Contacts of the strand formed by residues 210 - 216 (chain F) in PDB entry 2VIG
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 ILE 210 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154F LEU* 5.8 2.9 - - + -
163F ALA 4.2 2.9 - - - +
164F GLY* 3.5 40.4 - - - +
166F ALA* 4.2 13.9 - - + +
198F PHE* 4.1 17.5 - - + -
199F ALA 3.5 12.8 - - - +
200F SER* 4.5 7.6 - - - -
201F THR* 3.9 0.2 - - - -
209F SER* 1.3 86.8 - - - +
211F SER* 1.3 67.0 + - - +
258F GLY* 3.2 12.2 + - - +
260F GLY* 2.6 40.8 + - - -
261F PHE* 4.1 20.5 - - + +
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Residues in contact with SER 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F PHE* 3.3 6.1 - - - -
199F ALA 3.0 31.1 + - - -
201F THR* 2.8 23.5 + - - +
210F ILE* 1.3 71.3 - - - +
212F ALA* 1.3 58.7 + - - +
213F PHE* 3.6 29.3 - - - -
253F ILE* 3.8 10.5 - - - -
256F GLU 4.9 1.3 - - - -
257F PRO* 3.4 8.1 - - - +
258F GLY 3.1 18.6 + - - -
259F MET 5.0 0.2 - - - +
260F GLY* 3.7 8.1 - - - +
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Residues in contact with ALA 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F VAL* 4.5 2.0 - - + -
197F VAL 3.4 5.4 - - - +
198F PHE* 3.8 26.7 - - + -
211F SER* 1.3 74.2 - - - +
213F PHE* 1.3 56.0 + - - +
253F ILE* 3.4 11.3 - - - +
254F LEU* 2.8 50.7 + - + +
256F GLU 5.7 0.2 + - - -
260F GLY* 3.9 3.0 - - - +
263F ILE* 4.0 21.1 - - + -
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Residues in contact with PHE 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ALA* 3.5 31.2 - - + -
177F TRP* 3.6 34.8 - + + -
179F LEU* 5.0 5.2 - - + -
195F ALA 3.4 1.6 - - - +
196F VAL* 3.3 7.3 - - - +
197F VAL* 2.8 42.8 + - + +
199F ALA* 4.0 11.7 - - + -
201F THR* 3.9 7.2 - - + -
211F SER* 3.6 34.8 - - - -
212F ALA* 1.3 77.5 - - - +
214F LEU* 1.3 62.4 + - - +
215F VAL* 3.7 7.4 + - + -
248F ILE* 3.7 29.8 - - + -
252F SER 3.6 3.6 - - - -
253F ILE* 3.8 17.7 - - + -
254F LEU* 4.4 0.9 - - - +
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Residues in contact with LEU 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F TYR* 5.2 0.2 - - + -
127F ILE* 3.7 35.4 - - + -
135F GLN* 3.6 35.7 - - + +
139F TRP* 3.5 54.8 - - + +
195F ALA 3.6 3.4 - - - +
196F VAL* 4.3 13.2 - - + -
213F PHE* 1.3 70.4 - - - +
215F VAL* 1.3 61.6 + - - +
216F PRO* 4.2 1.9 - - - +
248F ILE* 4.4 0.9 - - - +
252F SER* 2.9 39.2 + - - +
254F LEU* 4.5 16.2 - - + -
504F EDO 4.7 0.9 - - - +
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Residues in contact with VAL 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F TRP* 3.7 4.1 - - - -
179F LEU* 4.2 9.9 - - + -
194F ALA* 3.3 2.4 - - - -
195F ALA* 2.9 33.9 + - + +
197F VAL* 3.6 31.9 - - + -
213F PHE* 4.2 2.7 - - + +
214F LEU* 1.3 78.2 - - - +
216F PRO* 1.4 82.9 - - + +
217F MET* 4.2 0.6 - - + +
219F THR* 4.0 14.4 - - + -
222F LEU* 4.3 5.4 - - + -
243F PHE* 4.2 15.9 - - + -
248F ILE* 4.0 27.4 - - + -
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Residues in contact with PRO 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F TRP* 3.6 20.1 - - + -
193F SER 3.9 7.0 - - - +
214F LEU 4.2 2.2 - - - +
215F VAL* 1.4 97.6 - - + +
217F MET* 1.3 64.8 + - - +
218F PRO 3.6 7.4 - - - +
219F THR* 3.4 36.9 + - - +
222F LEU* 4.0 0.9 - - - +
248F ILE* 4.6 8.5 - - + -
249F PRO* 6.0 3.1 - - + -
252F SER* 5.9 0.7 - - - +
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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