Figure 5.

Determining conservation of interaction modes. The cyclin domain (cd00043) is shown in green interacting with a protein kinase domain (cd00180) in purple to illustrate the definition of CBMs. On the left, three different structures are shown containing this interaction, with interacting residues highlighted in red. On the right, structural superpositions are shown between these structures to determine conserved binding modes. In the alignment of 1GY3 to 1E9H, a sufficient fraction of the interfacial residues overlap, and the two structures create a conserved binding mode. The alignment of 1E9H to 1OL2, however, fails the definition of overlap to be grouped in the same binding mode. The 1OL2 interaction is, in fact, due to crystal packing and is isolated as a nonconserved mode.