Hi

You can use NUCPLOT it is free software for protein-nucleic acid interaction.You can use it for protein-protein interaction study also but both chain of dimer should have different chain identifier. It gives hydrogen and hydrophobic interaction between interacting residues.

Dear Sangita Kachhap

As you said the NUCPLOT used for protein-nucleic acid interaction. Whether the results are valuable for protein-protein interaction and reporting in research papers?

Yes it is, because it gives interaction result based on distance and angle criteria for hydrogen bond and distance criteria for hydrophobic interaction. You can use default values of these criteria or you can change accordingly. I have checked it for protein-protein interaction from protein-DNA ternary complex and I have got protein-protein interaction which were already known in literature.

Dear Ms Farrokh,

Try PDBePISA tool for the exploration of macromolecular interfaces. This tool can calculate the Hydrogen Bonds, Salt Bridges and disulphide bonds for both archived PDB files and your own PDB or mmCIF files. It's also easy to use.

Good Luck