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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