The peptide:MHC binding energy covariance (PMBEC) matrix. The 20 amino acid residues are shown at the top and right. Each matrix entry corresponds to the covariance in peptide:MHC binding energies between two residues. Values greater than 0.05 indicate similarity between residues, and are colored green. Values less than -0.05 indicate dissimilarity between residues, and are colored red. Note that the diagonal values are the residue specific statistical variances (defined as the average squared values), which indicate how much the binding energies associated with the residue varies over all alleles and positions. Cysteine (C), Glycine (G), Asparagine (N), and Glutamine (Q) are relative outliers because they have no partner residue with absolute covariance > 0.05. Agglomerative clustering with complete linkage was used to group the amino acid residues, corresponding to ordering the matrix rows and columns. The distance measure between two residues aa and aa' used for clustering is (K - PMBEC(aa, aa')), where K is the maximum value in the PMBEC matrix. The resulting dendrogram on the right provides a classification of amino acids which largely corresponds to classical groupings of amino acids by physicochemical properties.