Contacts of the strand formed by residues 210 - 216 (chain A) in PDB entry 2WIN
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 PHE 210 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A PRO* 3.7 5.1 - - - +
209A SER* 1.3 94.3 - - - +
211A GLU* 1.3 69.4 + - - +
212A VAL* 3.8 15.3 - - + -
235A ALA* 4.4 1.8 - - + -
236A ARG 3.3 13.7 - - - +
237A PHE* 3.5 9.6 - + + +
238A LEU* 3.9 9.3 - - - +
243A VAL* 3.6 19.7 - - + -
308A VAL* 3.8 33.4 - - + -
310A LEU* 3.8 29.2 - - + -
315A ASP* 3.5 22.7 - - + -
316A MET* 4.4 1.1 - - - -
317A VAL* 3.3 42.9 - - + +
582A VAL* 4.2 3.3 - - - +
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Residues in contact with GLU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 1.3 75.0 - - - +
212A VAL* 1.3 65.7 + - - +
213A ILE* 4.3 21.4 - - + +
234A THR 3.9 0.3 - - - +
235A ALA* 3.4 5.4 - - - +
236A ARG* 2.9 62.1 + - + +
237A PHE 5.1 2.4 - - - +
238A LEU* 4.5 8.5 - - + +
578A LYS* 4.1 27.8 + - - -
582A VAL* 4.0 24.8 - - + +
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 3.8 13.2 - - + -
211A GLU* 1.3 80.6 - - - +
213A ILE* 1.3 67.5 + - - +
214A VAL* 5.3 0.3 - - - +
233A ILE* 4.1 16.8 - - + -
234A THR 3.5 4.0 - - - +
235A ALA* 4.3 2.5 - - + -
306A ALA* 4.6 5.8 - - + -
308A VAL* 3.7 33.9 - - + +
317A VAL* 3.7 26.5 - - + +
319A ALA* 3.4 35.9 - - + +
582A VAL* 4.9 2.5 - - - +
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Residues in contact with ILE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 4.3 24.5 - - + +
212A VAL* 1.3 79.2 - - - +
214A VAL* 1.3 64.1 + - - +
215A GLU* 3.6 35.0 - - + +
232A THR 3.4 3.1 - - - +
233A ILE* 3.6 4.2 - - - +
234A THR* 2.7 53.6 + - + +
236A ARG* 4.7 15.5 - - + +
321A ARG* 5.9 0.4 - - - +
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Residues in contact with VAL 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A VAL* 4.9 0.4 - - + -
213A ILE* 1.3 78.1 - - - +
215A GLU* 1.3 60.6 + - - +
216A PRO* 3.5 4.8 - - - +
231A VAL* 4.5 7.0 - - + -
232A THR 3.6 2.7 - - - -
233A ILE* 3.5 28.0 - - + -
304A VAL* 4.5 10.1 - - + -
306A ALA* 3.8 22.4 - - + +
319A ALA* 4.6 7.0 - - + -
320A GLU 3.8 11.7 - - - +
321A ARG* 3.4 56.9 + - + +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ILE* 3.6 29.9 - - + +
214A VAL* 1.3 72.3 - - - +
216A PRO* 1.3 69.7 - - + +
217A THR 3.7 0.9 + - - -
231A VAL* 4.4 0.9 - - - +
232A THR* 3.0 40.7 + - - +
234A THR* 5.3 5.8 + - - +
321A ARG* 3.9 13.9 - - - +
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Residues in contact with PRO 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A VAL 3.5 9.9 - - - +
215A GLU* 1.3 89.3 - - - +
217A THR* 1.3 65.8 + - - +
218A GLU 3.1 21.5 + - - +
219A LYS* 5.5 3.0 - - - +
229A LEU* 4.1 13.5 - - + -
230A GLU 3.2 14.6 - - - +
231A VAL* 4.0 11.9 - - + -
304A VAL* 5.3 0.7 - - + -
321A ARG* 3.6 24.9 - - + +
324A ILE* 3.7 28.0 - - + -
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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