Secondary structure and accessibility

Secondary structure assignments and accessibilities were defined by the Definition of Secondary Structure in Proteins program (DSSP; Kabsch and Sander, 1983). Secondary structure assignments were converted to a three state representation for simplicity: helix = DSSP -helix ,-helix; beta = DSSP -ladder, -bridge; coil = DSSP not (-helix ,-helix, -ladder, or -bridge). Relative accessibilities were calculated by dividing the DSSP accessibility by the accessibility for a GXG tripeptide given by Rose &Dworkin (1989). When one chain or domain was extracted from a PDB file, DSSP was run on the domain separately, excluding heteroatoms, such as substrates, not integral to the 3D structure.