The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centers of the two atoms.
The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterium was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably aren't there anyway.
Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction.
161 CL ( 173 ) CL -- 170 HOH (HOH ) 291 1.117 1.683 INTER 16 LYS ( 16 ) O -- 17 ILE ( 17 ) C 0.325 2.475 INTRA BF 25 TYR ( 25 ) N -- 34 THR ( 34 ) CG2 0.310 2.790 INTRA BF 14 ARG ( 14 ) NH1 -- 163 HOH (HOH ) 236 0.251 2.299 INTRA BF 17 ILE ( 17 ) CG2 -- 18 TYR ( 18 ) N 0.246 2.854 INTRA 69 ASP ( 72 ) OD2 -- 93 ARG ( 96 ) NH1 0.241 2.309 INTER HB 16 LYS ( 16 ) CE -- 54 VAL ( 57 ) CG2 0.212 2.988 INTRA BF 82 LYS ( 85 ) N -- 83 PRO ( 86 ) CD 0.207 2.793 INTRA 16 LYS ( 16 ) CD -- 54 VAL ( 57 ) CG2 0.207 2.993 INTRA BF 99 MET ( 102 ) CE -- 103 MET ( 106 ) CE 0.200 3.000 INTRA 11 GLU ( 11 ) OE2 -- 142 ARG ( 145 ) NH1 0.195 2.355 INTRA HB 26 THR ( 26 ) CG2 -- 27 ILE ( 27 ) N 0.167 2.933 INTRA 20 ASP ( 20 ) O -- 23 GLY ( 23 ) N 0.162 2.388 INTRA BF 137 ASN ( 140 ) ND2 -- 167 HOH (HOH ) 300 0.156 2.394 INTRA HB 62 LYS ( 65 ) NZ -- 169 HOH (HOH ) 273 0.147 2.403 INTER BF 45 LYS ( 48 ) CE -- 170 HOH (HOH ) 197 0.136 2.664 INTER 142 ARG ( 145 ) O -- 143 ALA ( 146 ) C 0.131 2.669 INTRA 129 ASN ( 132 ) O -- 130 LEU ( 133 ) C 0.118 2.682 INTRA 73 ARG ( 76 ) CD -- 167 HOH (HOH ) 328 0.113 2.687 INTER BF 74 GLY ( 77 ) O -- 75 ILE ( 78 ) C 0.110 2.690 INTRA 20 ASP ( 20 ) C -- 22 GLU ( 22 ) N 0.109 2.791 INTRA BF 11 GLU ( 11 ) CD -- 142 ARG ( 145 ) NH1 0.104 2.996 INTRA 49 ARG ( 52 ) NH2 -- 163 HOH (HOH ) 196 0.098 2.452 INTRA BF 51 THR ( 54 ) C -- 53 GLY ( 56 ) N 0.098 2.802 INTRA BF 1 MET ( 1 ) CG -- 155 TRP ( 158 ) CD2 0.094 3.106 INTRA BF 21 THR ( 21 ) CB -- 170 HOH (HOH ) 323 0.090 2.710 INTER BF 13 LEU ( 13 ) C -- 14 ARG ( 14 ) CG 0.089 3.111 INTRA BF 78 ASN ( 81 ) OD1 -- 80 LYS ( 83 ) N 0.079 2.471 INTRA HB 21 THR ( 21 ) CA -- 170 HOH (HOH ) 323 0.075 2.725 INTER BF 16 LYS ( 16 ) C -- 17 ILE ( 17 ) O 0.065 2.735 INTRA BF 27 ILE ( 27 ) CG1 -- 28 GLY ( 28 ) N 0.064 3.036 INTRA 22 GLU ( 22 ) OE2 -- 134 ARG ( 137 ) NH1 0.063 2.487 INTRA BF 139 THR ( 142 ) CA -- 140 PRO ( 143 ) CD 0.061 2.739 INTRA B3 143 ALA ( 146 ) O -- 144 LYS ( 147 ) C 0.061 2.739 INTRA 1 MET ( 1 ) CG -- 155 TRP ( 158 ) CE3 0.059 3.141 INTRA BF 62 LYS ( 65 ) CD -- 169 HOH (HOH ) 297 0.057 2.743 INTER BF 73 ARG ( 76 ) O -- 74 GLY ( 77 ) C 0.054 2.746 INTRA 118 LEU ( 121 ) O -- 119 GLN ( 122 ) C 0.045 2.755 INTRA 86 ASP ( 89 ) OD1 -- 167 HOH (HOH ) 328 0.042 2.208 INTER HB 52 ASN ( 55 ) CB -- 52 ASN ( 55 ) ND2 0.040 3.060 INTER BF 123 TRP ( 126 ) NE1 -- 170 HOH (HOH ) 323 0.040 2.510 INTRA HB 16 LYS ( 16 ) C -- 17 ILE ( 17 ) C 0.031 2.769 INTRA B3 139 THR ( 142 ) N -- 140 PRO ( 143 ) CD 0.030 2.970 INTRA 68 VAL ( 71 ) O -- 69 ASP ( 72 ) C 0.028 2.772 INTRA 16 LYS ( 16 ) CE -- 53 GLY ( 56 ) O 0.027 2.773 INTRA BF 7 LEU ( 7 ) O -- 8 ARG ( 8 ) C 0.025 2.775 INTRA 24 TYR ( 24 ) C -- 25 TYR ( 25 ) CA 0.024 2.276 INTRA B2 14 ARG ( 14 ) CD -- 163 HOH (HOH ) 236 0.024 2.776 INTRA BF 32 LEU ( 32 ) CD1 -- 33 LEU ( 33 ) N 0.023 3.077 INTRA 22 GLU ( 22 ) N -- 23 GLY ( 23 ) N 0.019 2.581 INTRA BF 77 ARG ( 80 ) N -- 78 ASN ( 81 ) N 0.019 2.581 INTRA B3 12 GLY ( 12 ) C -- 163 HOH (HOH ) 298 0.018 2.782 INTRA BF 103 MET ( 106 ) C -- 104 GLY ( 107 ) CA 0.017 2.283 INTRA B2 123 TRP ( 126 ) CZ2 -- 170 HOH (HOH ) 323 0.016 2.784 INTRA 92 ARG ( 95 ) O -- 93 ARG ( 96 ) C 0.015 2.785 INTRA 41 SER ( 44 ) O -- 42 GLU ( 45 ) C 0.013 2.787 INTRA 25 TYR ( 25 ) O -- 32 LEU ( 32 ) CD1 0.012 2.788 INTRA 42 GLU ( 45 ) OE2 -- 113 ASN ( 116 ) ND2 0.011 2.539 INTER HB 111 PHE ( 114 ) O -- 112 THR ( 115 ) C 0.008 2.792 INTRA 81 LEU ( 84 ) C -- 83 PRO ( 86 ) CD 0.007 3.193 INTRA 87 SER ( 90 ) O -- 121 LYS ( 124 ) NZ 0.007 2.543 INTRA HB 162 CL ( 178 ) CL -- 164 HOH (HOH ) 215 0.006 2.794 INTRA 158 TYR ( 161 ) N -- 159 LYS ( 162 ) N 0.002 2.598 INTRA B3 105 GLU ( 108 ) CD -- 166 HOH (HOH ) 289 0.002 2.798 INTRA BF 14 ARG ( 14 ) CG -- 163 HOH (HOH ) 298 0.000 2.800 INTRA BF