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Table 2 Representative clusters from each primary branch in ubiquitin

From: Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

Cluster Sites Highest pattern residual k Structural relationship Functional factors
1 7,9–11 25.9 4 Double bond between 7 and the other sites 11 is a binding site
2 12,14–17,20 57.6 6   12 is adjacent to binding site 11
3 18–19,21 13.4 3 Double bond between 18 and 21  
4 23,25–27 6.7 4 Double bond between 23 and other sites 27 is a binding site
5 29–31,41 22.6 4 30 in Van der Waals contact with 41 29 is a binding site
6 34–36,38 27.9 4 Van der Waals contact 34 & 36 34 is adjacent to binding site 33
7 37,39–40,43 20.8 4 37 bonds to 40 43 is adjacent to possible external recognition site 42 and external contact site 44
8 44–47 646.1 4 Van der Waals contact 44 & 47 sites 44 and 47 are external contact points, 47 is adjacent to major binding site 48
9 49–50,52 7.5 3   site 49 is an external contact point
10 54–59 31.0 6 8 internal H-bonds  
11 60,63–64 29.9 3   63 is a major binding site
12 66,68–70 27.8 4   site 70 is an external contact point
13 43,69,74 13.0 3 43 in tight Van der Waals contact with 69 74 is a possible external recognition site
14 70,72–73 22.6 3   70 is an external contact point, 73 is an external recognition site