Contacts of the helix formed by residues 203 - 215 (chain C) in PDB entry 2OQH
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 203 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C ALA 4.0 1.4 + - - -
202C TRP* 1.3 74.0 - - - +
204C VAL* 1.3 58.3 - - - +
205C PRO* 3.3 12.3 - - - +
206C ASP* 3.2 34.3 + - - +
207C SER* 2.8 29.4 + - - -
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Residues in contact with VAL 204 (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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203C SER* 1.3 72.5 - - - +
205C PRO* 1.3 73.4 - - + +
207C SER* 3.0 7.3 + - - -
208C VAL* 2.9 29.1 + - + +
226C CYS* 4.0 13.2 - - + +
227C VAL* 5.3 2.7 - - + +
231C GLY* 3.6 29.6 - - - +
234C GLN* 3.8 27.4 - - + -
235C VAL* 4.2 7.0 - - + -
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Residues in contact with PRO 205 (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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203C SER* 3.3 14.1 - - - +
204C VAL* 1.3 96.8 - - + +
206C ASP* 1.3 58.3 + - - +
208C VAL* 3.3 7.2 + - + +
209C ARG* 3.1 34.4 + - - +
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Residues in contact with ASP 206 (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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175C CYS* 3.8 28.1 - - + +
202C TRP* 4.5 2.2 - - + -
203C SER* 3.2 27.0 + - - +
205C PRO* 1.3 79.2 - - - +
207C SER* 1.3 61.0 + - - +
209C ARG* 3.9 25.7 + - - +
210C ALA* 2.9 31.4 + - - +
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Residues in contact with SER 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TRP* 3.3 29.0 + - - +
203C SER 2.8 23.4 + - - -
204C VAL* 3.0 6.3 + - - -
206C ASP* 1.3 74.0 - - - +
208C VAL* 1.3 57.1 + - - +
210C ALA* 4.0 0.2 - - - +
211C GLY* 2.7 32.2 + - - -
222C LEU* 5.0 1.2 - - - +
225C PRO* 3.6 19.1 - - - +
226C CYS* 3.7 4.2 - - - +
235C VAL* 3.7 24.2 - - - +
239C VAL* 4.0 4.2 - - - +
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Residues in contact with VAL 208 (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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204C VAL* 2.9 29.8 + - + +
205C PRO* 3.6 9.2 - - + +
207C SER* 1.3 75.0 - - - +
209C ARG* 1.3 67.0 + - + +
211C GLY* 3.8 0.3 - - - -
212C ILE* 2.9 49.1 + - + +
234C GLN* 4.8 2.2 - - + +
235C VAL* 4.6 12.6 - - - -
238C LYS* 4.1 33.4 - - + +
239C VAL* 3.9 6.9 - - + +
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Residues in contact with ARG 209 (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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205C PRO* 3.1 20.7 + - - +
206C ASP* 3.9 23.3 + - - +
208C VAL* 1.3 78.6 - - + +
210C ALA* 1.3 63.6 + - - +
212C ILE* 3.4 9.8 + - + +
213C ALA* 3.1 21.1 + - - +
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Residues in contact with ALA 210 (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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175C CYS* 4.6 10.1 - - + -
179C VAL* 4.0 19.7 - - + +
202C TRP* 3.6 29.8 - - + -
206C ASP 2.9 19.5 + - - +
207C SER 4.0 0.2 - - - +
209C ARG* 1.3 77.6 - - - +
211C GLY* 1.3 63.9 + - - +
213C ALA* 3.0 7.8 + - - +
214C LEU* 2.9 26.3 + - + +
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Residues in contact with GLY 211 (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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202C TRP* 5.0 0.6 - - - -
207C SER 2.7 23.8 + - - -
208C VAL 3.8 0.7 - - - -
210C ALA* 1.3 72.7 - - - +
212C ILE* 1.3 61.5 + - - +
214C LEU* 2.9 13.3 + - - +
215C GLU* 3.1 15.8 + - - +
222C LEU* 4.5 7.9 - - - -
239C VAL* 3.8 22.2 - - - -
241C ILE* 3.4 10.4 - - - +
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Residues in contact with ILE 212 (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* 2.9 45.1 + - + +
209C ARG* 3.6 8.1 - - + +
210C ALA 3.2 0.2 - - - -
211C GLY* 1.3 74.9 - - - +
213C ALA* 1.3 62.8 + - - +
214C LEU 3.3 0.3 + - - -
215C GLU* 3.4 34.5 + - - +
216C GLU* 4.7 0.7 + - - +
238C LYS* 5.3 9.0 - - + +
239C VAL* 4.2 6.2 - - + +
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Residues in contact with ALA 213 (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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179C VAL* 4.0 14.1 - - + -
183C ARG* 3.7 25.8 + - - +
209C ARG 3.1 9.8 + - - +
210C ALA* 3.0 12.2 + - - +
212C ILE* 1.3 81.1 - - - +
214C LEU* 1.3 60.9 + - - +
215C GLU 3.6 0.2 + - - -
216C GLU* 3.8 23.9 + - - +
217C LEU* 4.9 0.9 - - - +
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Residues in contact with LEU 214 (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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179C VAL* 4.2 21.3 - - + -
182C LEU* 3.4 37.7 - - + -
196C VAL* 4.2 9.6 - - + -
202C TRP* 4.4 13.5 - - + -
210C ALA 2.9 21.2 + - - +
211C GLY* 2.9 10.3 + - - +
213C ALA* 1.3 74.7 - - - +
215C GLU* 1.3 65.4 + - - +
216C GLU 3.1 2.7 - - - -
217C LEU* 3.0 42.3 + - + +
218C ASP 3.9 2.4 + - - -
219C LEU* 4.1 16.5 - - + +
222C LEU* 4.6 6.5 - - + -
241C ILE* 3.7 12.5 - - + +
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Residues in contact with GLU 215 (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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211C GLY 3.1 14.9 + - - +
212C ILE* 3.4 26.6 + - - +
214C LEU* 1.3 76.1 - - - +
216C GLU* 1.3 63.2 + - - +
217C LEU 3.1 1.6 + - - -
218C ASP* 3.1 14.5 + - - +
238C LYS 4.1 2.8 - - - +
239C VAL* 3.7 6.8 - - - +
240C ARG* 2.7 50.9 + - + +
241C ILE* 4.1 18.6 - - + -
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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