Contacts of the helix formed by residues 284 - 298 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244U PRO* 2.8 24.4 + - + +
246U ILE* 4.3 19.2 - - + +
252U THR* 3.5 15.8 + - + -
283U PRO* 1.3 73.5 - - - +
285U LEU* 1.3 51.7 + - - +
286U ALA* 3.4 4.7 + - - +
287U MET* 2.5 63.9 + - + +
288U LYS* 2.8 15.7 + - - +
246V ILE* 4.1 4.9 - - + -
252V THR* 4.3 0.5 + - - -
284V ASN* 2.6 43.4 + - - +
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Residues in contact with LEU 285 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283U PRO* 3.2 23.3 + - + +
284U ASN* 1.3 70.2 - - - +
286U ALA* 1.4 56.2 - - - +
288U LYS* 2.7 35.9 + - + +
289U GLU* 3.1 21.6 + - - +
249V SER 4.1 6.3 - - - +
250V GLY* 2.8 39.4 + - - +
251V ILE* 4.6 10.8 - - + -
252V THR 5.4 0.2 - - - +
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Residues in contact with ALA 286 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284U ASN* 3.5 5.6 - - - +
285U LEU* 1.4 77.2 - - - +
287U MET* 1.3 62.6 + - - +
289U GLU* 3.4 14.6 + - - +
290U VAL* 3.1 27.2 + - - +
231V TYR* 5.1 7.8 - - - +
241V MET* 6.1 0.7 - - + -
252V THR* 2.7 33.8 + - - +
287V MET* 3.6 21.8 - - + -
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Residues in contact with MET 287 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231U TYR 4.8 7.4 - - - +
232U LEU* 5.5 5.2 - - - -
241U MET* 5.7 3.8 - - + -
244U PRO* 3.8 14.4 - - + -
252U THR* 4.6 6.3 - - + -
284U ASN* 2.5 43.9 + - + +
286U ALA* 1.3 76.2 - - - +
288U LYS* 1.3 65.4 + - - +
290U VAL* 3.8 6.6 - - - +
291U ILE* 2.9 32.2 + - + +
286V ALA* 2.8 55.2 - - + +
287V MET* 2.9 26.9 - - - +
290V VAL* 3.2 17.5 - - + -
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Residues in contact with LYS 288 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242U ARG* 5.9 3.2 - - - +
243U GLU* 5.4 5.7 - - + +
244U PRO* 4.0 22.9 - - + -
284U ASN 2.8 9.2 + - - +
285U LEU* 2.7 21.6 + - + +
287U MET* 1.3 82.2 - - - +
289U GLU* 1.4 66.4 + - + +
291U ILE* 3.4 7.7 + - + +
292U ASP* 3.0 56.9 + - - +
295U ILE* 5.5 3.4 - - - +
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Residues in contact with GLU 289 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285U LEU* 3.1 22.5 + - - +
286U ALA* 3.6 9.0 - - - +
288U LYS* 1.4 74.2 - - + +
290U VAL* 1.4 55.2 + - - +
292U ASP* 2.3 38.8 + - - +
293U ALA* 3.3 4.9 + - - +
231V TYR* 2.5 50.5 - - + +
235V LYS* 5.3 4.3 + - - +
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Residues in contact with VAL 290 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232U LEU* 5.0 10.8 - - + -
286U ALA 3.1 22.6 + - - +
287U MET* 3.8 6.7 - - - +
289U GLU* 1.4 75.0 - - - +
291U ILE* 1.3 69.9 + - - +
292U ASP 3.0 0.3 + - - -
293U ALA* 3.0 18.2 - - + +
294U PHE* 3.2 7.7 + - + +
231V TYR* 4.0 33.0 - - + +
287V MET* 3.7 31.0 - - + -
290V VAL* 3.6 33.0 - - + -
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Residues in contact with ILE 291 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232U LEU* 3.6 31.2 - - + +
240U LEU* 4.6 11.4 - - + -
241U MET* 3.3 46.9 - - + +
242U ARG* 5.7 0.7 - - - -
244U PRO* 3.7 24.9 - - + -
287U MET* 2.9 23.7 + - + +
288U LYS* 3.6 7.0 - - + +
290U VAL* 1.3 78.3 - - - +
292U ASP* 1.4 57.6 + - - +
294U PHE* 3.3 4.9 + - + +
295U ILE* 2.6 60.3 + - + -
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Residues in contact with ASP 292 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288U LYS* 3.0 52.3 + - - +
289U GLU* 2.3 30.7 + - - +
291U ILE* 1.4 67.1 - - - +
293U ALA* 1.4 51.8 - - - +
295U ILE* 3.2 25.3 + - - +
296U SER* 2.5 39.8 + - - -
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Residues in contact with ALA 293 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289U GLU 3.3 4.0 + - - -
290U VAL* 3.0 12.8 - - + +
292U ASP* 1.4 67.0 - - - +
294U PHE* 1.3 62.2 - - + +
296U SER* 2.8 9.6 + - - -
297U GLU* 2.6 45.4 + - - +
231V TYR* 3.0 33.8 - - + +
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Residues in contact with PHE 294 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228U ILE* 4.0 29.2 - - + -
229U PRO* 3.8 23.3 - - + -
232U LEU* 5.1 11.2 - - + -
240U LEU* 4.5 24.2 - - + -
290U VAL* 3.6 8.1 - - + +
291U ILE* 3.3 9.6 - - + +
293U ALA* 1.3 82.4 - - + +
295U ILE* 1.4 66.8 + - - +
297U GLU* 5.1 1.3 + - - -
298U ASN* 2.9 64.6 + - + +
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Residues in contact with ILE 295 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240U LEU* 4.1 24.7 - - + -
242U ARG* 4.6 19.7 - - + -
288U LYS* 5.5 2.7 - - - +
291U ILE* 2.6 31.6 + - + +
292U ASP* 3.2 26.7 + - - +
294U PHE* 1.4 75.7 - - - +
296U SER* 1.4 60.3 + - - +
298U ASN 2.8 22.1 - - - +
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Residues in contact with SER 296 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292U ASP 2.5 27.1 + - - -
293U ALA* 2.8 8.2 + - - -
295U ILE* 1.4 78.2 - - - +
297U GLU* 1.4 67.2 + - - +
298U ASN 3.0 10.9 - - - +
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Residues in contact with GLU 297 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293U ALA* 2.6 31.5 + - - +
294U PHE* 5.1 0.7 + - - -
296U SER* 1.4 78.7 + - - +
298U ASN* 1.3 73.5 + - - +
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Residues in contact with ASN 298 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294U PHE* 2.9 62.8 + - + +
295U ILE 2.8 22.7 - - - +
296U SER 3.0 8.5 - - - +
297U GLU* 1.3 89.3 + - - +
299U GLY 1.3 46.6 + - - +
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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