Figure 8: Equilibrium properties of the simulated protein (a) the distribution of similarity q between the conformations ofD0 , (b) the average contact map of mHIV-1-PR1-95, (c) the average contact map limited to native contacts, (d) the average contact map limited to non-native contacts
A cluster analysis was performed for the simulated conformations ofD0 at 300K with the Ward algorithm. The fractionq of common contacts was used as underlying metrics for the clustering instead of the more common RMSD because of the reasons described above. We could identify 17 clusters. In Fig. 9, we displayed the three most populated clusters (others can be found in Fig. S15). The most populated cluster (labelled A) has a population of 21% and is poorly structured; it contains most conformations with a low number of contacts. The only stable structure is a turn involving P63. Clusters B and C have a population of 8% each. Cluster B displays a non-native β-hairpin involving residues 39-45 and the native, C-terminal α-helix. Cluster C displays a β-hairpin involving residues 56-63, a β-turn 80-83 and tertiary contacts between this and the N-terminal region 4-6.
In the other clusters (cf. Fig. S15) particular recurrent non-native contacts in the region 40-50 and the native α-helix are seen.