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Table 1 Prevalence of H-bonds in special configurations.

From: Towards accurate modeling of noncovalent interactions for protein rigidity analysis

 

1htg

1vgc

1bbp

total

146

173

553

bifurcated D

1.3%

2.3%

5.8%

bifurcated A

15%

20%

21%

trifurcated A

0%

1.7%

3.8%

multi-base A

4.8%

6.4%

6.0%

  1. We examined the H-bonds calculated with HBPLUS [36] on 3 example proteins from [15]: HIV-1 protease (1htg), serine protease (1vgc), and bilin binding protein (1bbp). We counted how many H-bonds were found in each configuration type shown in Figure 3, which are of special interest in mechanical modeling.