Contacts of the strand formed by residues 57 - 67 (chain B) in PDB entry 2BXJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B VAL* 5.3 0.2 - - - +
12B PRO* 3.3 28.7 - - + +
45B LEU* 4.6 20.4 - - + +
46B ARG 3.6 11.4 - - - +
47B ARG* 4.8 9.6 - - + +
48B LEU* 3.7 12.2 - - - +
55B ASP* 2.9 15.8 + - - +
56B PRO* 1.3 92.6 - - + +
58B GLY* 1.3 58.7 + - - +
86B ARG* 4.4 2.8 + - - +
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Residues in contact with GLY 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.7 15.7 - - - -
10B LEU 3.7 9.9 - - - -
12B PRO* 3.9 2.7 - - - +
45B LEU* 3.4 7.2 - - - -
46B ARG 3.1 31.0 + - - -
48B LEU* 4.1 4.1 - - - +
57B GLN* 1.3 77.1 - - - +
59B TYR* 1.3 61.7 + - - -
60B PHE* 3.4 9.1 - - - -
86B ARG* 5.9 0.2 - - - -
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Residues in contact with TYR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE 3.7 0.7 - - - +
9B VAL* 3.5 1.4 - - - -
10B LEU* 2.8 49.1 + - + +
11B ASN 4.2 10.5 - - - +
12B PRO* 4.3 3.5 - - + +
19B LEU* 3.4 40.4 - - + +
42B GLU* 2.7 35.4 + - + +
44B GLY* 3.6 28.2 - - - -
45B LEU* 4.1 18.1 - - + +
58B GLY* 1.3 72.5 - - - -
60B PHE* 1.3 78.3 + - - +
61B LEU* 3.9 7.4 + - + -
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASN* 5.8 8.7 - - + -
8B ILE 3.5 4.5 - - - -
9B VAL* 3.6 21.8 - - + -
42B GLU* 3.8 3.8 - - - -
43B LEU* 2.9 45.2 + - + -
44B GLY 2.9 17.9 + - - +
46B ARG* 3.4 54.7 - - + -
47B ARG 5.9 0.2 - - - -
48B LEU* 3.7 26.2 - - + -
58B GLY 3.4 17.0 - - - -
59B TYR* 1.3 78.1 - - - +
61B LEU* 1.3 62.3 + - - +
87B ARG* 3.6 21.1 - - - -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B VAL 3.7 1.2 - - - +
7B ASN* 3.7 3.3 - - - +
8B ILE* 2.9 38.7 + - + +
10B LEU* 3.4 33.4 - - + -
19B LEU* 6.1 0.4 - - + -
23B LYS* 3.6 41.7 - - + -
26B ILE* 4.0 19.7 - - + -
40B VAL* 5.1 1.6 - - + -
41B GLU 3.6 3.8 - - - +
42B GLU* 3.6 22.0 - - + -
43B LEU* 4.3 0.6 - - - +
59B TYR* 4.7 7.0 - - + -
60B PHE* 1.3 79.4 - - - +
62B TRP* 1.3 62.6 + - - +
63B TYR* 4.0 16.2 - - + +
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Residues in contact with TRP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLU* 3.3 49.2 + - + +
6B VAL 3.5 2.7 - - - -
7B ASN* 3.2 26.2 + - - +
39B LYS* 3.9 28.7 - - + -
40B VAL* 3.4 4.5 - - - +
41B GLU* 2.8 48.7 + - + +
43B LEU* 3.4 28.9 - - + -
61B LEU* 1.3 76.4 - - - +
63B TYR* 1.3 68.8 + - - +
64B GLN* 3.5 25.4 - - + -
97B PHE* 3.4 37.0 - + - -
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR 3.7 0.3 - - - +
5B GLU* 3.3 5.0 - - - +
6B VAL* 2.7 54.7 + - + +
8B ILE* 4.0 12.6 - - + -
23B LYS* 3.2 37.8 + - - +
26B ILE* 3.6 25.2 - - + +
27B GLN* 4.4 18.8 - - + -
37B VAL* 4.1 13.0 - - + -
39B LYS 3.3 3.4 - - - -
40B VAL* 3.5 37.0 - - + -
61B LEU* 4.0 22.6 - - + +
62B TRP* 1.3 84.6 - - - +
64B GLN* 1.3 60.1 + - - +
65B VAL* 3.9 10.4 + - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ARG* 3.7 18.8 - - + +
4B TYR 3.5 9.6 - - - +
5B GLU* 4.9 4.3 - - + +
37B VAL 3.7 0.3 - - - -
38B GLU* 2.8 56.8 + - - +
39B LYS* 2.8 18.7 + - + +
62B TRP* 3.5 27.9 - - + -
63B TYR* 1.3 72.2 - - - +
65B VAL* 1.3 63.8 + - - +
93B SER* 4.7 1.7 + - - -
96B PRO* 3.7 4.6 - - - +
97B PHE* 2.9 54.6 + - - +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ARG 3.7 0.2 - - - +
3B ARG* 3.2 7.4 - - - +
4B TYR* 2.7 51.9 + - + +
6B VAL* 4.3 16.8 - - + -
30B ALA* 5.3 4.9 - - + -
35B ALA* 4.2 10.8 - - + -
36B ARG 3.3 9.0 - - - +
37B VAL* 4.0 24.7 - - + -
38B GLU* 4.4 3.1 - - - +
63B TYR* 3.9 17.5 - - + -
64B GLN* 1.3 80.3 - - - +
66B GLU* 1.3 60.5 + - - +
67B MET* 4.2 25.8 - - + -
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.0 41.2 - - + +
2B ARG* 3.1 15.9 - - - +
3B ARG* 4.1 20.6 + - - +
36B ARG* 2.8 42.7 + - + +
38B GLU* 4.3 15.9 - - - +
65B VAL* 1.3 75.5 - - - +
67B MET* 1.3 60.3 + - - +
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Residues in contact with MET 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 3.2 9.6 - - - +
2B ARG 2.9 25.6 + - - +
4B TYR* 3.9 12.3 - - + -
6B VAL* 6.1 1.6 - - - -
30B ALA* 4.8 3.1 - - - +
33B TYR* 3.9 33.4 - - + +
35B ALA* 3.4 26.5 - - + -
65B VAL* 4.2 11.4 - - + -
66B GLU* 1.3 76.9 - - - +
68B PRO* 1.3 82.7 - - + +
69B GLU 3.2 1.4 + - - -
71B ARG 3.9 6.3 - - - +
72B VAL* 3.9 39.3 - - + -
75B ALA* 4.2 9.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il