Contacts of the strand formed by residues 210 - 216 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154G LEU* 5.7 4.0 - - + -
163G ALA 3.9 8.1 - - - +
164G GLY* 3.7 36.6 - - - +
166G ALA* 4.1 13.2 - - + +
198G PHE* 4.2 17.5 - - + -
199G ALA 3.6 8.1 - - - +
200G SER* 4.6 10.8 - - - -
201G THR* 3.9 0.2 - - - -
206G GLN 3.7 13.2 - - - +
207G ASN 4.3 2.3 + - - +
208G LYS 3.7 1.6 - - - -
209G SER* 1.3 79.1 - - - +
211G SER* 1.3 66.3 + - - +
258G GLY* 3.1 13.3 - - - +
260G GLY* 2.8 41.3 + - - -
261G PHE* 3.9 20.4 - - + +
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Residues in contact with SER 211 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198G PHE* 3.4 4.2 - - - -
199G ALA 2.8 30.6 + - - -
201G THR* 3.1 23.4 + - - +
210G ILE* 1.3 72.7 - - - +
212G ALA* 1.3 59.4 + - - +
213G PHE* 3.3 30.4 - - - -
253G ILE* 4.0 7.8 - - - +
256G GLU 5.1 0.9 - - - -
257G PRO* 3.3 11.4 - - - +
258G GLY 3.2 16.2 + - - +
259G MET 5.0 0.2 - - - +
260G GLY* 3.8 8.5 - - - +
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Residues in contact with ALA 212 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G VAL* 4.7 2.2 - - + -
197G VAL 3.5 4.3 - - - +
198G PHE* 3.7 26.0 - - + -
211G SER* 1.3 71.5 - - - +
213G PHE* 1.3 62.6 + - - +
253G ILE* 3.5 5.8 - - - +
254G LEU* 2.7 58.6 + - + +
256G GLU 5.5 0.6 + - - -
260G GLY* 3.8 3.4 - - - +
263G ILE* 4.0 15.5 - - + -
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Residues in contact with PHE 213 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G ALA* 3.5 29.8 - - + -
177G TRP* 3.6 42.6 - + + -
179G LEU* 4.7 7.2 - - + -
195G ALA 3.4 1.2 - - - +
196G VAL* 3.3 7.2 - - - -
197G VAL* 2.8 45.3 + - - +
199G ALA* 4.0 11.9 - - + -
201G THR* 4.0 5.8 - - + -
211G SER* 3.3 41.3 - - - -
212G ALA* 1.3 77.1 - - - +
214G LEU* 1.3 62.6 + - - +
215G VAL* 3.9 5.5 + - + -
248G ILE* 4.1 22.9 - - + -
252G SER 3.5 3.6 - - - +
253G ILE* 4.0 18.6 - - + -
254G LEU* 5.1 0.7 - - - -
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Residues in contact with LEU 214 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G TYR* 5.2 0.2 - - + -
127G ILE* 3.6 35.0 - - + -
135G GLN* 3.8 32.1 - - + +
139G TRP* 3.3 57.3 - - + +
195G ALA 3.5 2.5 - - - +
196G VAL* 4.0 14.4 - - + -
213G PHE* 1.3 72.1 - - - +
215G VAL* 1.3 62.0 + - - +
216G PRO* 4.2 1.6 - - - +
248G ILE* 4.2 1.6 - - - +
252G SER* 2.9 36.6 + - - +
254G LEU* 4.5 16.2 - - + -
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Residues in contact with VAL 215 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G TRP* 3.8 4.8 - - - -
179G LEU* 3.9 12.3 - - + -
194G ALA* 3.3 1.9 - - - -
195G ALA* 2.9 39.6 + - + +
197G VAL* 3.7 27.6 - - + -
213G PHE* 4.2 4.5 - - + +
214G LEU* 1.3 77.7 - - - +
216G PRO* 1.4 80.3 - - + +
217G MET* 4.0 0.6 - - + +
219G THR* 4.2 9.9 - - + -
222G LEU* 4.6 3.8 - - + -
243G PHE* 3.9 24.2 - - + -
246G CYS* 5.1 0.4 - - - -
248G ILE* 3.7 26.0 - - + -
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Residues in contact with PRO 216 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G TRP* 3.5 21.1 - - + -
193G SER 3.7 7.9 - - - +
214G LEU 4.2 2.0 - - - +
215G VAL* 1.4 90.0 - - + +
217G MET* 1.3 63.3 + - - +
218G PRO 3.9 7.0 - - - +
219G THR* 3.2 41.8 - - - +
248G ILE* 4.5 13.7 - - + -
249G PRO* 6.1 2.9 - - + -
252G 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