Significant residue features revealed by eigenvalue decomposition analysis of BLOSUM matrices

Here we attempt to characterize protein evolution by residue features which dominate residue substitution in homologous proteins. Evolutionary information contained in residue substitution matrix is abstracted with the method of eigenvalue decomposition. Top eigenvectors in the eigenvalue spectrums are analyzed as function of the level of similarity, i.e. sequence identity (SI) between homologous proteins. It is found that hydrophobicity and volume are two significant residue features conserved in protein evolution. There is a transition point at SI≈45%. Residue hydrophobicity is a feature governing residue substitution as SI?45%. Whereas below this SI level, residue volume is a dominant feature.