  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: alpha-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 Cb and
Cg atoms of amino acid. alpha-helix admirers do not have polar heteroatoms on
Cb and Cg atoms, nor branching or aromatic group on Cb atom. Amino acids that
have aromatic groups or branching on Cb atom are strand admirers. Turn and bend
admirers have polar heteroatom on Cb or Cg atoms or do not have Cb 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 Cb or
Cg atoms.
