Figure 1

Procedure used to determine the trigger-ligand set. Two-domain proteins are depicted with a bending region, indicated as a curved line, linking two domains drawn as large ellipses. Different contact ligands (which have also been confirmed using KEGG to be functional ligands) are indicated in black as filled circles, triangles, squares, and ellipses. The contact ligand set is divided into two groups: those without a spanning ligand and those with a spanning ligand. A spanning ligand is one that is in contact with one domain as well as in contact with the other domain, or bending regions, or both. (A) The non-spanning trigger ligand set: Identical ligands in both conformations are removed (i.e. the triangle ligand) to leave the circle ligand as the non-spanning trigger-ligand. This pair of conformations is put in the non-spanning trigger-ligand set. (B) The spanning trigger ligand set: First non-spanning ligands are removed from both conformations (i.e. the ellipse and the square ligands on the conformation on the left), to leave the triangle ligand and the ellipse ligand both of which are spanning ligands. Then, identical ligands in both conformations are removed to leave the ellipse ligand as the spanning trigger-ligand. This pair is put in the spanning trigger-ligand set. Combined, the non-spanning trigger-ligand set (53 examples) and the spanning trigger-ligand set (150 examples) form the trigger-ligand set (203 examples).