PDB structure with multiple chains

This time we will use protein with two chains, lipoxygenase (PDB: 7LAF) which contain chain A and chain B. First, we will add missing hydrogens to the protein structures and then we will perform analysis of interactions between two chains.

Add missing hydrogen atoms to the structure

We start by fetching the PDB file and adding missing hydrogens using Openbabel.

In [1]: fetchPDB('7laf', compressed=False)

In [2]: addMissingAtoms('7laf.pdb', method='openbabel')

In [3]: atoms = parsePDB('addH_7laf.pdb').select('protein')
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 7laf downloaded (7laf.pdb)
@> PDB download via FTP completed (1 downloaded, 0 failed).
@> Hydrogens were added to the structure. Structure addH_7laf.pdb is saved in the local directry.
@> 21970 atoms and 1 coordinate set(s) were parsed in 0.24s.
In [4]: interactions = Interactions('7laf')

To compute all interactions:

In [5]: all_interactions = interactions.calcProteinInteractions(atoms)
@> Calculating interations.
@> Calculating hydrogen bonds.
@>      DONOR (res chid atom)   <--->       ACCEPTOR (res chid atom)    Distance  Angle
@>     ASP505    A      OD2_3935  <--->     TYR496    A       OH_3867     2.2    29.5
@>     ASP666    B     OD1_10390  <--->     SER648    B      OG_10241     2.3    17.8
@>     HIS394    A        N_3026  <--->     GLU141    A      OE2_1006     2.4    35.5
@>     ARG390    B      NH1_8204  <--->     TYR149    B        O_6273     2.4    35.6
@>     GLN641    A      NE2_4984  <--->     GLY621    A        O_4815     2.4     8.5
@>     ARG649    B     NH1_10251  <--->     GLU653    B     OE1_10281     2.4     4.9
@>     ARG463    B      NH1_8796  <--->     ASP459    B      OD1_8759     2.4    30.6
@>     TYR318    B        N_7621  <--->     LEU327    B        O_7687     2.4     4.3
@>     ASN301    A      ND2_2299  <--->     ASP428    A        O_3307     2.4    29.3
@>     ARG474    A      NH1_3686  <--->     ILE468    A        O_3625     2.5    37.5
@>     ARG474    B      NH1_8890  <--->     VAL465    B        O_8805     2.5    21.1
@>     SER517    B       OG_9247  <--->     ASN522    B      ND2_9287     2.5    26.7
@>     ASN522    B      ND2_9287  <--->     SER517    B       OG_9247     2.5    33.0
@>     TRP481    B        N_8937  <--->     GLY477    B        O_8911     2.5     7.9
@>      LEU36    A         N_274  <--->      VAL24    A         O_194     2.5    21.5
@>     SER526    A       OG_4113  <--->     GLN523    A        O_4087     2.5    24.9
@>     ARG138    B      NH2_6183  <--->     GLU507    B      OE1_9158     2.5    28.0
@>     TRP109    A         N_743  <--->     ASN173    A      OD1_1279     2.5     7.1
@>     THR431    B      OG1_8538  <--->     VAL427    B        O_8504     2.5    24.5
@>     SER501    B       OG_9107  <--->     SER498    B        O_9082     2.5    35.7
@>     GLN143    B        N_6219  <--->     GLN139    B        O_6187     2.5    11.9
@>     LEU329    A        N_2495  <--->     LEU316    A        O_2404     2.5    21.1
@>     LEU110    A         N_757  <--->      TRP87    A         O_551     2.6    33.6
@>     HIS373    A        N_2854  <--->     HIS368    A        O_2818     2.6    19.3
@>     ASN413    B      ND2_8402  <--->     GLU382    B      OE1_8140     2.6    20.3
@>     ARG535    B      NH1_9382  <--->     TYR496    B        O_9063     2.6    29.4
@>     ARG649    A      NH1_5047  <--->     GLU653    A      OE2_5078     2.6    19.6
@>     TRP109    B        N_5947  <--->     ASN173    B      OD1_6483     2.6    37.3
@>     ARG429    B        N_8516  <--->     GLN425    B        O_8488     2.6    23.9
@>     GLN575    B      NE2_9683  <--->     LEU594    B        O_9812     2.6    14.9
@>      ARG68    A         N_482  <--->      SER25    A         O_201     2.6    14.5
@>      HIS70    A         N_500  <--->      SER23    A         O_188     2.6    12.3
@>     ARG215    A      NH2_1620  <--->     GLU168    B      OE1_6442     2.6    24.8
@>     THR462    A        N_3576  <--->     GLU458    A        O_3543     2.6    22.5
@>     ARG463    B      NH2_8797  <--->     TYR471    B       OH_8856     2.6    19.7
@>     HIS405    A      ND1_3124  <--->     ASN672    A        O_5230     2.6    25.8
@>     GLN335    A      NE2_2547  <--->     ALA312    A        O_2377     2.6    10.5
@>     LEU110    B        N_5961  <--->      TRP87    B        O_5770     2.6    37.7
@>     TYR495    B       OH_9059  <--->     GLU630    B     OE1_10098     2.6    12.0
@>     ARG463    A      NH2_3593  <--->     ILE251    A        O_1918     2.6    39.3
@>     GLN319    B      NE2_7641  <--->     GLY324    B        O_7668     2.6    28.2
@>     HIS373    B        N_8058  <--->     HIS368    B        O_8022     2.6    20.9
@>     GLU364    B        N_7982  <--->     VAL360    B        O_7954     2.6    28.1
@>      TRP87    A         N_548  <--->     LEU110    A         O_760     2.6     8.9
@>     TYR408    A       OH_3157  <--->     ASP616    A      OD1_4775     2.6    37.7
@>     GLY493    B        N_9036  <--->     SER489    B        O_9008     2.6    32.4
@>     LEU354    B        N_7900  <--->     LYS350    B        O_7858     2.6    22.3
@>     LEU142    A        N_1007  <--->     ARG138    A         O_972     2.6     5.8
@>     VAL488    A        N_3794  <--->     VAL484    A        O_3759     2.6    11.4
@>     ASN655    A      ND2_5097  <--->     TYR662    A        O_5144     2.6    17.4
@>      THR95    A         N_632  <--->       ARG5    A          O_52     2.6    12.4
@>     ARG208    A        N_1551  <--->     GLU212    A      OE1_1591     2.6    21.7
@>     ARG463    A      NH2_3593  <--->     TYR471    A       OH_3652     2.6    35.2
@>     ARG208    B        N_6755  <--->     GLU212    B      OE1_6795     2.6    34.4
@>     SER550    B       OG_9500  <--->     ILE546    B        O_9466     2.6    22.5
@>     GLN119    B      NE2_6029  <--->     GLN137    B      OE1_6171     2.6    28.1
@>     LEU327    B        N_7684  <--->     TYR318    B        O_7624     2.6     6.3
@>     LEU420    A        N_3247  <--->     ALA416    A        O_3217     2.6    34.5
@>     CYS106    A         N_716  <--->      ARG90    A         O_582     2.7    36.5
@>     LEU607    B        N_9900  <--->     VAL603    B        O_9875     2.7    12.6
@>     VAL488    B        N_8998  <--->     VAL484    B        O_8963     2.7     4.8
@>     GLY583    B        N_9735  <--->     ASP352    B      OD2_7885     2.7    15.8
@>      SER25    A         N_198  <--->      ARG68    A         O_485     2.7    38.0
@>     ASN301    A      ND2_2299  <--->     THR431    A        O_3332     2.7    28.3
@>     ARG407    A      NH2_3145  <--->     ASP616    A        O_4772     2.7    29.7
@>     GLN509    B      NE2_9176  <--->     LEU532    B        O_9352     2.7    37.1
@>     ARG407    A      NH1_3144  <--->     ASP616    A      OD2_4776     2.7    11.0
@>     SER489    A        N_3801  <--->     GLU485    A        O_3766     2.7    24.6
@>     ARG215    A      NH1_1619  <--->     GLU168    B      OE2_6443     2.7    28.7
@>     ARG253    A        N_1934  <--->     ARG463    A        O_3586     2.7    10.7
@>     PHE288    B        N_7398  <--->     LEU317    B        O_7616     2.7    18.1
@>     GLN509    A      NE2_3972  <--->     LEU532    A        O_4148     2.7    27.8
@>     THR409    A      OG1_3163  <--->     VAL674    A        O_5244     2.7    37.9
@>     PHE309    B        N_7556  <--->     MET574    B        O_9670     2.7    12.8
@>     ASN445    B        N_8639  <--->     LEU441    B        O_8606     2.7    23.6
@>     GLY583    A        N_4531  <--->     ASP352    A      OD2_2681     2.7    14.6
@>     TYR451    B        N_8689  <--->     SER526    B        O_9315     2.7    38.7
@>       ARG5    A          N_49  <--->      THR95    A         O_635     2.7    15.9
@>     CYS106    B        N_5920  <--->      ARG90    B        O_5801     2.7    32.5
@>     TYR149    A        N_1066  <--->     ARG145    A        O_1032     2.7     8.1
@>     GLN575    A        N_4471  <--->     THR593    A        O_4601     2.7    15.0
@>     HIS160    A        N_1167  <--->     LYS518    A        O_4047     2.7    35.5
@>     PHE547    B        N_9471  <--->     THR543    B        O_9444     2.7    33.0
@>     ARG253    B        N_7138  <--->     ARG463    B        O_8790     2.7    16.2
@>     ASN655    A        N_5090  <--->     ILE651    A        O_5056     2.7    28.0
@>     LEU345    B        N_7817  <--->     ASP348    B      OD2_7846     2.7    14.0
@>     ASP504    A        N_3920  <--->     GLU500    A        O_3892     2.7    37.2
@>     ARG203    A      NH1_1514  <--->     GLU212    A      OE2_1592     2.7    38.1
@>     ASN569    A      ND2_4434  <--->     SER563    A        O_4384     2.7     2.5
@>     TRP481    A        N_3733  <--->     GLY477    A        O_3707     2.7     5.8
@>     ASN362    A        N_2765  <--->     THR358    A        O_2729     2.7    34.3
@>     MET314    A        N_2386  <--->     GLN332    A        O_2519     2.7    23.3
@>     SER430    B        N_8527  <--->     VAL426    B        O_8497     2.7    13.0
@>      TRP87    B        N_5767  <--->     LEU110    B        O_5964     2.7    31.2
@>     HIS368    B        N_8019  <--->     GLU364    B        O_7985     2.7    24.6
@>     ILE492    B        N_9028  <--->     VAL488    B        O_9001     2.7     2.1
@>     ASN413    A      ND2_3198  <--->     HIS378    A        O_2899     2.7    35.7
@>     ARG390    A      NH1_3000  <--->     TYR149    A        O_1069     2.7    18.4
@>     ARG407    B      NH2_8349  <--->     ASP616    B        O_9976     2.7    31.8
@>     SER430    A        N_3323  <--->     VAL426    A        O_3293     2.7    37.6
@>     ARG654    A        N_5079  <--->     GLY650    A        O_5052     2.7    22.2
@>     ASN445    A        N_3435  <--->     LEU441    A        O_3402     2.7     9.8
@>     HIS376    B        N_8084  <--->     LEU371    B        O_8046     2.7    15.5
@>     LYS518    B        N_9248  <--->     GLU514    B        O_9217     2.7    30.5
@>     ARG444    B      NH2_8638  <--->     SER296    B        O_7465     2.7    14.5
@>     GLU440    A        N_3390  <--->     GLU436    A        O_3363     2.7    23.1
@>     LEU607    A        N_4696  <--->     VAL603    A        O_4671     2.7     6.3
@>     GLN641    A        N_4976  <--->     ILE637    A        O_4948     2.7    35.5
@>     ARG444    B        N_8628  <--->     GLU440    B        O_8597     2.7    20.9
@>     ASP202    A      OD2_1504  <--->     GLU418    B      OE2_8442     2.7    31.6
@>     ILE403    B        N_8307  <--->     PHE399    B        O_8274     2.7    13.4
@>     LEU278    A        N_2119  <--->     ASP265    A      OD1_2043     2.7    32.7
@>     GLN575    B        N_9675  <--->     THR593    B        O_9805     2.7    22.3
@>     GLN136    A       NE2_959  <--->     GLU140    A       OE2_997     2.7    16.6
@>     TYR496    B        N_9060  <--->     ILE492    B        O_9031     2.7    35.5
@>     GLU364    A        N_2778  <--->     VAL360    A        O_2750     2.8    29.9
@>     ALA188    A        N_1398  <--->     PHE184    A        O_1361     2.8    22.9
@>     ASN672    B       N_10431  <--->     ARG618    B        O_9993     3.3    14.1
@>     ARG461    A        N_3565  <--->     PRO457    A        O_3536     3.3    31.9
@>     SER636    A        N_4939  <--->     ALA632    A        O_4908     3.3    26.8
@>     GLN136    B      NE2_6163  <--->     GLU140    B      OE2_6201     3.3    15.4
@>     ALA370    A        N_2834  <--->     SER366    A        O_2801     3.3    16.7
@>     VAL360    A        N_2747  <--->     ALA356    A        O_2715     3.3    23.8
@>     PHE229    A        N_1729  <--->     ALA225    A        O_1703     3.3    33.3
@>     ASN362    A      ND2_2772  <--->     PRO571    A        O_4446     3.3    10.2
@>     CYS161    A        N_1177  <--->     LYS152    A        O_1104     3.3     8.3
@>     ALA370    B        N_8038  <--->     SER366    B        O_8005     3.3    30.9
@>     ASN413    B        N_8395  <--->     THR409    B        O_8365     3.3    36.3
@>     THR372    A        N_2847  <--->     PHE367    A        O_2807     3.3    18.6
@>     ARG215    B      NH1_6823  <--->     GLU212    B      OE2_6796     3.3    34.9
@>     ASN598    B      ND2_9845  <--->     ASN304    B      OD1_7525     3.3     7.3
@>     GLY424    B        N_8481  <--->     ASP428    B      OD2_8515     3.3    25.2
@>     ILE515    B        N_9223  <--->     TRP511    B        O_9185     3.3    19.4
@>     ARG361    A      NH1_2763  <--->     ASN569    A        O_4430     3.3    27.9
@>     CYS161    B        N_6381  <--->     LYS152    B        O_6308     3.3    19.0
@>      THR95    B      OG1_5856  <--->       ARG5    B        O_5309     3.3    14.8
@>     SER517    B       OG_9247  <--->     ASN522    B      OD1_9286     3.3    36.6
@>     ARG474    B      NH1_8890  <--->     ILE468    B        N_8826     3.3    28.8
@>     VAL268    A        N_2058  <--->     THR264    A        O_2033     3.3    27.6
@>     SER377    B        N_8094  <--->     THR372    B        O_8054     3.3    31.9
@>     ARG535    A        N_4169  <--->     ASP499    A      OD1_3887     3.3     1.1
@>     ARG634    B     NH2_10131  <--->     GLU626    B     OE1_10061     3.3    31.2
@>     ILE421    B        N_8459  <--->     ALA416    B        O_8421     3.3    24.8
@>      THR10    A          N_91  <--->      ALA49    A         O_335     3.3    21.1
@>     TYR473    B        N_8869  <--->     ASN244    B      OD1_7075     3.3    39.9
@>     GLN241    A      NE2_1845  <--->     ASN569    A      OD1_4433     3.3    38.6
@>     TYR495    A        N_3844  <--->     ILE491    A        O_3819     3.3    30.8
@>     ILE421    A        N_3255  <--->     ALA416    A        O_3217     3.3    34.5
@>       ARG5    B        N_5306  <--->      THR95    B        O_5854     3.3    34.8
@>     GLN139    A         N_980  <--->     GLN135    A         O_945     3.4    11.3
@>     GLN479    A        N_3716  <--->     ASP475    A        O_3691     3.4    33.6
@>     SER286    B        N_7384  <--->     GLU281    B        O_7348     3.4    16.8
@>     MET195    B        N_6647  <--->     ALA191    B        O_6620     3.4    27.9
@>     ARG618    A      NH1_4795  <--->     ASP625    A      OD2_4849     3.4     9.3
@>     VAL502    B        N_9108  <--->     SER498    B        O_9082     3.4    32.3
@>     ILE515    A        N_4019  <--->     TRP511    A        O_3981     3.4    28.7
@>     ARG407    B      NH2_8349  <--->     GLU671    B     OE2_10430     3.4    26.5
@>     ASN672    A        N_5227  <--->     ARG618    A        O_4789     3.4    31.4
@>     VAL167    B        N_6428  <--->     GLU418    B      OE1_8441     3.4    23.0
@>     SER320    B        N_7642  <--->     PRO325    B        O_7672     3.4    32.0
@>     HIS394    B        N_8230  <--->     GLU141    B      OE1_6209     3.4     4.5
@>     ARG203    A      NH1_1514  <--->     GLU212    A      OE1_1591     3.4    24.9
       ..
       ..
@> Number of detected hydrogen bonds: 669.
@> Calculating salt bridges.
@>     LYS196    A         NZ_1459  <--->     ASP202    A   OD1_1503_1504     2.4
@>     GLU168    B   OE1_6442_6443  <--->     ARG215    A   NH1_1619_1620     2.6
@>     ASP202    B   OD1_6707_6708  <--->     LYS196    B         NZ_6663     2.7
@>     ARG654    A   NH1_5088_5089  <--->     ASP476    A   OD1_3702_3703     2.8
@>     ASP505    B   OD1_9138_9139  <--->     HIS396    B        NE2_8255     2.9
@>     ARG203    A   NH1_1514_1515  <--->     GLU212    A   OE1_1591_1592     3.0
@>     GLU281    B   OE1_7352_7353  <--->     LYS284    B         NZ_7379     3.0
@>     ASP616    A   OD1_4775_4776  <--->     ARG407    A   NH1_3144_3145     3.0
@>     ASP505    A   OD1_3934_3935  <--->     HIS396    A        NE2_3051     3.0
@>     LYS582    B         NZ_9734  <--->     ASP348    B   OD1_7845_7846     3.1
@>     ARG635    A   NH1_4937_4938  <--->     GLU631    A   OE1_4903_4904     3.2
@>      GLU32    B   OE1_5509_5510  <--->      ARG68    B   NH1_5729_5730     3.3
@>     GLU212    B   OE1_6795_6796  <--->     ARG203    B   NH1_6718_6719     3.3
@>     ASP625    B OD1_10052_10053  <--->     ARG618    B  NH1_9999_10000     3.3
@>     ASP616    B   OD1_9979_9980  <--->     ARG407    B   NH1_8348_8349     3.3
@>     HIS292    A        NE2_2237  <--->     GLU364    A   OE1_2785_2786     3.4
@>     ARG618    A   NH1_4795_4796  <--->     ASP625    A   OD1_4848_4849     3.4
@>     ASP476    B   OD1_8906_8907  <--->     ARG654    B NH1_10292_10293     3.5
@>     ARG138    B   NH1_6182_6183  <--->     GLU507    B   OE1_9158_9159     3.5
@>     ARG649    B NH1_10251_10252  <--->     GLU653    B OE1_10281_10282     3.6
@>     ARG649    A   NH1_5047_5048  <--->     GLU653    A   OE1_5077_5078     3.6
@>     ARG634    B NH1_10130_10131  <--->     GLU626    B OE1_10061_10062     3.7
@>     GLU364    B   OE1_7989_7990  <--->     HIS292    B        NE2_7441     3.7
@>     ARG220    B   NH1_6872_6873  <--->     GLU194    B   OE1_6645_6646     3.8
@>     GLU507    A   OE1_3954_3955  <--->     ARG138    A     NH1_978_979     3.8
@>     ASP602    A   OD1_4666_4667  <--->     ARG429    A   NH1_3321_3322     3.9
@>     GLU626    A   OE1_4857_4858  <--->     ARG634    A   NH1_4926_4927     3.9
@>     ARG220    A   NH1_1668_1669  <--->     GLU194    A   OE1_1441_1442     3.9
@>     LYS357    B         NZ_7929  <--->     ASP235    B   OD1_7001_7002     3.9
@>     LYS175    A         NZ_1297  <--->     GLU168    A   OE1_1238_1239     4.0
@>     ASP235    A   OD1_1797_1798  <--->     LYS357    A         NZ_2725     4.0
@>     GLU141    B   OE1_6209_6210  <--->     ARG145    B   NH1_6242_6243     4.0
@>     ARG429    B   NH1_8525_8526  <--->     ASP602    B   OD1_9870_9871     4.0
@>     GLU613    A   OE1_4756_4757  <--->     LYS180    A         NZ_1336     4.0
@>       ARG7    A       NH1_76_77  <--->      ASP52    A     OD1_361_362     4.1
@>     ARG463    B   NH1_8796_8797  <--->     ASP459    B   OD1_8759_8760     4.1
@>     GLU382    A   OE1_2936_2937  <--->     ARG417    A   NH1_3228_3229     4.1
@>     ASP348    A   OD1_2641_2642  <--->     LYS582    A         NZ_4530     4.2
@>      ASP20    B   OD1_5424_5425  <--->      LYS71    B         NZ_5756     4.2
@>     GLU194    A   OE1_1441_1442  <--->     LYS198    A         NZ_1476     4.2
@>      GLU32    A     OE1_252_253  <--->      ARG68    A     NH1_491_492     4.3
@>     ARG463    A   NH1_3592_3593  <--->     ASP459    A   OD1_3555_3556     4.3
@>     ARG208    A   NH1_1560_1561  <--->     GLU111    B   OE1_5976_5977     4.3
@>     GLU141    A   OE1_1005_1006  <--->     ARG145    A   NH1_1038_1039     4.4
@>     ASP475    A   OD1_3694_3695  <--->     ARG474    A   NH1_3686_3687     4.4
@>     ASP616    A   OD1_4775_4776  <--->     LYS180    A         NZ_1336     4.5
@>     ARG390    A   NH1_3000_3001  <--->     GLU514    A   OE1_4017_4018     4.6
@>      ARG63    B   NH1_5687_5688  <--->     ASP129    B   OD1_6102_6103     4.6
@>     ARG461    B   NH1_8778_8779  <--->     GLU458    B   OE1_8751_8752     4.6
@>     ARG444    A   NH1_3433_3434  <--->     GLU440    A   OE1_3397_3398     4.6
@>     GLU369    A   OE1_2832_2833  <--->     HIS368    A        NE2_2824     4.6
@>     HIS231    B        NE2_6962  <--->     GLU234    B   OE1_6993_6994     4.6
@>     LYS165    A         NZ_1216  <--->     ASP163    A   OD1_1197_1198     4.6
@>     LYS612    B         NZ_9952  <--->     ASP562    B   OD1_9583_9584     4.7
@>      ASP20    A     OD1_167_168  <--->      LYS71    A          NZ_518     4.7
@>     GLU212    B   OE1_6795_6796  <--->     ARG208    B   NH1_6764_6765     4.7
@>     GLU369    B   OE1_8036_8037  <--->     HIS368    B        NE2_8028     4.8
@>     HIS231    A        NE2_1758  <--->     GLU234    A   OE1_1789_1790     4.8
@>     GLU168    B   OE1_6442_6443  <--->     LYS175    B         NZ_6501     4.8
@>     ARG417    B   NH1_8432_8433  <--->     GLU382    B   OE1_8140_8141     4.9
@>     ARG474    B   NH1_8890_8891  <--->     ASP475    B   OD1_8898_8899     4.9
@>     ARG215    A   NH1_1619_1620  <--->     GLU212    A   OE1_1591_1592     4.9
@>      GLU12    B   OE1_5366_5367  <--->      ARG90    B   NH1_5807_5808     4.9
@>     LYS198    B         NZ_6680  <--->     GLU194    B   OE1_6645_6646     5.0
@> Number of detected salt bridges: 64.
@> Calculating repulsive ionic bonding.
@>     ASP352    A   OD1_2680_2681  <--->     ASP349    A   OD1_2649_2650     3.3
@>     LYS165    A         NZ_1216  <--->     LYS152    A         NZ_1109     3.8
@>     ARG203    B   NH1_6718_6719  <--->     ARG208    B   NH1_6764_6765     4.3
@> Number of detected Repulsive Ionic Bonding interactions: 3.
@> Calculating Pi stacking interactions.
@>     HIS227       B        6923_6924_6925_6926_6927  <--->     HIS231       B        6958_6959_6960_6961_6962     4.1    23.4
@>     HIS227       A        1719_1720_1721_1722_1723  <--->     HIS231       A        1754_1755_1756_1757_1758     4.1    29.7
@>     PHE640       A   4970_4971_4972_4973_4974_4975  <--->     PHE487       A   3788_3789_3790_3791_3792_3793     4.3   177.8
@>     HIS411       B        8382_8383_8384_8385_8386  <--->     TYR176       B   6507_6508_6509_6510_6511_6512     4.5   173.1
@>     TRP566       B   9609_9611_9612_9613_9614_9615  <--->     PHE229       B   6938_6939_6940_6941_6942_6943     4.5   105.4
@>     PHE640       B10174_10175_10176_10177_10178_10179  <--->     PHE487       B   8992_8993_8994_8995_8996_8997     4.5   166.4
@>     HIS373       B        8063_8064_8065_8066_8067  <--->     HIS378       B        8105_8106_8107_8108_8109     4.5   123.3
@>     PHE229       A   1734_1735_1736_1737_1738_1739  <--->     TRP566       A   4405_4407_4408_4409_4410_4411     4.6    75.3
@>     TYR176       A   1303_1304_1305_1306_1307_1308  <--->     HIS411       A        3178_3179_3180_3181_3182     4.7    87.1
@>     TYR256       B   7170_7171_7172_7173_7174_7175  <--->     HIS255       B        7160_7161_7162_7163_7164     4.7    82.3
@>     HIS553       B        9520_9521_9522_9523_9524  <--->     HIS378       B        8105_8106_8107_8108_8109     4.7    99.2
@>     HIS255       A        1956_1957_1958_1959_1960  <--->     TYR256       A   1966_1967_1968_1969_1970_1971     4.8    66.4
@>     PHE399       A   3072_3073_3074_3075_3076_3077  <--->     HIS394       A        3031_3032_3033_3034_3035     4.8   125.6
@>     TRP109       B   5954_5956_5957_5958_5959_5960  <--->      PHE88       B   5786_5787_5788_5789_5790_5791     4.9    45.5
@>     HIS553       A        4316_4317_4318_4319_4320  <--->     HIS378       A        2901_2902_2903_2904_2905     4.9    95.9
@>     HIS373       A        2859_2860_2861_2862_2863  <--->     HIS378       A        2901_2902_2903_2904_2905     5.0    85.4
@> Number of detected Pi stacking interactions: 16.
@> Calculating cation-Pi interactions.
@>     PHE399   B   8276_8277_8278_8279_8280_8281  <--->     ARG145   B            NH1_6242_6243     3.8
@>     PHE229   B   6938_6939_6940_6941_6942_6943  <--->     LYS214   B                  NZ_6813     4.4
@>     PHE219   B   6857_6858_6859_6860_6861_6862  <--->     ARG220   B            NH1_6872_6873     4.5
@>     HIS376   A        2885_2886_2887_2888_2889  <--->     LYS552   A                  NZ_4310     4.5
@>     PHE219   A   1653_1654_1655_1656_1657_1658  <--->     ARG220   A            NH1_1668_1669     4.6
@>     TYR408   B   8355_8356_8357_8358_8359_8360  <--->     ARG407   B            NH1_8348_8349     4.6
@>     PHE399   A   3072_3073_3074_3075_3076_3077  <--->     ARG145   A            NH1_1038_1039     4.6
@>     TYR408   A   3151_3152_3153_3154_3155_3156  <--->     ARG407   A            NH1_3144_3145     4.6
@>     TYR154   B   6324_6325_6326_6327_6328_6329  <--->     LYS152   B                  NZ_6313     4.6
@>     PHE344   A   2607_2608_2609_2610_2611_2612  <--->     LYS582   A                  NZ_4530     4.7
@>     TYR408   B   8355_8356_8357_8358_8359_8360  <--->     LYS180   B                  NZ_6540     4.7
@>     TYR472   B   8862_8863_8864_8865_8866_8867  <--->     ARG654   B          NH1_10292_10293     4.8
@>     HIS160   B        6376_6377_6378_6379_6380  <--->     LYS518   B                  NZ_9256     4.8
@>     TYR107   A         727_728_729_730_731_732  <--->      ARG90   A              NH1_588_589     4.9
@>     TYR472   A   3658_3659_3660_3661_3662_3663  <--->     ARG654   A            NH1_5088_5089     4.9
@> Number of detected cation-pi interactions: 15.
@> Hydrophobic Overlaping Areas are computed.
@> Calculating hydrophobic interactions.
@>     ILE433    B   CD1_855114s  <--->     PHE438    B   CD1_8583     2.2    42.8
@>     MET446    A    SD_344914s  <--->     LEU449    A   CD1_3475     2.8    43.8
@>     ALA179    B    CB_653114s  <--->      PHE14    B   CE2_5382     2.9    48.5
@>     ILE421    A   CD1_326214s  <--->     TYR154    A    OH_1126     2.9    21.4
@>      PHE92    A    CE2_61314s  <--->      VAL69    A    CG2_499     3.0    33.3
@>     PHE438    A   CD1_337914s  <--->     ILE433    A   CG2_3346     3.0    43.4
@>     MET478    A    SD_371414s  <--->     ILE460    A   CD1_3564     3.0    30.7
@>     ILE460    B   CG2_876714s  <--->     VAL465    B   CG2_8808     3.0    42.3
@>       VAL6    B   CG2_532314s  <--->      LEU94    B   CD2_5850     3.1    23.4
@>     ARG474    B    CG_888614s  <--->     ILE460    B   CD1_8768     3.1    37.5
@>     LEU210    B   CD1_677814s  <--->     ILE591    B   CG1_9794     3.1    33.1
@>     TRP207    B   NE1_674914s  <--->     MET567    B    CE_9623     3.1    22.5
@>      VAL55    B   CG1_562614s  <--->      LEU36    B   CD1_5537     3.1    20.4
@>     ILE515    A   CG2_402514s  <--->     TYR541    A    OH_4229     3.2    29.9
@>     TYR472    B    OH_886814s  <--->     LEU658    B  CD2_10322     3.2    31.2
@>     ALA123    B    CB_605414s  <--->     TYR495    B   CE1_9056     3.2    30.9
@>     ARG220    B    CG_686814s  <--->     PHE219    B   CE2_6861     3.2    81.3
@>     LEU594    A   CD1_461114s  <--->     MET213    A    CE_1600     3.2    14.0
@>     ILE515    B   CG2_922914s  <--->     TYR541    B    OH_9433     3.2    29.6
@>     TRP158    B   CH2_636314s  <--->     ILE442    B   CD1_8618     3.2    45.7
@>     PHE367    A   CE2_281314s  <--->     ILE294    A   CG2_2248     3.2    17.1
@>       VAL8    A     CG2_8414s  <--->      PHE92    A    CD1_610     3.2    28.0
@>     PHE184    B   CD2_656914s  <--->     ILE197    A   CD1_1467     3.3    29.5
@>     TYR664    A   CD1_516614s  <--->     ALA558    A    CB_4348     3.3    38.4
@>     TRP608    B   NE1_991614s  <--->     ARG220    B    CG_6868     3.3    46.3
@>     LEU605    B   CD1_989314s  <--->     ALA191    B    CB_6621     3.3    16.4
@>     TYR472    A    OH_366414s  <--->     LEU658    A   CD2_5118     3.3    33.0
@>     LEU594    B   CD1_981514s  <--->     MET213    B    CE_6804     3.3    16.0
@>     ALA188    B    CB_660614s  <--->     LEU609    B   CD1_9928     3.3    30.9
@>     ALA370    A    CB_283814s  <--->     PHE438    A   CD2_3380     3.3    42.4
@>     LEU521    A   CD1_407414s  <--->     MET446    A    CE_3450     3.3    11.8
@>     LEU538    A   CD2_420114s  <--->     ILE492    A   CD1_3831     3.3    25.6
@>     LEU401    B   CD1_829714s  <--->     PHE487    B   CE2_8996     3.3    21.3
@>     TYR495    A   CE1_385214s  <--->     ALA123    A     CB_850     3.3    28.2
@>      VAL24    B   CG1_545314s  <--->      LEU67    B   CD1_5718     3.3    11.0
@>     PHE104    A    CE1_70614s  <--->      LEU94    A    CD1_630     3.3    16.3
@>     ILE468    A   CG2_362814s  <--->     TYR471    A   CD2_3648     3.3    15.5
@>     TRP359    B   CZ3_794914s  <--->     MET574    B    CG_9672     3.3    43.2
@>     LEU201    B   CD1_669914s  <--->     PHE192    B   CE1_6630     3.3    31.1
@>      PHE92    B   CE2_583214s  <--->       VAL8    B   CG2_5341     3.3    31.8
@>     TYR318    A   CD1_242314s  <--->     LEU272    A   CD2_2090     3.4    34.9
@>     LEU250    B   CD2_711814s  <--->     PHE367    B    CZ_8018     3.4    47.0
@>     LEU317    A   CD1_241514s  <--->     ILE251    A   CD1_1922     3.4    14.3
@>      ARG90    A     CG_58414s  <--->      PHE88    A    CE2_571     3.4    31.2
@>       PHE4    A     CD2_4514s  <--->      LEU57    A    CD1_403     3.4    14.5
@>     LEU441    A   CD1_340514s  <--->     ILE433    A   CD1_3347     3.4    15.4
@>     VAL290    A   CG2_221914s  <--->     LEU317    A   CD1_2415     3.4     9.6
@>     PHE547    A   CE1_427514s  <--->     ALA551    A    CB_4301     3.4    31.0
@>     PHE219    A   CE2_165714s  <--->     ARG220    A    CG_1664     3.4    91.6
@>      PHE45    A     CZ_31514s  <--->      LEU38    A    CD1_295     3.4    14.4
@>     MET148    A    CG_106314s  <--->     TYR149    A   CE2_1075     3.4    68.6
@>     LEU110    A    CD2_76414s  <--->      TRP87    A    CZ3_560     3.4    54.2
@>     PHE192    A    CZ_142814s  <--->     LYS196    A    CG_1456     3.4    36.2
@>     TYR473    A   CE2_367414s  <--->     ALA555    A    CB_4330     3.4    13.4
@>     PHE384    B   CD2_815614s  <--->     VAL545    B   CG1_9461     3.4    38.5
@>     TYR496    B   CD1_906614s  <--->     VAL502    B   CG2_9114     3.4    32.3
@>     ARG417    A    CG_322414s  <--->     ILE421    A   CD1_3262     3.4    19.2
@>     LEU210    A   CD2_157514s  <--->     MET213    A    CE_1600     3.4    42.7
@>     LEU456    B   CD1_873514s  <--->     ILE460    B   CD1_8768     3.4    39.6
@>     VAL263    A   CG2_202914s  <--->     PHE261    A    CZ_2015     3.4    35.6
@>     VAL597    A   CG2_463314s  <--->     TRP207    A   CD2_1544     3.4    51.7
@>     LEU355    B   CD1_791414s  <--->     TRP359    B   NE1_7945     3.4    38.6
@>     TRP511    A   CE3_398814s  <--->     LEU508    A   CD1_3962     3.4    36.6
@>     LEU605    A   CD1_468914s  <--->     ALA191    A    CB_1417     3.4    12.4
@>     LEU420    B   CD1_845714s  <--->     VAL426    B   CG1_8499     3.4    20.8
@>      VAL69    B   CG2_573714s  <--->      PHE92    B   CE1_5831     3.4    28.2
@>     LEU354    B   CD2_790714s  <--->     TRP232    B   CH2_6976     3.4    36.8
@>     VAL542    A   CG1_423514s  <--->     LEU401    A   CD2_3094     3.4     9.3
@>     VAL360    A   CG2_275314s  <--->     ILE331    A   CG2_2514     3.5    14.1
@>     VAL125    B   CG1_606914s  <--->     TRP127    B   CE2_6086     3.5    50.8
@>     LYS214    A    CD_160714s  <--->     PHE229    A    CZ_1739     3.5    36.1
@>     LEU329    B   CD2_770614s  <--->     VAL271    B   CG1_7285     3.5    17.7
@>     ILE294    B   CG2_745214s  <--->     LEU295    B   CD1_7460     3.5    41.1
@>     LEU419    B   CD1_844914s  <--->     LYS196    A    CD_1457     3.5    34.6
@>     LYS518    B    CG_925314s  <--->     TRP151    B   CE2_6300     3.5    61.9
@>     MET574    A    CG_446814s  <--->     TRP359    A   CZ3_2745     3.5    46.6
@>     PHE590    B   CE2_978714s  <--->     LEU594    B   CD1_9815     3.5    37.1
@>     ILE343    B   CG2_780414s  <--->     ALA330    B    CB_7711     3.5     3.4
@>     PHE547    B   CE2_948014s  <--->     ALA551    B    CB_9505     3.5    25.8
       ..
       ..

@> Number of detected hydrophobic interactions: 324.
@> Calculating disulfide bonds.
@> Number of detected disulfide bonds: 0.

To extract the interactions between protein’s complex, specify selection and selection2 and interaction type:

For hydrogen bonds:

In [6]: interactions.getHydrogenBonds(selection='chain A', selection2='chain B')
[['ARG215', 'NH2_1620', 'A', 'GLU168', 'OE1_6442', 'B', 2.5802, 24.8343],
 ['ARG215', 'NH1_1619', 'A', 'GLU168', 'OE2_6443', 'B', 2.6778, 28.6548],
 ['ASP202', 'OD2_1504', 'A', 'GLU418', 'OE2_8442', 'B', 2.744, 31.6383]]

For salt bridges:

In [7]: interactions.getSaltBridges(selection='chain A', selection2='chain B')
[['GLU168', 'OE1_6442_6443', 'B', 'ARG215', 'NH1_1619_1620', 'A', 2.6066],
 ['ARG208', 'NH1_1560_1561', 'A', 'GLU111', 'OE1_5976_5977', 'B', 4.3468]]

For hydrophobic interactions:

In [8]: interactions.getHydrophobic(selection='chain A', selection2='chain B')
[['PHE184', 'CD2_6569', 'B', 'ILE197', 'CD1_1467', 'A', 3.2502, 29.5284],
 ['LEU419', 'CD1_8449', 'B', 'LYS196', 'CD_1457', 'A', 3.4645, 34.5683],
 ['ALA182', 'CB_1349', 'A', 'ILE197', 'CD1_6671', 'B', 3.7348, 34.1782],
 ['ALA193', 'CB_6637', 'B', 'LEU186', 'CD1_1387', 'A', 4.2965, 20.2503]]

For Pi-stacking interaction:

In [9]: interactions.getPiStacking(selection='chain A', selection2='chain B')
[]

For Pi-cation interactions:

In [10]: interactions.getPiCation(selection='chain A', selection2='chain B')
[]

For repulsive ionic bonding interactions:

In [11]: interactions.getRepulsiveIonicBonding(selection='chain A', selection2='chain B')
[]

Non-zero interactions could be futher saved and used in VMD program to display them:

In [12]: showProteinInteractions_VMD(atoms, interactions.getHydrogenBonds(),
   ....:                              color='blue', filename='HBs_7laf.tcl')
   ....: 

In [13]: showProteinInteractions_VMD(atoms, interactions.getSaltBridges(),
   ....:                              color='yellow',filename='SBs_7laf.tcl')
   ....: 

In [14]: showProteinInteractions_VMD(atoms, interactions.getHydrophobic(),
   ....:                              color='silver',filename='HPh_7laf.tcl')
   ....: 
@> TCL file saved
@> TCL file saved
@> TCL file saved