Table 3

Contacts observed between inhibitor 2 and N9 NA; 3LV is the residue name assigned to the inhibitor by the PDB and 488 is the residue number of the inhibitor
Inhibitor atom N9 atom distance (Å) Angle(D-A-AA)°
Potential hydrogen bonds1
3LV488-O1 Arg118-NH1 2.84 117.3
3LV488-O1 Arg371-NH1 2.86 112.8
3LV488-O2 Arg292-NH1 3.34 97.1
3LV488-O2 Arg292-NH2 3.25 101.2
3LV488-O2 Arg371-NH2 2.84 124.9
3LV488-O2 HOH-747 2.85
HOH-747 3.25 Asn347 OD1
3LV488-O15 Arg152- NH1 2.54 145.9
3LV488-O20 HOH-612 2.72
HOH-612 2.82, 3.16 Glu227 OE2, Thr225 O
Van der Waals contacts2 (≤4.0 Å)
3LV488-C1 Tyr406-OH 2.97 119.4
Arg371-NH1 3.70 96.2
Arg371-NH2 3.49 106.5
Tyr406-CZ 3.83 42.5
3LV488-O1 Tyr406-OH 3.50 99.8
Arg118-CZ 3.65 43.7
Arg118-NH2 3.56 83.0
Arg371-CZ 3.59 47.2
Arg371-NH2 3.45 85.5
3LV488-C2 Tyr406-OH 2.80 136.4
3LV488-O2 Tyr406-OH 3.32 123.93
Arg371-CZ 3.76 38.3
Arg371-NH1 3.82 96.2
3LV488-C3 Tyr406-OH 3.19 161.8
3LV488-C6 Glu119-OE2 3.39 119.6
Asp151-CG 3.49 74.6
Asp151-OD1 3.37 84.4
Asp151-OD2 3.87 62.7
3LV488-C7 Glu119-OE2 3.49 136.6
Asp151-OD1 3.52 97.7
Asp151-CG 3.89 63.8
Tyr406-OH 3.23 118.0
Arg118-NH1 3.63 113.4
3LV488-C10 Ile222-CD1 3.63 122.8
3LV488-C11 Ala246-CB 3.90 115.5
Ile222-CD1 3.54 105.5
Ile222-CB 3.88 87.6
Arg224-CZ 3.43 79.4
Arg224-NE 3.78 64.8
Arg224-NH1 3.44 78.4
Arg224-NH2 3.81 63.4
HOH-945 2.82 ---
3LV488-C14 Arg292-NH24 3.50 140.0
3LV488-O15 Asp151-CB 3.59 100.5
Arg152-CG 3.84 73.6
Arg152-CD 3.71 83.0
Arg152-CZ 3.70 22.6
3LV488-C16 Trp178-CE3 3.59 91.2
Trp178-CZ3 3.88 67.8
Trp178-O 3.78 135.7
Arg152-CD 3.73 78.1
Arg152-CG 3.73 78.1
3LV488-C17 Trp178-O 3.43 139.6
Glu227-OE2 3.62 135.8
3LV488-C19 Trp178-O 3.19 167.7
Glu119-CD 3.88 85.8
3LV488-O19 Asp151-O 3.26 116.7
Asp151-CB 3.73 97.2
Arg156-NH1 3.68 139.0
Trp178-O 2.82 162.5
3LV488-C20 Glu227-CG 3.88 74.3
Glu227-CD 3.77 55.7
Glu227-OE2 3.23 105.4
Glu277-OE2 3.34 140.2
3LV488-O20 Glu227-OE2 3.68 115.2
Glu277-CG 3.80 70.4
Glu277-CD 3.59 31.9
Glu277-OE2 2.61 133.4
Water bridge – inhibitor – Glu276
3LV488-O20 HOH-612 2.72
612-HOH 553-HOH 2.64
553-HOH Glu276-OE1 2.82 142.2
Glu276 interactions
Glu276-OE1 Arg224-NE 2.72 114.2
Glu276-OE2 Arg224-NE 3.50 83.2
Glu276-OE2 Arg224-NH2 2.81 115.9
Glu276-OE2 His274-NE2 2.73 119.7

1Potential hydrogen bonds were identified using HBPLUS[29]. Potential hydrogen bonds were interactions between donor and acceptor atoms that met the following geometric requirements: (i) a donor acceptor distance (D-A) < 3.5 Å and a hydrogen acceptor distance (H-A) < 2.5 Å and (ii) a donor-acceptor-acceptor antecedent angle (D-A-AA), of > 90° [31].

2Favorable hydrophobic contacts were defined as non-bonded contacts between two carbon atoms at a distance of ≤4 Å [28].

3Freely rotating hydroxyl hydrogen atoms had the potential to form hydrogen bonds with two alternative acceptor atoms. Only the more probable acceptor atom at the shorter distance from the hydrogen atom was reported by HBPLUS.

4There were several conformations of the propyl chain C12-C14. We used the best, but it is of low occupancy so the interactions involving C14 contribute very little.

Venkatramani et al.

Venkatramani et al. BMC Structural Biology 2012 12:7   doi:10.1186/1472-6807-12-7

Open Data