How to identify Protein-Protein Interaction from a pdb file (except for manually checking residues one by one)? In particular, how to automatically show the sites of interaction in batch when dealing with a protein complex that has a large interface?
You look for pairs of atoms in the two interacting chains whose distance from each other is less than a specified cut-off distance: slightly more than the sum of the VdW radii of the atoms for direct VdW contacts, add 1.4 Å to that for solvent-excluding contacts.
See my Presentation Intermediate PyMOL
Page 7 for an example on how to identify, visualise and list contact residues in PyMOL.
Contact map of one chain w.r.t. other chain will solve your purpose.
PDBsum (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/) can provide contact maps. In case your structure is not released yet, they also offer a local installation.