I have docked two proteins using ClusPro. I want to see its interacting residues and interactions. I tried to use pdbsum for the analysis, but it considers both the proteins as a single chain and does not show any interaction. how can I analyze the interaction and find out interacting residues?
If the two proteins have the same chain letter, you will most likely need to change it. I think PDBsum is still your best choice when you have a correct PDB file. To calculate the contact interface area and energy, I suggest PISA: