Correlations of Amino Acids with Secondary Structure Types: Connection with Amino Acid Structure

The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were calculated for distances between -25 and 25. Shapes of the diagrams indicate that amino acids polarity and capability for hydrogen bonding have influence on the secondary structure at some distances. Clear preference of most of the amino acids towards certain secondary structure type classifies amino acids into four groups: α-helix admirers, strand admirers, turn and bend admirers and the others. Group four consists of His and Cis, the amino acids that do not show clear preference for any secondary structure. Amino acids from a group have similar physicochemical properties, and the same structural characteristics. The results suggest that amino acid preference for secondary structure type is based on the structural characteristics at Cβ and Cγ atoms of amino acid. α-helix admirers do not have polar heteroatoms on Cβ and Cγ atoms, nor branching or aromatic group on Cβ atom. Amino acids that have aromatic groups or branching on Cβ atom are strand admirers. Turn and bend admirers have polar heteroatom on Cβ or Cγ atoms or do not have Cβ atom at all. Our results indicate that polarity and capability for hydrogen bonding have influence on the secondary structure at some distance, and that amino acid preference for secondary structure is caused by structural properties at Cβ or Cγ atoms.