Statistical analysis of pair-wise compatibility of spatially nearest neighbor and adjacent residues in α-helix and β-strands: application to a minimal model for secondary structure prediction

Abstract

Secondary structural elements like α-helix and β-strands posses distinctly different structural features and thus the relative positioning of the nearest neighbor residues, and also the sequence-wise adjacent residues is important in determining the structural preference. In the present work we have statistically examined the pair-wise compatibility pattern of physically nearest neighbors and separately the adjacent residue pairs along the sequence in between the nearest neighbor partners in α-helices and β-strands. It has been demonstrated that the patterns and hence, the physical basis of the compatibility of adjacent residue pairs and the spatially nearest neighbors are significantly different in most cases. The influence of tertiary contacts on the pair-wise compatibility is shown to be significant for β-strands while it is small for α-helices. Based on the compatibility of physically nearest neighbors and the sequence-wise adjacent residue pairs, a minimal model has been constructed to predict the α-helices, β-strands and coils of a protein from its sequence. Application of this method to 100 sequences shows that it has a predictive capability comparable to that of other more sophisticated statistical methods.