An amino acid map of inter-residue contact energies using metric multi-dimensional scaling

We present an amino map based on their inter-residue contact energies using the Miyazawa–Jernigan matrix. This work is based on the method of metric multi-dimensional scaling (MMDS). The MMDS map shows, among other things, that the MJ contact energies imply the hydrophobic–hydrophilic nature of the amino acid residues. With the help of the map we are able to compare and draw inferences from uncorrelated data sets such as BLOSUM and PAM with MJ methods. We also use a hierarchical clustering method on our MMDS distance matrix to group the amino acids and arrive at an optimum number of groups for simplifying the amino acid set.