Figure 2

A two-dimensional representation of the amino acid vectors. The contact propensity distance matrix derived vectors are shown in (a) and it is clear that residues with similar hydropathies and sizes are grouped together. A similar vector space can be obtained from an evolutionary substitution rate matrix and this is shown in (b). The residue positions are similar in (a) and (b), but in (a) residues with opposite hydropathies appear to lie further apart. In contrast, the vector space derived from the MJ energy matrix appears to be roughly linear. Here, the residues group in essentially the same way as reported by Wang & Wang [6].