Independence divergence-generated binary trees of amino acids

The discovery of the relationship between amino acids is importantin terms of the replacement ability, as used in protein engineeringhomology studies, and gaining a better understanding of theroles which various properties of the residues play in the creationof a unique, stable, 3-D protein structure. Amino acid sequencesof proteins edited by evolution are anything but random. Themeasure of nonrandomness, i.e. the level of editing, can becharacterized by an independence divergence value. This parameteris used to generate binary tree relationships between aminoacids. The relationships of residues presented in this paperare based on protein building features and not on the physico-chemicalcharacteristics of amino acids. This approach is not biasedby the tautology present in all sequence similarity-based relationshipstudies. The roles which various physico-chemical characteristicsplay in the determination of the relationships between aminoacids are also discussed.