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Table 5 Number of contacts in the database between the defined ligand atom types and protein atom types, as extracted from the PDB2003 dataset

From: Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms

Ligand atom type

Number of contacts

Number of contacts with protein atom types *

  

ACC

NEG

DON

POS

HDX

PHO

ARM

C_l

11404

600

694

507

473

634

3145

5351

C_r

5900

304

79

171

168

228

1884

3066

N_+

569

80

263

15

19

57

37

98

N_d

1784

533

406

71

52

159

173

390

N_a

1407

33

23

169

165

150

393

474

N_r

231

43

0

1

2

7

53

125

O_a

3750

229

110

567

754

389

703

998

O_-

5147

307

181

818

2009

1313

216

303

O_h

3863

404

1333

473

565

380

275

433

Total

34055

2533

3089

2792

4207

3317

6879

11238

  1. *) Protein atoms types are: acceptor (ACC), negative (NEG), donor (DON), positive (POS), hydroxyl (HDX), hydrophobic (PHO) and aromatic (ARM).