Abstract: Analysis of protein-protein interface is crucial to understand protein interactions and to develop drugs targeting protein complexes. PP_SITE is a method developed by the author's group to deduce hydrogen bond and hydrophobic properties for protein-protein interface. We have used PP_SITE to perform statistical analysis on protein-protein interfaces. A two-chain non-redundant interface dataset from PDB was constructed and used in the study. According to the hydrophobicity and hydrogen bond characteristics, criteria were selected to differentiate protein interfaces into distinct groups. The size of interface, the proportion of hydrophobic and hydrophilic property and the extent of concentration in hydrophobicity were found to be important for interface classification.

Key words: Protein-protein interaction, PP_SITE procedure, Interface classification