Contacts of the strand formed by residues 210 - 216 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C LEU* 5.7 4.3 - - + -
163C ALA 4.4 4.9 - - - +
164C GLY* 3.5 39.9 - - - +
166C ALA* 4.4 11.0 - - + +
198C PHE* 4.0 18.4 - - + -
199C ALA 3.4 12.8 - - - +
200C SER* 4.4 9.2 - - - +
209C SER* 1.3 87.3 - - - +
211C SER* 1.3 74.0 + - - +
258C GLY* 3.0 14.8 + - - +
260C GLY* 2.8 30.0 + - - -
261C PHE* 4.0 25.0 - - + +
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Residues in contact with SER 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C PHE* 3.3 5.0 - - - -
199C ALA 2.9 32.3 + - - +
201C THR* 2.8 25.1 + - - +
210C ILE* 1.3 72.2 - - - +
212C ALA* 1.3 58.8 + - - +
213C PHE* 3.5 25.3 - - - -
253C ILE* 4.4 7.9 - - - -
256C GLU 4.8 1.3 - - - -
257C PRO* 3.2 12.7 - - - +
258C GLY 3.0 18.7 + - - +
259C MET 5.0 0.2 - - - +
260C GLY* 3.8 10.1 - - - +
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Residues in contact with ALA 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C VAL* 4.4 4.7 - - + -
197C VAL 3.4 4.3 - - - -
198C PHE* 3.7 24.5 - - + -
211C SER* 1.3 71.5 - - - +
213C PHE* 1.3 61.0 + - - +
253C ILE* 3.4 10.0 - - - +
254C LEU* 2.8 59.2 + - + +
260C GLY* 3.9 3.2 - - - +
263C ILE* 4.0 12.3 - - + -
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Residues in contact with PHE 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ALA* 3.2 32.3 - - + -
177C TRP* 3.5 40.8 - + - -
179C LEU* 4.7 5.8 - - + -
195C ALA 3.2 4.3 - - - +
196C VAL* 3.4 4.2 - - - -
197C VAL* 2.8 44.5 + - - +
199C ALA* 3.7 14.1 - - + -
201C THR* 3.8 7.2 - - + -
211C SER* 3.5 33.2 - - - -
212C ALA* 1.3 77.3 - - - +
214C LEU* 1.3 62.6 + - - +
215C VAL* 3.7 6.2 + - + -
248C ILE* 4.0 23.6 - - + -
252C SER 3.3 4.9 - - - +
253C ILE* 3.9 17.9 - - + -
254C LEU* 5.1 0.9 - - - -
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Residues in contact with LEU 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C TYR* 5.2 0.7 - - + -
127C ILE* 3.8 32.8 - - + -
135C GLN* 3.8 32.1 - - + +
139C TRP* 3.5 57.6 - - + +
195C ALA 3.7 2.5 - - - +
196C VAL* 4.0 15.3 - - + -
213C PHE* 1.3 72.7 - - - +
215C VAL* 1.3 59.8 + - - +
216C PRO* 4.2 1.7 - - - +
248C ILE* 4.3 1.6 - - - +
251C ASP 5.4 0.2 - - - +
252C SER* 2.7 39.3 + - - +
254C LEU* 4.5 16.8 - - + -
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Residues in contact with VAL 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TRP* 3.7 4.7 - - - -
179C LEU* 4.0 11.7 - - + -
194C ALA* 3.3 2.4 - - - -
195C ALA* 2.9 35.9 + - + +
197C VAL* 3.5 28.5 - - + -
213C PHE* 4.0 3.4 - - + +
214C LEU* 1.3 77.0 - - - +
216C PRO* 1.4 80.1 - - + +
217C MET* 4.3 2.3 - - + +
219C THR* 4.1 10.5 - - + -
222C LEU* 4.5 5.8 - - + -
243C PHE* 4.0 20.6 - - + -
248C ILE* 3.9 25.4 - - + -
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Residues in contact with PRO 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C TRP* 3.5 21.9 - - + -
193C SER 3.8 7.9 - - - +
214C LEU 4.2 2.2 - - - +
215C VAL* 1.4 93.9 - - + +
217C MET* 1.3 60.9 + - - +
218C PRO 3.7 6.5 - - - +
219C THR* 3.3 38.6 - - - +
248C ILE* 4.3 13.5 - - + -
249C PRO* 6.0 3.4 - - + -
252C SER* 5.8 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