Analyzing Protein-Protein Interaction Interfaces in PyMOL

Preprocessing

Save the code as InterfaceResidues.py, then place it in your PyMOL Working Directory.

Detailed Procedure

1. Run File -> Run Script... and select the InterfaceResidues.py file.
2. Load the model and color it by chain.
3. Remove waters from the model if they do not affect the interface.
4. Run get_chains $objSel in the command line to list the chains in the model.
5. Run interfaceResidues $objSel, chain $A, chain $B in the command line to identify the interface residues. The residues are saved in a new selection named (interface). Rename the selection before running the command again to analyze another interface.
6. Analyze the polar contacts: Actions -> Find -> Polar Contacts -> Between Chains.

References

1. InterfaceResidues - PyMOLWiki
2. Get Chains - PyMOLWiki
3. PyMOL - Analyzing Protein-Protein Interaction Interfaces - Bilibili