Skip to main content

Table 1 Hydrogen bonds atomic interaction frequency matrix

From: Prediction of TF target sites based on atomistic models of protein-DNA complexes

   T C A G
   O2 N3 O4 O2 N3 N4 N7 N6 N3 N7 O6 N2 N3
R NE 6 0 3 4 0 0 0 0 0 13 11 0 1
R NH1 21 0 2 9 4 0 2 0 8 48 39 0 4
R NH2 15 0 8 14 3 0 0 0 7 62 80 0 3
K NZ 15 0 9 9 1 0 6 0 7 33 38 0 2
S OG 4 0 2 2 0 5 4 1 2 7 9 3 1
T OG1 2 1 4 2 0 9 2 1 1 3 3 2 0
N OD1 0 1 0 0 0 8 0 23 0 0 0 6 0
N ND2 6 0 11 3 0 0 20 0 2 4 11 0 7
Q OE1 0 0 0 0 0 4 0 17 0 0 0 4 0
Q NE2 2 0 7 3 1 0 16 0 3 1 6 0 5
H ND1 1 0 0 0 0 0 0 0 0 2 5 0 0
H NE2 3 0 2 1 0 1 0 0 1 5 12 1 1
Y OH 1 0 4 3 0 1 1 3 1 2 2 3 1
E OE1 0 1 0 0 0 16 0 1 0 0 0 0 0
E OE2 0 2 0 0 0 11 0 2 0 0 0 1 0
D OD1 0 0 0 0 0 10 0 1 0 0 0 2 0
D OD2 0 3 0 0 0 13 0 1 0 0 0 5 0
C SG 0 0 1 0 0 0 0 2 0 0 0 0 0
M SD 0 0 0 0 0 0 0 0 0 0 0 0 0
W NE1 1 0 1 0 0 0 0 0 0 0 0 0 1
  1. Hydrogen bonds reported by HBPLUS [46] between pairs of atoms in the side-chains of amino acids and bases in the set of 210 protein-DNA complexes extracted from PDB were computed. Rows correspond to the hydrogen bond donor/acceptor atoms from the amino acids and columns to the hydrogen bond donor/acceptor atoms from bases (T, C, A, G) with their corresponding PDB atom codes. Each cell indicates the number of contacts found for a given pair of atoms.