Contacts of the helix formed by residues 219 - 231 (chain B) in PDB entry 2OG9
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 ASP 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B GLN 4.2 0.8 + - - -
218B TRP* 1.3 75.2 - - - +
220B ARG* 1.3 64.9 + - - +
221B PRO* 3.0 16.0 - - + +
222B THR* 2.6 45.8 + - - -
223B ALA* 2.9 17.2 + - - +
242B LEU* 3.5 2.7 - - - -
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Residues in contact with ARG 220 (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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219B ASP* 1.3 71.7 - - - +
221B PRO* 1.3 72.2 - - + +
223B ALA* 3.7 1.8 - - - +
224B GLN* 2.9 26.6 + - - +
242B LEU* 3.6 18.0 - - + +
246B ASP* 2.7 42.9 + - - +
248B GLU* 4.0 17.4 + - - +
249B GLY* 3.7 16.2 - - - +
253B LEU* 5.3 0.9 - - - +
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Residues in contact with PRO 221 (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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219B ASP* 3.0 16.8 - - + +
220B ARG* 1.3 95.2 - - + +
222B THR* 1.3 62.1 + - - +
224B GLN* 3.3 8.0 + - + +
225B ARG* 3.1 38.3 + - - +
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Residues in contact with THR 222 (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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218B TRP* 3.6 24.9 - - + +
219B ASP* 2.6 37.5 + - - -
221B PRO* 1.3 69.8 - - - +
223B ALA* 1.3 66.6 + - - +
225B ARG* 3.1 7.4 + - + +
226B MSE 2.9 31.8 + - + +
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Residues in contact with ALA 223 (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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218B TRP* 3.7 27.5 - - + +
219B ASP 2.9 16.2 + - - +
220B ARG 3.7 2.2 - - - +
222B THR* 1.3 76.1 - - - +
224B GLN* 1.3 58.2 + - - +
227B CYS* 2.9 36.2 + - - -
241B PRO* 4.3 2.0 - - + -
242B LEU* 3.6 21.8 - - + -
253B LEU* 4.1 18.8 - - + -
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Residues in contact with GLN 224 (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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220B ARG 2.9 14.0 + - - +
221B PRO* 3.3 13.5 - - + +
223B ALA* 1.3 77.5 - - - +
225B ARG* 1.3 67.4 + - + +
228B ARG* 3.2 24.7 + - - +
252B ALA* 5.5 3.8 - - - +
253B LEU* 3.6 21.0 + - - +
256B GLN* 3.7 18.4 + - - +
257B PHE* 3.4 35.1 - - - -
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Residues in contact with ARG 225 (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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221B PRO* 3.2 22.4 + - - +
222B THR* 3.1 8.6 + - + +
224B GLN* 1.3 80.1 - - + +
226B MSE 1.3 66.4 + - + +
228B ARG* 3.4 8.1 - - - +
229B ILE* 3.1 31.9 + - + +
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Residues in contact with MSE 226 (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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190B GLY* 3.6 38.8 - - - +
193B ASP* 4.2 11.4 - - + +
194B ILE* 4.0 13.0 - - + -
218B TRP* 3.6 45.1 - - + +
222B THR* 2.9 27.7 + - + +
223B ALA 4.0 0.2 - - - +
225B ARG* 1.3 74.4 - - + +
227B CYS* 1.3 67.5 + - - +
229B ILE* 3.2 20.9 + - + +
230B PHE* 3.0 46.3 + - + -
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Residues in contact with CYS 227 (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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218B TRP* 4.7 5.2 - - - -
223B ALA 2.9 25.4 + - - +
226B MSE 1.3 76.9 - - - +
228B ARG* 1.3 63.4 + - - +
230B PHE* 3.2 2.8 + - - +
231B GLU* 3.1 26.2 + - - +
238B ILE* 3.7 40.8 - - + +
241B PRO* 4.8 1.1 - - - -
253B LEU* 4.0 19.1 - - - -
257B PHE* 3.5 29.2 - - + -
261B ILE* 4.5 10.3 - - - -
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Residues in contact with ARG 228 (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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224B GLN* 3.2 16.0 + - - +
225B ARG* 3.4 14.1 - - - +
226B MSE 3.2 0.4 - - - -
227B CYS* 1.3 80.6 - - - +
229B ILE* 1.3 63.9 + - + +
231B GLU* 3.4 22.6 + - - +
232B PRO* 3.8 3.6 - - - +
256B GLN* 2.9 37.0 + - - +
257B PHE* 3.4 28.7 - - - -
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Residues in contact with ILE 229 (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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194B ILE* 3.4 50.5 - - + -
225B ARG* 3.1 18.3 + - + +
226B MSE 3.2 19.2 + - - +
228B ARG* 1.3 79.1 - - + +
230B PHE* 1.3 59.4 + - + +
232B PRO* 3.1 17.9 - - - +
233B PHE* 3.7 11.6 - - + -
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Residues in contact with PHE 230 (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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185B VAL* 4.5 10.8 - - + -
193B ASP* 4.7 3.6 - - + -
194B ILE* 4.6 10.3 - - + -
197B VAL* 3.8 35.9 - - + -
212B VAL* 4.5 9.2 - - + -
218B TRP* 4.0 24.5 - + - -
226B MSE 3.0 45.7 + - + +
227B CYS 3.2 4.2 + - - +
229B ILE* 1.3 76.8 - - + +
231B GLU* 1.3 65.6 + - - +
232B PRO* 3.3 0.4 - - - -
233B PHE* 2.9 42.7 + + - +
234B ASN 3.9 1.7 + - - -
235B LEU* 4.0 24.3 - - + +
238B ILE* 4.1 17.5 - - + -
259B THR* 4.5 4.3 + - - +
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Residues in contact with GLU 231 (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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227B CYS 3.1 18.5 + - - +
228B ARG* 3.4 15.8 + - - +
230B PHE* 1.3 76.3 - - - +
232B PRO* 1.3 71.0 - - + +
233B PHE 3.2 1.2 + - - -
234B ASN* 3.3 17.3 + - - +
256B GLN 5.0 0.7 - - - +
257B PHE* 3.7 23.9 - - + +
258B ASP* 3.1 34.4 + - - +
259B THR* 2.7 46.1 + - - -
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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