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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