Trajectory analysis

This example shows how to compute interactions for a trajectory performed using NAMD software for a small protein tyrosine phosphatase LMW-PTP in a complex with inhibitor MES (PDB: 5KQM) and visualize the results using Matplotlib library and VMD program.

In the tutorial, we will use already prepared files for simulation (PDB and DCD file).

Parse trajectory

We start by parsing PDB and DCD files, which contain LMW-PTP protein structure (available as tutorial files). PDB file contains the coordinates of protein structure with water and counter ions. DCD file is a binary file that contains a short simulation computed in NAMD package (20 frames). The commands shown below are explained in Trajectory Analysis tutorial.

In [1]: PDBfile = '5kqm_all_sci.pdb'

In [2]: DCDfile = 'NAMD_D2_co100.dcd'

In [3]: atoms = parsePDB(PDBfile)

In [4]: dcd = Trajectory(DCDfile)

In [5]: dcd.link(atoms)

In [6]: dcd.setCoords(atoms)
@> 19321 atoms and 1 coordinate set(s) were parsed in 0.17s.

To compute hydrogen bonds for each frame of the simulation use calcHydrogenBondsTrajectory() function:

In [7]: calcHydrogenBondsTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>     ARG101    P      NH1_1516  <--->      ASP98    P      OD1_1463     2.0    33.1
@>      HSE72    P      NE2_1042  <--->      ASN15    P       OD1_165     2.6    34.8
@>     GLN143    P      NE2_2192  <--->     GLU139    P      OE2_2126     2.7     9.2
@>      HSE66    P       NE2_957  <--->     GLU139    P      OE1_2125     2.7     6.4
@>      ARG40    P         N_561  <--->       LYS6    P          O_37     2.7    17.1
@>      ARG58    P         N_813  <--->      ASP56    P       OD1_788     2.7    30.0
@>      ALA45    P         N_634  <--->      ARG75    P        O_1097     2.8    35.1
@>      ASN53    P       ND2_747  <--->      GLU50    P       OE1_708     2.8    18.2
@>      ALA74    P        N_1064  <--->      ASN53    P         O_751     2.8    21.3
@>      ASP56    P         N_780  <--->      ILE16    P         O_189     2.8    27.0
@>     LYS110    P       NZ_1667  <--->      THR84    P        O_1240     2.8    38.2
@>     LEU116    P        N_1758  <--->      CYS90    P        O_1342     2.8    15.0
@>     SER103    P        N_1546  <--->      LEU99    P        O_1485     2.8    29.1
@>     ASN134    P        N_2045  <--->     ASP137    P      OD2_2091     2.8    22.6
@>     PHE152    P        N_2321  <--->     CYS148    P        O_2275     2.8     8.3
@>      ASN95    P        N_1398  <--->      ASP92    P      OD1_1368     2.8    12.6
@>       LYS6    P          N_16  <--->      ASN38    P         O_536     2.8    25.0
@>      ILE77    P        N_1115  <--->      ALA45    P         O_643     2.8    12.2
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.8    27.7
@>      LEU99    P        N_1467  <--->      ASN95    P        O_1411     2.8    15.5
@>     CYS149    P        N_2276  <--->     CYS145    P        O_2224     2.8     9.6
@>      GLY52    P         N_731  <--->      ALA74    P        O_1073     2.8     6.6
@>      ASP32    P         N_435  <--->      LYS28    P         O_385     2.8     8.8
@>      ILE88    P        N_1294  <--->     LYS112    P        O_1704     2.8    17.7
@>     GLN143    P        N_2180  <--->     GLU139    P        O_2128     2.8    21.7
@>      ARG27    P         N_340  <--->      GLU23    P         O_293     2.8    15.4
@>     TYR142    P        N_2159  <--->     PHE138    P        O_2113     2.9    14.2
@>     GLY133    P        N_2038  <--->     PRO130    P        O_1995     2.9    25.4
@>      PHE26    P         N_320  <--->      ALA22    P         O_278     2.9     4.9
@>      ASN15    P       ND2_166  <--->      SER19    P        OG_232     2.9    32.1
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.9    19.7
@>      ARG75    P      NH2_1093  <--->      ASP42    P       OD2_610     2.9    23.5
@>      ARG97    P        N_1431  <--->      GLU93    P        O_1386     2.9    22.2
@>      ARG65    P       NH2_941  <--->     GLU139    P      OE1_2125     2.9    32.3
@>      VAL25    P         N_304  <--->      ILE21    P         O_268     2.9     8.2
@>     LEU153    P        N_2341  <--->     CYS149    P        O_2286     2.9    12.5
@>       SER7    P          N_38  <--->      ASP86    P      OD2_1270     2.9    39.9
@>      ASP86    P        N_1261  <--->       SER7    P         OG_45     2.9    34.7
@>      ARG58    P       NH2_832  <--->     TYR131    P        O_2016     2.9    33.1
@>      THR46    P         N_644  <--->      CYS12    P         O_130     2.9    36.1
@>     GLN144    P        N_2197  <--->     THR140    P        O_2142     2.9    23.3
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.9    12.4
@>      LEU89    P        N_1313  <--->       LEU9    P          O_83     2.9    29.5
@>      THR31    P         N_421  <--->      ARG27    P         O_363     2.9    24.1
@>      CYS90    P        N_1332  <--->     GLU114    P        O_1738     2.9    24.6
..
..
@>      ARG40    P       NH1_577  <--->      THR84    P      OG1_1233     2.9     8.4
@>      ALA44    P         N_624  <--->      PHE10    P         O_103     2.9    33.2
@>     GLU154    P        N_2360  <--->     ARG150    P        O_2310     3.0    22.6
@>       VAL8    P          N_49  <--->      ARG40    P         O_584     3.0    25.0
@>      SER19    P         N_225  <--->      CYS12    P        SG_127     3.3     8.0
@>      PHE82    P        N_1197  <--->      LYS79    P        O_1169     3.4    37.7
@>      ASP81    P        N_1185  <--->      THR78    P      OG1_1140     3.5    39.5
@>     LYS102    P       NZ_1540  <--->      ASP98    P      OD2_1464     3.5    26.1
@>     ARG147    P      NH2_2260  <--->     GLN124    P      OE1_1892     3.5    33.9
@>     VAL106    P        N_1588  <--->     SER103    P        O_1556     3.5    34.2
@> Number of detected hydrogen bonds: 124.

@> Frame: 1
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>     LYS112    P       NZ_1699  <--->     GLU114    P      OE1_1735     2.5    20.8
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.5    15.6
@>      ARG27    P       NH2_359  <--->      GLU23    P       OE2_291     2.5    36.5
@>      THR78    P      OG1_1140  <--->      ASP81    P      OD2_1194     2.6    25.2
@>       SER7    P         OG_45  <--->      ASP86    P      OD2_1270     2.6    32.3
@>     LYS102    P       NZ_1540  <--->      ASP98    P      OD2_1464     2.6    18.6
@>     LYS112    P       NZ_1699  <--->     HSE157    P      OT1_2423     2.6    17.8
@>      ARG75    P      NH2_1093  <--->      ASP81    P      OD1_1193     2.6    17.6
@>     SER118    P       OG_1791  <--->     LEU115    P        O_1757     2.7    25.6
@>      ARG58    P        NE_826  <--->      ASP56    P       OD1_788     2.7     6.4
@>     GLN124    P        N_1881  <--->     ASP120    P      OD1_1824     2.7    17.2
@>     ARG147    P      NH1_2257  <--->     GLN124    P      OE1_1892     2.7    11.8
@>      ARG18    P       NH1_217  <--->      ASP92    P      OD2_1369     2.7    14.6
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.7    23.9
@>      TYR87    P       OH_1286  <--->     HSE157    P      OT1_2423     2.7    11.6
@>      SER43    P        OG_620  <--->      GLU23    P       OE1_290     2.7    15.2
@>      LYS28    P        NZ_380  <--->      ASP32    P       OD1_443     2.7     3.6
@>     LYS110    P       NZ_1667  <--->      ASP86    P      OD1_1269     2.7    25.2
@>     THR140    P      OG1_2135  <--->     SER136    P        O_2081     2.7     5.2
@>     LEU116    P        N_1758  <--->      CYS90    P        O_1342     2.7    24.4
@>       THR5    P         OG1_8  <--->      ASN38    P         O_536     2.7    38.6
@>      LYS64    P         N_900  <--->      GLN60    P         O_860     2.7    26.8
@>     ARG147    P      NH1_2257  <--->     ASP120    P      OD2_1825     2.7    15.2
@>      ARG27    P         N_340  <--->      GLU23    P         O_293     2.7    21.9
@>     TYR119    P       OH_1808  <--->     GLU114    P      OE1_1735     2.7    15.9
@>      ARG18    P       NH1_217  <--->     ILE127    P        O_1954     2.8    16.0
@>     SER103    P        N_1546  <--->      LEU99    P        O_1485     2.8    13.6
@>     LYS102    P        N_1524  <--->      ASP98    P        O_1466     2.8    15.9
@>      ARG58    P       NH1_829  <--->     GLY133    P        O_2044     2.8    31.9
@>      ARG75    P      NH2_1093  <--->      ASP42    P       OD2_610     2.8    13.0
@>     LYS112    P        N_1683  <--->      ASP86    P        O_1272     2.8    13.2
..
..
@>     ILE127    P        N_1936  <--->      MET91    P        O_1359     3.3    29.4
@>     ASN104    P        N_1557  <--->     ASN100    P        O_1499     3.4    12.6
@>     GLN105    P        N_1571  <--->     ARG101    P        O_1523     3.4    38.7
@>     ARG147    P        N_2241  <--->     GLN143    P        O_2196     3.4    10.9
@>      ASP56    P         N_780  <--->      ILE16    P         O_189     3.4    25.5
@>      ASN95    P        N_1398  <--->      ASP92    P      OD1_1368     3.5    32.5
@>      HSE72    P      NE2_1042  <--->      ASN15    P       OD1_165     3.5     7.1
@>     VAL106    P        N_1588  <--->     LYS102    P        O_1545     3.5    29.8
@>      ILE21    P         N_250  <--->      CYS17    P         O_200     3.5    34.9
@>      LEU96    P        N_1412  <--->      ASP92    P        O_1371     3.5     8.7
@> Number of detected hydrogen bonds: 123.

@> Frame: 2
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>      ARG18    P       NH1_217  <--->      ASP92    P      OD2_1369     2.5     4.9
@>      THR31    P       OG1_427  <--->      ARG27    P         O_363     2.5     5.5
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.6     8.2
@>     LYS112    P       NZ_1699  <--->     HSE157    P      OT1_2423     2.6    19.0
@>      ARG75    P      NH2_1093  <--->      ASP42    P       OD2_610     2.6    25.0
@>     TYR119    P       OH_1808  <--->     GLU114    P      OE2_1736     2.6    10.3
@>     LYS102    P       NZ_1540  <--->      ASP98    P      OD2_1464     2.6     7.9
@>      TYR87    P       OH_1286  <--->     HSE157    P      OT1_2423     2.7    14.1
@>      LYS64    P         N_900  <--->      GLN60    P         O_860     2.7     4.9
@>      SER43    P        OG_620  <--->      GLU23    P       OE1_290     2.7     8.6
@>      THR78    P      OG1_1140  <--->      ASP81    P      OD2_1194     2.7     6.5
@>      ILE88    P        N_1294  <--->     LYS112    P        O_1704     2.7    25.0
@>     SER118    P       OG_1791  <--->     LEU115    P        O_1757     2.7    26.9
@>      LYS28    P        NZ_380  <--->      ASP32    P       OD2_444     2.7    13.9
@>      THR84    P      OG1_1233  <--->      GLU80    P        O_1184     2.7    13.4
@>      LEU89    P        N_1313  <--->       LEU9    P          O_83     2.8    11.8
@>     ARG147    P      NH1_2257  <--->     GLN124    P      OE1_1892     2.8    15.1
@>      ARG27    P       NH2_359  <--->      GLU23    P       OE2_291     2.8    18.0
@>      ILE35    P         N_478  <--->      VAL30    P         O_420     2.8    20.7
@>      PHE26    P         N_320  <--->      ALA22    P         O_278     2.8    21.8
@>      VAL11    P         N_104  <--->      LEU89    P        O_1331     2.8    10.3
@>      VAL25    P         N_304  <--->      ILE21    P         O_268     2.8     9.2
@>       SER7    P         OG_45  <--->      ASP86    P      OD2_1270     2.8    29.4
@>      HSE72    P      NE2_1042  <--->      ASN15    P       OD1_165     2.8    37.1
@>      ASN34    P         N_464  <--->      THR31    P         O_434     2.8    19.7
@>     LYS110    P        N_1651  <--->      PHE82    P        O_1216     2.8     9.2
@>     LYS110    P       NZ_1667  <--->      ASP86    P      OD1_1269     2.8    13.5
@>      ARG58    P        NE_826  <--->      ASP56    P       OD1_788     2.8     8.0
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.8    14.9
@>       VAL8    P          N_49  <--->      ARG40    P         O_584     2.8    19.4
@>      ARG18    P       NH1_217  <--->     ILE127    P        O_1954     2.8     7.0
@>     LYS155    P        N_2375  <--->     ALA151    P        O_2320     2.8    15.1
@>      HSE66    P       NE2_957  <--->     GLU139    P      OE1_2125     2.8    28.9
@>     ARG147    P      NH1_2257  <--->     ASP120    P      OD2_1825     2.8    31.7
@>      ARG97    P        N_1431  <--->      GLU93    P        O_1386     2.8    15.2
@>     LYS123    P        N_1859  <--->     ASP120    P      OD1_1824     2.8    34.0
@>     LYS112    P        N_1683  <--->      ASP86    P        O_1272     2.8    10.3
@>      ASP86    P        N_1261  <--->       SER7    P         OG_45     2.8    22.0
@>      ARG65    P         N_922  <--->      SER61    P         O_871     2.8    24.4
@>     ILE127    P        N_1936  <--->      MET91    P        O_1359     2.8     4.1
@>     LYS112    P       NZ_1699  <--->     HSE157    P      ND1_2414     2.9    14.0
@>      GLY67    P         N_963  <--->      MET63    P         O_899     2.9    38.6
@>     SER103    P        N_1546  <--->      LEU99    P        O_1485     2.9    17.1
@>     LYS112    P       NZ_1699  <--->     GLU114    P      OE2_1736     2.9    18.1
@>      ARG75    P       NE_1087  <--->      ASP42    P       OD2_610     2.9    38.3
@>      ALA44    P         N_624  <--->      PHE10    P         O_103     2.9    30.1
@>      ILE68    P         N_970  <--->      MET63    P         O_899     2.9    12.9
@>      ARG58    P         N_813  <--->      ASP56    P       OD1_788     2.9    21.1
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.9    26.3
@>      ALA45    P         N_634  <--->      ARG75    P        O_1097     2.9    27.7
..
..
@>      HSE66    P         N_946  <--->      CYS62    P         O_882     2.9    17.6
@>      ASP32    P         N_435  <--->      LYS28    P         O_385     3.0    20.4
@>     VAL146    P        N_2225  <--->     TYR142    P        O_2179     3.0    20.7
@>     VAL106    P        N_1588  <--->     LYS102    P        O_1545     3.0    10.6
@>      ARG40    P         N_561  <--->       LYS6    P          O_37     3.4    33.1
@>     HSE157    P        N_2407  <--->     TYR119    P       OH_1808     3.4    27.6
@>      ARG65    P       NH1_938  <--->     GLU139    P      OE1_2125     3.4    32.0
@>     GLU114    P        N_1724  <--->      ILE88    P        O_1312     3.5    13.0
@>      ASP92    P        N_1360  <--->      ASN95    P      OD1_1406     3.5    35.4
@>      ASN15    P       ND2_166  <--->      SER43    P        OG_620     3.5    33.3
@> Number of detected hydrogen bonds: 113.
..
..
@> Frame: 20
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>      ARG97    P       NE_1444  <--->      GLU93    P      OE1_1383     2.5    12.5
@>      SER19    P        OG_232  <--->      ASN15    P       OD1_165     2.6    31.5
@>      ARG27    P       NH1_356  <--->      GLU23    P       OE1_290     2.6    19.1
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.6    21.5
@>     GLN122    P      NE2_1854  <--->     ASP120    P      OD2_1825     2.6    39.7
@>     SER118    P       OG_1791  <--->     GLU114    P      OE2_1736     2.6    24.5
@>      ARG65    P       NH1_938  <--->     GLU139    P      OE1_2125     2.7     6.1
@>      ARG65    P       NH2_941  <--->     ASP135    P      OD1_2067     2.7    15.6
@>      SER43    P        OG_620  <--->      GLU23    P       OE2_291     2.7    13.9
@>      ARG75    P       NE_1087  <--->      ASP42    P       OD1_609     2.7    26.5
@>     ARG150    P       NE_2300  <--->     GLU154    P      OE2_2372     2.7     4.9
@>     VAL106    P        N_1588  <--->     LYS102    P        O_1545     2.7    16.2
@>      LYS28    P         N_364  <--->      ALA24    P         O_303     2.7    38.8
@>     HSE157    P      NE2_2418  <--->     PHE152    P        O_2340     2.7    28.5
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.7    19.3
@>      ARG97    P      NH2_1450  <--->      GLU93    P      OE2_1384     2.7    15.8
@>      ARG75    P      NH2_1093  <--->      ASP42    P       OD1_609     2.7    30.5
@>      ALA45    P         N_634  <--->      ARG75    P        O_1097     2.7    22.3
@>      ARG75    P      NH2_1093  <--->      ASP81    P      OD1_1193     2.7    19.2
@>      THR31    P       OG1_427  <--->      ARG27    P         O_363     2.7    13.1
@>     ARG150    P      NH2_2306  <--->     GLU154    P      OE1_2371     2.7     8.5
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.7    14.8
@>      GLY67    P         N_963  <--->      MET63    P         O_899     2.7    25.3
@>      LEU89    P        N_1313  <--->       LEU9    P          O_83     2.8    18.4
@>     ARG101    P      NH1_1516  <--->      ASP98    P      OD2_1464     2.8    11.5
@>      ILE77    P        N_1115  <--->      ALA45    P         O_643     2.8    39.9
@>     LYS110    P        N_1651  <--->      PHE82    P        O_1216     2.8    32.3
@>      LEU29    P         N_386  <--->      VAL25    P         O_319     2.8     5.4
@>     ASN100    P        N_1486  <--->      LEU96    P        O_1430     2.8     6.7
@>     LYS102    P        N_1524  <--->      ASP98    P        O_1466     2.8     4.9
@>      THR78    P      OG1_1140  <--->      ASP81    P      OD2_1194     2.8    10.5
@>       VAL8    P          N_49  <--->      ARG40    P         O_584     2.8    16.8
@>     GLU154    P        N_2360  <--->     ARG150    P        O_2310     2.8    15.1
@>     LYS110    P       NZ_1667  <--->      ASP86    P      OD2_1270     2.8    32.5
@>      ARG58    P        NE_826  <--->      ASP56    P       OD1_788     2.8     3.3
@>      ILE35    P         N_478  <--->      VAL30    P         O_420     2.8     7.9
@>      ARG58    P       NH1_829  <--->     GLY133    P        O_2044     2.8    34.3
@>     GLN105    P        N_1571  <--->     ARG101    P        O_1523     2.8    29.9
@>       SER7    P          N_38  <--->      ASP86    P      OD1_1269     2.8    10.5
@>     ARG101    P      NH2_1519  <--->      ASP98    P      OD1_1463     2.8    17.5
@>     GLN143    P        N_2180  <--->     GLU139    P        O_2128     2.8    20.5
@>     CYS149    P        N_2276  <--->     CYS145    P        O_2224     2.8    16.0
@>     SER103    P       OG_1553  <--->      LEU99    P        O_1485     2.9    21.4
@>      ARG18    P       NH1_217  <--->      ASP92    P      OD2_1369     2.9     6.7
@>      CYS90    P        N_1332  <--->     GLU114    P        O_1738     2.9     7.9
..
..
@>     ALA151    P        N_2311  <--->     ARG147    P        O_2264     3.3    28.5
@>      ILE88    P        N_1294  <--->     LYS112    P        O_1704     3.3     8.1
@>      CYS12    P         N_120  <--->      ALA44    P         O_633     3.4    24.0
@>     GLN124    P      NE2_1893  <--->     ILE126    P        O_1935     3.4     3.3
@>      ARG97    P        N_1431  <--->      GLU93    P        O_1386     3.4    28.8
@>      SER61    P         N_861  <--->      TYR57    P         O_812     3.4    29.6
@>     GLN122    P      NE2_1854  <--->     ASP120    P      OD1_1824     3.5    17.2
@> Number of detected hydrogen bonds: 114.

Similarly, it can be done with other interaction types. Salt bridges (residues with opposite changes) with calcSaltBridgesTrajectory():

In [8]: calcSaltBridgesTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating salt bridges.
@>     GLU139    P   OE1_2125_2126  <--->      HSE66    P         NE2_957     2.8
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.9
@>      ASP32    P     OD1_443_444  <--->      LYS28    P          NZ_380     3.0
@>      ASP98    P   OD1_1463_1464  <--->     ARG101    P   NH1_1516_1519     3.1
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     3.7
@>     GLU139    P   OE1_2125_2126  <--->      ARG65    P     NH1_938_941     3.8
@>     LYS102    P         NZ_1540  <--->      ASP98    P   OD1_1463_1464     3.9
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.9
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     4.1
@>     GLU114    P   OE1_1735_1736  <--->     LYS112    P         NZ_1699     4.1
@>     ASP120    P   OD1_1824_1825  <--->     ARG147    P   NH1_2257_2260     4.2
@>      ASP86    P   OD1_1269_1270  <--->     LYS110    P         NZ_1667     4.2
@>     HSE157    P        NE2_2418  <--->     GLU114    P   OE1_1735_1736     4.4
@>      ARG18    P     NH1_217_220  <--->     ASP129    P   OD1_1978_1979     4.6
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.6
@>      GLU23    P     OE1_290_291  <--->      HSE72    P        NE2_1042     5.0
@> Number of detected salt bridges: 16.

@> Frame: 1
@> Calculating salt bridges.
@>      ASP32    P     OD1_443_444  <--->      LYS28    P          NZ_380     2.6
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.6
@>      ASP98    P   OD1_1463_1464  <--->     ARG101    P   NH1_1516_1519     2.8
@>     GLU114    P   OE1_1735_1736  <--->     LYS112    P         NZ_1699     3.1
@>     HSE157    P        NE2_2418  <--->     GLU114    P   OE1_1735_1736     3.2
@>      ASP86    P   OD1_1269_1270  <--->     LYS110    P         NZ_1667     3.3
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     3.4
@>     GLU139    P   OE1_2125_2126  <--->      ARG65    P     NH1_938_941     3.4
@>     LYS102    P         NZ_1540  <--->      ASP98    P   OD1_1463_1464     3.5
@>     ASP120    P   OD1_1824_1825  <--->     ARG147    P   NH1_2257_2260     3.8
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.8
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     3.8
@>     GLU139    P   OE1_2125_2126  <--->      HSE66    P         NE2_957     4.0
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.5
@> Number of detected salt bridges: 14.

@> Frame: 2
@> Calculating salt bridges.
@>     GLU114    P   OE1_1735_1736  <--->     LYS112    P         NZ_1699     2.6
@>      ASP32    P     OD1_443_444  <--->      LYS28    P          NZ_380     2.6
@>     GLU139    P   OE1_2125_2126  <--->      ARG65    P     NH1_938_941     2.7
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.9
@>     LYS102    P         NZ_1540  <--->      ASP98    P   OD1_1463_1464     3.1
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.6
@>     GLU139    P   OE1_2125_2126  <--->      HSE66    P         NE2_957     3.6
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     3.7
@>      ASP86    P   OD1_1269_1270  <--->     LYS110    P         NZ_1667     3.7
@>     ASP120    P   OD1_1824_1825  <--->     ARG147    P   NH1_2257_2260     3.8
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     3.9
@>     HSE157    P        NE2_2418  <--->     GLU114    P   OE1_1735_1736     4.2
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.3
@>      ARG18    P     NH1_217_220  <--->     ASP129    P   OD1_1978_1979     4.6
@>      ASP86    P   OD1_1269_1270  <--->       LYS6    P           NZ_32     5.0
@> Number of detected salt bridges: 15.

..
..

@> Frame: 18
@> Calculating salt bridges.
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.6
@>      ASP32    P     OD1_443_444  <--->      LYS28    P          NZ_380     2.7
@>     ASP135    P   OD1_2067_2068  <--->      ARG65    P     NH1_938_941     2.8
@>     LYS102    P         NZ_1540  <--->      ASP98    P   OD1_1463_1464     3.0
@>      GLU23    P     OE1_290_291  <--->      HSE72    P        NE2_1042     3.4
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     3.6
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.6
@>      ASP98    P   OD1_1463_1464  <--->     ARG101    P   NH1_1516_1519     3.9
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     4.2
@>      ARG97    P   NH1_1447_1450  <--->      GLU93    P   OE1_1383_1384     4.5
@>     ARG150    P   NH1_2303_2306  <--->     GLU154    P   OE1_2371_2372     4.5
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.5
@>      ARG18    P     NH1_217_220  <--->     ASP129    P   OD1_1978_1979     4.7
@> Number of detected salt bridges: 13.

@> Frame: 19
@> Calculating salt bridges.
@>     ASP135    P   OD1_2067_2068  <--->      ARG65    P     NH1_938_941     2.7
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.9
@>     LYS102    P         NZ_1540  <--->      ASP98    P   OD1_1463_1464     3.1
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     3.3
@>      ASP98    P   OD1_1463_1464  <--->     ARG101    P   NH1_1516_1519     3.7
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.7
@>      ARG97    P   NH1_1447_1450  <--->      GLU93    P   OE1_1383_1384     3.7
@>      ASP86    P   OD1_1269_1270  <--->     LYS110    P         NZ_1667     3.9
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     3.9
@>      GLU23    P     OE1_290_291  <--->      HSE72    P        NE2_1042     4.0
@>     ARG150    P   NH1_2303_2306  <--->     GLU154    P   OE1_2371_2372     4.2
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.6
@> Number of detected salt bridges: 12.

@> Frame: 20
@> Calculating salt bridges.
@>     ASP135    P   OD1_2067_2068  <--->      ARG65    P     NH1_938_941     2.5
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.7
@>      ASP98    P   OD1_1463_1464  <--->     ARG101    P   NH1_1516_1519     2.8
@>      ASP86    P   OD1_1269_1270  <--->     LYS110    P         NZ_1667     3.4
@>      ARG97    P   NH1_1447_1450  <--->      GLU93    P   OE1_1383_1384     3.5
@>     ARG150    P   NH1_2303_2306  <--->     GLU154    P   OE1_2371_2372     3.7
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.7
@>     GLU139    P   OE1_2125_2126  <--->      HSE66    P         NE2_957     3.9
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     4.0
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     4.0
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.4
@>      GLU23    P     OE1_290_291  <--->      HSE72    P        NE2_1042     4.7
@>     GLU139    P   OE1_2125_2126  <--->      ARG65    P     NH1_938_941     4.8
@>      ARG18    P     NH1_217_220  <--->     ASP129    P   OD1_1978_1979     5.0
@> Number of detected salt bridges: 14.

Repulsive Ionic Bonding using calcRepulsiveIonicBondingTrajectory() for residues with the same charges:

In [9]: calcRepulsiveIonicBondingTrajectory(atoms, dcd, distA=7)
@> Frame: 0
@> Calculating repulsive ionic bonding.
@>     LYS102    P         NZ_1540  <--->     ARG101    P   NH1_1516_1519     4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 1
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 2
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 3
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 4
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 5
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 6
@> Calculating repulsive ionic bonding.
@>     LYS102    P         NZ_1540  <--->     ARG101    P   NH1_1516_1519     4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 7
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 8
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
@> Frame: 9
@> Calculating repulsive ionic bonding.
@>     LYS102    P         NZ_1540  <--->     ARG101    P   NH1_1516_1519     4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Frame: 10
@> Calculating repulsive ionic bonding.
@> Number of detected Repulsive Ionic Bonding interactions: 0.
..
..
@> Frame: 20
@> Calculating repulsive ionic bonding.
@>     ARG147    P   NH1_2257_2260  <--->     LYS123    P         NZ_1875     4.5
@> Number of detected Repulsive Ionic Bonding interactions: 1.

Pi-Stacking interactions using calcPiStackingTrajectory():

In [10]: calcPiStackingTrajectory(atoms, dcd, distA=5)
@> Frame: 0
@> Calculating Pi stacking interactions.
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     3.9   162.1
@>     HSE157       P2414_2415_2416_2418_2420_2423_2424  <--->     TYR119       P   1802_1803_1805_1807_1810_1812     4.4     3.0
@>      PHE26       P         327_328_330_332_334_336  <--->      TRP39       P         549_550_551_553_555_557     4.8    75.5
@>     TYR132       P   2024_2025_2027_2029_2032_2034  <--->     TYR131       P   2003_2004_2006_2008_2011_2013     4.9    91.4
@> Number of detected Pi stacking interactions: 4.
@> Frame: 1
@> Calculating Pi stacking interactions.
@>      PHE26       P         327_328_330_332_334_336  <--->      TRP39       P         549_550_551_553_555_557     4.8    71.0
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     4.8   138.9
@> Number of detected Pi stacking interactions: 2.
@> Frame: 2
@> Calculating Pi stacking interactions.
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     3.6   174.2
@> Number of detected Pi stacking interactions: 1.
@> Frame: 3
@> Calculating Pi stacking interactions.
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     4.1   143.3
@> Number of detected Pi stacking interactions: 1.
@> Frame: 4
@> Calculating Pi stacking interactions.
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     4.3   137.5
@>      TYR87       P   1280_1281_1283_1285_1288_1290  <--->     PHE152       P   2328_2329_2331_2333_2335_2337     5.0    73.7
@> Number of detected Pi stacking interactions: 2.
..
..
@> Frame: 19
@> Calculating Pi stacking interactions.
@>     TYR132       P   2024_2025_2027_2029_2032_2034  <--->     TYR131       P   2003_2004_2006_2008_2011_2013     4.6    62.2
@>     TYR119       P   1802_1803_1805_1807_1810_1812  <--->     PHE152       P   2328_2329_2331_2333_2335_2337     4.9    60.8
@> Number of detected Pi stacking interactions: 2.
@> Frame: 20
@> Calculating Pi stacking interactions.
@>     TYR119       P   1802_1803_1805_1807_1810_1812  <--->     PHE152       P   2328_2329_2331_2333_2335_2337     4.7   125.5
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     4.8   165.0
@>     TYR132       P   2024_2025_2027_2029_2032_2034  <--->     TYR131       P   2003_2004_2006_2008_2011_2013     4.9   116.3
@> Number of detected Pi stacking interactions: 3.

Pi-Cation interactions using calcPiCationTrajectory():

In [11]: calcPiCationTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.7
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.5
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     4.8
@> Number of detected cation-pi interactions: 3.
@> Frame: 1
@> Calculating cation-Pi interactions.
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     3.5
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.9
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.9
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     4.9
@>     TYR131   P   2003_2004_2006_2008_2011_2013  <--->      ARG58   P                     NH1_829_832     4.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 2
@> Calculating cation-Pi interactions.
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     2.7
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.1
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.5
@> Number of detected cation-pi interactions: 3.
@> Frame: 3
@> Calculating cation-Pi interactions.
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     2.6
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.6
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     3.8
@> Number of detected cation-pi interactions: 3.
@> Frame: 4
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.9
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.8
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS155   P                         NZ_2391     4.8
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     4.9
@> Number of detected cation-pi interactions: 4.
..
..
@> Frame: 19
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.9
@> Number of detected cation-pi interactions: 1.
@> Frame: 20
@> Calculating cation-Pi interactions.
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.0
@> Number of detected cation-pi interactions: 1.

Hydrophobic interactions using calcHydrophohicTrajectory():

In [12]: calcHydrophohicTrajectory(atoms, dcd)
@> Frame: 0
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@>     ALA156    P    CB_240114s  <--->      TYR87    P    OH_1286     3.0    22.0
@>      ALA24    P     CB_29814s  <--->      MET63    P     CE_894     3.3     5.2
@>      ILE68    P    CG2_97614s  <--->      MET63    P     CE_894     3.3    52.4
@>     TYR142    P    CZ_217114s  <--->     VAL146    P   CG2_2235     3.5    49.7
@>      PHE10    P     CD1_9214s  <--->      ALA22    P     CB_273     3.5    31.2
@>       LYS6    P      CD_2614s  <--->      TRP39    P    CZ2_555     3.5    68.7
@>      PHE26    P    CE2_33614s  <--->      VAL30    P    CG1_411     3.6    21.1
@>      ILE88    P    CD_130714s  <--->     ALA111    P    CB_1677     3.6    21.2
@>      VAL11    P    CG2_11414s  <--->      ILE88    P   CG2_1300     3.6     9.3
@>      VAL41    P    CG2_59514s  <--->      PHE26    P    CD2_334     3.6    16.6
@>     PHE152    P   CE1_233114s  <--->     ALA156    P    CB_2401     3.7    17.5
@>      LYS79    P    CG_115514s  <--->     VAL106    P   CG2_1598     3.7    25.1
@>      LEU99    P   CD2_148014s  <--->      ILE77    P    CD_1128     3.7    12.0
@>      PHE82    P   CD1_120514s  <--->      ILE88    P    CD_1307     3.7    17.6
@>     LEU116    P   CD2_177114s  <--->     ILE127    P    CD_1949     3.7    17.4
@>       VAL8    P     CG1_5514s  <--->      PHE26    P    CE2_336     3.7    12.1
@>      LEU96    P   CD1_142114s  <--->     ILE113    P   CG2_1711     3.7    17.0
@>       LEU9    P     CD2_7814s  <--->      ILE77    P    CD_1128     3.7    15.4
@>      LEU89    P   CD1_132214s  <--->       VAL8    P     CG2_59     3.8    15.9
@>     ILE126    P    CD_193014s  <--->     LEU125    P   CD1_1907     3.8    54.2
@>     VAL141    P   CG1_214914s  <--->     ILE127    P   CG2_1942     3.9    11.5
@>      MET91    P    SD_135314s  <--->     ILE127    P    CD_1949     3.9    35.9
@>      ALA44    P     CB_62814s  <--->       LEU9    P     CD1_74     3.9    15.1
@>      VAL25    P    CG2_31414s  <--->     TYR142    P   CE1_2169     3.9    12.0
@>      ILE21    P    CG2_25614s  <--->      MET63    P     SD_893     4.0    20.8
@>     LEU153    P   CD1_235014s  <--->      TRP39    P    NE1_547     4.0     9.4
@>      PHE85    P    CZ_125314s  <--->       LEU9    P     CD1_74     4.0    32.1
@>      ILE35    P     CD_49114s  <--->      TRP39    P    NE1_547     4.0    26.0
@>      LEU29    P    CD1_39514s  <--->      VAL25    P    CG1_310     4.1    19.7
@>      ALA74    P    CB_106814s  <--->      ILE16    P    CG2_177     4.1     6.7
@>      ARG75    P    CG_108114s  <--->      ALA44    P     CB_628     4.1    36.2
@>      ARG18    P     CG_20814s  <--->     VAL141    P   CG1_2149     4.1    20.3
@>     LYS102    P    CD_153414s  <--->      ILE77    P   CG2_1121     4.1    17.5
@>     TYR119    P   CE1_180514s  <--->      LEU89    P   CD2_1326     4.1    11.6
@>      ARG40    P     CG_56814s  <--->      PHE85    P   CE2_1257     4.3    60.9
@>      LYS28    P     CG_37114s  <--->      ILE68    P     CD_983     4.3    21.8
@>     PHE138    P   CD2_210814s  <--->      ILE21    P     CD_263     4.3     6.6
@>     TYR131    P   CE1_200614s  <--->      ILE16    P     CD_184     4.3     8.9
@>      ARG58    P     CG_82014s  <--->     PHE138    P   CE1_2104     4.5    59.4
@> Number of detected hydrophobic interactions: 39.
@> Frame: 1
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@>      MET63    P     SD_89314s  <--->     TYR142    P   CD1_2167     3.3    26.8
@>      ALA24    P     CB_29814s  <--->      MET63    P     CE_894     3.4     7.1
@>       VAL8    P     CG2_5914s  <--->      PHE10    P      CZ_96     3.4    27.8
@>      LEU96    P   CD1_142114s  <--->     ILE113    P   CG2_1711     3.4    13.3
@>     LEU116    P   CD1_176714s  <--->      PHE10    P     CE1_94     3.5    13.5
@>      PHE82    P    CZ_120914s  <--->      ILE77    P    CD_1128     3.6    20.4
@>      ILE68    P     CD_98314s  <--->     TYR142    P    OH_2172     3.6    27.4
@>      PHE26    P    CE2_33614s  <--->      VAL30    P    CG1_411     3.6    28.1
@>     ALA156    P    CB_240114s  <--->     PHE152    P   CD1_2329     3.6    24.5
@>      VAL11    P    CG2_11414s  <--->      ILE88    P   CG2_1300     3.6     8.6
@>     LYS102    P    CD_153414s  <--->      ILE77    P   CG2_1121     3.7    18.2
@>      LEU99    P   CD2_148014s  <--->      ILE77    P    CD_1128     3.7     8.0
@>     LEU153    P   CD1_235014s  <--->      VAL30    P    CG1_411     3.7    14.5
@>       LEU9    P     CD2_7814s  <--->      ILE77    P    CD_1128     3.7    16.0
@>      TRP39    P    CD1_54514s  <--->      VAL30    P    CG1_411     3.7    14.9
@>     PHE138    P   CD2_210814s  <--->      ILE21    P     CD_263     3.8    15.8
@>     TYR119    P    OH_180814s  <--->     ALA156    P    CB_2401     3.8    18.6
@>     VAL146    P   CG2_223514s  <--->     TYR142    P    CZ_2171     3.8    40.5
@>      VAL25    P    CG2_31414s  <--->     TYR142    P   CD1_2167     3.8    14.3
@>      MET91    P    CE_135414s  <--->     LEU116    P   CD2_1771     3.8    19.1
@>      ILE35    P     CD_49114s  <--->     LEU153    P   CD1_2350     3.9    17.2
@>      VAL41    P    CG2_59514s  <--->      PHE26    P    CD2_334     3.9    21.9
@>     ILE127    P    CD_194914s  <--->     LEU116    P   CD2_1771     3.9    11.7
@>      LEU29    P    CD1_39514s  <--->      VAL25    P    CG1_310     3.9    25.1
@>      ALA22    P     CB_27314s  <--->     LEU116    P   CD2_1771     4.0     7.3
@>     ALA111    P    CB_167714s  <--->      ILE88    P    CD_1307     4.0    14.9
@>      ARG75    P    CG_108114s  <--->      ALA44    P     CB_628     4.0    36.8
@>     ILE126    P    CD_193014s  <--->     LEU125    P    CG_1905     4.0    53.2
@>     VAL106    P   CG2_159814s  <--->      PHE82    P   CD2_1211     4.0    13.1
@>      PHE85    P    CZ_125314s  <--->       LEU9    P     CD1_74     4.1    28.5
@>      ARG40    P     CG_56814s  <--->      PHE85    P   CE2_1257     4.1    50.3
@>      TYR87    P   CD1_128114s  <--->      LEU89    P   CD2_1326     4.2    14.7
@>      LYS28    P     CG_37114s  <--->      ILE68    P    CG2_976     4.2    15.9
@>      LYS79    P    CG_115514s  <--->     VAL106    P   CG2_1598     4.2    20.4
@>      ARG18    P     CG_20814s  <--->     VAL141    P   CG1_2149     4.3    10.9
@>      ARG58    P     CG_82014s  <--->     PHE138    P   CD1_2102     4.3    48.8
@>      ALA74    P    CB_106814s  <--->      ILE16    P    CG2_177     4.4     4.3
@>     ARG150    P    CG_229414s  <--->      LEU29    P    CD2_399     4.5    22.3
@> Number of detected hydrophobic interactions: 38.
..
..
@> Frame: 20
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@>      LEU96    P   CD1_142114s  <--->     ILE113    P   CG2_1711     3.3    21.1
@>      ILE88    P    CD_130714s  <--->      PHE82    P   CD2_1211     3.4    25.2
@>      VAL11    P    CG2_11414s  <--->      LEU99    P   CD1_1476     3.4    11.5
@>      MET63    P     SD_89314s  <--->     TYR142    P   CE1_2169     3.4    37.7
@>      TRP39    P    NE1_54714s  <--->     LEU153    P   CD1_2350     3.4    19.2
@>     ALA111    P    CB_167714s  <--->      ILE88    P    CD_1307     3.5    23.0
@>      ILE35    P     CD_49114s  <--->     LEU153    P   CD1_2350     3.5    16.4
@>      VAL30    P    CG1_41114s  <--->     LEU153    P   CD2_2354     3.5     9.8
@>       LEU9    P     CD2_7814s  <--->      ILE77    P    CD_1128     3.5    17.0
@>      PHE10    P     CE1_9414s  <--->      LEU89    P   CD1_1322     3.5    25.4
@>     TYR119    P   CE1_180514s  <--->      LEU89    P   CD2_1326     3.6    18.5
@>      ALA24    P     CB_29814s  <--->      MET63    P     CE_894     3.6    13.8
@>      PHE26    P     CZ_33214s  <--->     LEU153    P   CD1_2350     3.6    27.1
@>       VAL8    P     CG2_5914s  <--->      LEU89    P   CD1_1322     3.6    13.0
@>      ALA22    P     CB_27314s  <--->      PHE10    P     CD1_92     3.6    29.5
@>      MET91    P    CE_135414s  <--->      ALA22    P     CB_273     3.7     9.1
@>      VAL41    P    CG2_59514s  <--->      PHE26    P    CD2_334     3.7    17.5
@>     LEU116    P   CD2_177114s  <--->      MET91    P    SD_1353     3.7    21.9
@>      ALA44    P     CB_62814s  <--->      VAL11    P    CG1_110     3.7    34.2
@>       LYS6    P      CD_2614s  <--->      TRP39    P    CH2_557     3.7    44.8
@>     VAL146    P   CG2_223514s  <--->     TYR142    P   CE2_2176     3.8    39.4
@>      PHE85    P   CE1_125114s  <--->       LEU9    P     CD1_74     3.8    31.6
@>      ILE21    P    CG2_25614s  <--->      VAL25    P    CG2_314     3.8    25.0
@>     VAL141    P   CG1_214914s  <--->      ILE21    P     CD_263     3.9    13.0
@>      ILE68    P    CG1_98014s  <--->      MET63    P     CE_894     3.9    37.2
@>     PHE152    P    CZ_233314s  <--->      LEU89    P   CD1_1322     3.9    18.0
@>      ARG18    P     CG_20814s  <--->     VAL141    P   CG1_2149     4.0    26.2
@>      ARG75    P    CG_108114s  <--->      ALA44    P     CB_628     4.2    27.4
@>     ILE127    P    CD_194914s  <--->     LEU116    P   CD2_1771     4.3     7.9
@>      LYS79    P    CG_115514s  <--->     VAL106    P   CG2_1598     4.3    15.6
@>      LEU29    P     CG_39314s  <--->      VAL25    P    CG1_310     4.3    21.7
@>     ILE126    P   CG1_192714s  <--->     LEU125    P    CG_1905     4.4    55.6
@> Number of detected hydrophobic interactions: 32.

In this particular example you will not have disulfide bonds, but you can compute it using calcDisulfideBondsTrajectory():

In [13]: calcDisulfideBondsTrajectory(atoms, dcd)
@> Frame: 0
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 1
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 2
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 3
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> Frame: 4
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
..
..

Compute all availabe types of interactions

First, we instantiate a InteractionsTrajectory instance, which stores all the information about interactions for protein structure for multiple frames. With InteractionsTrajectory.calcProteinInteractionsTrajectory(), we can compute all types of interactions such as hydrogen bonds, salt bridges, repulsive ionic bonding, Pi-cation, Pi-stacking, and hydrophobic) at once. Be aware that those computations may take a while, depending on the size of the system and the number of frames that are stored by the DCD file. Therefore, we recommend saving the results as a filename file. filename file, here calcProteinInteractionsTrajectory.pkl, can be reloaded and used with all available functions and methods.

In [14]: interactionsTrajectory = InteractionsTrajectory('trajectory')

In [15]: interactionsTrajectory.calcProteinInteractionsTrajectory(atoms, dcd,
   ....:     filename='calcProteinInteractionsTrajectory')
   ....: 
@> Frame: 0
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>     ARG101    P      NH1_1516  <--->      ASP98    P      OD1_1463     2.0    33.1
@>      HSE72    P      NE2_1042  <--->      ASN15    P       OD1_165     2.6    34.8
@>     GLN143    P      NE2_2192  <--->     GLU139    P      OE2_2126     2.7     9.2
@>      HSE66    P       NE2_957  <--->     GLU139    P      OE1_2125     2.7     6.4
@>      ARG40    P         N_561  <--->       LYS6    P          O_37     2.7    17.1
@>      ARG58    P         N_813  <--->      ASP56    P       OD1_788     2.7    30.0
@>      ALA45    P         N_634  <--->      ARG75    P        O_1097     2.8    35.1
@>      ASN53    P       ND2_747  <--->      GLU50    P       OE1_708     2.8    18.2
@>      ALA74    P        N_1064  <--->      ASN53    P         O_751     2.8    21.3
@>      ASP56    P         N_780  <--->      ILE16    P         O_189     2.8    27.0
@>     LYS110    P       NZ_1667  <--->      THR84    P        O_1240     2.8    38.2
@>     LEU116    P        N_1758  <--->      CYS90    P        O_1342     2.8    15.0
@>     SER103    P        N_1546  <--->      LEU99    P        O_1485     2.8    29.1
@>     ASN134    P        N_2045  <--->     ASP137    P      OD2_2091     2.8    22.6
@>     PHE152    P        N_2321  <--->     CYS148    P        O_2275     2.8     8.3
@>      ASN95    P        N_1398  <--->      ASP92    P      OD1_1368     2.8    12.6
@>       LYS6    P          N_16  <--->      ASN38    P         O_536     2.8    25.0
@>      ILE77    P        N_1115  <--->      ALA45    P         O_643     2.8    12.2
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.8    27.7
@>      LEU99    P        N_1467  <--->      ASN95    P        O_1411     2.8    15.5
@>     CYS149    P        N_2276  <--->     CYS145    P        O_2224     2.8     9.6
@>      GLY52    P         N_731  <--->      ALA74    P        O_1073     2.8     6.6
@>      ASP32    P         N_435  <--->      LYS28    P         O_385     2.8     8.8
@>      ILE88    P        N_1294  <--->     LYS112    P        O_1704     2.8    17.7
@>     GLN143    P        N_2180  <--->     GLU139    P        O_2128     2.8    21.7
@>      ARG27    P         N_340  <--->      GLU23    P         O_293     2.8    15.4
@>     TYR142    P        N_2159  <--->     PHE138    P        O_2113     2.9    14.2
@>     GLY133    P        N_2038  <--->     PRO130    P        O_1995     2.9    25.4
@>      PHE26    P         N_320  <--->      ALA22    P         O_278     2.9     4.9
@>      ASN15    P       ND2_166  <--->      SER19    P        OG_232     2.9    32.1
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.9    19.7
@>      ARG75    P      NH2_1093  <--->      ASP42    P       OD2_610     2.9    23.5
@>      ARG97    P        N_1431  <--->      GLU93    P        O_1386     2.9    22.2
@>      ARG65    P       NH2_941  <--->     GLU139    P      OE1_2125     2.9    32.3
@>      VAL25    P         N_304  <--->      ILE21    P         O_268     2.9     8.2
@>     LEU153    P        N_2341  <--->     CYS149    P        O_2286     2.9    12.5
@>       SER7    P          N_38  <--->      ASP86    P      OD2_1270     2.9    39.9
@>      ASP86    P        N_1261  <--->       SER7    P         OG_45     2.9    34.7
@>      ARG58    P       NH2_832  <--->     TYR131    P        O_2016     2.9    33.1
@>      THR46    P         N_644  <--->      CYS12    P         O_130     2.9    36.1
@>     GLN144    P        N_2197  <--->     THR140    P        O_2142     2.9    23.3
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.9    12.4
@>      LEU89    P        N_1313  <--->       LEU9    P          O_83     2.9    29.5
@>      THR31    P         N_421  <--->      ARG27    P         O_363     2.9    24.1
@>      CYS90    P        N_1332  <--->     GLU114    P        O_1738     2.9    24.6
@>     CYS148    P        N_2265  <--->     GLN144    P        O_2213     2.9     9.3
@>      GLU23    P         N_279  <--->      SER19    P         O_235     2.9    15.4
@>      ILE68    P         N_970  <--->      MET63    P         O_899     2.9    13.0
@>      PHE10    P          N_84  <--->      ASP42    P         O_612     2.9    22.8
@>     LYS112    P        N_1683  <--->      ASP86    P        O_1272     2.9    10.1
@>      SER61    P         N_861  <--->      TYR57    P         O_812     2.9    35.1
@>     CYS145    P        N_2214  <--->     VAL141    P        O_2158     2.9    15.9
@>      ARG27    P       NH2_359  <--->      GLU23    P       OE2_291     2.9    31.5
@>      LYS64    P         N_900  <--->      GLN60    P         O_860     2.9    22.9
@>       LEU9    P          N_65  <--->      TYR87    P        O_1293     2.9    16.4
@>      ASN38    P         N_523  <--->      ILE35    P         O_496     2.9    29.1
@>      VAL11    P         N_104  <--->      LEU89    P        O_1331     2.9    29.7
@>     ASN100    P        N_1486  <--->      LEU96    P        O_1430     2.9    10.3
..
..
@> Number of detected hydrogen bonds: 124.
@> Calculating salt bridges.
@>     GLU139    P   OE1_2125_2126  <--->      HSE66    P         NE2_957     2.8
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.9
@>      ASP32    P     OD1_443_444  <--->      LYS28    P          NZ_380     3.0
@>      ASP98    P   OD1_1463_1464  <--->     ARG101    P   NH1_1516_1519     3.1
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     3.7
@>     GLU139    P   OE1_2125_2126  <--->      ARG65    P     NH1_938_941     3.8
@>     LYS102    P         NZ_1540  <--->      ASP98    P   OD1_1463_1464     3.9
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.9
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     4.1
@>     GLU114    P   OE1_1735_1736  <--->     LYS112    P         NZ_1699     4.1
@>     ASP120    P   OD1_1824_1825  <--->     ARG147    P   NH1_2257_2260     4.2
@>      ASP86    P   OD1_1269_1270  <--->     LYS110    P         NZ_1667     4.2
@>     HSE157    P        NE2_2418  <--->     GLU114    P   OE1_1735_1736     4.4
@>      ARG18    P     NH1_217_220  <--->     ASP129    P   OD1_1978_1979     4.6
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.6
@>      GLU23    P     OE1_290_291  <--->      HSE72    P        NE2_1042     5.0
@> Number of detected salt bridges: 16.
@> Calculating repulsive ionic bonding.
@>     LYS102    P         NZ_1540  <--->     ARG101    P   NH1_1516_1519     4.3
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Calculating Pi stacking interactions.
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     3.9   162.1
@>     HSE157       P2414_2415_2416_2418_2420_2423_2424  <--->     TYR119       P   1802_1803_1805_1807_1810_1812     4.4     3.0
@>      PHE26       P         327_328_330_332_334_336  <--->      TRP39       P         549_550_551_553_555_557     4.8    75.5
@>     TYR132       P   2024_2025_2027_2029_2032_2034  <--->     TYR131       P   2003_2004_2006_2008_2011_2013     4.9    91.4
@> Number of detected Pi stacking interactions: 4.
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.7
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.5
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     4.8
@> Number of detected cation-pi interactions: 3.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@>     ALA156    P    CB_240114s  <--->      TYR87    P    OH_1286     3.0    22.0
@>      ALA24    P     CB_29814s  <--->      MET63    P     CE_894     3.3     5.2
@>      ILE68    P    CG2_97614s  <--->      MET63    P     CE_894     3.3    52.4
@>     TYR142    P    CZ_217114s  <--->     VAL146    P   CG2_2235     3.5    49.7
@>      PHE10    P     CD1_9214s  <--->      ALA22    P     CB_273     3.5    31.2
@>       LYS6    P      CD_2614s  <--->      TRP39    P    CZ2_555     3.5    68.7
@>      PHE26    P    CE2_33614s  <--->      VAL30    P    CG1_411     3.6    21.1
@>      ILE88    P    CD_130714s  <--->     ALA111    P    CB_1677     3.6    21.2
@>      VAL11    P    CG2_11414s  <--->      ILE88    P   CG2_1300     3.6     9.3
@>      VAL41    P    CG2_59514s  <--->      PHE26    P    CD2_334     3.6    16.6
@>     PHE152    P   CE1_233114s  <--->     ALA156    P    CB_2401     3.7    17.5
@>      LYS79    P    CG_115514s  <--->     VAL106    P   CG2_1598     3.7    25.1
@>      LEU99    P   CD2_148014s  <--->      ILE77    P    CD_1128     3.7    12.0
@>      PHE82    P   CD1_120514s  <--->      ILE88    P    CD_1307     3.7    17.6
@>     LEU116    P   CD2_177114s  <--->     ILE127    P    CD_1949     3.7    17.4
@>       VAL8    P     CG1_5514s  <--->      PHE26    P    CE2_336     3.7    12.1
@>      LEU96    P   CD1_142114s  <--->     ILE113    P   CG2_1711     3.7    17.0
@>       LEU9    P     CD2_7814s  <--->      ILE77    P    CD_1128     3.7    15.4
@>      LEU89    P   CD1_132214s  <--->       VAL8    P     CG2_59     3.8    15.9
@>     ILE126    P    CD_193014s  <--->     LEU125    P   CD1_1907     3.8    54.2
@>     VAL141    P   CG1_214914s  <--->     ILE127    P   CG2_1942     3.9    11.5
@>      MET91    P    SD_135314s  <--->     ILE127    P    CD_1949     3.9    35.9
@>      ALA44    P     CB_62814s  <--->       LEU9    P     CD1_74     3.9    15.1
@>      VAL25    P    CG2_31414s  <--->     TYR142    P   CE1_2169     3.9    12.0
@>      ILE21    P    CG2_25614s  <--->      MET63    P     SD_893     4.0    20.8
@>     LEU153    P   CD1_235014s  <--->      TRP39    P    NE1_547     4.0     9.4
@>      PHE85    P    CZ_125314s  <--->       LEU9    P     CD1_74     4.0    32.1
@>      ILE35    P     CD_49114s  <--->      TRP39    P    NE1_547     4.0    26.0
@>      LEU29    P    CD1_39514s  <--->      VAL25    P    CG1_310     4.1    19.7
@>      ALA74    P    CB_106814s  <--->      ILE16    P    CG2_177     4.1     6.7
@>      ARG75    P    CG_108114s  <--->      ALA44    P     CB_628     4.1    36.2
@>      ARG18    P     CG_20814s  <--->     VAL141    P   CG1_2149     4.1    20.3
@>     LYS102    P    CD_153414s  <--->      ILE77    P   CG2_1121     4.1    17.5
@>     TYR119    P   CE1_180514s  <--->      LEU89    P   CD2_1326     4.1    11.6
@>      ARG40    P     CG_56814s  <--->      PHE85    P   CE2_1257     4.3    60.9
@>      LYS28    P     CG_37114s  <--->      ILE68    P     CD_983     4.3    21.8
@>     PHE138    P   CD2_210814s  <--->      ILE21    P     CD_263     4.3     6.6
@>     TYR131    P   CE1_200614s  <--->      ILE16    P     CD_184     4.3     8.9
@>      ARG58    P     CG_82014s  <--->     PHE138    P   CE1_2104     4.5    59.4
@> Number of detected hydrophobic interactions: 39.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
..
..
@> Frame: 20
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>      ARG97    P       NE_1444  <--->      GLU93    P      OE1_1383     2.5    12.5
@>      SER19    P        OG_232  <--->      ASN15    P       OD1_165     2.6    31.5
@>      ARG27    P       NH1_356  <--->      GLU23    P       OE1_290     2.6    19.1
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.6    21.5
@>     GLN122    P      NE2_1854  <--->     ASP120    P      OD2_1825     2.6    39.7
@>     SER118    P       OG_1791  <--->     GLU114    P      OE2_1736     2.6    24.5
@>      ARG65    P       NH1_938  <--->     GLU139    P      OE1_2125     2.7     6.1
@>      ARG65    P       NH2_941  <--->     ASP135    P      OD1_2067     2.7    15.6
@>      SER43    P        OG_620  <--->      GLU23    P       OE2_291     2.7    13.9
@>      ARG75    P       NE_1087  <--->      ASP42    P       OD1_609     2.7    26.5
@>     ARG150    P       NE_2300  <--->     GLU154    P      OE2_2372     2.7     4.9
@>     VAL106    P        N_1588  <--->     LYS102    P        O_1545     2.7    16.2
@>      LYS28    P         N_364  <--->      ALA24    P         O_303     2.7    38.8
@>     HSE157    P      NE2_2418  <--->     PHE152    P        O_2340     2.7    28.5
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.7    19.3
@>      ARG97    P      NH2_1450  <--->      GLU93    P      OE2_1384     2.7    15.8
@>      ARG75    P      NH2_1093  <--->      ASP42    P       OD1_609     2.7    30.5
@>      ALA45    P         N_634  <--->      ARG75    P        O_1097     2.7    22.3
@>      ARG75    P      NH2_1093  <--->      ASP81    P      OD1_1193     2.7    19.2
@>      THR31    P       OG1_427  <--->      ARG27    P         O_363     2.7    13.1
@>     ARG150    P      NH2_2306  <--->     GLU154    P      OE1_2371     2.7     8.5
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.7    14.8
@>      GLY67    P         N_963  <--->      MET63    P         O_899     2.7    25.3
@>      LEU89    P        N_1313  <--->       LEU9    P          O_83     2.8    18.4
@>     ARG101    P      NH1_1516  <--->      ASP98    P      OD2_1464     2.8    11.5
@>      ILE77    P        N_1115  <--->      ALA45    P         O_643     2.8    39.9
@>     LYS110    P        N_1651  <--->      PHE82    P        O_1216     2.8    32.3
@>      LEU29    P         N_386  <--->      VAL25    P         O_319     2.8     5.4
@>     ASN100    P        N_1486  <--->      LEU96    P        O_1430     2.8     6.7
@>     LYS102    P        N_1524  <--->      ASP98    P        O_1466     2.8     4.9
@>      THR78    P      OG1_1140  <--->      ASP81    P      OD2_1194     2.8    10.5
@>       VAL8    P          N_49  <--->      ARG40    P         O_584     2.8    16.8
@>     GLU154    P        N_2360  <--->     ARG150    P        O_2310     2.8    15.1
@>     LYS110    P       NZ_1667  <--->      ASP86    P      OD2_1270     2.8    32.5
@>      ARG58    P        NE_826  <--->      ASP56    P       OD1_788     2.8     3.3
@>      ILE35    P         N_478  <--->      VAL30    P         O_420     2.8     7.9
@>      ARG58    P       NH1_829  <--->     GLY133    P        O_2044     2.8    34.3
@>     GLN105    P        N_1571  <--->     ARG101    P        O_1523     2.8    29.9
@>       SER7    P          N_38  <--->      ASP86    P      OD1_1269     2.8    10.5
@>     ARG101    P      NH2_1519  <--->      ASP98    P      OD1_1463     2.8    17.5
@>     GLN143    P        N_2180  <--->     GLU139    P        O_2128     2.8    20.5
@>     CYS149    P        N_2276  <--->     CYS145    P        O_2224     2.8    16.0
@>     SER103    P       OG_1553  <--->      LEU99    P        O_1485     2.9    21.4
@>      ARG18    P       NH1_217  <--->      ASP92    P      OD2_1369     2.9     6.7
@>      CYS90    P        N_1332  <--->     GLU114    P        O_1738     2.9     7.9
@>      ARG18    P       NH1_217  <--->     ILE127    P        O_1954     2.9    13.0
@>     LYS155    P       NZ_2391  <--->     TYR119    P        O_1815     2.9    27.9
@>     ARG150    P        N_2287  <--->     VAL146    P        O_2240     2.9    39.3
@>      ARG65    P       NH1_938  <--->     ASP135    P      OD2_2068     2.9    39.2
@>      VAL30    P         N_405  <--->      PHE26    P         O_339     2.9     2.0
@>      VAL11    P         N_104  <--->      LEU89    P        O_1331     2.9    19.9
@>     GLN144    P        N_2197  <--->     THR140    P        O_2142     2.9    16.4
@>     LEU116    P        N_1758  <--->      CYS90    P        O_1342     2.9    22.2
@>     SER103    P        N_1546  <--->      LEU99    P        O_1485     2.9    35.6
@>      ASP56    P         N_780  <--->      ILE16    P         O_189     2.9     5.0
@>     GLU139    P        N_2114  <--->     ASP135    P        O_2070     2.9    33.1
@>      PHE10    P          N_84  <--->      ASP42    P         O_612     2.9    11.4
@>     LYS155    P        N_2375  <--->     ALA151    P        O_2320     2.9    39.0
@>      PHE26    P         N_320  <--->      ALA22    P         O_278     2.9    21.1
@>     THR140    P        N_2129  <--->     SER136    P        O_2081     3.0    36.4
@>      ALA74    P        N_1064  <--->      ASN53    P         O_751     3.0    20.8
@>       LYS6    P          N_16  <--->      ASN38    P         O_536     3.0    12.1
@>      ARG65    P         N_922  <--->      SER61    P         O_871     3.0    15.7
@>       LEU9    P          N_65  <--->      TYR87    P        O_1293     3.0     6.8
..
..
@> Number of detected hydrogen bonds: 114.
@> Calculating salt bridges.
@>     ASP135    P   OD1_2067_2068  <--->      ARG65    P     NH1_938_941     2.5
@>      ASP81    P   OD1_1193_1194  <--->      ARG75    P   NH1_1090_1093     2.7
@>      ASP98    P   OD1_1463_1464  <--->     ARG101    P   NH1_1516_1519     2.8
@>      ASP86    P   OD1_1269_1270  <--->     LYS110    P         NZ_1667     3.4
@>      ARG97    P   NH1_1447_1450  <--->      GLU93    P   OE1_1383_1384     3.5
@>     ARG150    P   NH1_2303_2306  <--->     GLU154    P   OE1_2371_2372     3.7
@>      ARG58    P     NH1_829_832  <--->      ASP56    P     OD1_788_789     3.7
@>     GLU139    P   OE1_2125_2126  <--->      HSE66    P         NE2_957     3.9
@>      ARG18    P     NH1_217_220  <--->      ASP92    P   OD1_1368_1369     4.0
@>      ARG27    P     NH1_356_359  <--->      GLU23    P     OE1_290_291     4.0
@>      ARG75    P   NH1_1090_1093  <--->      ASP42    P     OD1_609_610     4.4
@>      GLU23    P     OE1_290_291  <--->      HSE72    P        NE2_1042     4.7
@>     GLU139    P   OE1_2125_2126  <--->      ARG65    P     NH1_938_941     4.8
@>      ARG18    P     NH1_217_220  <--->     ASP129    P   OD1_1978_1979     5.0
@> Number of detected salt bridges: 14.
@> Calculating repulsive ionic bonding.
@>     ARG147    P   NH1_2257_2260  <--->     LYS123    P         NZ_1875     4.5
@> Number of detected Repulsive Ionic Bonding interactions: 1.
@> Calculating Pi stacking interactions.
@>     TYR119       P   1802_1803_1805_1807_1810_1812  <--->     PHE152       P   2328_2329_2331_2333_2335_2337     4.7   125.5
@>      HSE66       P             953_954_955_957_959  <--->     TYR142       P   2166_2167_2169_2171_2174_2176     4.8   165.0
@>     TYR132       P   2024_2025_2027_2029_2032_2034  <--->     TYR131       P   2003_2004_2006_2008_2011_2013     4.9   116.3
@> Number of detected Pi stacking interactions: 3.
@> Calculating cation-Pi interactions.
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.0
@> Number of detected cation-pi interactions: 1.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@>      LEU96    P   CD1_142114s  <--->     ILE113    P   CG2_1711     3.3    21.1
@>      ILE88    P    CD_130714s  <--->      PHE82    P   CD2_1211     3.4    25.2
@>      VAL11    P    CG2_11414s  <--->      LEU99    P   CD1_1476     3.4    11.5
@>      MET63    P     SD_89314s  <--->     TYR142    P   CE1_2169     3.4    37.7
@>      TRP39    P    NE1_54714s  <--->     LEU153    P   CD1_2350     3.4    19.2
@>     ALA111    P    CB_167714s  <--->      ILE88    P    CD_1307     3.5    23.0
@>      ILE35    P     CD_49114s  <--->     LEU153    P   CD1_2350     3.5    16.4
@>      VAL30    P    CG1_41114s  <--->     LEU153    P   CD2_2354     3.5     9.8
@>       LEU9    P     CD2_7814s  <--->      ILE77    P    CD_1128     3.5    17.0
@>      PHE10    P     CE1_9414s  <--->      LEU89    P   CD1_1322     3.5    25.4
@>     TYR119    P   CE1_180514s  <--->      LEU89    P   CD2_1326     3.6    18.5
@>      ALA24    P     CB_29814s  <--->      MET63    P     CE_894     3.6    13.8
@>      PHE26    P     CZ_33214s  <--->     LEU153    P   CD1_2350     3.6    27.1
@>       VAL8    P     CG2_5914s  <--->      LEU89    P   CD1_1322     3.6    13.0
@>      ALA22    P     CB_27314s  <--->      PHE10    P     CD1_92     3.6    29.5
@>      MET91    P    CE_135414s  <--->      ALA22    P     CB_273     3.7     9.1
@>      VAL41    P    CG2_59514s  <--->      PHE26    P    CD2_334     3.7    17.5
@>     LEU116    P   CD2_177114s  <--->      MET91    P    SD_1353     3.7    21.9
@>      ALA44    P     CB_62814s  <--->      VAL11    P    CG1_110     3.7    34.2
@>       LYS6    P      CD_2614s  <--->      TRP39    P    CH2_557     3.7    44.8
@>     VAL146    P   CG2_223514s  <--->     TYR142    P   CE2_2176     3.8    39.4
@>      PHE85    P   CE1_125114s  <--->       LEU9    P     CD1_74     3.8    31.6
@>      ILE21    P    CG2_25614s  <--->      VAL25    P    CG2_314     3.8    25.0
@>     VAL141    P   CG1_214914s  <--->      ILE21    P     CD_263     3.9    13.0
@>      ILE68    P    CG1_98014s  <--->      MET63    P     CE_894     3.9    37.2
@>     PHE152    P    CZ_233314s  <--->      LEU89    P   CD1_1322     3.9    18.0
@>      ARG18    P     CG_20814s  <--->     VAL141    P   CG1_2149     4.0    26.2
@>      ARG75    P    CG_108114s  <--->      ALA44    P     CB_628     4.2    27.4
@>     ILE127    P    CD_194914s  <--->     LEU116    P   CD2_1771     4.3     7.9
@>      LYS79    P    CG_115514s  <--->     VAL106    P   CG2_1598     4.3    15.6
@>      LEU29    P     CG_39314s  <--->      VAL25    P    CG1_310     4.3    21.7
@>     ILE126    P   CG1_192714s  <--->     LEU125    P    CG_1905     4.4    55.6
@> Number of detected hydrophobic interactions: 32.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.
@> File with interactions saved.

The results are displayed on the screen and they can be fetch by using InteractionsTrajectory.getInteractions() method.

In [16]: interactionsTrajectory.getInteractions()
[[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
   ['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
   ['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
   ['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
   ['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
   ['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
   ['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
   ['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
   ['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
   ['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
   ['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
   ['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
   ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
   ['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
   ['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
   ['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
   ['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
   ['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
   ['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
   ['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
   ['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
   ['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
   ['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
   ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
   ['GLN143', 'N_2180', 'P', 'GLU139', 'O_2128', 'P', 2.8445, 21.6714],
   ['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.8446, 15.4167],
   ['TYR142', 'N_2159', 'P', 'PHE138', 'O_2113', 'P', 2.8515, 14.2061],
   ['GLY133', 'N_2038', 'P', 'PRO130', 'O_1995', 'P', 2.854, 25.4301],
   ['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8541, 4.8732],
   ['ASN15', 'ND2_166', 'P', 'SER19', 'OG_232', 'P', 2.8592, 32.1244],
   ['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8632, 19.6664],
   ['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.8649, 23.5083],
   ['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8654, 22.24],
   ['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8655, 32.3239],
   ['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.8666, 8.2255],
   ['LEU153', 'N_2341', 'P', 'CYS149', 'O_2286', 'P', 2.8707, 12.4931],
   ['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.8732, 39.8839],
   ['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8753, 34.7426],
   ..
  [['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.5487, 20.8176],
   ['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.5494, 15.6392],
   ['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.5496, 36.5043],
   ['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.5756, 25.1514],
   ['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.5904, 32.2995],
   ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.5963, 18.6089],
   ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6334, 17.8203],
   ['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 2.6367, 17.6426],
   ['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.6547, 25.6442],
   ['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 2.6611, 6.4459],
   ['GLN124', 'N_1881', 'P', 'ASP120', 'OD1_1824', 'P', 2.6666, 17.1571],
   ['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 2.6875, 11.8479],
   ['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.6879, 14.5803],
   ['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.6889, 23.9375],
   ['TYR87', 'OH_1286', 'P', 'HSE157', 'OT1_2423', 'P', 2.6945, 11.5603],
   ['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.6978, 15.166],
   ['LYS28', 'NZ_380', 'P', 'ASP32', 'OD1_443', 'P', 2.7003, 3.632],
   ['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.7025, 25.1511],
   ['THR140', 'OG1_2135', 'P', 'SER136', 'O_2081', 'P', 2.71, 5.2209],
   ['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.7125, 24.3959],
   ['THR5', 'OG1_8', 'P', 'ASN38', 'O_536', 'P', 2.7162, 38.6072],
   ['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.7222, 26.7806],
   ['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD2_1825', 'P', 2.731, 15.2446],
   ['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.7341, 21.9432],
   ['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.735, 15.8502],
   ['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.7501, 16.0113],
   ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7535, 13.6202],
   ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7626, 15.9446],
   ['ARG58', 'NH1_829', 'P', 'GLY133', 'O_2044', 'P', 2.7673, 31.8828],
   ['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.7744, 13.0389],
   ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7935, 13.2257],
   ['GLU23', 'N_279', 'P', 'SER19', 'O_235', 'P', 2.8067, 10.8775],
   ['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.813, 38.9132],
   ['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.8182, 13.801],
   ['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8212, 18.2267],
   ['LEU9', 'N_65', 'P', 'TYR87', 'O_1293', 'P', 2.8249, 34.2551],
   ['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8308, 14.8745],
   ['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8328, 9.2758],
   ..
  [['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.5097, 4.9218],
   ['THR31', 'OG1_427', 'P', 'ARG27', 'O_363', 'P', 2.5496, 5.4538],
   ['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.5525, 8.1856],
   ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.5902, 19.0335],
   ['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.6114, 24.975],
   ['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6441, 10.2991],
   ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6466, 7.8982],
   ['TYR87', 'OH_1286', 'P', 'HSE157', 'OT1_2423', 'P', 2.6516, 14.0793],
   ['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.6643, 4.9246],
   ['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.7024, 8.6062],
   ['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.7158, 6.5273],
   ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7184, 24.9984],
   ['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7238, 26.9156],
   ['LYS28', 'NZ_380', 'P', 'ASP32', 'OD2_444', 'P', 2.7274, 13.9298],
   ['THR84', 'OG1_1233', 'P', 'GLU80', 'O_1184', 'P', 2.7314, 13.4406],
   ['LEU89', 'N_1313', 'P', 'LEU9', 'O_83', 'P', 2.7581, 11.8493],
   ['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 2.7633, 15.0984],
   ['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.765, 17.97],
   ['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.7659, 20.7163],
   ['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.7663, 21.7712],
   ['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.767, 10.3325],
   ['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.7679, 9.2024],
   ['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.7682, 29.4143],
   ['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.7756, 37.1399],
   ['ASN34', 'N_464', 'P', 'THR31', 'O_434', 'P', 2.7794, 19.6803],
   ['LYS110', 'N_1651', 'P', 'PHE82', 'O_1216', 'P', 2.7863, 9.1814],
   ['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.7932, 13.508],
   ['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 2.8021, 8.0221],
   ['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8066, 14.9419],
   ['VAL8', 'N_49', 'P', 'ARG40', 'O_584', 'P', 2.8114, 19.4027],
   ['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.8173, 6.9549],
   ['LYS155', 'N_2375', 'P', 'ALA151', 'O_2320', 'P', 2.8212, 15.1026],
   ['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.8239, 28.9105],
   ['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD2_1825', 'P', 2.8257, 31.6579],
   ['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8291, 15.1587],
   ['LYS123', 'N_1859', 'P', 'ASP120', 'OD1_1824', 'P', 2.8292, 34.0011],
   ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8381, 10.253],
   ['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8406, 22.034],
   ['ARG65', 'N_922', 'P', 'SER61', 'O_871', 'P', 2.8423, 24.4142],
   ['ILE127', 'N_1936', 'P', 'MET91', 'O_1359', 'P', 2.8469, 4.126],
   ['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8616, 14.018],
   ['GLY67', 'N_963', 'P', 'MET63', 'O_899', 'P', 2.8626, 38.6183],
   ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8761, 17.0562],
   ['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8761, 18.0626],
   ['ARG75', 'NE_1087', 'P', 'ASP42', 'OD2_610', 'P', 2.8795, 38.3078],
   ['ALA44', 'N_624', 'P', 'PHE10', 'O_103', 'P', 2.8798, 30.1431],
   ['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8902, 12.9079],
   ['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.903, 21.0711],
   ['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.9152, 26.3475],
   ['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.9235, 27.7222],
   ..
  [['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.5321, 12.1754],
   ['SER7', 'OG_45', 'P', 'ASP86', 'OD2_1270', 'P', 2.5681, 8.2326],
   ['SER43', 'OG_620', 'P', 'GLU23', 'OE1_290', 'P', 2.5908, 6.4741],
   ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.5911, 17.069],
   ['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.6234, 15.5609],
   ['THR78', 'OG1_1140', 'P', 'ASP81', 'OD2_1194', 'P', 2.6239, 11.6022],
   ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6274, 12.9418],
   ['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.6388, 5.0129],
   ['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.6571, 20.4048],
   ['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6666, 5.0368],
   ['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.677, 21.8922],
   ['ARG18', 'NH2_220', 'P', 'ASP92', 'OD2_1369', 'P', 2.6813, 31.3689],
   ['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.6844, 12.4337],
   ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7018, 15.5273],
   ['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.7094, 34.9749],
   ['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7146, 21.3402],
   ['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.719, 23.3583],
   ['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.7207, 8.4795],
   ['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.7283, 14.8893],
   ['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 2.7353, 26.7201],
   ['THR31', 'OG1_427', 'P', 'ARG27', 'O_363', 'P', 2.7466, 22.4844],
   ['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.7489, 16.6396],
   ['ARG58', 'NH1_829', 'P', 'TYR132', 'O_2037', 'P', 2.7511, 23.6002],
   ['ARG147', 'NH1_2257', 'P', 'ASP120', 'OD1_1824', 'P', 2.7592, 19.3384],
   ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7625, 21.1367],
   ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7703, 4.1752],
   ['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.7726, 18.0115],
   ['ARG65', 'NH1_938', 'P', 'GLU139', 'OE1_2125', 'P', 2.7749, 18.9952],
   ['GLY133', 'N_2038', 'P', 'ASP137', 'OD2_2091', 'P', 2.7764, 32.7458],
   ['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 2.7783, 16.8911],
   ['TYR87', 'OH_1286', 'P', 'HSE157', 'OT2_2424', 'P', 2.7928, 9.9286],
   ['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.7945, 6.0583],
   ['LYS28', 'NZ_380', 'P', 'ASP32', 'OD2_444', 'P', 2.7993, 35.4827],
   ['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8, 5.5477],
   ['LYS110', 'NZ_1667', 'P', 'ASP86', 'OD1_1269', 'P', 2.8021, 14.2767],
   ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.813, 11.6498],
   ['GLN60', 'N_844', 'P', 'ASP56', 'O_791', 'P', 2.8156, 25.2584],
   ['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.8209, 30.082],
   ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8375, 24.3092],
   ['ARG150', 'N_2287', 'P', 'VAL146', 'O_2240', 'P', 2.8394, 21.6561],
   ..
   ..
[['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.2931, 21.0747],
   ['ILE88', 'CD_1307', 'P', 'PHE82', 'CD2_1211', 'P', 3.3689, 25.2319],
   ['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.3771, 11.4804],
   ['MET63', 'SD_893', 'P', 'TYR142', 'CE1_2169', 'P', 3.3896, 37.7382],
   ['TRP39', 'NE1_547', 'P', 'LEU153', 'CD1_2350', 'P', 3.4345, 19.2142],
   ['ALA111', 'CB_1677', 'P', 'ILE88', 'CD_1307', 'P', 3.4669, 22.9943],
   ['ILE35', 'CD_491', 'P', 'LEU153', 'CD1_2350', 'P', 3.4868, 16.4472],
   ['VAL30', 'CG1_411', 'P', 'LEU153', 'CD2_2354', 'P', 3.4938, 9.7531],
   ['LEU9', 'CD2_78', 'P', 'ILE77', 'CD_1128', 'P', 3.5133, 16.9544],
   ['PHE10', 'CE1_94', 'P', 'LEU89', 'CD1_1322', 'P', 3.5468, 25.3848],
   ['TYR119', 'CE1_1805', 'P', 'LEU89', 'CD2_1326', 'P', 3.554, 18.5297],
   ['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.5859, 13.7697],
   ['PHE26', 'CZ_332', 'P', 'LEU153', 'CD1_2350', 'P', 3.6118, 27.1048],
   ['VAL8', 'CG2_59', 'P', 'LEU89', 'CD1_1322', 'P', 3.6199, 12.9537],
   ['ALA22', 'CB_273', 'P', 'PHE10', 'CD1_92', 'P', 3.6246, 29.4846],
   ['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.6628, 9.0978],
   ['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6792, 17.4783],
   ['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6984, 21.9302],
   ['ALA44', 'CB_628', 'P', 'VAL11', 'CG1_110', 'P', 3.7022, 34.2417],
   ['LYS6', 'CD_26', 'P', 'TRP39', 'CH2_557', 'P', 3.7135, 44.8],
   ['VAL146', 'CG2_2235', 'P', 'TYR142', 'CE2_2176', 'P', 3.7622, 39.414],
   ['PHE85', 'CE1_1251', 'P', 'LEU9', 'CD1_74', 'P', 3.8118, 31.6126],
   ['ILE21', 'CG2_256', 'P', 'VAL25', 'CG2_314', 'P', 3.825, 25.047],
   ['VAL141', 'CG1_2149', 'P', 'ILE21', 'CD_263', 'P', 3.8615, 13.036],
   ['ILE68', 'CG1_980', 'P', 'MET63', 'CE_894', 'P', 3.8698, 37.1931],
   ['PHE152', 'CZ_2333', 'P', 'LEU89', 'CD1_1322', 'P', 3.9131, 17.9674],
   ['ARG18', 'CG_208', 'P', 'VAL141', 'CG1_2149', 'P', 3.9881, 26.173],
   ['ARG75', 'CG_1081', 'P', 'ALA44', 'CB_628', 'P', 4.1878, 27.3996],
   ['ILE127', 'CD_1949', 'P', 'LEU116', 'CD2_1771', 'P', 4.2643, 7.8575],
   ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2738, 15.6412],
   ['LEU29', 'CG_393', 'P', 'VAL25', 'CG1_310', 'P', 4.3325, 21.7286],
   ['ILE126', 'CG1_1927', 'P', 'LEU125', 'CG_1905', 'P', 4.4374, 55.6364]]],
 [[],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  [],
  []]]

Moreover, we can display the evolution of each interaction type during the simulation. There are the following types of plots: hydrogen bonds (blue), salt bridges (yellow), hydrophobic interactions (silver), Pi-stacking (green), Pi-cation (orange), repulsive ionic bonding (red), disulfide bonds(black).

In [17]: interactionsTrajectory.getTimeInteractions()
../../_images/insty_traj_counts.png

If the structure is stable, we will not observe a lot of changes in protein structure.

Similar to the single PDB analysis, we have an access to each interaction type by using: InteractionsTrajectory.getHydrogenBonds() method, etc.

In [18]: interactionsTrajectory.getHydrogenBonds()
[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
  ['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
  ['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
  ['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
  ['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
  ['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
  ['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
  ['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
  ['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
  ['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
  ['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
  ['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
  ['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
  ['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
  ['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
  ['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
  ['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
  ['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
  ['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
  ['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
  ['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
  ['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
  ['GLN143', 'N_2180', 'P', 'GLU139', 'O_2128', 'P', 2.8445, 21.6714],
  ['ARG27', 'N_340', 'P', 'GLU23', 'O_293', 'P', 2.8446, 15.4167],
  ['TYR142', 'N_2159', 'P', 'PHE138', 'O_2113', 'P', 2.8515, 14.2061],
  ['GLY133', 'N_2038', 'P', 'PRO130', 'O_1995', 'P', 2.854, 25.4301],
  ['PHE26', 'N_320', 'P', 'ALA22', 'O_278', 'P', 2.8541, 4.8732],
  ['ASN15', 'ND2_166', 'P', 'SER19', 'OG_232', 'P', 2.8592, 32.1244],
  ['ARG75', 'NH1_1090', 'P', 'ASP81', 'OD2_1194', 'P', 2.8632, 19.6664],
  ['ARG75', 'NH2_1093', 'P', 'ASP42', 'OD2_610', 'P', 2.8649, 23.5083],
  ['ARG97', 'N_1431', 'P', 'GLU93', 'O_1386', 'P', 2.8654, 22.24],
  ['ARG65', 'NH2_941', 'P', 'GLU139', 'OE1_2125', 'P', 2.8655, 32.3239],
  ['VAL25', 'N_304', 'P', 'ILE21', 'O_268', 'P', 2.8666, 8.2255],
  ['LEU153', 'N_2341', 'P', 'CYS149', 'O_2286', 'P', 2.8707, 12.4931],
  ['SER7', 'N_38', 'P', 'ASP86', 'OD2_1270', 'P', 2.8732, 39.8839],
  ['ASP86', 'N_1261', 'P', 'SER7', 'OG_45', 'P', 2.8753, 34.7426],
  ['ARG58', 'NH2_832', 'P', 'TYR131', 'O_2016', 'P', 2.8815, 33.1098],
  ['THR46', 'N_644', 'P', 'CYS12', 'O_130', 'P', 2.883, 36.1279],
  ['GLN144', 'N_2197', 'P', 'THR140', 'O_2142', 'P', 2.8836, 23.2545],
  ['THR78', 'N_1134', 'P', 'ASP81', 'OD2_1194', 'P', 2.8869, 12.4465],
  ['LEU89', 'N_1313', 'P', 'LEU9', 'O_83', 'P', 2.8946, 29.5105],
  ['THR31', 'N_421', 'P', 'ARG27', 'O_363', 'P', 2.896, 24.1287],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8975, 24.576],
  ['CYS148', 'N_2265', 'P', 'GLN144', 'O_2213', 'P', 2.8976, 9.3165],
  ['GLU23', 'N_279', 'P', 'SER19', 'O_235', 'P', 2.8979, 15.4146],
  ['ILE68', 'N_970', 'P', 'MET63', 'O_899', 'P', 2.8986, 12.9903],
  ['PHE10', 'N_84', 'P', 'ASP42', 'O_612', 'P', 2.9026, 22.751],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.912, 10.1158],
  ['SER61', 'N_861', 'P', 'TYR57', 'O_812', 'P', 2.9132, 35.1196],
  ['CYS145', 'N_2214', 'P', 'VAL141', 'O_2158', 'P', 2.9144, 15.8507],
  ['ARG27', 'NH2_359', 'P', 'GLU23', 'OE2_291', 'P', 2.9199, 31.5487],
  ['LYS64', 'N_900', 'P', 'GLN60', 'O_860', 'P', 2.9211, 22.8783],
  ['LEU9', 'N_65', 'P', 'TYR87', 'O_1293', 'P', 2.9229, 16.439],
  ['ASN38', 'N_523', 'P', 'ILE35', 'O_496', 'P', 2.9255, 29.091],
  ['VAL11', 'N_104', 'P', 'LEU89', 'O_1331', 'P', 2.9316, 29.7192],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.933, 10.3321],
  ['GLN124', 'N_1881', 'P', 'ASP120', 'OD2_1825', 'P', 2.9333, 27.4547],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9361, 9.2855],
  ['GLN76', 'NE2_1110', 'P', 'THR46', 'O_657', 'P', 2.9381, 31.3836],
  ['ARG40', 'NH1_577', 'P', 'THR84', 'OG1_1233', 'P', 2.9482, 8.3748],
  ['ALA44', 'N_624', 'P', 'PHE10', 'O_103', 'P', 2.9499, 33.1771],
  ['GLU154', 'N_2360', 'P', 'ARG150', 'O_2310', 'P', 2.956, 22.5898],
  ['VAL8', 'N_49', 'P', 'ARG40', 'O_584', 'P', 2.9631, 25.0079],
  ['MET63', 'N_883', 'P', 'GLY59', 'O_843', 'P', 2.9733, 18.2731],
  ['GLN60', 'N_844', 'P', 'ASP56', 'O_791', 'P', 2.9795, 35.5229],
  ['ILE35', 'N_478', 'P', 'VAL30', 'O_420', 'P', 2.9811, 23.5092],
  ['VAL146', 'N_2225', 'P', 'TYR142', 'O_2179', 'P', 2.9914, 31.4798],
  ['ARG58', 'NH1_829', 'P', 'TYR131', 'O_2016', 'P', 2.9942, 38.0937],
  ['ASN53', 'N_738', 'P', 'GLU50', 'O_711', 'P', 2.995, 28.587],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9952, 32.2712],
  ['ARG18', 'NH1_217', 'P', 'ILE127', 'O_1954', 'P', 2.9957, 25.9507],
  ['ARG75', 'N_1074', 'P', 'ASN15', 'OD1_165', 'P', 3.0026, 25.0853],
  ['GLN144', 'NE2_2209', 'P', 'ILE126', 'O_1935', 'P', 3.0038, 18.2744],
  ['ASN34', 'N_464', 'P', 'THR31', 'O_434', 'P', 3.0041, 18.2465],
  ['ASN15', 'ND2_166', 'P', 'SER43', 'OG_620', 'P', 3.0129, 25.6996],
  ['ARG58', 'NE_826', 'P', 'ASP56', 'OD1_788', 'P', 3.017, 22.2284],
  ['ARG27', 'NH1_356', 'P', 'GLU23', 'OE2_291', 'P', 3.0175, 36.9342],
  ['ILE127', 'N_1936', 'P', 'MET91', 'O_1359', 'P', 3.018, 17.5601],
  ['TYR119', 'OH_1808', 'P', 'HSE157', 'N_2407', 'P', 3.0224, 28.0923],
  ['HSE157', 'N_2407', 'P', 'TYR119', 'OH_1808', 'P', 3.0224, 19.1804],
  ['GLU139', 'N_2114', 'P', 'ASP135', 'O_2070', 'P', 3.0245, 27.9246],
  ['LEU29', 'N_386', 'P', 'VAL25', 'O_319', 'P', 3.0299, 19.1089],
  ['SER47', 'N_658', 'P', 'LEU13', 'O_149', 'P', 3.0386, 28.8029],
  ['VAL30', 'N_405', 'P', 'PHE26', 'O_339', 'P', 3.0394, 17.6883],
  ['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.0464, 19.6807],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.051, 21.4045],
  ['LYS155', 'N_2375', 'P', 'ALA151', 'O_2320', 'P', 3.0555, 21.3244],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.059, 24.1606],
  ['ASP120', 'N_1816', 'P', 'GLY117', 'O_1783', 'P', 3.0623, 12.666],
  ['CYS62', 'N_872', 'P', 'ARG58', 'O_836', 'P', 3.0651, 20.443],
  ['ARG18', 'NH1_217', 'P', 'ASP92', 'OD2_1369', 'P', 3.0679, 4.2778],
  ['ALA24', 'N_294', 'P', 'PRO20', 'O_249', 'P', 3.0751, 29.9487],
  ['ARG150', 'N_2287', 'P', 'VAL146', 'O_2240', 'P', 3.078, 12.7022],
  ['LYS28', 'N_364', 'P', 'ALA24', 'O_303', 'P', 3.0783, 19.9504],
  ['VAL141', 'N_2143', 'P', 'ASP137', 'O_2093', 'P', 3.081, 18.4811],
  ['ASP98', 'N_1455', 'P', 'SER94', 'O_1397', 'P', 3.0844, 19.56],
  ['LEU96', 'N_1412', 'P', 'ASP92', 'O_1371', 'P', 3.085, 36.3254],
  ['ALA22', 'N_269', 'P', 'ARG18', 'O_224', 'P', 3.088, 21.873],
  ['ALA151', 'N_2311', 'P', 'ARG147', 'O_2264', 'P', 3.0991, 15.5713],
  ['GLY67', 'N_963', 'P', 'LYS64', 'O_921', 'P', 3.122, 22.7833],
  ['ASP42', 'N_601', 'P', 'VAL8', 'O_64', 'P', 3.1331, 35.5671],
  ['ARG65', 'N_922', 'P', 'SER61', 'O_871', 'P', 3.1339, 23.3682],
  ['TRP39', 'N_537', 'P', 'SER36', 'O_507', 'P', 3.1343, 15.1775],
  ['LYS123', 'N_1859', 'P', 'ASP120', 'O_1827', 'P', 3.1375, 18.6589],
  ['MET91', 'N_1343', 'P', 'ASN95', 'OD1_1406', 'P', 3.1581, 39.0427],
  ['THR140', 'N_2129', 'P', 'SER136', 'O_2081', 'P', 3.1742, 30.2937],
  ['PHE85', 'N_1241', 'P', 'ASP81', 'O_1196', 'P', 3.1845, 20.2243],
  ['ASN15', 'N_157', 'P', 'CYS12', 'SG_127', 'P', 3.2043, 37.4576],
  ['ALA111', 'N_1673', 'P', 'PHE82', 'O_1216', 'P', 3.2054, 20.58],
  ['ARG147', 'N_2241', 'P', 'GLN143', 'O_2196', 'P', 3.2416, 12.0678],
  ['ARG75', 'NH2_1093', 'P', 'ASP81', 'OD1_1193', 'P', 3.2447, 29.3403],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 3.2687, 28.6743],
  ['ARG147', 'NH1_2257', 'P', 'GLN124', 'OE1_1892', 'P', 3.3008, 29.853],
  ['PHE138', 'N_2094', 'P', 'ASN134', 'O_2058', 'P', 3.3062, 31.0247],
  ['SER7', 'OG_45', 'P', 'THR84', 'O_1240', 'P', 3.3227, 35.5231],
  ['CYS12', 'N_120', 'P', 'ALA44', 'O_633', 'P', 3.3349, 36.1006],
  ..
  ..
In [19]: interactionsTrajectory.getSaltBridges()
[[['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 2.8359],
  ['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.9163],
  ['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 3.037],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
  ['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.7148],
  ['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 3.7799],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359],
  ['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.9486],
  ['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 4.0693],
  ['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 4.0787],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.1543],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.1879],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.3835],
  ['ARG18', 'NH1_217_220', 'P', 'ASP129', 'OD1_1978_1979', 'P', 4.5608],
  ['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.5612],
  ['GLU23', 'OE1_290_291', 'P', 'HSE72', 'NE2_1042', 'P', 4.99]],
 [['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5568],
  ['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.6325],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
  ['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.0552],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.2384],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3269],
  ['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.4115],
  ['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 3.4427],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8015],
  ['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.8017],
  ['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 3.8368],
  ['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 3.9677],
  ['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.5207]],
 [['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5925],
  ['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5955],
  ['GLU139', 'OE1_2125_2126', 'P', 'ARG65', 'NH1_938_941', 'P', 2.6677],
  ['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.945],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796],
  ['ARG58', 'NH1_829_832', 'P', 'ASP56', 'OD1_788_789', 'P', 3.6],
  ['GLU139', 'OE1_2125_2126', 'P', 'HSE66', 'NE2_957', 'P', 3.6121],
  ['ARG18', 'NH1_217_220', 'P', 'ASP92', 'OD1_1368_1369', 'P', 3.6951],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7353],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8213],
  ['ARG27', 'NH1_356_359', 'P', 'GLU23', 'OE1_290_291', 'P', 3.897],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.2197],
  ['ARG75', 'NH1_1090_1093', 'P', 'ASP42', 'OD1_609_610', 'P', 4.3401],
  ['ARG18', 'NH1_217_220', 'P', 'ASP129', 'OD1_1978_1979', 'P', 4.6103],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS6', 'NZ_32', 'P', 4.9726]],
 [['ASP32', 'OD1_443_444', 'P', 'LYS28', 'NZ_380', 'P', 2.5045],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
  ['ASP81', 'OD1_1193_1194', 'P', 'ARG75', 'NH1_1090_1093', 'P', 2.8842],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.2487],
  ..
  ..
In [20]: interactionsTrajectory.getHydrophobic()
[[['ALA156', 'CB_2401', 'P', 'TYR87', 'OH_1286', 'P', 3.0459, 21.959],
  ['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3105, 5.1584],
  ['ILE68', 'CG2_976', 'P', 'MET63', 'CE_894', 'P', 3.3306, 52.4165],
  ['TYR142', 'CZ_2171', 'P', 'VAL146', 'CG2_2235', 'P', 3.4815, 49.7427],
  ['PHE10', 'CD1_92', 'P', 'ALA22', 'CB_273', 'P', 3.5334, 31.1973],
  ['LYS6', 'CD_26', 'P', 'TRP39', 'CZ2_555', 'P', 3.5427, 68.7284],
  ['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5603, 21.127],
  ['ILE88', 'CD_1307', 'P', 'ALA111', 'CB_1677', 'P', 3.5627, 21.2201],
  ['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6386, 9.3289],
  ['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6448, 16.55],
  ['PHE152', 'CE1_2331', 'P', 'ALA156', 'CB_2401', 'P', 3.6594, 17.4765],
  ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
  ['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
  ['PHE82', 'CD1_1205', 'P', 'ILE88', 'CD_1307', 'P', 3.692, 17.6138],
  ['LEU116', 'CD2_1771', 'P', 'ILE127', 'CD_1949', 'P', 3.7057, 17.4094],
  ['VAL8', 'CG1_55', 'P', 'PHE26', 'CE2_336', 'P', 3.7106, 12.1392],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7263, 16.9718],
  ['LEU9', 'CD2_78', 'P', 'ILE77', 'CD_1128', 'P', 3.745, 15.4175],
  ['LEU89', 'CD1_1322', 'P', 'VAL8', 'CG2_59', 'P', 3.7672, 15.9262],
  ['ILE126', 'CD_1930', 'P', 'LEU125', 'CD1_1907', 'P', 3.7885, 54.1512],
  ['VAL141', 'CG1_2149', 'P', 'ILE127', 'CG2_1942', 'P', 3.8659, 11.4623],
  ['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.8864, 35.855],
  ['ALA44', 'CB_628', 'P', 'LEU9', 'CD1_74', 'P', 3.8992, 15.0915],
  ['VAL25', 'CG2_314', 'P', 'TYR142', 'CE1_2169', 'P', 3.92, 12.0265],
  ['ILE21', 'CG2_256', 'P', 'MET63', 'SD_893', 'P', 3.9614, 20.7701],
  ['LEU153', 'CD1_2350', 'P', 'TRP39', 'NE1_547', 'P', 3.967, 9.4118],
  ['PHE85', 'CZ_1253', 'P', 'LEU9', 'CD1_74', 'P', 4.0119, 32.0573],
  ['ILE35', 'CD_491', 'P', 'TRP39', 'NE1_547', 'P', 4.0172, 25.9805],
  ['LEU29', 'CD1_395', 'P', 'VAL25', 'CG1_310', 'P', 4.0642, 19.7098],
  ['ALA74', 'CB_1068', 'P', 'ILE16', 'CG2_177', 'P', 4.0772, 6.6731],
  ['ARG75', 'CG_1081', 'P', 'ALA44', 'CB_628', 'P', 4.0853, 36.2109],
  ['ARG18', 'CG_208', 'P', 'VAL141', 'CG1_2149', 'P', 4.104, 20.3057],
  ['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1048, 17.4819],
  ['TYR119', 'CE1_1805', 'P', 'LEU89', 'CD2_1326', 'P', 4.1435, 11.5628],
  ['ARG40', 'CG_568', 'P', 'PHE85', 'CE2_1257', 'P', 4.2669, 60.8933],
  ['LYS28', 'CG_371', 'P', 'ILE68', 'CD_983', 'P', 4.2707, 21.8011],
  ['PHE138', 'CD2_2108', 'P', 'ILE21', 'CD_263', 'P', 4.3082, 6.5618],
  ['TYR131', 'CE1_2006', 'P', 'ILE16', 'CD_184', 'P', 4.3352, 8.9118],
  ['ARG58', 'CG_820', 'P', 'PHE138', 'CE1_2104', 'P', 4.4781, 59.4126]],
 [['MET63', 'SD_893', 'P', 'TYR142', 'CD1_2167', 'P', 3.3036, 26.7569],
  ['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3592, 7.0868],
  ['VAL8', 'CG2_59', 'P', 'PHE10', 'CZ_96', 'P', 3.3808, 27.8216],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.429, 13.2977],
  ['LEU116', 'CD1_1767', 'P', 'PHE10', 'CE1_94', 'P', 3.549, 13.546],
  ['PHE82', 'CZ_1209', 'P', 'ILE77', 'CD_1128', 'P', 3.5608, 20.4262],
  ['ILE68', 'CD_983', 'P', 'TYR142', 'OH_2172', 'P', 3.5692, 27.4475],
  ['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5789, 28.1292],
  ['ALA156', 'CB_2401', 'P', 'PHE152', 'CD1_2329', 'P', 3.6255, 24.4807],
  ['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6421, 8.6093],
  ..
  ..
In [21]: interactionsTrajectory.getPiCation()
[[['PHE85',
   '1248_1249_1251_1253_1255_1257',
   'P',
   'ARG40',
   'NH1_577_580',
   'P',
   3.6523],
  ['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.5323],
  ['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   4.828]],
 [['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   3.4611],
  ['PHE85',
   '1248_1249_1251_1253_1255_1257',
   'P',
   'ARG40',
   'NH1_577_580',
   'P',
   3.924],
  ['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.8561],
  ['TYR87',
   '1280_1281_1283_1285_1288_1290',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   4.9287],
  ['TYR131',
   '2003_2004_2006_2008_2011_2013',
   'P',
   'ARG58',
   'NH1_829_832',
   'P',
   4.9441]],
 [['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   2.693],
  ['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.0971],
  ['PHE85',
   '1248_1249_1251_1253_1255_1257',
   'P',
   'ARG40',
   'NH1_577_580',
   'P',
   4.4856]],
 [['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   2.5938],
  ['PHE85',
   '1248_1249_1251_1253_1255_1257',
   'P',
   'ARG40',
   'NH1_577_580',
   'P',
   3.5816],
  ['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 3.8296]],
 [['PHE85',
   '1248_1249_1251_1253_1255_1257',
   'P',
   'ARG40',
   'NH1_577_580',
   'P',
   3.9363],
  ['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.7618],
  ['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS155',
   'NZ_2391',
   'P',
   4.8181],
  ['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   4.8867]],
 [['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.2935],
  ['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   4.3158]],
 [['PHE85',
   '1248_1249_1251_1253_1255_1257',
   'P',
   'ARG40',
   'NH1_577_580',
   'P',
   3.8709],
  ['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.4195],
  ['PHE138',
   '2101_2102_2104_2106_2108_2110',
   'P',
   'ARG58',
   'NH1_829_832',
   'P',
   4.9708]],
  ..
  ..
In [22]: interactionsTrajectory.getPiStacking()
[[['HSE66',
   '953_954_955_957_959',
   'P',
   'TYR142',
   '2166_2167_2169_2171_2174_2176',
   'P',
   3.8882,
   162.1245],
  ['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'TYR119',
   '1802_1803_1805_1807_1810_1812',
   'P',
   4.3605,
   3.0063],
  ['PHE26',
   '327_328_330_332_334_336',
   'P',
   'TRP39',
   '549_550_551_553_555_557',
   'P',
   4.8394,
   75.4587],
  ['TYR132',
   '2024_2025_2027_2029_2032_2034',
   'P',
   'TYR131',
   '2003_2004_2006_2008_2011_2013',
   'P',
   4.8732,
   91.4358]],
 [['PHE26',
   '327_328_330_332_334_336',
   'P',
   'TRP39',
   '549_550_551_553_555_557',
   'P',
   4.8046,
   70.9506],
  ['HSE66',
   '953_954_955_957_959',
   'P',
   'TYR142',
   '2166_2167_2169_2171_2174_2176',
   'P',
   4.8351,
   138.8872]],
 [['HSE66',
   '953_954_955_957_959',
   'P',
   'TYR142',
   '2166_2167_2169_2171_2174_2176',
   'P',
   3.6419,
   174.2245]],
 [['HSE66',
   '953_954_955_957_959',
   'P',
   'TYR142',
   '2166_2167_2169_2171_2174_2176',
   'P',
   4.1376,
   143.3286]],
 [['HSE66',
   '953_954_955_957_959',
   'P',
   'TYR142',
   '2166_2167_2169_2171_2174_2176',
   'P',
   4.2999,
   137.4965],
  ['TYR87',
   '1280_1281_1283_1285_1288_1290',
   'P',
   'PHE152',
   '2328_2329_2331_2333_2335_2337',
   'P',
   4.9646,
   73.7093]],
 [['HSE66',
   '953_954_955_957_959',
   'P',
   'TYR142',
   '2166_2167_2169_2171_2174_2176',
   'P',
   4.2623,
   158.0688],
   ..
   ..

Once we compute interactions, we can also select two that are interesting for us by using selection or selection and selection2 if we want to compare two chains of protein structure. Here, we can display all interactions with residues with numbers between 100 and 106.

In [23]: interactionsTrajectory.getInteractions(selection='resid 100 to 106')
[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.933, 10.3321],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9361, 9.2855],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9952, 32.2712],
  ['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.0464, 19.6807],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 3.4548, 26.1223],
  ['VAL106', 'N_1588', 'P', 'SER103', 'O_1556', 'P', 3.4974, 34.2367]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.5963, 18.6089],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7535, 13.6202],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7626, 15.9446],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.9067, 16.7879],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0125, 16.6445],
  ['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 3.0551, 13.8509],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 3.1649, 39.2608],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2195, 25.4359],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.3521, 12.6376],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.3904, 38.6896],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.46, 29.7639]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6466, 7.8982],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8761, 17.0562],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9269, 16.8394],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.984, 10.6183],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.101, 38.8603],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.2553, 38.5648]],
 [['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.5911, 17.069],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6274, 12.9418],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7018, 15.5273],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8801, 16.6129],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9348, 25.5713],
  ['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 2.9562, 38.6882],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 3.1464, 36.9083],
  ['LYS102', 'NZ_1540', 'P', 'SER47', 'OG_665', 'P', 3.155, 33.2035],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.2314, 26.449]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6718, 15.3661],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.6858, 28.5654],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.7479, 25.7898],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7584, 9.5766],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.8029, 24.9678],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.9645, 18.3577],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0085, 24.3135],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2018, 39.9842],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.2421, 26.211],
  ['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.3623, 38.1443]],
 [['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6595, 13.3173],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.8351, 14.4292],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.8423, 25.7739],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8761, 36.221],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.9016, 29.2602],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9501, 21.9519],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9534, 4.572],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9715, 13.2817],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0385, 28.4861],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.0741, 22.6725],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0961, 21.9463]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6673, 5.897],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.8621, 21.3715],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.9062, 37.2809],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.9467, 14.2625],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.0105, 15.1965],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.1835, 33.0481],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2504, 29.8412],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.4557, 26.8981]],
 [['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.6955, 15.9473],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7336, 13.04],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7844, 21.0059],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.7921, 34.0413],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8616, 30.9582],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9622, 35.633],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9862, 9.5713],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.992, 28.725],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 3.0439, 38.4803],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2289, 6.3339],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.3376, 16.6525],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.3409, 32.703]],
 [['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6495, 18.2239],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD1_1463', 'P', 2.675, 14.3671],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.6999, 16.6616],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7186, 10.5368],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8422, 23.6928],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8537, 21.8508],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8826, 12.651],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9711, 26.7601],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.1186, 14.3141],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.2655, 29.3262]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6587, 11.1386],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7047, 15.6631],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.791, 11.1184],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.801, 22.9498],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.9519, 31.5282],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0148, 11.0913],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.3007, 38.2386],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.3317, 21.1],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.4041, 33.0264]],
 [['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.5558, 15.1737],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.7324, 21.7444],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8949, 31.6832],
  ['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.9391, 22.8993],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 3.1202, 21.236],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.1673, 16.8727],
  ['GLN105', 'N_1571', 'P', 'LYS102', 'O_1545', 'P', 3.1973, 19.7715],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.271, 31.13],
  ['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.3052, 14.7978]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.671, 37.3323],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.739, 34.0943],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 2.7588, 35.9299],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.8159, 18.3284],
  ['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.8621, 29.9939],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.8717, 34.7545],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.9076, 6.0046],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.079, 29.8594],
  ['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.4094, 37.1284],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.4107, 38.1571]],
 [['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.6803, 15.1718],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7669, 25.5278],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.8242, 31.1474],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 3.0011, 28.4159],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0907, 32.962],
  ['ASN104', 'N_1557', 'P', 'ARG101', 'O_1523', 'P', 3.0944, 31.0232],
  ['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 3.1066, 31.2941],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 3.153, 7.2531],
  ['ARG101', 'NE_1513', 'P', 'ASP98', 'OD2_1464', 'P', 3.1683, 35.5334]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.5916, 5.2678],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7483, 9.7499],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7533, 23.1952],
  ['GLN105', 'NE2_1583', 'P', 'ARG101', 'O_1523', 'P', 2.8947, 9.5954],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9874, 36.0359],
  ['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 2.9944, 17.1267],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0055, 24.8374],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0528, 29.1184],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0686, 20.4109],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.1474, 24.7453]],
 [['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.7044, 10.5924],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7509, 8.0677],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8112, 11.4161],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8136, 16.1535],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.8215, 39.6551],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.8508, 18.2442],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9434, 34.3129],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9806, 20.0253],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.1026, 29.4155]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.6685, 15.0847],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.757, 19.0853],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.7715, 5.5688],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.7976, 24.804],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.869, 19.5567],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.9269, 20.4698],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.1468, 8.581],
  ['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.2707, 39.8715],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.2959, 34.2995]],
 [['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.6797, 11.1273],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7404, 22.8181],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.8344, 21.332],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.8389, 18.5308],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8491, 12.329],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 2.9264, 7.5038],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.9504, 10.3511],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0236, 6.9167],
  ['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.106, 38.5309],
  ['ASN100', 'ND2_1495', 'P', 'LEU96', 'O_1430', 'P', 3.2461, 4.2582]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.6103, 19.241],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.6343, 15.3945],
  ['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD2_1464', 'P', 2.6543, 10.2308],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7596, 12.1992],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.7949, 12.7041],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.9188, 34.6284],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9977, 39.8669],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.162, 37.02],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.1719, 26.513],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2101, 36.7681]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463', 'P', 2.7558, 29.536],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD2_1464', 'P', 2.7988, 8.8578],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8421, 28.9541],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.9436, 3.1426],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0155, 38.3833],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0202, 2.421],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 3.2096, 28.1311],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 3.4213, 14.8714]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD2_1464', 'P', 2.6129, 19.7326],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.6911, 19.978],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.7089, 22.225],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 2.7963, 25.158],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8504, 16.7766],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.8915, 21.1984],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 3.0135, 31.6808],
  ['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 3.0372, 20.7935],
  ['ASN104', 'N_1557', 'P', 'ASN100', 'O_1499', 'P', 3.0379, 38.205],
  ['GLN105', 'NE2_1583', 'P', 'ARG101', 'O_1523', 'P', 3.2845, 28.1096],
  ['CYS109', 'SG_1647', 'P', 'SER103', 'OG_1553', 'P', 3.4421, 25.6483]],
 [['VAL106', 'N_1588', 'P', 'LYS102', 'O_1545', 'P', 2.6793, 16.1937],
  ['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD2_1464', 'P', 2.7584, 11.5432],
  ['ASN100', 'N_1486', 'P', 'LEU96', 'O_1430', 'P', 2.775, 6.6534],
  ['LYS102', 'N_1524', 'P', 'ASP98', 'O_1466', 'P', 2.7754, 4.8907],
  ['GLN105', 'N_1571', 'P', 'ARG101', 'O_1523', 'P', 2.8177, 29.9366],
  ['ARG101', 'NH2_1519', 'P', 'ASP98', 'OD1_1463', 'P', 2.8304, 17.4803],
  ['SER103', 'OG_1553', 'P', 'LEU99', 'O_1485', 'P', 2.856, 21.4102],
  ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.9243, 35.6267],
  ['ARG101', 'N_1500', 'P', 'ARG97', 'O_1454', 'P', 3.0156, 9.3534]],
 [['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359]],
 [['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.5055]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5251],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6639]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.784],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7415]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7833],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6905]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.118],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.7333]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9802],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3115]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1925],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3314]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1321],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.377]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5465],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.1424]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8662],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7765]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.4575],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7844]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7106],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2495]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9739],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3131]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0533],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.8328]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.2511],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6196]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.955],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.9277]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1188],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6654]],
 [['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.7506]],
 [['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2655]],
 [],
 [],
 [],
 [],
 [],
 [['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2903]],
 [],
 [],
 [['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3093]],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
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 [],
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 [],
 [],
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 [],
 [],
 [],
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 [],
 [],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
  ['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1048, 17.4819]],
 [['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 3.6601, 18.1513],
  ['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 4.0401, 13.1367],
  ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2489, 20.4475]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.9579, 24.0447],
  ['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 3.993, 10.9852]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG1_1594', 'P', 3.7771, 25.8417],
  ['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2695, 6.7328]],
 [['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.7581, 24.2415],
  ['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.3995, 30.7521]],
 [['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 3.9758, 19.5257],
  ['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2315, 11.0609]],
 [['VAL106', 'CG1_1594', 'P', 'PHE82', 'CG_1204', 'P', 3.8971, 17.973],
  ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.0318, 20.1861]],
 [['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.9504, 18.2026],
  ['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.0183, 24.7812],
  ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.354, 18.5823]],
 [['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.1345, 9.1889],
  ['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 4.1488, 19.0544]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7492, 21.5977]],
 [['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 3.7532, 20.5214],
  ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.1843, 21.2188]],
 [['LYS79', 'CD_1158', 'P', 'VAL106', 'CG2_1598', 'P', 4.1132, 33.2299],
  ['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.2545, 30.9532]],
 [['VAL106', 'CG1_1594', 'P', 'PHE82', 'CG_1204', 'P', 4.2115, 22.6531],
  ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.4451, 30.8638]],
 [['LYS102', 'CD_1534', 'P', 'PHE82', 'CE2_1213', 'P', 4.1132, 21.6908],
  ['VAL106', 'CG2_1598', 'P', 'PHE82', 'CD2_1211', 'P', 4.301, 14.4692]],
 [['VAL106', 'CG1_1594', 'P', 'PHE82', 'CD1_1205', 'P', 3.769, 29.2683]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7591, 26.6179]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG1_1594', 'P', 3.7466, 15.362],
  ['LYS102', 'CD_1534', 'P', 'PHE82', 'CZ_1209', 'P', 4.3692, 20.969]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.7838, 20.4368],
  ['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.2006, 12.5337]],
 [['LYS102', 'CD_1534', 'P', 'PHE82', 'CZ_1209', 'P', 4.3001, 14.6918]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2078, 41.8606],
  ['LYS102', 'CD_1534', 'P', 'ILE77', 'CG2_1121', 'P', 4.3141, 10.5395]],
 [['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 4.2738, 15.6412]],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
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 [],
 []]

We can apply the same selection to any type of interaction, for example:

In [24]: interactionsTrajectory.getHydrophobic(selection='chain P and resid 90 to 100')
[[['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7263, 16.9718],
  ['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.8864, 35.855]],
 [['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.429, 13.2977],
  ['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6871, 7.95],
  ['MET91', 'CE_1354', 'P', 'LEU116', 'CD2_1771', 'P', 3.8434, 19.1277]],
 [['ILE88', 'CG2_1300', 'P', 'LEU99', 'CD1_1476', 'P', 3.5436, 9.3247],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.57, 23.3065],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6654, 17.4729]],
 [['LEU99', 'CD1_1476', 'P', 'ILE88', 'CG2_1300', 'P', 3.5506, 10.5506],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.6132, 25.5246],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.6989, 21.7296]],
 [['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.681, 13.3699],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7838, 19.4208],
  ['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.8538, 35.0746],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CD_1718', 'P', 3.993, 32.6427],
  ['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.3995, 30.7521]],
 [['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.4473, 9.6836],
  ['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.7931, 33.4972],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.8599, 15.7656],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG1_1715', 'P', 4.0839, 25.8005]],
 [['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6656, 11.2061],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CD_1718', 'P', 3.7465, 13.9407],
  ['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 4.1873, 5.8643]],
 [['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.577, 21.8565],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7311, 16.6688],
  ['LEU99', 'CD1_1476', 'P', 'ILE77', 'CD_1128', 'P', 3.7918, 13.9645],
  ['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.0183, 24.7812]],
 [['LEU99', 'CD1_1476', 'P', 'ILE88', 'CG2_1300', 'P', 3.493, 12.0525],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8477, 17.8661],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.9465, 13.0407],
  ['ARG18', 'CG_208', 'P', 'MET91', 'CG_1350', 'P', 4.4773, 45.2545]],
 [['MET91', 'SD_1353', 'P', 'ILE127', 'CD_1949', 'P', 3.6073, 35.8986],
  ['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG1_110', 'P', 3.8196, 19.5026],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.8266, 8.1345]],
 [['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.688, 16.5389],
  ['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.8303, 12.8658],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.9125, 20.3824],
  ['ARG18', 'CG_208', 'P', 'MET91', 'CG_1350', 'P', 4.3469, 47.3018]],
 [['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.4146, 25.9366],
  ['LEU99', 'CD2_1480', 'P', 'PHE82', 'CZ_1209', 'P', 3.6458, 17.5698],
  ['ILE113', 'CG2_1711', 'P', 'LEU99', 'CD1_1476', 'P', 3.7998, 30.7151],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 4.0071, 18.0266],
  ['LYS102', 'CD_1534', 'P', 'LEU99', 'CD2_1480', 'P', 4.2545, 30.9532]],
 [['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.5757, 19.6775],
  ['LEU99', 'CD2_1480', 'P', 'ILE88', 'CG2_1300', 'P', 3.8102, 10.1337],
  ['ILE113', 'CG2_1711', 'P', 'LEU96', 'CG_1419', 'P', 3.8694, 28.8723]],
 [['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.5696, 9.6273],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8426, 17.9602]],
 [['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.511, 19.586],
  ['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG2_114', 'P', 3.5732, 10.7329],
  ['MET91', 'CE_1354', 'P', 'LEU116', 'CD2_1771', 'P', 3.9678, 13.6217]],
 [['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.6543, 13.7308],
  ['ILE113', 'CG2_1711', 'P', 'LEU96', 'CG_1419', 'P', 3.7456, 22.5419],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.8152, 17.9895]],
 [['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.4849, 12.5888],
  ['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.5767, 9.5877],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7229, 15.3003],
  ['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 4.274, 35.6655]],
 [['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6286, 22.7844],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.6984, 12.3956],
  ['ALA22', 'CB_273', 'P', 'MET91', 'CE_1354', 'P', 3.7795, 8.4161],
  ['LEU99', 'CD2_1480', 'P', 'ILE88', 'CG2_1300', 'P', 3.7921, 7.4352]],
 [['ILE127', 'CD_1949', 'P', 'MET91', 'SD_1353', 'P', 3.4598, 42.01],
  ['LEU99', 'CD1_1476', 'P', 'ILE113', 'CG2_1711', 'P', 3.6609, 33.0336],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7378, 17.5379],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.7686, 14.0166]],
 [['LEU99', 'CD1_1476', 'P', 'VAL11', 'CG2_114', 'P', 3.518, 18.8799],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'CE_1354', 'P', 3.5399, 12.2359],
  ['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.7165, 21.0434]],
 [['LEU96', 'CD1_1421', 'P', 'ILE113', 'CG2_1711', 'P', 3.2931, 21.0747],
  ['VAL11', 'CG2_114', 'P', 'LEU99', 'CD1_1476', 'P', 3.3771, 11.4804],
  ['MET91', 'CE_1354', 'P', 'ALA22', 'CB_273', 'P', 3.6628, 9.0978],
  ['LEU116', 'CD2_1771', 'P', 'MET91', 'SD_1353', 'P', 3.6984, 21.9302]]]
In [25]: interactionsTrajectory.getHydrogenBonds(selection='chain P and resid 112 to 115')
[[['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8429, 17.7147],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8975, 24.576],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.912, 10.1158],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.051, 21.4045],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.059, 24.1606],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 3.2687, 28.6743]],
 [['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.5487, 20.8176],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6334, 17.8203],
  ['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.6547, 25.6442],
  ['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.735, 15.8502],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7935, 13.2257],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8946, 17.9316],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9523, 13.8795],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0323, 8.8409],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2094, 37.0837],
  ['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.2322, 23.7336],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE2_1736', 'P', 3.253, 23.8402]],
 [['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.5902, 19.0335],
  ['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6441, 10.2991],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7184, 24.9984],
  ['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7238, 26.9156],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8381, 10.253],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8616, 14.018],
  ['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8761, 18.0626],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0416, 27.2343],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.195, 38.6534],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.4603, 13.0317]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.5321, 12.1754],
  ['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6666, 5.0368],
  ['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.6844, 12.4337],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7625, 21.1367],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7703, 4.1752],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.813, 11.6498],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8375, 24.3092],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'ND1_2414', 'P', 2.8399, 24.5852],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9985, 12.7544]],
 [['TYR119', 'OH_1808', 'P', 'GLU114', 'OE2_1736', 'P', 2.6438, 28.5062],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7748, 6.971],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8324, 30.6076],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8567, 3.076],
  ['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE2_1736', 'P', 2.8677, 22.3219],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9251, 9.0077],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0506, 7.4102],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.4475, 19.9922]],
 [['TYR119', 'OH_1808', 'P', 'GLU114', 'OE1_1735', 'P', 2.6085, 18.3035],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7054, 1.3697],
  ['LYS112', 'NZ_1699', 'P', 'GLU114', 'OE1_1735', 'P', 2.7093, 27.1289],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8128, 18.817],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0762, 12.1723],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1037, 10.0101],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.1356, 19.0662],
  ['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.3017, 27.3282],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.3047, 11.3911]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.652, 10.3503],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.762, 14.1022],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7884, 21.6503],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7994, 5.7305],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8628, 30.0771],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9474, 28.4869],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.4304, 27.1097]],
 [['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7778, 28.0614],
  ['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.7868, 18.8919],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8504, 18.6098],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.9351, 15.9934],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.9391, 14.958]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.6858, 23.9752],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8512, 7.2231],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 2.9951, 23.9118],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0881, 6.5417],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.1217, 14.0883],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.2069, 19.3312],
  ['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.2331, 32.7145]],
 [['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT1_2423', 'P', 2.6385, 22.7134],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.6967, 1.035],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7267, 17.2895],
  ['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.8598, 29.0811],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9766, 16.8905],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.0616, 27.2229],
  ['CYS90', 'SG_1339', 'P', 'GLU114', 'O_1738', 'P', 3.4089, 25.9472]],
 [['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.8001, 13.1653],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8336, 11.5184],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8683, 15.5308],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8949, 10.1824],
  ['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.9677, 16.3497],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.089, 17.9789]],
 [['LYS112', 'NZ_1699', 'P', 'HSE157', 'OT2_2424', 'P', 2.7045, 11.8564],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8002, 5.9828],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8444, 31.549],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0718, 34.4381],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.3002, 12.0528]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.549, 18.6576],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7292, 11.3872],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7951, 19.2119],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.861, 9.3445],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 2.8723, 5.3509],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2056, 13.0868]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7432, 12.0576],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8455, 10.8341],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.8979, 18.8959],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.9513, 25.3055],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2646, 30.184]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7509, 33.4365],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7569, 15.9129],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8989, 5.3091],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.0521, 14.9906],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2193, 17.7506]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.9107, 11.3311],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.9279, 24.4459],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.9572, 22.8551],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0531, 39.2571],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2647, 19.7898]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE1_1735', 'P', 2.7301, 6.4912],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.0067, 19.0131],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 3.0515, 32.6929],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.0654, 16.9354],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.2584, 28.3632]],
 [['SER118', 'OG_1791', 'P', 'LEU115', 'O_1757', 'P', 2.7161, 4.3692],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7665, 15.6553],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.833, 1.7101],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.9604, 20.771],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1924, 36.5103],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.3101, 22.7426]],
 [['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.7306, 1.388],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 2.7477, 25.8134],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.7669, 4.8657],
  ['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.7852, 20.1148]],
 [['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8181, 19.759],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 2.8698, 4.299],
  ['LYS112', 'N_1683', 'P', 'ASP86', 'O_1272', 'P', 3.0671, 23.7084],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.1112, 27.1195],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.1262, 21.7619]],
 [['SER118', 'OG_1791', 'P', 'GLU114', 'OE2_1736', 'P', 2.6334, 24.4833],
  ['CYS90', 'N_1332', 'P', 'GLU114', 'O_1738', 'P', 2.8598, 7.853],
  ['SER118', 'N_1784', 'P', 'LEU115', 'O_1757', 'P', 3.0172, 19.6851],
  ['GLU114', 'N_1724', 'P', 'ILE88', 'O_1312', 'P', 3.2603, 11.1927],
  ['ILE88', 'N_1294', 'P', 'LYS112', 'O_1704', 'P', 3.3213, 8.0609]]]
In [26]: interactionsTrajectory.getSaltBridges(selection='chain P and resid 100 to 120')
[[['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.0699],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.9359],
  ['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 4.0787],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.1543],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.1879],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.3835]],
 [['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.8263],
  ['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.0552],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.2384],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3269],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.5063],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8015]],
 [['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5925],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0796],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7353],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.8213],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.2197]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8527],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.2487],
  ['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 3.281],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 3.4289],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.5055],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.7295]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5251],
  ['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5476],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.8031],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.7693],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6639]],
 [['GLU114', 'OE1_1735_1736', 'P', 'LYS112', 'NZ_1699', 'P', 2.5445],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.784],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.9545],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4269],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7415]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7833],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.7841],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6393],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.6905],
  ['HSE157', 'NE2_2418', 'P', 'GLU114', 'OE1_1735_1736', 'P', 4.9985]],
 [['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.7718],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.118],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.7333],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.385]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9802],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.1049],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3115],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4854]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1925],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.3668],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3314],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6386]],
 [['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 2.7461],
  ['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1321],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.377]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.5465],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.7315],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.886],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.1424]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.8662],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7765],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 4.9921]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.4575],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.6085],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9194],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.3166],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.7844]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.7106],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.7026],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.794],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2495]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.9739],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.397],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.5529],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.9267],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3131]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.0533],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG147', 'NH1_2257_2260', 'P', 3.7951],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.8215],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9526],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.8328]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.2511],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6196],
  ['ASP120', 'OD1_1824_1825', 'P', 'ARG150', 'NH1_2303_2306', 'P', 3.9186]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 2.955],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.9277]],
 [['LYS102', 'NZ_1540', 'P', 'ASP98', 'OD1_1463_1464', 'P', 3.1188],
  ['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 3.6654],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.9234]],
 [['ASP98', 'OD1_1463_1464', 'P', 'ARG101', 'NH1_1516_1519', 'P', 2.7506],
  ['ASP86', 'OD1_1269_1270', 'P', 'LYS110', 'NZ_1667', 'P', 3.4341]]]
In [27]: interactionsTrajectory.getRepulsiveIonicBonding(selection='chain P')
[[['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2655]],
 [],
 [],
 [],
 [],
 [],
 [['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.2903]],
 [],
 [],
 [['LYS102', 'NZ_1540', 'P', 'ARG101', 'NH1_1516_1519', 'P', 4.3093]],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [],
 [['ARG147', 'NH1_2257_2260', 'P', 'LYS123', 'NZ_1875', 'P', 4.4846]]]

Change selection criteria for interaction type

The interactionsTrajectory.calcProteinInteractionsTrajectory() method computes interactions using default parameters for interactions. However, it can be changed according to our needs. To do that, we need to recalculate the selected types of interactions.

We can do it using the following functions: calcHydrogenBondsTrajectory(), calcHydrogenBondsTrajectory(), calcSaltBridgesTrajectory(), calcRepulsiveIonicBondingTrajectory(), calcPiStackingTrajectory(), calcPiCationTrajectory(), calcHydrophohicTrajectory(), and use InteractionsTrajectory.setNewHydrogenBondsTrajectory(), InteractionsTrajectory.setNewSaltBridgesTrajectory(), InteractionsTrajectory.setNewRepulsiveIonicBondingTrajectory(), InteractionsTrajectory.setNewPiStackingTrajectory(), InteractionsTrajectory.setNewPiCationTrajectory(), InteractionsTrajectory.setNewHydrophohicTrajectory() method to replace it in the main Instance.

For example:

Repulsive ionic bonding:

In [28]: newRIB = calcRepulsiveIonicBondingTrajectory(atoms, dcd, distA=8)

In [29]: interactionsTrajectory.setNewRepulsiveIonicBondingTrajectory(newRIB)
@> Frame: 0
@> Calculating repulsive ionic bonding.
@>      ARG75    P   NH1_1090_1093  <--->      ARG40    P     NH1_577_580     6.7
@>      ASP81    P   OD1_1193_1194  <--->      GLU80    P   OE1_1181_1182     7.0
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.6
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 1
@> Calculating repulsive ionic bonding.
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     4.5
@>      ASP92    P   OD1_1368_1369  <--->      GLU93    P   OE1_1383_1384     7.9
@> Number of detected Repulsive Ionic Bonding interactions: 2.
@> Frame: 2
@> Calculating repulsive ionic bonding.
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     6.8
@>     ASP137    P   OD1_2090_2091  <--->     GLU128    P   OE1_1966_1967     7.7
@>      ASP81    P   OD1_1193_1194  <--->      GLU80    P   OE1_1181_1182     7.9
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 3
@> Calculating repulsive ionic bonding.
@>      GLU80    P   OE1_1181_1182  <--->      ASP81    P   OD1_1193_1194     6.3
@>      ASP42    P     OD1_609_610  <--->      ASP81    P   OD1_1193_1194     6.8
@> Number of detected Repulsive Ionic Bonding interactions: 2.
@> Frame: 4
@> Calculating repulsive ionic bonding.
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     6.0
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     6.8
@>      ARG75    P   NH1_1090_1093  <--->      ARG40    P     NH1_577_580     7.0
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 5
@> Calculating repulsive ionic bonding.
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     6.1
@>      ASP42    P     OD1_609_610  <--->      ASP81    P   OD1_1193_1194     6.6
@>      LYS79    P         NZ_1164  <--->     LYS102    P         NZ_1540     7.8
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 6
@> Calculating repulsive ionic bonding.
@>      ASP42    P     OD1_609_610  <--->      ASP81    P   OD1_1193_1194     6.1
@>     LYS112    P         NZ_1699  <--->       LYS6    P           NZ_32     6.4
@>      LYS79    P         NZ_1164  <--->     LYS107    P         NZ_1620     7.1
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 7
@> Calculating repulsive ionic bonding.
@>     ARG147    P   NH1_2257_2260  <--->     LYS123    P         NZ_1875     4.8
@>      ASP42    P     OD1_609_610  <--->      GLU23    P     OE1_290_291     5.9
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     6.4
@>      ARG75    P   NH1_1090_1093  <--->      ARG40    P     NH1_577_580     6.9
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 8
@> Calculating repulsive ionic bonding.
@>     LYS123    P         NZ_1875  <--->     ARG147    P   NH1_2257_2260     5.1
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.0
@>      ASP81    P   OD1_1193_1194  <--->      GLU80    P   OE1_1181_1182     7.2
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 9
@> Calculating repulsive ionic bonding.
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     4.3
@>      GLU93    P   OE1_1383_1384  <--->     GLU128    P   OE1_1966_1967     6.2
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     6.4
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 10
@> Calculating repulsive ionic bonding.
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     4.6
@>     LYS123    P         NZ_1875  <--->     ARG147    P   NH1_2257_2260     4.7
@>      ASP92    P   OD1_1368_1369  <--->     GLU128    P   OE1_1966_1967     6.4
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.4
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 11
@> Calculating repulsive ionic bonding.
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     5.3
@>      ASP42    P     OD1_609_610  <--->      ASP81    P   OD1_1193_1194     6.6
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.7
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 12
@> Calculating repulsive ionic bonding.
@>     LYS123    P         NZ_1875  <--->     ARG147    P   NH1_2257_2260     5.9
@>      ARG75    P   NH1_1090_1093  <--->      ARG40    P     NH1_577_580     6.2
@>     ARG150    P   NH1_2303_2306  <--->     ARG147    P   NH1_2257_2260     7.2
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 13
@> Calculating repulsive ionic bonding.
@>      ASP42    P     OD1_609_610  <--->      ASP81    P   OD1_1193_1194     6.6
@>     ASP129    P   OD1_1978_1979  <--->     GLU128    P   OE1_1966_1967     6.6
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     7.8
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.8
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 14
@> Calculating repulsive ionic bonding.
@>     LYS123    P         NZ_1875  <--->     ARG147    P   NH1_2257_2260     7.0
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.1
@>      ASP81    P   OD1_1193_1194  <--->      GLU80    P   OE1_1181_1182     7.2
@>      ASP92    P   OD1_1368_1369  <--->     GLU128    P   OE1_1966_1967     8.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 15
@> Calculating repulsive ionic bonding.
@>     LYS123    P         NZ_1875  <--->     ARG147    P   NH1_2257_2260     6.5
@>     GLU154    P   OE1_2371_2372  <--->     ASP120    P   OD1_1824_1825     6.5
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     6.6
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Frame: 16
@> Calculating repulsive ionic bonding.
@>      ASP42    P     OD1_609_610  <--->      GLU23    P     OE1_290_291     5.6
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     7.1
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.2
@>     ASP129    P   OD1_1978_1979  <--->     GLU128    P   OE1_1966_1967     7.2
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 17
@> Calculating repulsive ionic bonding.
@>     ARG101    P   NH1_1516_1519  <--->     LYS102    P         NZ_1540     4.9
@>      ASP42    P     OD1_609_610  <--->      ASP81    P   OD1_1193_1194     6.5
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.4
@>     GLU128    P   OE1_1966_1967  <--->     ASP129    P   OD1_1978_1979     8.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 18
@> Calculating repulsive ionic bonding.
@>      ASP42    P     OD1_609_610  <--->      GLU23    P     OE1_290_291     5.7
@>     ASP135    P   OD1_2067_2068  <--->     GLU139    P   OE1_2125_2126     5.9
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     6.8
@>      ASP92    P   OD1_1368_1369  <--->     GLU128    P   OE1_1966_1967     6.8
@>      GLU93    P   OE1_1383_1384  <--->     GLU128    P   OE1_1966_1967     7.3
@> Number of detected Repulsive Ionic Bonding interactions: 5.
@> Frame: 19
@> Calculating repulsive ionic bonding.
@>     LYS123    P         NZ_1875  <--->     ARG147    P   NH1_2257_2260     5.3
@>     GLU139    P   OE1_2125_2126  <--->     ASP135    P   OD1_2067_2068     6.0
@>      LYS79    P         NZ_1164  <--->     LYS107    P         NZ_1620     6.1
@>      ASP81    P   OD1_1193_1194  <--->      GLU80    P   OE1_1181_1182     7.0
@> Number of detected Repulsive Ionic Bonding interactions: 4.
@> Frame: 20
@> Calculating repulsive ionic bonding.
@>     LYS123    P         NZ_1875  <--->     ARG147    P   NH1_2257_2260     4.5
@>     ASP135    P   OD1_2067_2068  <--->     GLU139    P   OE1_2125_2126     5.5
@>     ASP129    P   OD1_1978_1979  <--->      ASP92    P   OD1_1368_1369     7.1
@>      LYS79    P         NZ_1164  <--->     LYS102    P         NZ_1540     7.9
@> Number of detected Repulsive Ionic Bonding interactions: 4.

@> Repulsive Ionic Bonding are replaced

Pi-cation interactions:

In [30]: newPiCation = calcPiCationTrajectory(atoms, dcd, distA=6)

In [31]: interactionsTrajectory.setNewPiCationTrajectory(newPiCation)
@> Frame: 0
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.7
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.5
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     4.8
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.0
@>     TYR131   P   2003_2004_2006_2008_2011_2013  <--->      ARG58   P                     NH1_829_832     5.1
@> Number of detected cation-pi interactions: 5.
@> Frame: 1
@> Calculating cation-Pi interactions.
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     3.5
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.9
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.9
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     4.9
@>     TYR131   P   2003_2004_2006_2008_2011_2013  <--->      ARG58   P                     NH1_829_832     4.9
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.7
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     6.0
@> Number of detected cation-pi interactions: 7.
@> Frame: 2
@> Calculating cation-Pi interactions.
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     2.7
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.1
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.5
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 3
@> Calculating cation-Pi interactions.
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     2.6
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.6
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     3.8
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.3
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.3
@> Number of detected cation-pi interactions: 5.
@> Frame: 4
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.9
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.8
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS155   P                         NZ_2391     4.8
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     4.9
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.3
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.4
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->       LYS6   P                           NZ_32     5.6
@> Number of detected cation-pi interactions: 7.
@> Frame: 5
@> Calculating cation-Pi interactions.
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.3
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     4.3
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     5.2
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.8
@> Number of detected cation-pi interactions: 4.
@> Frame: 6
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.9
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.4
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.0
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     5.0
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->       LYS6   P                           NZ_32     5.3
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.5
@> Number of detected cation-pi interactions: 6.
@> Frame: 7
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.9
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.2
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     4.9
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.7
@> Number of detected cation-pi interactions: 4.
@> Frame: 8
@> Calculating cation-Pi interactions.
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     3.8
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.5
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     5.4
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 9
@> Calculating cation-Pi interactions.
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.4
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.8
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     5.2
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.4
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.5
@>     PHE152   P   2328_2329_2331_2333_2335_2337  <--->       LYS6   P                           NZ_32     5.8
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG75   P                   NH1_1090_1093     5.8
@> Number of detected cation-pi interactions: 7.
@> Frame: 10
@> Calculating cation-Pi interactions.
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.8
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     4.9
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     5.0
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.2
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG75   P                   NH1_1090_1093     5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 11
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.1
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS155   P                         NZ_2391     4.4
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.8
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     5.4
       HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS112   P                         NZ_1699     5.8
@>
@> Number of detected cation-pi interactions: 5.
@> Frame: 12
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.3
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.4
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.4
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.5
@>      HSE72   P        1038_1039_1040_1042_1044  <--->      ARG27   P                     NH1_356_359     5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 13
@> Calculating cation-Pi interactions.
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     4.4
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.7
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.2
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG75   P                   NH1_1090_1093     5.8
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->     LYS155   P                         NZ_2391     5.9
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     6.0
@> Number of detected cation-pi interactions: 6.
@> Frame: 14
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.6
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->       LYS6   P                           NZ_32     5.2
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.3
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     5.6
@> Number of detected cation-pi interactions: 4.
@> Frame: 15
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.4
@>     HSE157   P2414_2415_2416_2418_2420_2423_2424  <--->       LYS6   P                           NZ_32     5.1
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.7
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     5.8
@> Number of detected cation-pi interactions: 4.
@> Frame: 16
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     3.8
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->       LYS6   P                           NZ_32     5.4
@> Number of detected cation-pi interactions: 2.
@> Frame: 17
@> Calculating cation-Pi interactions.
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.4
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     5.6
@> Number of detected cation-pi interactions: 2.
@> Frame: 18
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.5
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.2
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     5.3
@>      TYR87   P   1280_1281_1283_1285_1288_1290  <--->     LYS112   P                         NZ_1699     5.7
@>      HSE72   P        1038_1039_1040_1042_1044  <--->      ARG27   P                     NH1_356_359     5.8
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     6.0
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG75   P                   NH1_1090_1093     6.0
@> Number of detected cation-pi interactions: 7.
@> Frame: 19
@> Calculating cation-Pi interactions.
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     4.9
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     5.0
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.2
@>      HSE66   P             953_954_955_957_959  <--->      ARG65   P                     NH1_938_941     5.9
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG75   P                   NH1_1090_1093     5.9
@> Number of detected cation-pi interactions: 5.
@> Frame: 20
@> Calculating cation-Pi interactions.
@>     PHE138   P   2101_2102_2104_2106_2108_2110  <--->      ARG58   P                     NH1_829_832     5.0
@>      TRP39   P         549_550_551_553_555_557  <--->       LYS6   P                           NZ_32     5.6
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG40   P                     NH1_577_580     5.7
@>      PHE85   P   1248_1249_1251_1253_1255_1257  <--->      ARG75   P                   NH1_1090_1093     5.8
@> Number of detected cation-pi interactions: 4.
   Pi-Cation interactions are replaced

We can check whether the interactions were replaced. The repulsive ionic bonding can be found by using getInteractions() and selecting 2 (0 - hydrogen bonds, 1 - salt bridges, 2 - repulsive ionic bonding, 3 - Pi-Stacking, 4 - Pi-Cation, 5 - hydrophobic, 6 - disulfide bonds).

In [32]: interactionsTrajectory.getInteractions()[2]
[[['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.666],
  ['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 6.9843],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.6316]],
 [['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.5002],
  ['ASP92', 'OD1_1368_1369', 'P', 'GLU93', 'OE1_1383_1384', 'P', 7.9458]],
 [['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.8023],
  ['ASP137', 'OD1_2090_2091', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.7429],
  ['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.9228]],
 [['GLU80', 'OE1_1181_1182', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.2655],
  ['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.8064]],
 [['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 6.0034],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.8451],
  ['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 7.0306]],
 [['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.1332],
  ['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.6231],
  ['LYS79', 'NZ_1164', 'P', 'LYS102', 'NZ_1540', 'P', 7.81]],
 [['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.1141],
  ['LYS112', 'NZ_1699', 'P', 'LYS6', 'NZ_32', 'P', 6.4258],
  ['LYS79', 'NZ_1164', 'P', 'LYS107', 'NZ_1620', 'P', 7.0898]],
 [['ARG147', 'NH1_2257_2260', 'P', 'LYS123', 'NZ_1875', 'P', 4.8418],
  ['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.8605],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.3776],
  ['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.9162]],
 [['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.1095],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.9653],
  ['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.1885]],
 [['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.3093],
  ['GLU93', 'OE1_1383_1384', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.2251],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.3655]],
 [['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.6267],
  ['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.6563],
  ['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.4486],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.3554]],
 [['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 5.2803],
  ['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.6125],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.7231]],
 [['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.903],
  ['ARG75', 'NH1_1090_1093', 'P', 'ARG40', 'NH1_577_580', 'P', 6.2264],
  ['ARG150', 'NH1_2303_2306', 'P', 'ARG147', 'NH1_2257_2260', 'P', 7.2115]],
 [['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.5807],
  ['ASP129', 'OD1_1978_1979', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.6156],
  ['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 7.7691],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.8267]],
 [['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 6.9607],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.0793],
  ['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 7.1994],
  ['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.9662]],
 [['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 6.4558],
  ['GLU154', 'OE1_2371_2372', 'P', 'ASP120', 'OD1_1824_1825', 'P', 6.5391],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.6406]],
 [['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.5599],
  ['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 7.1302],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.1991],
  ['ASP129', 'OD1_1978_1979', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.2499]],
 [['ARG101', 'NH1_1516_1519', 'P', 'LYS102', 'NZ_1540', 'P', 4.913],
  ['ASP42', 'OD1_609_610', 'P', 'ASP81', 'OD1_1193_1194', 'P', 6.4678],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.3594],
  ['GLU128', 'OE1_1966_1967', 'P', 'ASP129', 'OD1_1978_1979', 'P', 7.9788]],
 [['ASP42', 'OD1_609_610', 'P', 'GLU23', 'OE1_290_291', 'P', 5.6704],
  ['ASP135', 'OD1_2067_2068', 'P', 'GLU139', 'OE1_2125_2126', 'P', 5.9135],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 6.7566],
  ['ASP92', 'OD1_1368_1369', 'P', 'GLU128', 'OE1_1966_1967', 'P', 6.7899],
  ['GLU93', 'OE1_1383_1384', 'P', 'GLU128', 'OE1_1966_1967', 'P', 7.3464]],
 [['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 5.3159],
  ['GLU139', 'OE1_2125_2126', 'P', 'ASP135', 'OD1_2067_2068', 'P', 6.0087],
  ['LYS79', 'NZ_1164', 'P', 'LYS107', 'NZ_1620', 'P', 6.0679],
  ['ASP81', 'OD1_1193_1194', 'P', 'GLU80', 'OE1_1181_1182', 'P', 6.9706]],
 [['LYS123', 'NZ_1875', 'P', 'ARG147', 'NH1_2257_2260', 'P', 4.4846],
  ['ASP135', 'OD1_2067_2068', 'P', 'GLU139', 'OE1_2125_2126', 'P', 5.4686],
  ['ASP129', 'OD1_1978_1979', 'P', 'ASP92', 'OD1_1368_1369', 'P', 7.0978],
  ['LYS79', 'NZ_1164', 'P', 'LYS102', 'NZ_1540', 'P', 7.9242]]]
In [33]: interactionsTrajectory.getInteractions()[4]
[[['PHE85',
   '1248_1249_1251_1253_1255_1257',
   'P',
   'ARG40',
   'NH1_577_580',
   'P',
   3.6523],
  ['HSE66', '953_954_955_957_959', 'P', 'ARG65', 'NH1_938_941', 'P', 4.5323],
  ['HSE157',
   '2414_2415_2416_2418_2420_2423_2424',
   'P',
   'LYS112',
   'NZ_1699',
   'P',
   4.828],
  ['PHE138',
   '2101_2102_2104_2106_2108_2110',
   'P',
   'ARG58',
   'NH1_829_832',
   'P',
   5.0448],
  ['TYR131',
   '2003_2004_2006_2008_2011_2013',
   'P',
   'ARG58',
   'NH1_829_832',
   'P',
   5.0915]],
   ..
   ..

Statistics

Using calcStatisticsInteractions() function, we can compute the statistics of interaction in the trajectory, such as the average distance between residues (usually the center of the mass; details are described in the function which computes the specific type of interactions), standard deviation for the distance value and weight. Weight is the number of counts for the whole trajectory and is divided by the number of frames in the dcd file. Weight equal to 1 corresponds to the contact that was main the whole time of the simulation. Note that weight can be >1 when multiple contacts are present between the same residues.

For example:

In [34]: interactions = interactionsTrajectory.getPiCation()

In [35]: calcStatisticsInteractions(interactions)
@> Statistics for PHE85P-ARG40P:
@>   Average [Ang.]: 4.385379791259766
@>   Standard deviation [Ang.]: 0.5366479754447937
@>   Weight: 0.952381
@> Statistics for HSE66P-ARG65P:
@>   Average [Ang.]: 4.717772006988525
@>   Standard deviation [Ang.]: 0.6487299799919128
@>   Weight: 0.857143
@> Statistics for HSE157P-LYS112P:
@>   Average [Ang.]: 4.388020038604736
@>   Standard deviation [Ang.]: 1.0506110191345215
@>   Weight: 0.47619
@> Statistics for PHE138P-ARG58P:
@>   Average [Ang.]: 5.318399906158447
@>   Standard deviation [Ang.]: 0.24265700578689575
@>   Weight: 0.809524
@> Statistics for TYR87P-LYS112P:
@>   Average [Ang.]: 5.441559791564941
@>   Standard deviation [Ang.]: 0.25401198863983154
@>   Weight: 0.47619
@> Statistics for TRP39P-LYS6P:
@>   Average [Ang.]: 5.522061824798584
@>   Standard deviation [Ang.]: 0.31886300444602966
@>   Weight: 0.380952
@> Statistics for PHE85P-ARG75P:
@>   Average [Ang.]: 5.877999782562256
@>   Standard deviation [Ang.]: 0.06788399815559387
@>   Weight: 0.285714
In [36]: calcStatisticsInteractions(interactionsTrajectory.getHydrogenBonds())
@> Statistics for ARG101P-ASP98P:
@>   Average [Ang.]: 2.793931
@>   Standard deviation [Ang.]: 0.205527
@>   Weight: 1.52381
@> Statistics for HSE72P-ASN15P:
@>   Average [Ang.]: 2.989283
@>   Standard deviation [Ang.]: 0.270697
@>   Weight: 0.285714
@> Statistics for GLN143P-GLU139P:
@>   Average [Ang.]: 3.051633
@>   Standard deviation [Ang.]: 0.20753
@>   Weight: 1.285714
@> Statistics for HSE66P-GLU139P:
@>   Average [Ang.]: 2.900411
@>   Standard deviation [Ang.]: 0.169455
@>   Weight: 0.428571
@> Statistics for ARG40P-LYS6P:
@>   Average [Ang.]: 3.055475
@>   Standard deviation [Ang.]: 0.213814
@>   Weight: 0.380952
@> Statistics for ARG58P-ASP56P:
@>   Average [Ang.]: 2.827481
@>   Standard deviation [Ang.]: 0.171087
@>   Weight: 2.952381
@> Statistics for ALA45P-ARG75P:
@>   Average [Ang.]: 2.840721
@>   Standard deviation [Ang.]: 0.105565
@>   Weight: 0.904762
@> Statistics for ASN53P-GLU50P:
@>   Average [Ang.]: 2.980214
@>   Standard deviation [Ang.]: 0.147229
@>   Weight: 0.333333
@> Statistics for ALA74P-ASN53P:
@>   Average [Ang.]: 2.98522
@>   Standard deviation [Ang.]: 0.148331
@>   Weight: 0.952381
@> Statistics for ASP56P-ILE16P:
@>   Average [Ang.]: 3.085957
@>   Standard deviation [Ang.]: 0.21134
@>   Weight: 0.666667
@> Statistics for LYS110P-THR84P:
@>   Average [Ang.]: 2.774475
@>   Standard deviation [Ang.]: 0.080304
@>   Weight: 0.380952
@> Statistics for LEU116P-CYS90P:
@>   Average [Ang.]: 2.887425
@>   Standard deviation [Ang.]: 0.118768
@>   Weight: 0.952381
@> Statistics for SER103P-LEU99P:
@>   Average [Ang.]: 2.897324
@>   Standard deviation [Ang.]: 0.17182
@>   Weight: 1.380952
@> Statistics for ASN134P-ASP137P:
@>   Average [Ang.]: 2.917242
@>   Standard deviation [Ang.]: 0.160488
@>   Weight: 0.904762
@> Statistics for PHE152P-CYS148P:
@>   Average [Ang.]: 2.956784
@>   Standard deviation [Ang.]: 0.160039
@>   Weight: 0.904762
@> Statistics for ASN95P-ASP92P:
@>   Average [Ang.]: 3.061373
@>   Standard deviation [Ang.]: 0.215848
@>   Weight: 0.714286
@> Statistics for LYS6P-ASN38P:
@>   Average [Ang.]: 3.006786
@>   Standard deviation [Ang.]: 0.154497
@>   Weight: 0.333333
@> Statistics for ILE77P-ALA45P:
@>   Average [Ang.]: 2.819429
@>   Standard deviation [Ang.]: 0.092538
@>   Weight: 0.666667
@> Statistics for LEU99P-ASN95P:
@>   Average [Ang.]: 3.027242
@>   Standard deviation [Ang.]: 0.19744
@>   Weight: 0.904762
@> Statistics for CYS149P-CYS145P:
@>   Average [Ang.]: 2.928052
@>   Standard deviation [Ang.]: 0.146811
@>   Weight: 1.190476
@> Statistics for GLY52P-ALA74P:
@>   Average [Ang.]: 2.887583
@>   Standard deviation [Ang.]: 0.088417
@>   Weight: 0.285714
@> Statistics for ASP32P-LYS28P:
@>   Average [Ang.]: 2.86277
@>   Standard deviation [Ang.]: 0.119982
@>   Weight: 0.952381
@> Statistics for ILE88P-LYS112P:
@>   Average [Ang.]: 2.906433
@>   Standard deviation [Ang.]: 0.147086
@>   Weight: 1.0
@> Statistics for ARG27P-GLU23P:
@>   Average [Ang.]: 2.790357
@>   Standard deviation [Ang.]: 0.140396
@>   Weight: 2.0
@> Statistics for TYR142P-PHE138P:
@>   Average [Ang.]: 3.094219
@>   Standard deviation [Ang.]: 0.152889
@>   Weight: 1.0
@> Statistics for PHE26P-ALA22P:
@>   Average [Ang.]: 3.023619
@>   Standard deviation [Ang.]: 0.150087
@>   Weight: 1.0
@> Statistics for ASN15P-SER19P:
@>   Average [Ang.]: 2.96532
@>   Standard deviation [Ang.]: 0.213496
@>   Weight: 0.238095
@> Statistics for ARG75P-ASP81P:
@>   Average [Ang.]: 2.782441
@>   Standard deviation [Ang.]: 0.185369
@>   Weight: 2.095238
@> Statistics for ARG75P-ASP42P:
@>   Average [Ang.]: 2.760572
@>   Standard deviation [Ang.]: 0.134486
@>   Weight: 1.380952
@> Statistics for ARG97P-GLU93P:
@>   Average [Ang.]: 2.881173
@>   Standard deviation [Ang.]: 0.223159
@>   Weight: 1.952381
@> Statistics for ARG65P-GLU139P:
@>   Average [Ang.]: 2.826732
@>   Standard deviation [Ang.]: 0.198775
@>   Weight: 1.047619
@> Statistics for VAL25P-ILE21P:
@>   Average [Ang.]: 2.975267
@>   Standard deviation [Ang.]: 0.121046
@>   Weight: 1.0
@> Statistics for LEU153P-CYS149P:
@>   Average [Ang.]: 3.04695
@>   Standard deviation [Ang.]: 0.1793
@>   Weight: 0.952381
@> Statistics for SER7P-ASP86P:
@>   Average [Ang.]: 2.758983
@>   Standard deviation [Ang.]: 0.122097
@>   Weight: 1.142857
..
..
@> Statistics for ALA83P-LYS79P:
@>   Average [Ang.]: 3.225643
@>   Standard deviation [Ang.]: 0.148806
@>   Weight: 0.333333
@> Statistics for GLN60P-MET70P:
@>   Average [Ang.]: 2.902757
@>   Standard deviation [Ang.]: 0.162208
@>   Weight: 0.333333
@> Statistics for GLN124P-ILE126P:
@>   Average [Ang.]: 2.98456
@>   Standard deviation [Ang.]: 0.198396
@>   Weight: 0.238095
@> Statistics for SER19P-ASN15P:
@>   Average [Ang.]: 2.691612
@>   Standard deviation [Ang.]: 0.10843
@>   Weight: 0.380952
@> Statistics for ASN95P-THR46P:
@>   Average [Ang.]: 3.056129
@>   Standard deviation [Ang.]: 0.197107
@>   Weight: 0.333333
@> Statistics for ARG150P-ASP120P:
@>   Average [Ang.]: 2.752571
@>   Standard deviation [Ang.]: 0.112541
@>   Weight: 0.333333
@> Statistics for LYS155P-HSE157P:
@>   Average [Ang.]: 2.833843
@>   Standard deviation [Ang.]: 0.185712
@>   Weight: 0.333333
@> Statistics for ARG65P-ASP135P:
@>   Average [Ang.]: 2.86488
@>   Standard deviation [Ang.]: 0.213607
@>   Weight: 0.47619

For better visualization of the results, we can use showInteractionsGraph(), which displays results as a graph with residue-residue pairs of interactions. The intensity of the color of the lines connecting two residues corresponds to the number of counts. Darker lines are assigned to the most frequent appearance of interaction. The distance between pairs corresponds to the average distance across all the frames. Moreover, ovals with residue names are color-coded: acidic residues: red, basic: blue, polar: green, non-polar: silver, and proline: pink. The same function can be applied to ensemble PDB (more examples can be found there). We will also change the region of protein structure, which we would like to analyze from residue 1 to 100.

In [37]: statistics = calcStatisticsInteractions(interactionsTrajectory.getHydrogenBonds(selection='resid 5 to 100'))

In [38]: showInteractionsGraph(statistics, code='1-letter', cutoff=0.5)
@> Statistics for ARG101P-ASP98P:
@>   Average [Ang.]: 2.793931
@>   Standard deviation [Ang.]: 0.205527
@>   Weight: 1.52381
@> Statistics for HSE72P-ASN15P:
@>   Average [Ang.]: 2.989283
@>   Standard deviation [Ang.]: 0.270697
@>   Weight: 0.285714
@> Statistics for HSE66P-GLU139P:
@>   Average [Ang.]: 2.900411
@>   Standard deviation [Ang.]: 0.169455
@>   Weight: 0.428571
@> Statistics for ARG40P-LYS6P:
@>   Average [Ang.]: 3.055475
@>   Standard deviation [Ang.]: 0.213814
@>   Weight: 0.380952
@> Statistics for ARG58P-ASP56P:
@>   Average [Ang.]: 2.827481
@>   Standard deviation [Ang.]: 0.171087
@>   Weight: 2.952381
@> Statistics for ALA45P-ARG75P:
@>   Average [Ang.]: 2.840721
@>   Standard deviation [Ang.]: 0.105565
@>   Weight: 0.904762
@> Statistics for ASN53P-GLU50P:
@>   Average [Ang.]: 2.980214
@>   Standard deviation [Ang.]: 0.147229
@>   Weight: 0.333333
@> Statistics for ALA74P-ASN53P:
@>   Average [Ang.]: 2.98522
@>   Standard deviation [Ang.]: 0.148331
@>   Weight: 0.952381
@> Statistics for ASP56P-ILE16P:
@>   Average [Ang.]: 3.085957
@>   Standard deviation [Ang.]: 0.21134
@>   Weight: 0.666667
@> Statistics for LYS110P-THR84P:
@>   Average [Ang.]: 2.774475
@>   Standard deviation [Ang.]: 0.080304
@>   Weight: 0.380952
@> Statistics for LEU116P-CYS90P:
@>   Average [Ang.]: 2.887425
@>   Standard deviation [Ang.]: 0.118768
@>   Weight: 0.952381
@> Statistics for SER103P-LEU99P:
@>   Average [Ang.]: 2.897324
@>   Standard deviation [Ang.]: 0.17182
@>   Weight: 1.380952
@> Statistics for ASN95P-ASP92P:
@>   Average [Ang.]: 3.061373
@>   Standard deviation [Ang.]: 0.215848
@>   Weight: 0.714286
@> Statistics for LYS6P-ASN38P:
@>   Average [Ang.]: 3.006786
@>   Standard deviation [Ang.]: 0.154497
@>   Weight: 0.333333
@> Statistics for ILE77P-ALA45P:
@>   Average [Ang.]: 2.819429
@>   Standard deviation [Ang.]: 0.092538
@>   Weight: 0.666667
@> Statistics for LEU99P-ASN95P:
@>   Average [Ang.]: 3.027242
@>   Standard deviation [Ang.]: 0.19744
@>   Weight: 0.904762
@> Statistics for GLY52P-ALA74P:
@>   Average [Ang.]: 2.887583
@>   Standard deviation [Ang.]: 0.088417
@>   Weight: 0.285714
..
..
../../_images/insty_traj_graph1.png

Compare two independent frames

With this analysis, we can also compare interactions between frames. Below, we will compute hydrogen bonds for frame 0 and frame 18 and we will compare them using the compareInteractions() function. That function will be helpful in checking the difference between interactions. The results will be saved as diff_fr0_vsfr18.dat file.

Let’s check the interactions for the initail frame in our trajectory:

In [39]: frame0 = dcd.getFrame(0)

In [40]: at0 = frame0.getAtoms()

In [41]: hb0 = calcHydrogenBonds(at0.select('protein'))
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>     ARG101    P      NH1_1516  <--->      ASP98    P      OD1_1463     2.0    33.1
@>      HSE72    P      NE2_1042  <--->      ASN15    P       OD1_165     2.6    34.8
@>     GLN143    P      NE2_2192  <--->     GLU139    P      OE2_2126     2.7     9.2
@>      HSE66    P       NE2_957  <--->     GLU139    P      OE1_2125     2.7     6.4
@>      ARG40    P         N_561  <--->       LYS6    P          O_37     2.7    17.1
@>      ARG58    P         N_813  <--->      ASP56    P       OD1_788     2.7    30.0
@>      ALA45    P         N_634  <--->      ARG75    P        O_1097     2.8    35.1
@>      ASN53    P       ND2_747  <--->      GLU50    P       OE1_708     2.8    18.2
@>      ALA74    P        N_1064  <--->      ASN53    P         O_751     2.8    21.3
@>      ASP56    P         N_780  <--->      ILE16    P         O_189     2.8    27.0
@>     LYS110    P       NZ_1667  <--->      THR84    P        O_1240     2.8    38.2
@>     LEU116    P        N_1758  <--->      CYS90    P        O_1342     2.8    15.0
@>     SER103    P        N_1546  <--->      LEU99    P        O_1485     2.8    29.1
@>     ASN134    P        N_2045  <--->     ASP137    P      OD2_2091     2.8    22.6
@>     PHE152    P        N_2321  <--->     CYS148    P        O_2275     2.8     8.3
@>      ASN95    P        N_1398  <--->      ASP92    P      OD1_1368     2.8    12.6
@>       LYS6    P          N_16  <--->      ASN38    P         O_536     2.8    25.0
@>      ILE77    P        N_1115  <--->      ALA45    P         O_643     2.8    12.2
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.8    27.7
@>      LEU99    P        N_1467  <--->      ASN95    P        O_1411     2.8    15.5
@>     CYS149    P        N_2276  <--->     CYS145    P        O_2224     2.8     9.6
@>      GLY52    P         N_731  <--->      ALA74    P        O_1073     2.8     6.6
@>      ASP32    P         N_435  <--->      LYS28    P         O_385     2.8     8.8
@>      ILE88    P        N_1294  <--->     LYS112    P        O_1704     2.8    17.7
@>     GLN143    P        N_2180  <--->     GLU139    P        O_2128     2.8    21.7
@>      ARG27    P         N_340  <--->      GLU23    P         O_293     2.8    15.4
@>     TYR142    P        N_2159  <--->     PHE138    P        O_2113     2.9    14.2
@>     GLY133    P        N_2038  <--->     PRO130    P        O_1995     2.9    25.4
@>      PHE26    P         N_320  <--->      ALA22    P         O_278     2.9     4.9
@>      ASN15    P       ND2_166  <--->      SER19    P        OG_232     2.9    32.1
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.9    19.7
@>      ARG75    P      NH2_1093  <--->      ASP42    P       OD2_610     2.9    23.5
@>      ARG97    P        N_1431  <--->      GLU93    P        O_1386     2.9    22.2
@>      ARG65    P       NH2_941  <--->     GLU139    P      OE1_2125     2.9    32.3
@>      VAL25    P         N_304  <--->      ILE21    P         O_268     2.9     8.2
@>     LEU153    P        N_2341  <--->     CYS149    P        O_2286     2.9    12.5
@>       SER7    P          N_38  <--->      ASP86    P      OD2_1270     2.9    39.9
@>      ASP86    P        N_1261  <--->       SER7    P         OG_45     2.9    34.7
@>      ARG58    P       NH2_832  <--->     TYR131    P        O_2016     2.9    33.1
@>      THR46    P         N_644  <--->      CYS12    P         O_130     2.9    36.1
@>     GLN144    P        N_2197  <--->     THR140    P        O_2142     2.9    23.3
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.9    12.4
@>      LEU89    P        N_1313  <--->       LEU9    P          O_83     2.9    29.5
@>      THR31    P         N_421  <--->      ARG27    P         O_363     2.9    24.1
@>      CYS90    P        N_1332  <--->     GLU114    P        O_1738     2.9    24.6
@>     CYS148    P        N_2265  <--->     GLN144    P        O_2213     2.9     9.3
@>      GLU23    P         N_279  <--->      SER19    P         O_235     2.9    15.4
@>      ILE68    P         N_970  <--->      MET63    P         O_899     2.9    13.0
@>      PHE10    P          N_84  <--->      ASP42    P         O_612     2.9    22.8
@>     LYS112    P        N_1683  <--->      ASP86    P        O_1272     2.9    10.1
@>      SER61    P         N_861  <--->      TYR57    P         O_812     2.9    35.1
@>     CYS145    P        N_2214  <--->     VAL141    P        O_2158     2.9    15.9
@>      ARG27    P       NH2_359  <--->      GLU23    P       OE2_291     2.9    31.5
@>      LYS64    P         N_900  <--->      GLN60    P         O_860     2.9    22.9
@>       LEU9    P          N_65  <--->      TYR87    P        O_1293     2.9    16.4
@>      ASN38    P         N_523  <--->      ILE35    P         O_496     2.9    29.1
@>      VAL11    P         N_104  <--->      LEU89    P        O_1331     2.9    29.7
@>     ASN100    P        N_1486  <--->      LEU96    P        O_1430     2.9    10.3
@>     GLN124    P        N_1881  <--->     ASP120    P      OD2_1825     2.9    27.5
@>     LYS102    P        N_1524  <--->      ASP98    P        O_1466     2.9     9.3
@>      GLN76    P      NE2_1110  <--->      THR46    P         O_657     2.9    31.4
@>      ARG40    P       NH1_577  <--->      THR84    P      OG1_1233     2.9     8.4
@>      ALA44    P         N_624  <--->      PHE10    P         O_103     2.9    33.2
@>     GLU154    P        N_2360  <--->     ARG150    P        O_2310     3.0    22.6
@>       VAL8    P          N_49  <--->      ARG40    P         O_584     3.0    25.0
@>      MET63    P         N_883  <--->      GLY59    P         O_843     3.0    18.3
@>      GLN60    P         N_844  <--->      ASP56    P         O_791     3.0    35.5
@>      ILE35    P         N_478  <--->      VAL30    P         O_420     3.0    23.5
@>     VAL146    P        N_2225  <--->     TYR142    P        O_2179     3.0    31.5
@>      ARG58    P       NH1_829  <--->     TYR131    P        O_2016     3.0    38.1
@>      ASN53    P         N_738  <--->      GLU50    P         O_711     3.0    28.6
@>     ARG101    P        N_1500  <--->      ARG97    P        O_1454     3.0    32.3
@>      ARG18    P       NH1_217  <--->     ILE127    P        O_1954     3.0    26.0
@>      ARG75    P        N_1074  <--->      ASN15    P       OD1_165     3.0    25.1
@>     GLN144    P      NE2_2209  <--->     ILE126    P        O_1935     3.0    18.3
@>      ASN34    P         N_464  <--->      THR31    P         O_434     3.0    18.2
@>      ASN15    P       ND2_166  <--->      SER43    P        OG_620     3.0    25.7
@>      ARG58    P        NE_826  <--->      ASP56    P       OD1_788     3.0    22.2
@>      ARG27    P       NH1_356  <--->      GLU23    P       OE2_291     3.0    36.9
@>     ILE127    P        N_1936  <--->      MET91    P        O_1359     3.0    17.6
@>     TYR119    P       OH_1808  <--->     HSE157    P        N_2407     3.0    28.1
@>     HSE157    P        N_2407  <--->     TYR119    P       OH_1808     3.0    19.2
@>     GLU139    P        N_2114  <--->     ASP135    P        O_2070     3.0    27.9
@>      LEU29    P         N_386  <--->      VAL25    P         O_319     3.0    19.1
@>      SER47    P         N_658  <--->      LEU13    P         O_149     3.0    28.8
@>      VAL30    P         N_405  <--->      PHE26    P         O_339     3.0    17.7
@>     GLN105    P        N_1571  <--->     LYS102    P        O_1545     3.0    19.7
@>     SER118    P        N_1784  <--->     LEU115    P        O_1757     3.1    21.4
@>     LYS155    P        N_2375  <--->     ALA151    P        O_2320     3.1    21.3
@>     GLU114    P        N_1724  <--->      ILE88    P        O_1312     3.1    24.2
@>     ASP120    P        N_1816  <--->     GLY117    P        O_1783     3.1    12.7
@>      CYS62    P         N_872  <--->      ARG58    P         O_836     3.1    20.4
@>      ARG18    P       NH1_217  <--->      ASP92    P      OD2_1369     3.1     4.3
@>      ALA24    P         N_294  <--->      PRO20    P         O_249     3.1    29.9
@>     ARG150    P        N_2287  <--->     VAL146    P        O_2240     3.1    12.7
@>      LYS28    P         N_364  <--->      ALA24    P         O_303     3.1    20.0
@>     VAL141    P        N_2143  <--->     ASP137    P        O_2093     3.1    18.5
@>      ASP98    P        N_1455  <--->      SER94    P        O_1397     3.1    19.6
@>      LEU96    P        N_1412  <--->      ASP92    P        O_1371     3.1    36.3
@>      ALA22    P         N_269  <--->      ARG18    P         O_224     3.1    21.9
@>     ALA151    P        N_2311  <--->     ARG147    P        O_2264     3.1    15.6
@>      GLY67    P         N_963  <--->      LYS64    P         O_921     3.1    22.8
@>      ASP42    P         N_601  <--->       VAL8    P          O_64     3.1    35.6
@>      ARG65    P         N_922  <--->      SER61    P         O_871     3.1    23.4
@>      TRP39    P         N_537  <--->      SER36    P         O_507     3.1    15.2
@>     LYS123    P        N_1859  <--->     ASP120    P        O_1827     3.1    18.7
@>      MET91    P        N_1343  <--->      ASN95    P      OD1_1406     3.2    39.0
@>     THR140    P        N_2129  <--->     SER136    P        O_2081     3.2    30.3
@>      PHE85    P        N_1241  <--->      ASP81    P        O_1196     3.2    20.2
@>      ASN15    P         N_157  <--->      CYS12    P        SG_127     3.2    37.5
@>     ALA111    P        N_1673  <--->      PHE82    P        O_1216     3.2    20.6
@>     ARG147    P        N_2241  <--->     GLN143    P        O_2196     3.2    12.1
@>      ARG75    P      NH2_1093  <--->      ASP81    P      OD1_1193     3.2    29.3
@>     LYS112    P       NZ_1699  <--->     HSE157    P      OT2_2424     3.3    28.7
@>     ARG147    P      NH1_2257  <--->     GLN124    P      OE1_1892     3.3    29.9
@>     PHE138    P        N_2094  <--->     ASN134    P        O_2058     3.3    31.0
@>       SER7    P         OG_45  <--->      THR84    P        O_1240     3.3    35.5
@>      CYS12    P         N_120  <--->      ALA44    P         O_633     3.3    36.1
@>      SER19    P         N_225  <--->      CYS12    P        SG_127     3.3     8.0
@>      PHE82    P        N_1197  <--->      LYS79    P        O_1169     3.4    37.7
@>      ASP81    P        N_1185  <--->      THR78    P      OG1_1140     3.5    39.5
@>     LYS102    P       NZ_1540  <--->      ASP98    P      OD2_1464     3.5    26.1
@>     ARG147    P      NH2_2260  <--->     GLN124    P      OE1_1892     3.5    33.9
@>     VAL106    P        N_1588  <--->     SER103    P        O_1556     3.5    34.2
@> Number of detected hydrogen bonds: 124.

Let’s check the interactions for frame number 18 in our trajectory:

In [42]: frame18 = dcd.getFrame(18)

In [43]: at18 = frame18.getAtoms()

In [44]: hb18 = calcHydrogenBonds(at18.select('protein'))
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>      ARG75    P      NH2_1093  <--->      ASP81    P      OD1_1193     2.6    18.5
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.6    21.5
@>      ARG27    P       NH2_359  <--->      GLU23    P       OE2_291     2.7    18.4
@>      LYS28    P        NZ_380  <--->      ASP32    P       OD2_444     2.7    25.9
@>     ARG150    P       NE_2300  <--->     GLU154    P      OE1_2371     2.7    22.4
@>      ARG18    P       NH1_217  <--->      ASP92    P      OD2_1369     2.7    25.9
@>      ARG75    P       NE_1087  <--->      ASP42    P       OD1_609     2.7    16.1
@>      ARG58    P        NE_826  <--->      ASP56    P       OD1_788     2.7     2.1
@>      SER19    P        OG_232  <--->      ASN15    P       OD1_165     2.7     8.1
@>      ILE88    P        N_1294  <--->     LYS112    P        O_1704     2.7     1.4
@>       VAL8    P          N_49  <--->      ARG40    P         O_584     2.7    11.5
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.7    28.1
@>     ASN134    P        N_2045  <--->     ASP137    P      OD1_2090     2.7    12.5
@>     LYS155    P       NZ_2391  <--->     HSE157    P      OT2_2424     2.7    38.9
@>     LYS112    P        N_1683  <--->      ASP86    P        O_1272     2.7    25.8
@>     CYS145    P        N_2214  <--->     VAL141    P        O_2158     2.7    13.7
@>     LYS102    P       NZ_1540  <--->      ASP98    P      OD1_1463     2.8    29.5
@>     GLN143    P        N_2180  <--->     GLU139    P        O_2128     2.8    21.3
@>      LEU29    P         N_386  <--->      VAL25    P         O_319     2.8    16.9
@>      THR84    P      OG1_1233  <--->      GLU80    P        O_1184     2.8    10.5
@>      CYS90    P        N_1332  <--->     GLU114    P        O_1738     2.8     4.9
@>      THR31    P       OG1_427  <--->      ARG27    P         O_363     2.8    21.2
@>      ASP98    P        N_1455  <--->      SER94    P        O_1397     2.8     6.1
@>      SER43    P        OG_620  <--->      GLU23    P       OE1_290     2.8    13.9
@>     LYS110    P        N_1651  <--->      PHE82    P        O_1216     2.8    36.4
@>     SER118    P       OG_1791  <--->     GLU114    P      OE2_1736     2.8    20.1
@>      ARG65    P       NH1_938  <--->     ASP135    P      OD2_2068     2.8    12.3
@>      LYS64    P         N_900  <--->      GLN60    P         O_860     2.8     3.3
@>     ARG101    P      NH2_1519  <--->      ASP98    P      OD2_1464     2.8     8.9
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD2_1194     2.8    25.1
@>      ARG65    P         N_922  <--->      SER61    P         O_871     2.8    24.3
@>      ARG58    P       NH1_829  <--->     GLY133    P        O_2044     2.8    34.0
@>     ILE127    P        N_1936  <--->      MET91    P        O_1359     2.8    22.3
@>      THR78    P      OG1_1140  <--->      ASP81    P      OD2_1194     2.8    12.4
@>      THR84    P        N_1227  <--->      GLU80    P        O_1184     2.8    10.8
@>      GLN33    P         N_447  <--->      LEU29    P         O_404     2.8     6.2
@>       SER7    P          N_38  <--->      ASP86    P      OD1_1269     2.8    25.3
@>      ASP32    P         N_435  <--->      LYS28    P         O_385     2.8    16.9
@>      ASP86    P        N_1261  <--->       SER7    P          O_48     2.8    35.1
@>     LYS102    P        N_1524  <--->      ASP98    P        O_1466     2.8    29.0
@>      ASP42    P         N_601  <--->       VAL8    P          O_64     2.9    25.5
@>      SER61    P         N_861  <--->      TYR57    P         O_812     2.9    32.8
@>     CYS149    P        N_2276  <--->     CYS145    P        O_2224     2.9     2.6
@>     VAL146    P        N_2225  <--->     TYR142    P        O_2179     2.9     9.7
@>      GLN60    P         N_844  <--->      ASP56    P         O_791     2.9    25.1
@>     LYS155    P        N_2375  <--->     ARG150    P        O_2310     2.9    13.4
@>      ALA74    P        N_1064  <--->      ASN53    P         O_751     2.9    16.2
@>      TYR87    P        N_1273  <--->       SER7    P          O_48     2.9    18.2
@>     GLN144    P        N_2197  <--->     THR140    P        O_2142     2.9    16.3
@>      LEU89    P        N_1313  <--->       LEU9    P          O_83     2.9    28.6
@>     ARG101    P        N_1500  <--->      ARG97    P        O_1454     2.9     3.1
@>      CYS12    P        SG_127  <--->      SER19    P        OG_232     3.0    35.8
@>      ASN53    P       ND2_747  <--->      GLU50    P       OE2_709     3.0    21.4
@>      ALA45    P         N_634  <--->      ARG75    P        O_1097     3.0    11.5
@>      ASP56    P         N_780  <--->      ILE16    P         O_189     3.0    15.2
@>      ARG58    P         N_813  <--->      ASP56    P       OD1_788     3.0    14.2
@>      ILE77    P        N_1115  <--->      ALA45    P         O_643     3.0    12.8
@>      GLY67    P         N_963  <--->      MET63    P         O_899     3.0    16.3
@>      ARG18    P       NH1_217  <--->     ILE127    P        O_1954     3.0    33.1
@>      ARG75    P      NH1_1090  <--->      ASP81    P      OD1_1193     3.0    39.7
@>     THR140    P        N_2129  <--->     SER136    P        O_2081     3.0    18.5
@>     LEU153    P        N_2341  <--->     CYS149    P        O_2286     3.0    12.0
@>     ASN104    P        N_1557  <--->     ASN100    P        O_1499     3.0    38.4
@>      CYS62    P         N_872  <--->      ARG58    P         O_836     3.0    39.7
@>      VAL11    P         N_104  <--->      LEU89    P        O_1331     3.0    15.4
@>     VAL106    P        N_1588  <--->     LYS102    P        O_1545     3.0     2.4
@>     ALA151    P        N_2311  <--->     ARG147    P        O_2264     3.0    21.7
@>      ARG40    P         N_561  <--->       LYS6    P          O_37     3.0    33.0
@>       LEU9    P          N_65  <--->      TYR87    P        O_1293     3.0    39.7
@>      ARG27    P         N_340  <--->      GLU23    P         O_293     3.0    17.9
@>      ASN95    P      ND2_1407  <--->      THR46    P       OG1_650     3.0    38.8
@>      ARG27    P       NH2_359  <--->      VAL41    P         O_600     3.0    32.9
@>      LEU99    P        N_1467  <--->      ASN95    P        O_1411     3.0    21.7
@>     GLU154    P        N_2360  <--->     ARG150    P        O_2310     3.0    37.1
@>     ALA111    P        N_1673  <--->      PHE82    P        O_1216     3.0    18.4
@>     ARG150    P      NH2_2306  <--->     GLU154    P      OE1_2371     3.0    31.0
@>      VAL25    P         N_304  <--->      ILE21    P         O_268     3.0    10.3
@>      ASN15    P       ND2_166  <--->      SER43    P        OG_620     3.1    18.8
@>      MET63    P         N_883  <--->      GLY59    P         O_843     3.1    15.7
@>      VAL30    P         N_405  <--->      PHE26    P         O_339     3.1     6.2
@>     ARG150    P        N_2287  <--->     VAL146    P        O_2240     3.1    30.1
@>     PHE138    P        N_2094  <--->     ASN134    P        O_2058     3.1    10.8
@>     VAL141    P        N_2143  <--->     ASP137    P        O_2093     3.1    10.8
@>      PHE10    P          N_84  <--->      ASP42    P         O_612     3.1    17.6
@>     CYS148    P        N_2265  <--->     GLN144    P        O_2213     3.1    23.2
@>      PHE26    P         N_320  <--->      ALA22    P         O_278     3.1     9.0
@>      GLN76    P      NE2_1110  <--->      THR46    P         O_657     3.1    11.9
@>     LEU116    P        N_1758  <--->      CYS90    P        O_1342     3.2    18.5
@>      GLU23    P         N_279  <--->      SER19    P         O_235     3.2     2.4
@>      ALA44    P         N_624  <--->      PHE10    P         O_103     3.2    38.7
@>      ARG65    P       NH2_941  <--->     ASP135    P      OD1_2067     3.2    19.6
@>      ASN34    P         N_464  <--->      THR31    P         O_434     3.2    38.6
@>      ARG97    P        N_1431  <--->      GLU93    P        O_1386     3.2    17.8
@>      ALA22    P         N_269  <--->      ARG18    P         O_224     3.2    11.6
@>     GLN105    P        N_1571  <--->     ARG101    P        O_1523     3.2    28.1
@>       LYS6    P          N_16  <--->      ASN38    P         O_536     3.2    31.6
@>      ASN95    P        N_1398  <--->      ASP92    P      OD1_1368     3.2    11.6
@>     CYS145    P       SG_2221  <--->     VAL141    P        O_2158     3.3    30.4
@>      HSE66    P         N_946  <--->      CYS62    P         O_882     3.3    14.7
@>     ARG147    P        N_2241  <--->     GLN143    P        O_2196     3.3    26.0
@>     TYR142    P        N_2159  <--->     PHE138    P        O_2113     3.3    11.5
@>      TRP39    P         N_537  <--->      ILE35    P         O_496     3.4    35.3
@>     GLN124    P        N_1881  <--->     GLN144    P      OE1_2208     3.4    35.9
@>      CYS12    P         N_120  <--->      ALA44    P         O_633     3.4    35.7
@>     SER103    P       OG_1553  <--->      LEU99    P        O_1485     3.4    14.9
@>      PHE85    P        N_1241  <--->      ASP81    P        O_1196     3.4    24.1
@>      SER19    P         N_225  <--->      CYS12    P        SG_127     3.5     7.6
@> Number of detected hydrogen bonds: 107.

And compare them using compareInteractions(). We will obtain information on which interactions are newly maintained, which are stable, and which ones were lost.

In [45]: compareInteractions(hb0, hb18, filename='diff_fr0_vsfr18.dat')
@> Which interactions disappeared: 23
@> TYR87P <---> SER7P
@> SER43P <---> GLU23P
@> ASN104P <---> ASN100P
@> LYS155P <---> HSE157P
@> ARG150P <---> GLU154P
@> ASN95P <---> THR46P
@> LYS110P <---> PHE82P
@> SER19P <---> ASN15P
@> LYS155P <---> ARG150P
@> SER118P <---> GLU114P
@> GLY67P <---> MET63P
@> ARG65P <---> ASP135P
@> TRP39P <---> ILE35P
@> THR84P <---> GLU80P
@> HSE66P <---> CYS62P
@> GLN105P <---> ARG101P
@> CYS12P <---> SER19P
@> ARG58P <---> GLY133P
@> VAL106P <---> LYS102P
@> LYS28P <---> ASP32P
@> GLN124P <---> GLN144P
@> ARG27P <---> VAL41P
@> GLN33P <---> LEU29P

Which interactions appeared: 41
@> SER118P <---> LEU115P
@> GLY67P <---> LYS64P
@> GLU139P <---> ASP135P
@> ARG75P <---> ASN15P
@> PHE82P <---> LYS79P
@> ARG147P <---> GLN124P
@> GLY52P <---> ALA74P
@> ASP81P <---> THR78P
@> GLN144P <---> ILE126P
@> ASN38P <---> ILE35P
@> SER47P <---> LEU13P
@> ARG58P <---> TYR131P
@> LYS155P <---> ALA151P
@> MET91P <---> ASN95P
@> PHE152P <---> CYS148P
@> LYS28P <---> ALA24P
@> ASN100P <---> LEU96P
@> VAL106P <---> SER103P
@> SER7P <---> THR84P
@> ALA24P <---> PRO20P
@> HSE66P <---> GLU139P
@> GLU114P <---> ILE88P
@> LEU96P <---> ASP92P
@> GLN105P <---> LYS102P
@> LYS123P <---> ASP120P
@> GLY133P <---> PRO130P
@> TYR119P <---> HSE157P
@> ASN15P <---> SER19P
@> ILE35P <---> VAL30P
@> ARG65P <---> GLU139P
@> HSE157P <---> TYR119P
@> ASP120P <---> GLY117P
@> ARG40P <---> THR84P
@> ILE68P <---> MET63P
@> ASN15P <---> CYS12P
@> HSE72P <---> ASN15P
@> LYS110P <---> THR84P
@> GLN124P <---> ASP120P
@> TRP39P <---> SER36P
@> THR46P <---> CYS12P
@> LYS112P <---> HSE157P

@> Which interactions are the same: 73
@> GLN60P <---> ASP56P
@> ARG150P <---> VAL146P
@> ARG101P <---> ASP98P
@> ILE77P <---> ALA45P
@> VAL11P <---> LEU89P
@> SER61P <---> TYR57P
@> ARG18P <---> ASP92P
@> ALA22P <---> ARG18P
@> THR31P <---> ARG27P
@> ALA44P <---> PHE10P
@> LEU153P <---> CYS149P
@> ARG58P <---> ASP56P
@> ALA111P <---> PHE82P
@> CYS62P <---> ARG58P
@> VAL146P <---> TYR142P
@> GLU23P <---> SER19P
@> ARG27P <---> GLU23P
@> CYS149P <---> CYS145P
@> LYS64P <---> GLN60P
@> VAL8P <---> ARG40P
@> ARG40P <---> LYS6P
@> ARG65P <---> SER61P
@> ASP32P <---> LYS28P
@> ILE88P <---> LYS112P
@> ALA45P <---> ARG75P
@> PHE26P <---> ALA22P
@> ASN95P <---> ASP92P
@> VAL30P <---> PHE26P
@> THR140P <---> SER136P
@> LEU89P <---> LEU9P
@> SER103P <---> LEU99P
@> LEU116P <---> CYS90P
@> PHE10P <---> ASP42P
@> ASN15P <---> SER43P
@> TYR142P <---> PHE138P
@> ASN34P <---> THR31P
@> ASN134P <---> ASP137P
@> LEU99P <---> ASN95P
@> ASP98P <---> SER94P
@> GLN144P <---> THR140P
@> ARG97P <---> GLU93P
@> GLN76P <---> THR46P
@> LYS6P <---> ASN38P
@> ARG75P <---> ASP81P
@> ASN53P <---> GLU50P
@> THR78P <---> ASP81P
@> VAL141P <---> ASP137P
@> SER19P <---> CYS12P
@> GLN143P <---> GLU139P
@> LEU29P <---> VAL25P
@> ALA151P <---> ARG147P
@> GLU154P <---> ARG150P
@> ALA74P <---> ASN53P
@> CYS148P <---> GLN144P
@> SER7P <---> ASP86P
@> LYS102P <---> ASP98P
@> MET63P <---> GLY59P
@> ASP56P <---> ILE16P
@> PHE138P <---> ASN134P
@> CYS90P <---> GLU114P
@> ASP42P <---> VAL8P
@> CYS145P <---> VAL141P
@> ARG147P <---> GLN143P
@> PHE85P <---> ASP81P
@> VAL25P <---> ILE21P
@> LEU9P <---> TYR87P
@> ASP86P <---> SER7P
@> ARG101P <---> ARG97P
@> ILE127P <---> MET91P
@> LYS112P <---> ASP86P
@> CYS12P <---> ALA44P
@> ARG75P <---> ASP42P
@> ARG18P <---> ILE127P

We can also all the tools that are shown for single PDB analysis in this tutorial. For example, we can compute all interactions for frame0 and frame18 and display the interactions:

In [46]: interactions0 = Interactions()

In [47]: interactions0.calcProteinInteractions(at0)

In [48]: matrix0 = interactions0.buildInteractionMatrix()
In [49]: interactions0.showCumulativeInteractionTypes()
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
../../_images/insty_traj_cum1.png
In [50]: interactions18 = Interactions()

In [51]: interactions18.calcProteinInteractions(at18)

In [52]: matrix18 = interactions18.buildInteractionMatrix()
@> Calculating interations.
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>      ARG75    P      NH2_1093  <--->      ASP81    P      OD1_1193     2.6    18.5
@>      ARG58    P       NH2_832  <--->      ASP56    P       OD2_789     2.6    21.5
@>      ARG27    P       NH2_359  <--->      GLU23    P       OE2_291     2.7    18.4
@>      LYS28    P        NZ_380  <--->      ASP32    P       OD2_444     2.7    25.9
@>     ARG150    P       NE_2300  <--->     GLU154    P      OE1_2371     2.7    22.4
@>      ARG18    P       NH1_217  <--->      ASP92    P      OD2_1369     2.7    25.9
@>      ARG75    P       NE_1087  <--->      ASP42    P       OD1_609     2.7    16.1
@>      ARG58    P        NE_826  <--->      ASP56    P       OD1_788     2.7     2.1
@>      SER19    P        OG_232  <--->      ASN15    P       OD1_165     2.7     8.1
@>      ILE88    P        N_1294  <--->     LYS112    P        O_1704     2.7     1.4
@>       VAL8    P          N_49  <--->      ARG40    P         O_584     2.7    11.5
@>      THR78    P        N_1134  <--->      ASP81    P      OD2_1194     2.7    28.1
@>     ASN134    P        N_2045  <--->     ASP137    P      OD1_2090     2.7    12.5
@>     LYS155    P       NZ_2391  <--->     HSE157    P      OT2_2424     2.7    38.9
@>     LYS112    P        N_1683  <--->      ASP86    P        O_1272     2.7    25.8
In [53]: interactions18.showCumulativeInteractionTypes()
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
@> Calculating interactions
../../_images/insty_traj_cum2.png

Parse previously saved data

To upload and further use the interactions data use InteractionsTrajectory.parseInteractions() function:

In [54]: interactionsTrajectory2 = InteractionsTrajectory('5kqm_import')

In [55]: interactionsTrajectory2.parseInteractions('calcProteinInteractionsTrajectory.pkl')
[[[['ARG101', 'NH1_1516', 'P', 'ASP98', 'OD1_1463', 'P', 1.998, 33.1238],
   ['HSE72', 'NE2_1042', 'P', 'ASN15', 'OD1_165', 'P', 2.5997, 34.752],
   ['GLN143', 'NE2_2192', 'P', 'GLU139', 'OE2_2126', 'P', 2.7287, 9.1822],
   ['HSE66', 'NE2_957', 'P', 'GLU139', 'OE1_2125', 'P', 2.7314, 6.3592],
   ['ARG40', 'N_561', 'P', 'LYS6', 'O_37', 'P', 2.7479, 17.1499],
   ['ARG58', 'N_813', 'P', 'ASP56', 'OD1_788', 'P', 2.7499, 29.9737],
   ['ALA45', 'N_634', 'P', 'ARG75', 'O_1097', 'P', 2.7609, 35.0983],
   ['ASN53', 'ND2_747', 'P', 'GLU50', 'OE1_708', 'P', 2.7702, 18.2336],
   ['ALA74', 'N_1064', 'P', 'ASN53', 'O_751', 'P', 2.7782, 21.3375],
   ['ASP56', 'N_780', 'P', 'ILE16', 'O_189', 'P', 2.7793, 27.0481],
   ['LYS110', 'NZ_1667', 'P', 'THR84', 'O_1240', 'P', 2.7977, 38.2213],
   ['LEU116', 'N_1758', 'P', 'CYS90', 'O_1342', 'P', 2.8072, 15.0239],
   ['SER103', 'N_1546', 'P', 'LEU99', 'O_1485', 'P', 2.8075, 29.107],
   ['ASN134', 'N_2045', 'P', 'ASP137', 'OD2_2091', 'P', 2.8132, 22.562],
   ['PHE152', 'N_2321', 'P', 'CYS148', 'O_2275', 'P', 2.8141, 8.2562],
   ['ASN95', 'N_1398', 'P', 'ASP92', 'OD1_1368', 'P', 2.8148, 12.5701],
   ['LYS6', 'N_16', 'P', 'ASN38', 'O_536', 'P', 2.8178, 25.0306],
   ['ILE77', 'N_1115', 'P', 'ALA45', 'O_643', 'P', 2.8179, 12.1856],
   ['ARG58', 'NH2_832', 'P', 'ASP56', 'OD2_789', 'P', 2.8204, 27.6617],
   ['LEU99', 'N_1467', 'P', 'ASN95', 'O_1411', 'P', 2.8205, 15.4867],
   ['CYS149', 'N_2276', 'P', 'CYS145', 'O_2224', 'P', 2.8247, 9.5914],
   ['GLY52', 'N_731', 'P', 'ALA74', 'O_1073', 'P', 2.832, 6.6442],
   ['ASP32', 'N_435', 'P', 'LYS28', 'O_385', 'P', 2.8357, 8.8318],
   ..
   ..

After uploading, we have access to all data, for example:

In [56]: interactionsTrajectory2.getHydrophohic()
[[['ALA156', 'CB_2401', 'P', 'TYR87', 'OH_1286', 'P', 3.0459, 21.959],
  ['ALA24', 'CB_298', 'P', 'MET63', 'CE_894', 'P', 3.3105, 5.1584],
  ['ILE68', 'CG2_976', 'P', 'MET63', 'CE_894', 'P', 3.3306, 52.4165],
  ['TYR142', 'CZ_2171', 'P', 'VAL146', 'CG2_2235', 'P', 3.4815, 49.7427],
  ['PHE10', 'CD1_92', 'P', 'ALA22', 'CB_273', 'P', 3.5334, 31.1973],
  ['LYS6', 'CD_26', 'P', 'TRP39', 'CZ2_555', 'P', 3.5427, 68.7284],
  ['PHE26', 'CE2_336', 'P', 'VAL30', 'CG1_411', 'P', 3.5603, 21.127],
  ['ILE88', 'CD_1307', 'P', 'ALA111', 'CB_1677', 'P', 3.5627, 21.2201],
  ['VAL11', 'CG2_114', 'P', 'ILE88', 'CG2_1300', 'P', 3.6386, 9.3289],
  ['VAL41', 'CG2_595', 'P', 'PHE26', 'CD2_334', 'P', 3.6448, 16.55],
  ['PHE152', 'CE1_2331', 'P', 'ALA156', 'CB_2401', 'P', 3.6594, 17.4765],
  ['LYS79', 'CG_1155', 'P', 'VAL106', 'CG2_1598', 'P', 3.6828, 25.1359],
  ['LEU99', 'CD2_1480', 'P', 'ILE77', 'CD_1128', 'P', 3.6917, 11.9735],
  ['PHE82', 'CD1_1205', 'P', 'ILE88', 'CD_1307', 'P', 3.692, 17.6138],
  ['LEU116', 'CD2_1771', 'P', 'ILE127', 'CD_1949', 'P', 3.7057, 17.4094],
  ..
  ..
In [57]: calcStatisticsInteractions(interactionsTrajectory2.getHydrogenBonds())
@> Statistics for ARG101P-ASP98P:
@>   Average [Ang.]: 2.793931
@>   Standard deviation [Ang.]: 0.205527
@>   Weight: 1.52381
@> Statistics for HSE72P-ASN15P:
@>   Average [Ang.]: 2.989283
@>   Standard deviation [Ang.]: 0.270697
@>   Weight: 0.285714
@> Statistics for GLN143P-GLU139P:
@>   Average [Ang.]: 3.051633
@>   Standard deviation [Ang.]: 0.20753
@>   Weight: 1.285714
@> Statistics for HSE66P-GLU139P:
@>   Average [Ang.]: 2.900411
@>   Standard deviation [Ang.]: 0.169455
@>   Weight: 0.428571
@> Statistics for ARG40P-LYS6P:
@>   Average [Ang.]: 3.055475
@>   Standard deviation [Ang.]: 0.213814
@>   Weight: 0.380952
@> Statistics for ARG58P-ASP56P:
@>   Average [Ang.]: 2.827481
@>   Standard deviation [Ang.]: 0.171087
@>   Weight: 2.952381
..
..
In [58]: interactionsTrajectory2.getTimeInteractions()
../../_images/insty_traj_counts2.png