Contacts of the helix formed by residues 236 - 245 (chain C) in PDB entry 6V3O
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 THR 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234C GLN 5.1 2.5 - - - +
235C PRO* 1.3 75.7 - - - +
237C PRO* 1.3 70.9 - - - +
238C GLN* 3.6 13.0 + - - +
239C ASP* 3.1 33.3 + - - +
240C GLU* 2.9 26.0 + - - +
298C ARG* 4.2 5.4 - - - +
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Residues in contact with PRO 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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236C THR* 1.3 88.3 - - - +
238C GLN* 1.3 61.2 + - - +
240C GLU* 3.4 15.0 + - + +
241C MET* 3.0 28.2 + - - +
289C MET* 4.9 0.5 - - - +
290C GLY* 4.8 10.8 + - - +
298C ARG* 4.1 43.1 - - + +
299C VAL* 4.4 15.5 - - + -
303C VAL* 3.8 23.3 - - + -
307C VAL* 4.3 3.7 - - - +
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Residues in contact with GLN 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C THR* 3.2 12.7 + - - +
237C PRO* 1.3 82.8 - - - +
239C ASP* 1.3 65.5 + - - +
241C MET* 3.2 4.9 + - - +
242C ARG* 3.0 30.9 + - - +
302C GLU* 5.2 0.8 - - - +
303C VAL* 3.8 31.8 - - - +
306C ASP* 3.5 28.1 + - + +
307C VAL* 3.8 22.4 - - + -
310C LEU* 4.2 17.3 - - + -
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Residues in contact with ASP 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C PRO* 4.0 14.9 - - + +
236C THR* 3.1 29.0 + - - +
238C GLN* 1.3 74.8 - - - +
240C GLU* 1.3 66.4 + - - +
242C ARG* 3.0 33.2 + - - +
243C TYR* 2.9 48.8 + - + -
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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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176C ALA* 3.7 29.3 - - + +
177C HIS 4.9 4.0 - - - +
235C PRO* 4.3 21.5 - - + +
236C THR 2.9 15.6 + - - +
237C PRO* 3.5 16.9 - - + +
239C ASP* 1.3 75.2 - - - +
241C MET* 1.3 63.1 + - - +
243C TYR* 3.5 8.1 + - - +
244C GLY* 3.0 17.0 + - - -
289C MET* 3.7 20.7 - - + +
298C ARG* 4.7 5.3 + - - -
758C SER* 4.3 17.7 + - - -
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Residues in contact with MET 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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237C PRO 3.0 14.2 + - - +
238C GLN 3.4 5.2 - - - +
240C GLU* 1.3 76.6 - - - +
242C ARG* 1.3 76.2 + - + +
244C GLY* 3.0 3.3 + - - -
245C MET* 3.0 47.7 + - + +
287C SER* 5.0 2.9 - - - +
289C MET* 4.0 31.8 - - + +
307C VAL* 3.6 32.1 - - + +
310C LEU* 3.6 43.5 - - + -
311C ALA* 5.0 4.5 - - - -
314C MET* 3.9 6.3 - - + +
451C VAL* 6.4 0.9 - - + -
453C LEU* 6.1 0.2 - - + -
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Residues in contact with ARG 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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238C GLN* 3.0 23.8 + - - +
239C ASP* 3.0 32.6 + - - +
241C MET* 1.3 87.5 - - + +
243C TYR* 1.3 77.6 + - + +
245C MET* 3.2 13.2 + - - +
246C SER* 3.3 10.2 + - - -
310C LEU* 4.6 19.2 - - + +
314C MET* 3.7 25.6 - - + +
365D ILE* 5.0 13.7 - - - +
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Residues in contact with TYR 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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181C SER* 4.7 14.4 - - - -
182C ALA* 3.4 43.6 - - + +
183C ARG* 4.4 7.2 - - + -
184C ARG 5.4 0.7 - - - -
231C ARG* 5.2 8.1 - - - -
235C PRO* 4.4 16.3 - - + +
239C ASP* 2.9 44.9 + - + +
240C GLU* 4.0 6.7 - - + +
242C ARG* 1.3 92.8 + - + +
244C GLY* 1.3 59.5 + - - +
246C SER* 2.5 24.3 + - - -
247C TYR* 4.5 1.9 - - - -
1002C SO4 3.6 25.9 + - - -
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Residues in contact with GLY 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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174C PHE* 5.1 9.2 - - - -
182C ALA* 5.8 0.2 - - - -
240C GLU 3.0 15.6 + - - -
241C MET 3.0 4.7 + - - -
243C TYR* 1.3 76.5 - - - +
245C MET* 1.3 67.5 + - - +
246C SER 3.1 2.9 + - - -
247C TYR* 3.9 14.1 + - - +
248C ILE* 4.6 5.0 + - - +
289C MET* 4.0 16.6 - - - -
677C ILE* 5.9 6.3 - - - +
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Residues in contact with MET 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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174C PHE* 5.0 4.5 - - + -
241C MET* 3.0 27.4 + - - +
242C ARG 3.2 8.7 + - - +
244C GLY* 1.3 79.4 - - - +
246C SER* 1.3 63.0 + - - +
247C TYR 3.3 0.9 - - - -
248C ILE* 3.1 29.3 + - + +
249C HIS* 3.0 29.3 + - + -
287C SER* 4.6 3.6 - - - +
289C MET* 4.2 17.3 - - + -
311C ALA* 5.7 3.6 - - - -
314C MET* 3.7 28.5 - - - +
450C LEU* 4.4 15.0 - - + -
451C VAL* 3.8 32.1 - - + -
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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