Polymer, Vol.43, No.22, 6037-6047, 2002
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 Tip are easy to form the long-range contacts, and the average number of long-range contacts per residue is 5.008 when R-c = 0.80 nm. Here R-c is the minimum distance between two C-alpha 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 R-c = 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 R-c = 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 R-c and two cases of R-c = 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.