Contacts of the strand formed by residues 55 - 63 (chain B) in PDB entry 6WCW
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 ARG 55 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B VAL* 4.2 19.2 - - + +
51B MET* 3.4 5.4 - - - -
52B VAL 3.1 36.6 + - - +
53B ASP* 2.7 26.6 + - - +
54B ASP* 1.3 73.3 - - - +
56B LEU* 1.3 72.1 + - - +
57B VAL* 3.6 11.4 + - + +
174B LEU* 3.5 31.3 - - - +
178B THR* 5.5 6.3 - - - +
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Residues in contact with LEU 56 (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 VAL* 4.2 13.9 + - - +
49B GLU* 4.3 18.8 - - + +
50B VAL 3.4 19.5 - - - +
51B MET* 3.5 22.9 - - + -
54B ASP 3.8 3.4 + - - -
55B ARG* 1.3 77.4 - - - +
57B VAL* 1.3 69.4 + - - +
58B THR* 3.8 19.5 - - - +
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 3.6 22.9 - - + +
9B LEU* 5.0 14.4 - - + -
49B GLU* 3.6 4.0 - - - +
50B VAL* 2.8 60.5 + - + +
52B VAL* 4.2 15.3 - - + +
55B ARG* 3.9 21.3 - - + +
56B LEU* 1.3 82.1 - - - +
58B THR* 1.3 63.0 + - - +
59B MET* 5.6 0.2 - - + -
170B ALA* 5.8 0.7 - - + -
174B LEU* 4.2 22.0 - - + -
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Residues in contact with THR 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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7B VAL 3.2 13.4 + - - -
8B LEU* 3.4 18.4 - - + +
9B LEU* 2.8 28.2 + - - +
47B THR* 4.6 12.8 - - + -
48B LYS 3.7 6.3 - - - +
49B GLU* 3.7 23.0 - - + +
56B LEU* 3.8 15.1 - - - +
57B VAL* 1.3 76.7 + - - +
59B MET* 1.3 69.8 + - - +
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Residues in contact with MET 59 (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 LEU* 3.5 16.8 - - + +
11B VAL* 3.4 30.1 - - + -
28B TYR* 4.3 14.8 - - - -
46B LEU 3.8 0.2 - - - +
47B THR* 3.2 27.7 - - - -
48B LYS* 2.9 18.6 + - + +
50B VAL* 4.7 12.3 - - + -
57B VAL* 5.6 0.2 - - + -
58B THR* 1.3 75.9 - - - +
60B GLN* 1.3 59.3 + - - +
61B ILE* 4.0 25.2 + - + +
166B PHE* 4.0 9.9 - - + +
169B ILE* 3.6 20.2 - - + -
170B ALA* 3.7 33.2 - - + +
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Residues in contact with GLN 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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8B LEU* 4.6 25.6 - - + +
9B LEU 2.7 15.7 + - - +
10B LYS* 3.4 17.5 - - - +
11B VAL 2.7 33.5 + - - +
45B PHE* 3.6 41.3 - - + -
46B LEU 3.5 2.9 - - - -
47B THR* 4.7 5.7 - - + +
59B MET* 1.3 73.8 - - - +
61B ILE* 1.3 55.6 + - - +
62B TRP* 3.1 32.0 + - - +
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Residues in contact with ILE 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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11B VAL* 3.4 17.0 - - + -
13B ILE* 3.5 19.5 - - + -
25B MET* 3.0 33.7 - - + +
28B TYR* 4.0 17.5 - - + -
29B VAL* 4.7 10.5 - - + -
45B PHE* 3.2 3.6 - - - -
46B LEU* 2.9 36.0 + - + +
48B LYS* 5.4 2.9 - - + +
59B MET* 4.2 21.5 - - + +
60B GLN* 1.3 75.0 - - - +
62B TRP* 1.3 60.7 + - - +
166B PHE* 3.5 32.3 - - + -
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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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882A MET 4.8 4.0 - - - -
883A LEU* 4.3 6.5 - - + -
886A ALA* 3.8 29.4 - - + -
10B LYS* 3.8 22.3 - - + +
11B VAL 2.7 21.3 + - - +
12B ILE* 4.2 5.2 - - + -
13B ILE* 2.7 35.7 + - - +
25B MET* 3.6 2.0 - - - -
43B ALA* 4.0 8.7 - - + -
44B ASP* 3.4 32.8 - - - -
45B PHE* 3.6 34.8 - + + -
60B GLN* 3.1 35.9 + - - +
61B ILE* 1.3 72.5 - - - +
63B ASP* 1.3 58.4 + - - +
64B THR* 4.5 0.9 - - - +
77B PHE* 3.7 41.3 - + + -
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Residues in contact with ASP 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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13B ILE* 4.0 9.4 - - + -
21B LYS* 4.5 13.9 - - + -
22B THR* 2.9 36.3 + - - +
25B MET* 3.4 30.8 - - + +
40B THR* 3.7 8.2 - - - +
42B GLY 4.5 1.2 - - - +
43B ALA* 3.4 23.0 - - - +
44B ASP* 3.2 17.2 + - - +
62B TRP* 1.3 74.7 - - - +
64B THR* 1.3 64.0 + - - +
1402B MG 3.6 3.5 - - - -
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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