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.