Core structure

Figure 6 shows how the percentage of structural equivalence (i.e., the fraction of the smallest structure that lies within structurally similar regions) behaves as a function of . Proteins having detectable sequence similarity (i.e., ) generally have over structural equivalence, or common structural regions. However, as drops, the percentage of structural equivalence drops to as low as . This is a consequence of distantly related protein structures being similar only within their core secondary structures and having loop/turn regions that differ substantially. This fraction is somewhat less than that reported by Chothia &Lesk (1986), who found a minimum of , though their protein structure pairs were more closely related than the pairs used in this study. For example, the globin fold family studied by Chothia and Lesk contained only haem containing globins and lacked the more distantly related phycocyanin and colicin A structures, which are included in this study.