Contacts of the strand formed by residues 85 - 90 (chain B) in PDB entry 2WNW
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 LEU 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ASP* 3.6 21.1 - - + +
47B GLY* 3.2 38.8 - - - +
48B PHE 3.0 9.8 + - - +
49B GLY* 3.1 20.2 - - - +
50B GLY 3.7 1.6 + - - -
83B TYR* 4.4 0.5 - - - +
84B THR* 1.3 86.3 + - - +
86B ALA* 1.3 65.2 + - - +
137B MET* 3.5 10.9 - - - +
138B LYS* 3.5 35.0 - - + +
291B LEU* 4.5 4.9 - - + -
327B GLY* 4.4 5.4 - - - -
328B PHE 3.8 15.7 - - - +
329B ILE* 4.0 20.0 - - + -
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Residues in contact with ALA 86 (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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50B GLY 3.1 15.3 - - - +
52B PHE* 3.5 30.7 - - + -
76B PHE* 5.9 0.2 - - + -
85B LEU* 1.3 80.3 - - - +
87B ARG* 1.3 62.4 + - - +
88B MET* 5.9 0.7 - - - -
137B MET* 3.8 4.3 - - + -
138B LYS 3.2 5.6 + - - +
139B LEU* 3.6 16.3 - - + -
140B MET* 2.9 29.1 + - - +
329B ILE* 4.0 8.2 - - - +
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Residues in contact with ARG 87 (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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50B GLY 3.3 4.9 + - - -
51B SER* 3.1 19.9 + - - +
52B PHE* 2.8 26.5 + - - +
86B ALA* 1.3 76.9 - - - +
88B MET* 1.3 67.0 + - - +
140B MET* 3.1 19.9 - - + +
142B SER* 3.0 25.9 + - - +
144B TRP* 3.4 22.7 - - + -
195B ASN* 3.0 21.2 + - - -
239B ASP* 2.9 32.3 + - - -
268B HIS* 4.5 0.2 - - - -
293B SER* 3.5 21.8 + - - -
294B GLU* 3.0 35.6 + - - +
329B ILE* 3.8 11.6 - - + +
331B TRP* 4.3 5.1 - - + -
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Residues in contact with MET 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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51B SER* 5.5 0.4 - - - -
52B PHE* 3.4 20.2 - - + +
86B ALA* 6.2 0.4 - - - -
87B ARG* 1.3 78.7 - - - +
89B PRO* 1.3 72.4 - - + +
123B LEU* 5.5 2.9 - - + -
127B ILE* 3.7 27.1 - - + -
139B LEU* 4.2 26.0 - - + -
140B MET 2.9 12.4 + - - +
141B ALA* 3.3 9.1 - - + -
142B SER* 2.9 24.3 + - - +
144B TRP* 4.9 2.5 - - - -
177B TYR* 3.4 24.5 - - - +
181B TYR* 4.0 13.5 - - + +
186B ILE* 4.4 0.4 - - + -
188B VAL* 3.6 29.2 - - + -
331B TRP* 6.1 0.7 - - - -
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Residues in contact with PRO 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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52B PHE 3.0 18.4 - - - +
53B THR* 4.2 11.2 - - + -
54B GLU 5.0 1.3 - - - +
88B MET* 1.3 86.6 - - + +
90B ILE* 1.3 62.7 + - - +
91B GLN 3.4 18.7 + - - +
93B CYS* 4.2 21.1 - - + +
96B SER* 5.8 0.4 - - - +
100B TYR* 4.9 3.5 + - - +
102B TYR* 4.1 1.9 + - - -
123B LEU* 4.5 19.5 - - + +
142B SER 3.2 6.1 - - - +
144B TRP* 3.8 23.8 - - + -
177B TYR* 4.1 12.1 + - - -
181B TYR* 4.9 0.2 + - - -
331B TRP* 5.7 0.4 - - + -
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Residues in contact with ILE 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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89B PRO* 1.3 70.2 - - - +
91B GLN* 1.3 71.7 + - - +
102B TYR* 3.9 20.9 - - + -
141B ALA* 3.7 37.2 - - + -
142B SER 2.9 9.6 + - - +
143B PRO* 3.6 40.5 - - + +
144B TRP 4.1 3.6 + - - -
145B SER 4.5 1.4 - - - +
170B TRP* 4.2 18.6 - - + -
173B ILE* 5.5 0.2 - - + -
174B ILE* 4.3 17.0 - - + -
177B TYR* 3.8 25.6 - - + -
191B LEU* 4.0 13.7 - - + -
192B SER 5.5 0.2 - - - +
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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