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Table 4 Number of ligand atoms and number of contacts with protein amino acids by ligand atom type, extracted from the non-redundant set selected from the database

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

Atom Type

Number of atoms (Na)

Contacts (C)

C/Na

C_l

51223

23891

0.466

C_r

25287

12000

0.475

N_+

1633

1061

0.650

N_d

6257

4031

0.644

N_a

4722

3090

0.654

N_r

2448

426

0.174

O_a

15286

8272

0.541

O_-

12503

9277

0.742

O_h

9939

6893

0.694

Others *

4928

-

-

Total †

129298

68941

0.533

  1. *) Atoms corresponding to chemical elements other than C, O or N.
  2. †) The total values do not include the unclassified atoms ("others")
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BMC Bioinformatics

ISSN: 1471-2105

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