Ubiquitin. (A) The 3D structure of ubiquitin, using the 1UBQ solved structure. Part of cluster 13 s is also shown within the ubiquitin molecule. The three sites are all within van der Waals interaction distance of each other and may have an important role in the stability of the overall structure. (B) Module 1. This module contains two H-bonded clusters, which may play a role both in folding and then maintaining structural stability once folding is complete, especially cluster 1 with six H-bonds anchoring the loop. (C) Cluster 12 s, a strong example of a van der Waals cluster discovered by the k-modes algorithm.