Contacts of the helix formed by residues 235 - 247 (chain C) in PDB entry 2V10
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 SER 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234C GLY* 1.3 75.3 - - - +
236C THR* 1.3 59.9 + - - +
237C SER* 2.9 11.4 + - - -
238C SER* 2.8 32.0 + - - -
239C ILE* 2.8 23.6 + - - +
303C MET 4.0 3.5 + - - -
304C ASP* 3.4 15.0 - - - +
311C PRO* 5.5 11.4 - - - -
312C THR 4.9 5.6 + - - +
313C TRP* 5.2 1.8 - - - +
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Residues in contact with THR 236 (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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235C SER* 1.3 74.3 - - - +
237C SER* 1.3 66.4 + - - +
239C ILE* 3.8 0.6 - - - +
240C GLU* 2.8 51.1 + - - +
255C TYR* 5.2 1.0 + - - +
302C ALA* 3.9 22.4 - - + +
304C ASP* 2.6 31.1 + - - -
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Residues in contact with SER 237 (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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235C SER* 2.9 8.6 + - - -
236C THR* 1.3 90.1 + - - +
238C SER* 1.3 61.2 - - - +
240C GLU* 3.8 11.5 - - - +
241C LYS* 3.9 9.7 + - - +
304C ASP* 5.3 0.3 + - - -
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Residues in contact with SER 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C LEU* 2.8 42.2 - - - +
235C SER* 2.8 19.1 + - - -
237C SER* 1.3 74.0 - - - +
239C ILE* 1.4 68.1 + - - +
241C LYS* 3.2 2.6 - - - +
242C LEU* 3.0 11.3 + - - +
313C TRP* 4.1 22.3 + - - -
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Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C GLY* 3.4 11.0 - - - +
235C SER 2.8 19.8 + - - +
236C THR 4.2 0.4 - - - +
238C SER* 1.4 75.0 - - - +
240C GLU* 1.3 57.5 - - - +
242C LEU* 3.0 14.3 + - + +
243C MET* 2.6 43.4 + - + +
255C TYR* 3.6 24.0 - - + +
300C ILE* 3.9 20.9 - - + -
301C HIS* 2.8 28.7 - - - +
302C ALA* 3.6 22.4 - - + -
313C TRP* 4.0 20.9 - - + -
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Residues in contact with GLU 240 (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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236C THR* 2.8 37.1 + - - +
237C SER* 3.8 9.8 - - - +
239C ILE* 1.3 76.9 - - - +
241C LYS* 1.3 57.3 + - - +
243C MET* 3.4 5.4 + - - +
244C GLU* 3.0 35.3 + - - +
250C LYS* 5.0 6.8 - - - +
255C TYR* 3.6 27.0 + - - +
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Residues in contact with LYS 241 (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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215C LEU* 2.3 46.9 + - + +
216C LEU* 3.7 20.6 - - + -
218C GLU* 4.2 7.6 + - - -
237C SER 4.1 7.0 - - - +
238C SER* 3.2 12.9 + - - +
239C ILE 3.0 0.2 - - - -
240C GLU* 1.3 76.8 - - - +
242C LEU* 1.3 68.0 + - - +
243C MET 3.1 0.9 - - - -
244C GLU* 3.0 33.9 - - - +
245C ALA* 3.1 8.0 + - - +
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Residues in contact with LEU 242 (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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208C VAL* 4.4 11.2 - - + -
210C VAL* 3.6 27.6 - - + -
215C LEU* 5.7 0.4 - - - -
216C LEU* 4.0 14.3 - - + +
238C SER 3.0 9.2 + - - +
239C ILE* 3.1 20.6 - - + +
241C LYS* 1.3 78.8 - - - +
243C MET* 1.3 70.5 + - + +
245C ALA* 3.0 22.1 + - - +
246C LEU* 3.0 36.4 + - + -
268C ILE* 4.2 16.2 - - + -
270C PHE* 6.2 0.9 - - + -
300C ILE* 5.1 7.2 - - + -
313C TRP* 4.7 12.8 - - + -
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Residues in contact with MET 243 (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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239C ILE* 2.6 25.7 + - + +
240C GLU 3.4 6.7 - - - +
242C LEU* 1.3 79.7 - - + +
244C GLU* 1.3 55.2 + - - +
246C LEU* 3.6 20.5 + - + -
247C GLY 2.8 23.4 + - - -
248C ALA* 3.2 19.9 + - - +
255C TYR* 3.4 59.0 - - + -
298C LEU* 3.9 20.4 - - + -
300C ILE* 3.9 39.5 - - + +
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Residues in contact with GLU 244 (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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240C GLU* 3.0 22.2 + - - +
241C LYS* 3.0 26.6 + - - +
243C MET* 1.3 73.3 - - - +
245C ALA* 1.3 73.8 + - - +
247C GLY* 3.2 9.9 + - - -
248C ALA 5.3 2.0 - - - -
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Residues in contact with ALA 245 (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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210C VAL* 4.1 16.2 - - + -
215C LEU* 3.9 24.2 - - + -
241C LYS 3.1 6.6 + - - +
242C LEU* 3.0 13.8 + - - +
244C GLU* 1.3 87.1 - - - +
246C LEU* 1.4 56.8 - - - +
247C GLY* 2.6 10.2 + - - -
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Residues in contact with LEU 246 (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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210C VAL* 4.1 8.9 - - + +
242C LEU* 3.0 32.5 + - + +
243C MET* 3.7 25.4 - - + +
245C ALA* 1.4 77.7 - - - +
247C GLY* 1.3 61.0 + - - +
248C ALA* 4.5 4.3 - - + +
257C VAL* 5.0 2.2 - - + +
265C LEU* 4.7 22.3 - - + +
266C PRO* 3.9 21.3 - - + -
268C ILE* 3.8 18.2 - - + -
284C TYR* 3.7 24.5 - - + +
298C LEU* 4.0 15.9 - - + -
300C ILE* 4.9 2.2 - - + -
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Residues in contact with GLY 247 (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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243C MET 2.8 10.7 + - - -
244C GLU* 3.5 8.5 - - - -
245C ALA 2.6 12.1 + - - -
246C LEU* 1.3 78.5 - - - +
248C ALA* 1.4 56.0 - - - -
249C LYS* 3.6 18.6 + - - +
257C VAL* 4.0 8.9 - - - +
261C GLU* 4.5 2.1 - - - +
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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