Amino Acids in Nine Ligand-Prefer Ramachandran Regions

Figure 1

Probability for (a) left-handed helix residues and (b) non-left-handed helix residues observed at ligand-binding site. (a) shows the probability of left-handed helix residues being observed in a ligand-binding site; (b) illustrates the probability of non-left-handed helix residues observed at a ligand-binding site in the same region. The top three most frequent ligands contacted with left-handed helix residues (a) and non-left-handed helix residues (b) are also labelled as three-letter code in (a) and (b). (c) shows an example of non-left-handed helix residues at a ligand-binding site. In (a) and (b), the probability value, which is expressed as a percentage, is defined by the number of residues detected in the ligand-binding site divided by the total number of residues observed in the Ramachandran box. (c) and (d) show examples of non-left-handed helix residues (coloured residues) at a ligand-binding site in O-succinylbenzoate synthase with a ligand-free form in (c) (pdbid: 2opj) and a ligand-bound form in (d) (pdbid: 2qvh). The dihedral angles for the residues are noted in bold font, and the ligand is indicated by purple spheres.

(a)

(b)

(c)

(d)