Contacts of the helix formed by residues 284 - 296 (chain V) in PDB entry 2C2V
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 ASN 284 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246U ILE* 4.1 5.3 - - + +
284U ASN* 2.6 41.8 + - - +
244V PRO* 3.1 21.7 + - + +
245V CYS* 3.9 9.0 - - - -
246V ILE* 4.2 9.8 - - - +
252V THR* 3.7 19.9 + - + +
283V PRO* 1.3 71.2 - - - +
285V LEU* 1.4 61.5 + - - +
286V ALA 3.4 2.9 + - - -
287V MET* 2.7 52.3 + - + +
288V LYS* 3.1 14.5 + - - +
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Residues in contact with LEU 285 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246U ILE* 4.5 0.4 - - - +
249U SER 4.0 3.4 - - - +
250U GLY* 3.1 43.4 + - - +
251U ILE* 3.9 13.9 - - + -
283V PRO* 3.2 19.8 + - + +
284V ASN* 1.4 73.9 - - - +
286V ALA* 1.3 62.7 + - - +
288V LYS* 3.6 19.6 + - + +
289V GLU* 3.2 31.3 + - - +
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Residues in contact with ALA 286 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231U TYR* 4.6 12.0 - - + +
241U MET* 5.9 1.6 - - + -
250U GLY 4.4 4.9 + - - -
252U THR* 4.1 20.7 + - + +
287U MET* 2.8 37.1 - - + +
284V ASN* 3.3 2.9 + - - +
285V LEU* 1.3 72.5 - - - +
287V MET* 1.4 67.8 + - - +
289V GLU* 3.1 12.7 + - - +
290V VAL* 2.7 18.4 + - - +
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Residues in contact with MET 287 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286U ALA* 3.6 28.7 - - + -
287U MET* 2.9 27.1 - - - +
290U VAL* 3.7 24.7 - - + -
231V TYR 4.8 8.1 - - - +
232V LEU* 4.3 7.4 - - + -
241V MET* 4.9 6.1 - - + -
244V PRO* 3.4 21.1 - - + -
252V THR* 4.6 4.0 - - + +
284V ASN* 2.7 38.7 + - + +
286V ALA* 1.4 65.2 - - - +
288V LYS* 1.3 55.9 - - - +
289V GLU 2.7 1.6 + - - -
290V VAL* 2.4 38.9 + - + +
291V ILE* 3.1 33.2 + - + -
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Residues in contact with LYS 288 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242V ARG 4.0 15.3 - - - +
243V GLU* 3.5 35.2 + - - +
244V PRO* 3.2 23.3 + - + +
255V ARG* 6.0 0.4 - - - +
283V PRO* 4.9 11.3 - - - +
284V ASN 3.1 10.2 + - - +
285V LEU* 3.8 21.5 - - + +
287V MET* 1.3 72.4 - - - +
289V GLU* 1.3 58.3 + - - +
291V ILE* 4.3 5.8 - - - -
292V ASP* 2.8 49.8 + - - +
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Residues in contact with GLU 289 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231U TYR* 3.4 41.9 - - + +
235U LYS* 5.4 8.1 + - - -
285V LEU* 3.2 34.3 + - - +
286V ALA* 3.1 9.5 + - - +
287V MET 2.7 5.5 + - - -
288V LYS* 1.3 75.1 - - - +
290V VAL* 1.4 56.6 + - - +
292V ASP* 3.6 4.6 - - + +
293V ALA* 2.9 32.4 + - - +
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Residues in contact with VAL 290 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231U TYR* 4.0 29.6 - - + +
232U LEU* 4.8 1.3 - - + -
287U MET* 3.2 25.4 - - + -
290U VAL* 3.6 28.5 - - + -
231V TYR* 5.9 0.2 - - + -
232V LEU* 4.9 8.5 - - + -
286V ALA* 2.7 20.4 + - + +
287V MET* 2.4 25.7 + - + +
289V GLU* 1.4 65.4 - - - +
291V ILE* 1.3 70.5 + - - +
293V ALA* 3.3 4.0 + - + +
294V PHE* 3.2 21.1 + - + +
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Residues in contact with ILE 291 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232V LEU* 4.0 28.5 - - + +
240V LEU* 4.4 10.8 - - + -
241V MET* 3.4 36.6 - - + +
242V ARG* 5.7 0.4 - - + -
244V PRO* 4.7 2.9 - - + -
287V MET* 3.1 31.8 + - + +
288V LYS* 3.8 9.6 - - - +
290V VAL* 1.3 73.0 - - - +
292V ASP* 1.4 64.4 + - - +
294V PHE* 2.5 35.4 + - + +
295V ILE* 2.8 36.9 + - + -
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Residues in contact with ASP 292 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242V ARG* 5.4 3.8 - - - +
288V LYS* 2.8 43.9 + - - +
289V GLU* 3.1 6.2 + - + +
291V ILE* 1.4 85.3 - - - +
293V ALA* 1.3 56.2 + - - +
295V ILE* 3.4 15.1 + - - +
296V SER* 3.1 31.4 + - - -
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Residues in contact with ALA 293 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231U TYR* 3.4 33.2 - - + +
289V GLU 2.9 16.8 + - - +
290V VAL* 3.3 6.5 - - + +
292V ASP* 1.3 76.0 - - - +
294V PHE* 1.3 59.7 + - + +
296V SER* 3.0 17.7 - - - +
297V GLU* 3.4 9.9 - - - +
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Residues in contact with PHE 294 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229V PRO* 4.4 26.0 - - + -
232V LEU* 4.0 31.6 - - + -
240V LEU* 4.3 19.7 - - + -
290V VAL* 3.4 12.6 - - + +
291V ILE* 2.5 17.1 + - - +
293V ALA* 1.3 75.6 - - + +
295V ILE* 1.4 65.1 + - - +
296V SER 3.2 1.3 - - - -
297V GLU* 2.8 28.4 - - - +
298V ASN* 3.4 36.3 + - + +
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Residues in contact with ILE 295 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240V LEU* 4.2 19.5 - - + -
242V ARG* 5.1 18.2 - - + -
291V ILE* 2.8 32.9 + - + +
292V ASP* 3.6 19.7 - - - +
294V PHE* 1.4 79.4 - - + +
296V SER* 1.3 64.5 + - - +
297V GLU 2.8 7.1 + - - -
298V ASN 4.3 2.3 - - - +
299V GLY 3.8 11.8 + - - -
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Residues in contact with SER 296 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292V ASP 3.1 15.2 + - - -
293V ALA* 3.0 13.6 - - - +
295V ILE* 1.3 78.3 - - - +
297V GLU* 1.3 68.7 + - - +
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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