Contacts of the strand formed by residues 88 - 93 (chain B) in PDB entry 4WNP
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 VAL 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B LYS 4.0 5.5 - - - +
48B ILE* 3.7 25.5 + - + +
57B GLN* 3.8 35.7 - - + +
60B LEU* 3.9 27.8 - - + +
61B GLY* 4.5 1.1 - - - +
64B ILE* 3.8 28.0 - - + -
82B GLN 3.3 5.2 - - - +
83B GLU* 4.2 18.2 - - + +
87B SER* 1.3 81.2 - - - +
89B TYR* 1.3 73.7 + - - +
90B LEU* 3.9 3.1 - - + -
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Residues in contact with TYR 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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9B GLU* 3.3 20.0 + - - -
11B VAL* 3.9 36.8 - - + -
16B PHE* 4.3 6.7 - + - -
18B ARG* 3.7 15.6 + - - -
45B VAL* 4.4 7.2 - - + -
46B LYS 3.6 3.4 - - - +
47B CYS* 3.9 31.4 - - + -
48B ILE 5.8 0.2 - - - -
64B ILE* 4.2 1.2 - - - +
81B PHE* 3.2 6.6 - - - +
82B GLN* 2.7 57.6 + - - +
87B SER* 4.1 25.7 - - - -
88B VAL* 1.3 81.5 - - - +
90B LEU* 1.3 64.9 + - - +
91B VAL 4.2 0.2 - - - -
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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 3.4 2.6 - - - +
45B VAL* 3.4 4.9 - - - -
46B LYS* 2.9 43.0 + - + +
60B LEU* 3.7 26.0 - - + -
63B GLU* 3.9 36.3 - - + +
64B ILE* 3.6 33.4 - - + +
67B LEU* 4.5 1.6 - - + -
78B LEU* 3.8 18.4 - - + -
80B ASP 3.9 3.4 - - - -
81B PHE* 4.4 0.2 - - - -
88B VAL* 3.9 12.6 - - + -
89B TYR* 1.3 79.9 - - - +
91B VAL* 1.3 61.9 + - - +
92B MET* 3.4 10.6 + - - +
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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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11B VAL* 4.3 24.9 - - + +
14B PHE* 3.7 39.5 - - + -
43B VAL* 3.6 35.0 - - + -
44B ALA 3.9 2.5 - - - -
45B VAL* 4.7 9.2 - - + +
78B LEU* 3.8 1.9 - - - -
79B TYR* 2.9 29.9 + - + +
80B ASP* 2.8 30.1 + - + +
81B PHE* 4.9 0.4 - - - -
90B LEU* 1.3 73.0 - - - +
92B MET* 1.3 58.0 + - - +
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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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43B VAL* 3.3 11.8 - - - +
44B ALA* 2.7 42.3 + - + +
46B LYS* 4.6 8.5 - - + -
63B GLU* 5.2 4.0 - - - +
67B LEU* 3.7 20.9 - - + -
76B VAL* 3.5 39.7 - - + +
77B ALA 3.4 9.4 - - - +
78B LEU* 3.8 24.9 - - - -
79B TYR* 4.3 3.4 - - - -
90B LEU* 4.0 17.5 - - + +
91B VAL* 1.3 74.8 - - - +
93B GLU* 1.3 67.6 + - - +
164B ALA* 6.2 1.1 - - - -
165B ASP 6.2 1.1 - - - +
401B 3RJ 3.9 29.2 - - + -
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Residues in contact with GLU 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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72B HIS 5.5 0.3 - - - +
75B ILE 4.0 1.9 - - - +
76B VAL* 3.6 13.9 - - + +
77B ALA* 2.9 43.0 + - - +
79B TYR* 3.7 30.7 - - + +
92B MET* 1.3 74.1 - - - +
94B TYR* 1.3 71.7 + - - +
95B CYS* 3.8 1.7 + - - -
147B SER* 5.1 1.4 + - - -
162B LYS* 2.8 42.1 + - - -
401B 3RJ 2.8 20.1 + - - -
249D ALA* 4.6 10.8 - - - +
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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