Contacts of the strand formed by residues 87 - 93 (chain B) in PDB entry 2VWI
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 GLU 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B VAL* 5.0 4.2 - - - +
47B ARG* 2.8 52.9 + - - +
48B ILE 3.4 25.6 - - - +
49B ASN* 4.2 10.7 + - + +
50B LEU* 4.9 1.6 - - - -
83B VAL* 3.4 7.4 - - - +
84B VAL* 2.7 41.9 + - - +
85B LYS 3.4 0.8 + - - -
86B ASP* 1.3 84.2 - - - +
88B LEU* 1.3 58.6 + - - +
89B TRP* 3.0 14.8 + - - +
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Residues in contact with LEU 88 (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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46B LYS 3.3 4.5 - - - +
47B ARG* 3.6 0.5 - - - -
48B ILE* 2.7 49.1 + - + +
50B LEU* 4.2 14.5 - - + +
57B MET* 3.8 30.3 - - + -
60B LEU* 3.9 28.5 - - + -
64B ILE* 4.6 4.5 - - + -
81B SER* 4.4 12.8 - - - -
82B PHE 4.1 13.7 - - - +
83B VAL* 4.5 1.3 - - + +
87B GLU* 1.3 72.5 - - - +
89B TRP* 1.3 68.2 + - - +
90B LEU* 4.1 20.6 - - + -
167B VAL* 4.2 14.1 - - + -
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Residues in contact with TRP 89 (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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14B ARG* 3.8 32.3 - - + -
17B TYR* 4.8 6.5 - - + -
19B LEU* 3.7 36.3 - - + -
45B ILE* 3.7 32.1 - - + -
46B LYS 3.5 3.4 - - - -
47B ARG* 3.8 31.7 - - + +
81B SER* 3.3 10.6 - - - -
82B PHE* 3.0 58.9 + + + +
84B VAL* 3.6 34.2 - - + +
87B GLU* 3.0 26.9 + - + -
88B LEU* 1.3 79.1 - - - +
90B LEU* 1.3 61.2 + - - +
91B VAL* 3.9 1.9 + - - +
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Residues in contact with LEU 90 (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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44B ALA 3.5 2.6 - - - +
45B ILE* 3.2 5.7 - - - +
46B LYS* 2.9 45.1 + - + +
48B ILE* 3.8 20.4 - - + -
64B ILE* 5.3 0.7 - - + -
67B MET* 4.2 23.3 - - + -
78B TYR* 5.2 2.0 - - + -
80B THR 4.0 2.2 - - - -
81B SER* 3.3 20.0 - - - +
88B LEU* 4.1 22.2 - - + -
89B TRP* 1.3 74.3 - - - +
91B VAL* 1.3 61.8 + - - +
92B MET* 3.7 18.3 + - + +
167B VAL* 4.2 16.4 - - + -
168B SER* 3.8 22.9 - - - +
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Residues in contact with VAL 91 (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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10B TRP* 4.7 0.4 - - + -
17B TYR* 3.9 26.5 - - + +
43B VAL* 3.9 17.7 - - + -
44B ALA 3.8 2.7 - - - -
45B ILE* 4.0 17.3 - - + -
78B TYR* 3.8 4.6 - - - -
79B TYR* 2.8 41.4 + - + -
80B THR* 2.8 31.5 + - + +
82B PHE* 3.8 28.3 - - + -
89B TRP 4.7 2.2 - - - +
90B LEU* 1.3 73.0 - - - +
92B MET* 1.3 62.0 + - - +
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Residues in contact with MET 92 (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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31B VAL* 6.2 0.9 - - + -
43B VAL* 3.5 8.0 - - - +
44B ALA* 2.9 39.0 + - + +
46B LYS* 4.0 23.3 - - + +
67B MET* 6.1 2.5 - - + -
76B VAL* 4.2 14.1 - - + -
77B SER 3.3 15.0 - - - +
78B TYR* 4.4 6.1 - - + -
79B TYR* 3.6 8.3 - - - -
90B LEU* 3.7 37.7 - - + +
91B VAL* 1.3 74.9 - - - +
93B LYS* 1.3 58.9 + - - +
163B ALA* 5.9 1.3 - - - -
164B ASP* 5.2 11.2 - - - +
168B SER* 5.6 0.7 - - - +
1295B ANP 3.5 37.5 - - - +
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Residues in contact with LYS 93 (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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44B ALA 4.4 0.2 - - - -
76B VAL* 4.1 1.1 - - - +
77B SER* 2.9 35.5 + - - +
79B TYR* 3.4 27.6 - - + +
92B MET* 1.3 72.5 - - - +
94B LEU* 1.3 76.6 + - - +
95B LEU* 3.5 16.6 - - + +
155B GLY* 5.8 0.8 - - - -
156B GLU* 3.9 22.0 + - - -
157B ASP* 5.8 1.0 + - - -
161B GLN* 4.6 19.6 - - - +
1295B ANP 2.9 23.6 + - - -
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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