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Background:Protein-protein interactions are essential to many biological processes.The binding site information of protein-protein complexes is extremely useful to obtain their structures from biochemical experiments.Geometric description of protein structures is the precondition of protein binding site prediction and protein-protein interaction analysis.The previous description of protein surface residues is incomplete,and little attention are paid to the implication of residue types for binding site prediction.Methods:Here,we found three new geometric features to characterize protein surface residues which are very effective for protein-protein interface residue prediction.The new features and several commonly used descriptors were employed to train millions of residue type-nonspecific or specific protein binding site predictors.Results:The amino acid type-specific predictors are superior to the models without distinction of amino acid types.The performances of the best predictors are much better than those of the sophisticated methods developed before.Conclusions:The results demonstrate that the geometric properties and amino acid types are very likely to determine if a protein surface residue would become an interface one when the protein binds to its partner.