International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. F. ch. 20.1, pp. 484-485   | 1 | 2 |

Table 20.1.3.1 

U. Stockera and W. F. van Gunsterena

aLaboratory of Physical Chemistry, ETH-Zentrum, 8092 Zürich, Switzerland

Table 20.1.3.1 | top | pdf |
Occurrence of intramolecular hydrogen bonds (%) during the final 1.6 ns of the simulation

The criteria for a hydrogen bond to be present are angle donor–hydrogen–acceptor [\geq 135^{\circ}], distance hydrogen–acceptor [\leq 0.25] nm. Hydrogen bonds are shown if they are either present in the X-ray structure or if at least one of the four protein molecules in the unit cell shows the hydrogen bond of interest for at least 50% of the simulation time. The letter h appended to an amino-acid code indicates that the residue is protonated.

Hydrogen bonds X-ray structure Molecular dynamics
Backbone Backbone Molecule 1 Molecule 2 Molecule 3 Molecule 4
3Ile H 15Leu O 100 94 94 95 98
4Phe H 65Ser O 100 85 69 87 77
5Val H 13Ile O 100 80 90 87 93
6Lysh H 67Leu O 100 85 82 88 94
7Thr H 11Lysh O 100 65 49 54 62
8Leu H 69Leu O 0 5 52 19 55
10Gly H 7Thr O 100 0 0 0 0
13Ile H 5Val O 100 86 76 70 87
15Leu H 3Ile O 100 87 92 72 82
17Val H 1Met O 100 68 39 79 51
21Asp H 18Glu O 100 68 84 84 90
23Ile H 54Arg O 100 0 74 89 92
24Glu H 52Asp O 100 58 69 63 84
26Val H 22Thr O 100 92 69 78 61
27Lysh H 23Ile O 100 94 97 98 99
28Ala H 24Glu O 100 71 71 84 89
29Lysh H 25Asn O 100 91 79 94 88
30Ile H 26Val O 100 92 76 94 91
31Gln H 27Lysh O 100 85 53 66 93
32Asp H 28Ala O 100 82 27 87 77
33Lysh H 29Lysh O 100 23 13 81 51
33Lysh H 30Ile O 0 59 23 7 19
34Glu H 30Ile O 100 95 54 64 86
35Gly H 31Gln O 100 0 0 0 0
36Ile H 34Glu O 0 62 50 28 35
40Gln H 37Pro O 100 0 0 0 0
41Gln H 37Pro O 0 68 56 72 20
41Gln H 38Pro O 100 14 25 14 50
42Arg H 70Val O 100 82 82 83 88
44Ile H 68Hish O 100 84 96 93 95
45Phe H 48Lysh O 100 20 74 77 91
48Lysh H 45Phe O 100 24 62 59 44
50Leu H 43Leu O 100 29 88 92 85
54Arg H 51GluO 100 20 60 19 69
56Leu H 21Asp O 100 0 90 81 81
57Ser H 19Pro O 100 3 78 86 83
58Asp H 55Thr O 100 0 0 0 0
59Tyr H 55Thr O 100 58 86 92 85
59Tyr H 56Leu O 100 0 0 0 0
60Asn H 57Ser O 100 38 34 60 58
61Ile H 56Leu O 100 67 7 63 56
64Glu H 2Gln O 100 0 42 6 95
65Ser H 62Gln O 100 0 0 0 0
67Leu H 4Phe O 100 69 74 87 70
68Hish H 44Ile O 100 62 68 83 89
69Leu H 6Lysh O 100 79 72 92 90
70Val H 42Arg O 100 91 89 90 91
72Arg H 40Gln O 100 79 59 85 78

Hydrogen bond X-ray structure Molecular dynamics
Backbone Side chain Molecule 1 Molecule 2 Molecule 3 Molecule 4
2Gln H 64Glu OE2 0 63 7 84 0
9Thr H 7Thr OG1 100 0 0 0 0
11Lysh H 7Thr OG1 100 0 0 0 0
18Glu H 21Asp OD2 100 80 3 0 0
20Ser H 18Glu OE2 0 0 0 55 0
25Asn H 22Thr OG1 100 31 13 61 38
51Glu H 59Tyr OH 100 46 87 56 76
55Thr H 58Asp OD1 100 29 62 22 75
58Asp H 55Thr OG1 100 53 76 72 86
64Glu H 64Glu OE2 0 55 6 16 0

Hydrogen bond X-ray structure Molecular dynamics
Side chain Backbone Molecule 1 Molecule 2 Molecule 3 Molecule 4
29Lysh HZ2 16Glu O 100 0 0 0 0
33Lysh HZ2 14Thr O 100 0 0 0 0
41Gln HE21 27Lysh O 100 81 91 47 71
41Gln HE22 36Ile O 100 90 89 60 83
48Lysh HZ3 46Ala O 100 0 0 0 0

Hydrogen bond X-ray structure Molecular dynamics
Side chain Side chain Molecule 1 Molecule 2 Molecule 3 Molecule 4
11Lysh HZ2 34Glu OE2 100 0 0 0 0
20Ser HG 18Glu OE2 0 0 0 60 0
27Lysh HZ2 52Asp OD2 100 0 0 0 0
49Gln HE21 16Glu OE1 100 0 0 0 0
54Arg HH12 58Asp OD1 100 0 0 0 0
55Thr HG1 58Asp OD1 0 44 83 29 86