Propensities of Some Amino Acid Pairings in alpha-Helices Vary with Length

The results of secondary structure prediction methods are widely used in applications in biotechnology and bioinformatics. However, the accuracy limit of these methods could be improved up to 92%. One approach to achieve this goal is to harvest information from the primary structure of the peptide. This study aims to contribute to this goal by investigating the variations in propensity of amino acid pairings to alpha-helices in globular proteins depending on helix length. (n):(n + 4) residue pairings were determined using a comprehensive peptide data set according to backbone hydrogen bond criterion which states that backbone hydrogen bond is the dominant driving force of protein folding. Helix length is limited to 13 to 26 residues. Findings of this study show that propensities of ALA:GLY and GLY:GLU pairings to alpha-helix in globular protein increase with increasing helix length but of ALA:ALA and ALA:VAL decrease. While the frequencies of ILE:ALA, LEU:ALA, LEU:GLN, LEU:GLU, LEU:LEU, MET:ILE and VAL:LEU pairings remain roughly constant with length, the 25 residue pairings have varying propensities in narrow helix lengths. The remaining pairings have no prominent propensity to alpha-helices.