Physico-chemical properties of amino acids and arrangement of the genetic code.

Abstract

In order to carry out researches on existing relations between physico-chemical properties of amino acids, the substitution frequency of some amino acids by others in the proteins and natural partitioning found in the genetic code, a property vector was derived showing, in a generalized form, the hydrophobic and structural effects of amino acids. Coordinates were made up of the free energy of transfer of amino acids from water to octanol, the mean of solvent accessible surface area of the residue in standard state, the mean of area buried on transfer from the standard state to the folded protein, the mean of solvent accessible surface polar area of residue in standard state and the rate between this energy and these variables. Cluster analysis for 20 amino acids showed that amino acids with similar physico-chemical properties are grouped by identical second positions in their codon except those amino acids having guanine as a second codon: W; R; C; G. Besides, in the correlation analysis between distance matrix of amino acids and amino acids substitution matrices reported by Dayhoff et al and Gonnet et al, highly significant correlations were obtained from - 0.53 to - 0.95 with Dayhoff matrix and -0.79 to - 0.96 with Gonnet matrix, for all amino acids, except for cysteine, showing that the smaller the distance within amino acids, is the higher substitution frequency in the proteins. A closed connection was also evident between the genetic code organi-zation, physico-chemical properties of amino acids and protein evolution.