Analysis of the amino acid effect on protein folding by atom pair contacts

Abstract

New atomic pair contacts with considering the coordinates of each atom in a residue are introduced here. We analyze the ability of all the 20 amino acid residues to form long-range and short-range contacts by calculating the average numbers of short- and long-range contacts between different amino acid pairs. It is concluded that Phe-Phe, Leu-Phe and Leu-Leu have a high tendency to form contacts. The relative ability to form atom pair contact does not depend on the limiting value of R C. The average number of contacts per residue, which is the scale of the relative ability to form contacts for the 20 amino acid residue types, is also calculated. The result shows that hydrophobic residues with large numbers of long-range contacts more easily form long-range contacts, while the hydrophilic ones form long-range contacts less often. Linear regression analysis by a new method of counting contacts concludes that either contact order (CO) or total contact distance (TCD) parameter has a significant correlation with the logarithms of folding rates. The relative deviations between the experimentally observed ln k f and the two parameters CO and TCD are smaller than that with previous methods. Moreover, the values of CO λ-μ and TCD λ-μ between λ-type and μ-type amino acids are investigated. Comparisons between the Fauchere–Pliska hydrophobicity scale and the average number of contacts per residue formed are also made. The new knowledge of atomic pair contacts can help us understand the importance of amino acid residue type and its sequence in globular structure of the protein in detail.