Interatomic bumps. The list of all bumps. Date= 2012-04-24 18:38:10 The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction. 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 centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance. The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion 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). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively. 45 ARG ( 45 ) A NH1 <--> 68 ARG ( 68 ) A NH2 0.66 2.19 INTRA BF 44 ASN ( 44 ) A CB <--> 133 HOH ( 223 ) A O 0.31 2.49 INTRA 3 TYR ( 3 ) A OH <--> 88 LEU ( 88 ) A CD1 0.31 2.49 INTRA BL 3 TYR ( 3 ) A CZ <--> 88 LEU ( 88 ) A CD1 0.27 2.93 INTRA BL 45 ARG ( 45 ) A CZ <--> 68 ARG ( 68 ) A NH2 0.27 2.83 INTRA BF 35 GLU ( 35 ) A OE1 <--> 133 HOH ( 244 ) A O 0.26 2.14 INTRA BF 74 ASN ( 74 ) A N <--> 133 HOH ( 225 ) A O 0.19 2.51 INTRA 93 ARG ( 93 ) A NH1 <--> 133 HOH ( 184 ) A O 0.16 2.54 INTRA BF 131 NAG ( 131 ) A C1 <--> 132 NDG ( 132 ) A C4 0.16 2.14 INTRA B2 93 ARG ( 93 ) A NH2 <--> 133 HOH ( 226 ) A O 0.14 2.56 INTRA BF 10 ARG ( 10 ) A NH1 <--> 133 HOH ( 162 ) A O 0.13 2.57 INTRA 46 ASN ( 46 ) A N <--> 50 SER ( 50 ) A O 0.11 2.59 INTRA 103 ASN ( 103 ) A ND2 <--> 133 HOH ( 151 ) A O 0.10 2.60 INTRA 1 LYS ( 1 ) A N <--> 86 ASP ( 86 ) A OD1 0.10 2.60 INTRA 62 TYR ( 62 ) A CE2 <--> 131 NAG ( 131 ) A O6 0.09 2.71 INTRA BF 101 ASP ( 101 ) A CB <--> 102 PRO ( 102 ) A CD 0.08 3.02 INTRA 25 LEU ( 25 ) A N <--> 26 PRO ( 26 ) A CD 0.08 2.92 INTRA BL 52 ASP ( 52 ) A OD2 <--> 132 NDG ( 132 ) A C1 0.07 2.73 INTRA 127 CYS ( 127 ) A O <--> 133 HOH ( 162 ) A O 0.05 2.35 INTRA 52 ASP ( 52 ) A OD2 <--> 132 NDG ( 132 ) A O1L 0.04 2.36 INTRA 44 ASN ( 44 ) A CG <--> 133 HOH ( 223 ) A O 0.04 2.76 INTRA BF 64 CYS ( 64 ) A C <--> 80 CYS ( 80 ) A SG 0.03 3.37 INTRA BL 101 ASP ( 101 ) A CA <--> 102 PRO ( 102 ) A CD 0.03 2.77 INTRA B3 59 ASN ( 59 ) A N <--> 131 NAG ( 131 ) A O7 0.01 2.69 INTRA BL The bumps have been binned in 5 categories ranging from 'should deal with' till 'must fix'. Additionally, the integrated sum of all bumps, the squared sum of all bumps, and these latter two values normalized by the number of contacts are listed too for comparison purposes between, for example, small and large proteins. Total bump value: 3.697 Total bump value per residue: 0.183 Total number of bumps: 24 Total squared bump value: 1.032 Total number of bumps in the mildest bin: 18 Total number of bumps in the second bin: 5 Total number of bumps in the middle bin: 1 Total number of bumps in the fourth bin: 0 Total number of bumps in the worst bin: 0