ObjectivesDesigning a polypeptide sequence to interact with a preselected target polypeptide sequence of a protein has long been of interest, yet remains an elusive goal.ResultsHere, we propose a novel concept named Clustered Complementary Amino Acid Pairing (CCAAP), which plays an essential role in protein-protein interaction (PPI). Complementary amino acid pairing (CAAP) is a pairing between two amino acids encoded by a codon and its reverse complementary codon. CAAP interactions largely agree with the physicochemical and stereochemical requirements for probable amino acid pairings. Interestingly, 82 PPI structure data revealed that clusters of CAAP interactions (CCAAP boxes) are predominantly found in all PPI sites. Analysis of all amino acid pairings in the CCAAP boxes unveiled amino acid-pairing preferences and patterns for PPI that allowed us to develop a new method for designing an oligopeptide sequence to bind to a chosen polypeptide sequence of any target protein.ConclusionsDiscoveries in the present study provide proof of the CCAAP principle.