Effect of amino acid on forming residue–residue contacts in proteins

The long-range contacts contribute more function to the protein folding and play an active role in the stability of protein molecules. In this paper, we calculated the number of short- and long-range contacts from 278 globular proteins and analyzed the effects of amino acids on the long-range contacts by contrasting the average number of the long-range contacts between different amino acid residues in the protein sample. The amino acids of Leu, Val, Ile, Met, Phe, Tyr, Cys, and Trp are easy to form the long-range contacts, and the average number of long-range contacts per residue is 5.008 when Rc=0.80 nm. Here Rc is the minimum distance between two Cα atoms of residues. The amino acids of Glu, Gln, Asp, Asn, Lys, Ser, Arg, and Pro are difficult to form the long-range contacts, and the average number of long-range contacts per residue is only 3.232 when Rc=0.80 nm. However, the effect of amino acid on the short-range contact is negligible, and the average number of short-range contacts per residue ranges from 3.649 to 3.721 when Rc=0.80 nm. We also find that the highest preference is observed for Cys-Cys contact, and the lowest preference is Gln-His contact. The average number of contacts depends on Rc, and two cases of Rc=0.65 and 0.80 nm are discussed. The average distance of the residue–residue contacts is also concluded. Through these calculations, we can discuss how the amino acids affect the protein folding and how the proteins achieve the stability conformations.