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Table 3 Pockets and their characteristics recognized by our method for 1A6U protein atoms

From: A simple method for finding a protein’s ligand-binding pockets

Pocket Num.* Num. of Atoms Num. of Empty voxels Surface of Pocket Depth of Pocket NoA**HAaBonds NoA HDbBonds NoA vdW***Bonds NoA Ionic Bonds NoA Sulfur Bonds NoA cf cf
  C-Ring of the 1stAS, HAPc of the 2ndAS, AC1c
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
  1. *Pocket number indicates the number in the protein’s atomic positions convex hull surface rows, and they correspond to three vertices of triangles.
  2. **NoA means the number of atoms.
  3. ***vdW means van der Waals.
  4. aHA means hydrogen bond acceptor.
  5. bHD means hydrogen bond donor.
  6. cThese 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.