Contacts of the helix formed by residues 203 - 215 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ALA 4.0 0.8 + - - -
202A TRP* 1.3 74.4 - - - +
204A VAL* 1.3 60.8 + - - +
205A PRO* 3.4 10.9 - - - +
206A ASP* 3.0 36.0 + - - +
207A SER* 2.8 29.9 + - - -
226A CYS* 4.4 0.4 - - - -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 1.3 71.7 - - - +
205A PRO* 1.3 73.2 - - + +
207A SER* 3.0 7.8 + - - -
208A VAL* 3.0 29.4 + - + +
226A CYS* 4.2 10.8 - - + -
227A VAL* 5.4 2.5 - - + +
231A GLY* 3.7 29.6 - - - +
234A GLN* 3.9 26.5 - - + -
235A VAL* 4.3 6.3 - - + -
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Residues in contact with PRO 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 3.4 13.7 - - - +
204A VAL* 1.3 96.4 - - + +
206A ASP* 1.3 62.5 + - - +
208A VAL* 3.4 8.5 + - + +
209A ARG* 3.2 30.5 + - - +
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Residues in contact with ASP 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A CYS* 3.7 27.5 - - - +
202A TRP* 4.6 2.2 - - + -
203A SER* 3.0 29.5 + - - +
205A PRO* 1.3 77.1 - - - +
207A SER* 1.3 60.6 + - - +
209A ARG* 4.0 21.9 + - - +
210A ALA* 3.0 32.1 + - - +
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TRP* 3.3 26.1 - - - +
203A SER 2.8 22.9 + - - -
204A VAL* 3.0 6.3 + - - -
206A ASP* 1.3 77.4 - - - +
208A VAL* 1.3 57.7 + - - +
210A ALA* 4.2 0.2 - - - +
211A GLY* 2.8 27.5 + - - -
222A LEU* 4.9 1.7 - - - +
225A PRO* 3.5 23.9 + - - +
226A CYS* 3.8 2.3 - - - +
235A VAL* 3.7 23.8 - - - +
239A VAL* 4.1 4.2 - - - +
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Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL* 3.0 25.5 + - + +
205A PRO* 3.7 9.0 - - + +
207A SER* 1.3 75.6 - - - +
209A ARG* 1.3 61.4 + - + +
211A GLY* 3.8 0.2 - - - -
212A ILE* 2.9 53.0 + - + +
234A GLN 4.8 2.0 - - - +
235A VAL* 4.6 16.4 - - - -
238A LYS* 4.1 29.4 - - + +
239A VAL* 3.9 6.9 - - + +
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Residues in contact with ARG 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A PRO* 3.2 18.0 + - - +
206A ASP* 4.0 21.5 + - - +
208A VAL* 1.3 82.7 - - + +
210A ALA* 1.3 61.7 + - - +
212A ILE* 3.5 8.9 + - + +
213A ALA* 3.2 20.3 + - - +
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A CYS* 4.4 10.3 - - + -
179A VAL* 3.9 22.8 - - + +
202A TRP* 3.8 25.1 - - + -
206A ASP 3.0 18.8 + - - +
207A SER 4.2 0.2 - - - +
209A ARG* 1.3 72.4 - - - +
211A GLY* 1.3 66.9 + - - +
213A ALA* 3.0 6.8 + - - +
214A LEU* 2.9 27.7 + - - +
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A TRP* 5.0 0.4 - - - -
207A SER 2.8 23.2 + - - -
208A VAL 3.8 0.4 - - - -
210A ALA* 1.3 73.4 - - - +
212A ILE* 1.3 62.5 + - - +
214A LEU* 3.0 12.4 + - - +
215A GLU* 3.1 15.8 + - - +
222A LEU* 4.5 8.3 - - - -
239A VAL* 3.8 21.3 - - - -
241A ILE* 3.3 11.1 - - - +
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Residues in contact with ILE 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A VAL* 2.9 43.7 + - + +
209A ARG* 3.7 8.1 - - - +
210A ALA 3.2 0.2 - - - -
211A GLY* 1.3 75.4 - - - +
213A ALA* 1.3 63.9 + - - +
214A LEU 3.3 0.9 + - - -
215A GLU* 3.3 36.2 + - - +
216A GLU* 4.7 0.7 + - - +
238A LYS* 5.0 10.1 - - + +
239A VAL* 4.1 6.7 - - + +
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Residues in contact with ALA 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 4.2 10.3 - - + -
183A ARG* 3.8 26.0 + - - +
209A ARG 3.2 10.3 + - - +
210A ALA* 3.0 11.9 + - - +
212A ILE* 1.3 79.5 - - - +
214A LEU* 1.3 61.6 + - - +
215A GLU 3.4 0.2 - - - -
216A GLU* 3.6 24.9 - - - +
217A LEU* 4.8 1.2 - - - +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.8 25.8 - - + -
182A LEU* 3.5 33.7 - - + -
196A VAL* 4.4 4.5 - - + -
202A TRP* 4.3 20.4 - - + -
210A ALA 2.9 24.4 + - - +
211A GLY* 3.0 8.9 + - - +
213A ALA* 1.3 75.2 - - - +
215A GLU* 1.3 64.0 + - - +
216A GLU 3.1 3.4 - - - -
217A LEU* 2.9 41.2 + - + +
218A ASP 3.9 2.4 + - - -
219A LEU* 4.1 17.5 + - + +
222A LEU* 4.8 3.8 - - + -
241A ILE* 3.9 12.2 - - + +
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Residues in contact with GLU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLY 3.1 17.3 + - - +
212A ILE* 3.3 26.8 + - - +
214A LEU* 1.3 77.7 - - - +
216A GLU* 1.3 60.7 + - - +
217A LEU 3.1 1.4 + - - -
218A ASP* 3.3 13.0 + - - +
238A LYS 4.2 2.8 - - - +
239A VAL* 3.7 5.0 - - - -
240A ARG* 2.7 52.2 + - + +
241A ILE* 4.1 18.8 - - + -
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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