Accessibility

Three commonly used categories of relative accessibility were defined (, , ), corresponding to buried, half-buried and exposed (e.g., see Miller et al., 1987; Bowie et al., 1991). Positions within pairs of aligned structures were defined as conserved with respect to accessibility if structures had accessibilities in the same category. Figure 5 shows the percentage of these positions versus . Most pairs of structures have of such positions in common, though some pairs of structurally similar proteins have a degree of accessibility conservation similar to dissimilar structural pairs, which have between and conservation of these positions just by chance.

Defining conservation of accessibility after Miller et al. (1987) as those positions having an absolute accessibiility difference of less than Å gives a similar plot, though with a more steady drop in the percentage of conserved positions with decreasing sequence identity. Both observations suggest that many pairs of distantly related proteins have a degree of residue by residue accessibility conservation comparable to that observed for pairs of dissimilar protein structures.