Two indices can approximate four hundred and two amino acid properties

Abstract

We have developed a novel, general technique involving nonlinear transformation that summarizes the four hundred and two amino acid properties contained in the Nakai database in the form of two simply visualizable indices. The technique yields a higher fidelity of representation of the original data than linear methods, and results in a distribution of the amino acids which illustrates their dependence on size and hydrophobicity properties on the one hand, and their preference for belonging to loops vs. strands, on the other.