Variation of amino acid properties in protein secondary structures, alpha-helices and beta-strands

A study was made on the physical, chemical, energetic, conformational, geometric, and dynamic property potentials of amino acid residues in protein secondary structures: alpha-helix and beta-strand. Property patterns were obtained by computing the average property values for specified residue units partitioned longitudinally and transversely about the chain. It was found that in alpha-helices with not more than 15 residues, there exist longitudinally opposing portions, one characteristically higher in average property potentials than the other. The helical chain, in general, acquires either an increasing or decreasing average potential in the N-terminal to C-terminal direction. The sequence-wise and surface-wise variations of property potentials in the elements of beta-structure also revealed such general patterns. Possible wrong predictions in statistical methods of one secondary structural class over the other are pointed out.