Exceptional pairs of amino acid neighbors in α-helices

Abstract

Amino acids seem to have specific preferences for various locations in α-helices. These specific preferences, called singlet local propensity (SLP), have been determined by calculating the preference of occurrence of each amino acid in different positions of the α-helix. We have studied the occurrence of amino acids, single or pairs, in different positions, singlet or doublet, of α-helices in a database of 343 non-homologous proteins representing a unique superfamily from the SCOP database with a resolution better than 2.5 Å from the Protein Data Bank. The preference of single amino acids for various locations of the helix was shown by the relative entropy of each amino acid with respect to the background. Based on the total relative entropy of all amino acids occurring in a single position, the Ncap position was found to be the most selective position in the α-helix. A rigorous statistical analysis of amino acid pair occurrences showed that there are exceptional pairs for which, the observed frequency of occurrence in various doublet positions of the α-helix is significantly different from the expected frequency of occurrence in that position. The doublet local propensity (DLP) was defined as the preference of occurrences of amino acid pairs in different doublet positions of the α-helix. For most amino acid pairs, the observed DLP (DLPO) was nearly equal to the expected DLP (DLPE), which is the product of the related SLPs. However, for exceptional pairs of amino acids identified above, the DLPO and DLPE values were significantly different. Based on the relative values of DLPO and DLPE, exceptional amino acid pairs were divided into two categories. Those, for which the DLPO values are higher than DLPE, should have a strong tendency to pair together in the specified position. For those pairs which the DLPO values are less than DLPE, there exists a hindrance in neighboring of the two amino acids in that specific position of the α-helix. These cases have been identified and listed in various tables in this paper. The amount of mutual information carried by the exceptional pairs of amino acids was significantly higher than the average mutual information carried by other amino acid pairs. The average mutual information conveyed by amino acid pairs in each doublet position was found to be very small but non-zero.