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. 2014 Jul 19;14:18. doi: 10.1186/1472-6807-14-18

Table 3.

Pockets and their characteristics recognized by our method for 1A6U protein atoms

Pocket Num. *
Num. of Atoms
 Num. of Empty voxels
 Surface of Pocket
 Depth of Pocket
 NoA ** HA a Bonds
 NoA HD b Bonds
 NoA vdW *** Bonds
 NoA Ionic Bonds
 NoA Sulfur Bonds
 NoA
 cf
cf
  C-Ring of the 1 st AS, HAP c of the 2 nd AS, AC1 c
1
 63
 401
 116.25
 28.40
 5
 8
 0
 1
 0
 20
 0.31
 0.33
5
 80
 481
 21.83
 38.66
 2
 3
 10
 2
 0
 2
 0
 0
18
 101
 648
 187.27
 25.83
 5
 7
 6
 2
 0
 14
 0.12
 0.11
19
 67
 411
 84.36
 19.35
 1
 2
 5
 0
 0
 2
 0
 0
38
 44
 266
 138.90
 20.63
 1
 4
 1
 0
 0
 6
 0
 0
39
 85
 499
 82.58
 28.26
 3
 5
 2
 0
 0
 14
 0.31
 0.22
40
 21
 127
 77.97
 14.53
 2
 3
 0
 0
 0
 4
 0.06
 0
58
 118
 765
 340.90
 29.83
 5
 4
 7
 3
 0
 3
 0
 0
59
 86
 529
 253.20
 26.72
 4
 4
 4
 2
 0
 6
 0.06
 0
85
 226
 1360
 370.14
 36.18
 7
 7
 26
 3
 1
 27
 0
 0
89
 21
 141
 212.35
 21.47
 0
 1
 4
 1
 0
 4
 0
 0
90
 92
 573
 293.28
 28.54
 4
 2
 15
 2
 0
 11
 0
 0
112
 44
 241
 36.33
 27.39
 1
 2
 1
 0
 0
 6
 0.06
 0
117
 38
 215
 76.66
 17.42
 1
 3
 0
 0
 0
 8
 0
 0
137
 15
 99
 127.57
 17.53
 2
 4
 0
 0
 0
 3
 0.25
 0.33
143 55 354 259.10 24.24 4 8 0 1 0 20 0.43 0.55

*Pocket number indicates the number in the protein’s atomic positions convex hull surface rows, and they correspond to three vertices of triangles.

**NoA means the number of atoms.

***vdW means van der Waals.

a HA means hydrogen bond acceptor.

b HD means hydrogen bond donor.

c These are the cf-values (ratio of the number of correct residues to the total number of residues in the active site). For 1A6W in PDB two active sites (AS) are reported as HAP and AC1.