Contacts of the helix formed by residues 207 - 221 (chain B) in PDB entry 1ORR
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 GLY 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG* 5.5 0.2 - - - -
195B MET 5.3 4.5 - - - -
200B GLN* 4.0 25.1 - - - -
202B ALA* 3.3 5.8 - - - +
206B GLN* 1.3 71.5 - - - +
208B TRP* 1.3 64.6 + - - +
209B VAL 3.3 2.7 - - - -
210B GLY 3.3 1.5 + - - -
211B TRP* 2.8 31.6 + - - +
1300B NAD 5.9 3.1 - - - -
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Residues in contact with TRP 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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194B SER* 2.8 26.6 + - - -
206B GLN 5.0 0.2 - - - -
207B GLY* 1.3 76.2 - - - +
209B VAL* 1.3 75.8 + - + +
211B TRP* 3.2 5.7 + - - +
212B PHE* 3.0 39.3 + + + -
237B ARG* 3.9 15.0 - - + +
239B VAL* 3.6 25.4 - - + -
274B LEU* 4.2 23.3 - - + -
275B SER 4.7 1.3 - - - -
276B LEU* 3.9 24.9 - - + -
279B LEU* 3.3 30.5 - - + -
1301B CDP 3.6 69.1 + - + +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B SER* 5.2 2.5 - - - -
195B MET 5.5 0.7 - - - +
196B TYR* 3.8 39.9 - - + -
207B GLY* 3.3 0.8 - - - -
208B TRP* 1.3 116.2 - - + +
210B GLY* 1.3 62.0 + - - +
212B PHE* 3.3 2.3 + - - +
213B CYS* 2.9 31.9 + - - -
239B VAL* 4.0 15.9 - - + -
274B LEU* 5.5 0.9 - - + -
279B LEU* 4.3 8.7 - - + +
329B VAL* 4.3 20.0 - - + -
332B MET* 4.6 0.9 - - + -
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Residues in contact with GLY 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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200B GLN* 4.2 3.9 - - - +
202B ALA* 3.6 12.9 - - - +
207B GLY 3.3 6.4 + - - -
209B VAL* 1.3 80.3 - - - +
211B TRP* 1.3 63.5 + - - +
213B CYS* 3.2 5.6 + - - +
214B GLN* 2.9 23.2 + - - +
332B MET* 3.5 30.9 - - - +
336B THR* 4.7 2.8 + - - +
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Residues in contact with TRP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ALA* 3.3 9.7 - - + +
203B THR* 3.4 29.8 - - - +
204B TYR* 3.6 35.3 - + + +
207B GLY 2.8 19.5 + - - +
208B TRP* 3.5 5.6 - - - +
209B VAL 3.2 0.2 - - - -
210B GLY* 1.3 76.5 - - - +
212B PHE* 1.3 81.2 + + - +
214B GLN* 3.0 16.1 + - + +
215B LYS* 2.9 62.8 + - + +
227B PHE* 5.2 6.4 - - + +
228B THR 5.1 1.8 + - - -
1301B CDP 3.4 26.9 + - - -
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Residues in contact with PHE 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 TRP* 3.0 41.7 + + + +
211B TRP* 1.3 87.1 - + - +
213B CYS* 1.3 64.8 + - - +
215B LYS* 3.2 7.5 + - + +
216B ALA 3.0 17.2 + - - -
227B PHE* 3.8 22.0 - + - -
228B THR 3.8 15.7 - - - -
229B ILE* 4.0 12.6 - - + -
276B LEU* 4.2 14.4 - - + -
279B LEU* 3.9 12.8 - - + -
280B PHE* 3.7 27.6 - + + -
283B LEU* 3.6 4.2 - - + +
291B MET* 3.5 10.6 - - + +
1301B CDP 3.5 42.4 - + - -
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Residues in contact with CYS 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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209B VAL* 2.9 25.0 + - - -
210B GLY* 3.5 9.2 - - - +
212B PHE* 1.3 77.7 - - - +
214B GLN* 1.3 63.9 + - - +
216B ALA* 3.0 4.2 + - - +
217B VAL* 3.0 26.5 + - - +
279B LEU* 5.3 0.2 - - - -
283B LEU* 4.0 28.3 - - - -
329B VAL* 4.3 10.3 - - - -
332B MET* 3.7 26.7 - - - -
333B TYR* 4.1 10.6 - - - -
336B THR* 3.8 19.5 - - - +
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Residues in contact with GLN 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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202B ALA* 6.0 2.0 - - + +
210B GLY 2.9 12.9 + - - +
211B TRP* 3.2 20.4 - - + +
213B CYS* 1.3 78.4 - - - +
215B LYS* 1.3 69.8 + - - +
217B VAL* 3.2 8.4 + - - +
218B GLU* 3.0 60.8 + - - +
225B LYS* 5.2 0.2 - - - +
336B THR* 3.2 27.6 - - + +
339B ILE* 5.6 5.2 - - - +
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Residues in contact with LYS 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 TRP* 2.9 59.6 + - + +
212B PHE* 3.2 21.3 + - + +
214B GLN* 1.3 82.1 - - - +
216B ALA* 1.3 62.2 + - - +
218B GLU* 3.0 30.8 + - - +
219B ILE* 3.1 28.0 + - - +
225B LYS* 4.2 19.2 + - - +
227B PHE* 3.7 47.3 - - + +
291B MET* 4.1 7.2 - - + -
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Residues in contact with ALA 216 (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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212B PHE 3.0 12.0 + - - +
213B CYS 3.0 8.2 + - - +
215B LYS* 1.3 74.3 - - - +
217B VAL* 1.3 59.7 + - - +
219B ILE* 3.3 1.4 + - - -
220B LYS* 2.7 31.0 + - - +
283B LEU* 4.1 23.8 - - + -
287B CYS* 4.3 0.7 - - - -
289B ILE* 3.7 25.6 - - + +
291B MET* 4.1 5.8 - - - +
333B TYR* 4.0 14.8 - - + -
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Residues in contact with VAL 217 (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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213B CYS 3.0 18.1 + - - +
214B GLN* 3.2 14.1 + - - +
216B ALA* 1.3 74.7 - - - +
218B GLU* 1.3 60.7 + - + +
220B LYS* 3.1 0.9 + - - +
221B ASN* 2.7 50.9 + - + +
223B ILE* 5.6 0.9 - - + -
333B TYR* 3.5 30.3 - - + +
336B THR* 3.7 23.6 - - + +
337B SER* 3.9 25.8 - - - +
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Residues in contact with GLU 218 (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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214B GLN* 3.0 43.3 + - - +
215B LYS* 3.0 33.9 + - - +
217B VAL* 1.3 77.6 - - + +
219B ILE* 1.3 57.7 + - + +
221B ASN 3.0 1.6 + - - -
223B ILE* 2.6 66.6 + - + +
225B LYS* 2.9 42.4 + - - +
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Residues in contact with ILE 219 (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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215B LYS 3.1 18.6 + - - +
216B ALA* 3.7 5.2 - - - +
218B GLU* 1.3 76.3 - - + +
220B LYS* 1.3 66.4 + - - +
222B GLY* 2.8 15.9 + - - -
223B ILE 3.5 13.5 - - - +
227B PHE* 4.3 14.8 - - + -
289B ILE* 4.0 23.2 - - + +
290B ASP 4.0 13.7 - - - +
291B MET* 3.6 33.4 - - + -
292B ARG* 4.6 12.1 - - - +
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Residues in contact with LYS 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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216B ALA 2.7 19.1 + - - +
217B VAL 3.1 5.4 - - - +
219B ILE* 1.3 79.3 - - - +
221B ASN* 1.3 67.3 + - - +
222B GLY* 3.0 5.5 + - - -
287B CYS* 2.7 37.2 + - - +
288B ASN* 4.5 9.5 + - - +
289B ILE* 3.9 13.9 - - + -
333B TYR* 3.2 23.3 - - - +
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Residues in contact with ASN 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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217B VAL* 2.7 40.8 + - + +
218B GLU 3.0 0.4 + - - -
220B LYS* 1.3 88.6 - - - +
222B GLY* 1.3 54.8 + - - +
223B ILE* 3.0 34.6 + - + +
333B TYR* 4.7 1.0 + - - -
337B SER* 5.7 2.2 - - - -
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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