Contacts of the helix formed by residues 203 - 215 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ALA 4.1 1.0 + - - -
202B TRP* 1.3 74.5 - - - +
204B VAL* 1.3 59.1 + - - +
205B PRO* 3.4 10.9 - - - +
206B ASP* 3.2 34.1 + - - +
207B SER* 2.8 29.2 + - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B SER* 1.3 71.9 - - - +
205B PRO* 1.3 73.8 - - + +
207B SER* 3.0 8.1 + - - -
208B VAL* 2.9 28.9 + - + +
226B CYS* 4.0 12.3 - - + -
227B VAL 5.3 1.3 - - - +
231B GLY* 3.6 26.9 - - - -
234B GLN* 4.0 26.2 - - + -
235B VAL* 4.1 10.8 - - + -
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Residues in contact with PRO 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B SER* 3.4 13.7 - - - +
204B VAL* 1.3 95.7 - - + +
206B ASP* 1.3 62.1 + - - +
208B VAL* 3.4 7.3 + - + +
209B ARG* 3.1 30.9 + - - +
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Residues in contact with ASP 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B CYS* 3.9 27.6 - - + +
202B TRP* 4.6 2.0 - - - -
203B SER* 3.2 27.7 + - - +
205B PRO* 1.3 79.7 - - - +
207B SER* 1.3 60.3 + - - +
209B ARG* 3.8 22.8 + - - +
210B ALA* 3.0 31.4 + - - +
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B TRP* 3.3 25.5 - - - +
203B SER 2.8 22.9 + - - -
204B VAL* 3.0 6.5 + - - -
206B ASP* 1.3 77.9 - - - +
208B VAL* 1.3 57.9 + - - +
210B ALA* 4.2 0.2 - - - +
211B GLY* 2.8 27.9 + - - -
222B LEU* 4.9 1.6 - - - +
225B PRO* 3.5 24.4 + - - +
226B CYS* 3.7 3.1 - - - +
235B VAL* 3.7 24.2 - - - +
239B VAL* 4.1 3.5 - - - +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B VAL* 2.9 29.7 + - + +
205B PRO* 3.7 9.4 - - + +
207B SER* 1.3 74.8 - - - +
209B ARG* 1.3 60.6 + - + +
212B ILE* 2.9 55.0 + - + +
234B GLN* 4.7 2.5 - - + +
235B VAL* 4.4 16.8 - - - -
238B LYS* 4.1 30.3 - - + +
239B VAL* 4.0 7.5 - - + +
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205B PRO* 3.1 22.6 + - - +
206B ASP* 3.8 21.5 + - - +
208B VAL* 1.3 79.8 - - + +
210B ALA* 1.3 62.2 + - - +
212B ILE* 3.5 10.0 + - + +
213B ALA* 3.2 21.0 + - - +
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Residues in contact with ALA 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B CYS* 4.5 11.2 - - + -
179B VAL* 3.9 24.0 - - + -
202B TRP* 3.8 25.6 - - + -
206B ASP 3.0 18.1 + - - +
209B ARG* 1.3 73.2 - - - +
211B GLY* 1.3 62.0 + - - +
213B ALA* 2.9 6.8 + - - +
214B LEU* 2.8 33.7 + - - +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B TRP* 5.1 0.8 - - - -
207B SER 2.8 24.1 + - - -
208B VAL 3.9 0.2 - - - -
210B ALA* 1.3 73.7 - - - +
212B ILE* 1.3 61.5 + - - +
214B LEU* 3.0 12.4 + - - +
215B GLU* 3.1 12.0 + - - +
222B LEU* 4.4 8.7 - - - -
239B VAL* 3.8 20.9 - - - -
241B ILE* 3.2 14.9 - - - +
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B VAL* 2.9 45.5 + - + +
209B ARG* 3.7 8.7 - - + +
211B GLY* 1.3 75.7 - - - +
213B ALA* 1.3 64.4 + - - +
214B LEU 3.3 0.5 + - - -
215B GLU* 3.3 36.1 + - - +
216B GLU 4.7 0.9 + - - -
238B LYS* 5.2 9.2 - - + +
239B VAL* 4.3 5.1 - - + +
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Residues in contact with ALA 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B VAL* 4.2 14.4 - - + -
183B ARG* 3.5 34.9 + - - +
209B ARG 3.2 10.1 + - - +
210B ALA* 2.9 11.5 + - - +
212B ILE* 1.3 82.1 - - - +
214B LEU* 1.3 62.0 + - - +
215B GLU 3.4 0.4 + - - -
216B GLU* 3.8 14.2 - - - +
217B LEU* 5.0 0.5 - - - +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B VAL* 4.1 24.2 - - + -
182B LEU* 3.5 35.7 - - + -
196B VAL* 4.4 9.0 - - + -
202B TRP* 4.4 14.6 - - + -
210B ALA 2.8 23.2 + - - +
211B GLY* 3.0 10.0 + - - +
213B ALA* 1.3 76.7 - - - +
215B GLU* 1.3 64.1 + - - +
216B GLU 3.1 3.1 - - - -
217B LEU* 3.0 39.2 + - + +
218B ASP 4.0 2.4 + - - -
219B LEU* 4.2 17.2 + - + +
222B LEU* 4.7 4.9 - - + -
241B ILE* 3.8 11.9 - - + +
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Residues in contact with GLU 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B GLY 3.1 14.2 + - - +
212B ILE* 3.3 28.0 + - - +
214B LEU* 1.3 77.2 - - - +
216B GLU* 1.3 61.4 + - - +
217B LEU 3.1 1.4 + - - -
218B ASP* 3.2 13.9 + - - +
238B LYS 4.1 2.8 - - - +
239B VAL* 3.7 6.4 - - - -
240B ARG* 2.8 66.5 + - + +
241B ILE* 3.9 20.6 - - + -
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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