Contacts of the helix formed by residues 209 - 221 (chain B) in PDB entry 1QO0
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 209 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B ILE* 5.8 0.4 - - - +
181B PRO* 4.4 16.8 - - - -
186B LEU* 4.7 4.7 - - - +
205B VAL* 4.7 4.9 - - - -
208B THR* 1.3 77.6 - - - +
210B THR* 1.3 59.1 + - - +
211B ALA 4.5 0.2 - - - +
212B GLU* 3.2 28.2 + - - +
213B LEU* 2.8 32.8 + - - +
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Residues in contact with THR 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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205B VAL* 3.8 21.9 + - + +
206B VAL* 3.7 4.9 - - - -
207B GLY 2.6 35.8 + - - -
208B THR 3.7 0.2 + - - -
209B GLY* 1.3 79.5 - - - +
211B ALA* 1.3 62.9 + - - +
213B LEU* 3.1 2.2 + - - +
214B TYR* 3.1 40.5 + - + -
234B THR* 3.5 25.6 - - - +
238B GLU* 3.5 25.7 - - + +
242B MET* 4.3 1.8 - - + -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B GLY 3.4 1.0 - - - +
210B THR* 1.3 77.4 - - - +
212B GLU* 1.3 69.6 + - - +
214B TYR* 3.3 4.0 + - - +
215B ARG* 3.0 45.9 + - - +
238B GLU* 4.3 4.9 - - - +
241B LYS* 3.9 33.0 - - + +
242B MET* 4.2 19.0 - - + +
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Residues in contact with GLU 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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186B LEU* 4.0 18.8 - - + -
208B THR* 4.5 8.5 - - - +
209B GLY* 3.2 34.5 + - - +
211B ALA* 1.3 79.9 + - - +
213B LEU* 1.3 68.1 + - - +
215B ARG* 3.1 18.6 + - - +
216B ALA* 2.8 26.7 + - - +
241B LYS* 5.8 4.1 + - - -
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Residues in contact with LEU 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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146B ILE* 4.2 27.4 - - + -
177B ILE* 4.5 4.7 - - + -
186B LEU* 4.7 14.5 - - + +
189B ALA* 5.5 1.6 - - + -
190B VAL* 4.0 14.6 - - + -
193B ILE* 4.6 1.6 - - + -
203B SER* 4.4 4.5 - - - +
205B VAL* 3.4 40.4 - - + -
209B GLY 2.8 18.3 + - - +
210B THR* 3.3 5.8 - - - +
212B GLU* 1.3 79.0 - - - +
214B TYR* 1.3 63.2 + - + +
216B ALA* 3.3 3.5 + - - +
217B ILE* 2.9 48.9 + - + +
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Residues in contact with TYR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B SER* 4.6 9.9 - - - -
210B THR* 3.1 34.9 + - + +
211B ALA 3.8 6.3 - - - +
213B LEU* 1.3 82.6 - - + +
215B ARG* 1.3 59.8 + - - +
217B ILE* 3.8 3.0 + - - +
218B ALA* 3.2 24.1 + - - +
226B ARG* 5.7 0.2 - - - -
229B ILE* 3.4 46.8 + - + +
231B SER* 3.3 18.7 - - - -
234B THR* 2.7 33.1 + - + -
239B VAL* 6.2 0.7 - - + -
242B MET* 3.6 26.7 - - + -
246B VAL* 3.5 14.5 - - + +
250B GLN* 3.8 32.0 + - + +
251B VAL 5.0 1.4 + - - -
252B VAL* 5.4 0.5 - - - +
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Residues in contact with ARG 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 ALA* 3.0 35.2 + - - +
212B GLU* 3.1 17.6 + - - +
214B TYR* 1.3 74.7 - - - +
216B ALA* 1.3 59.7 + - - +
218B ALA* 3.0 7.2 + - - +
219B ARG* 2.9 64.7 + - + +
241B LYS* 3.5 23.1 + - - +
242B MET* 3.8 10.9 - - - +
243B GLU* 2.7 45.6 + - - +
246B VAL* 4.0 13.3 - - + +
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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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186B LEU* 5.3 4.0 - - + +
187B GLN* 3.7 23.2 + - - +
190B VAL* 3.6 23.8 - - + -
212B GLU 2.8 20.4 + - - +
213B LEU* 3.8 1.8 - - - +
215B ARG* 1.3 69.0 - - - +
217B ILE* 1.3 66.8 + - - +
218B ALA 3.2 0.2 + - - -
219B ARG* 3.3 10.7 + - - +
220B ARG* 2.8 27.2 + - - +
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Residues in contact with ILE 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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146B ILE* 5.3 0.9 - - + -
190B VAL* 3.7 15.9 - - + -
193B ILE* 4.1 24.0 - - + -
201B VAL* 4.4 13.7 - - + -
213B LEU* 2.9 43.2 + - + +
214B TYR 4.0 4.7 - - - +
216B ALA* 1.3 76.6 - - - +
218B ALA* 1.3 65.8 + - - +
220B ARG* 3.5 1.7 - - - +
221B TYR* 3.2 39.9 + - + +
226B ARG* 4.8 10.8 - - + -
227B PRO* 5.3 2.5 - - + +
229B ILE* 3.5 34.1 - - + -
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Residues in contact with ALA 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 TYR 3.2 13.3 + - - +
215B ARG 3.0 10.7 + - - +
217B ILE* 1.3 82.1 - - - +
219B ARG* 1.3 64.4 + - + +
221B TYR* 3.4 14.7 + - - +
223B ASP* 3.7 13.3 - - - +
226B ARG* 3.3 35.0 + - - +
245B ASP* 6.0 0.2 - - - +
246B VAL* 3.6 19.5 - - + -
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Residues in contact with ARG 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 ARG* 2.9 55.5 + - + +
216B ALA* 4.1 6.7 - - - +
218B ALA* 1.3 69.4 - - + +
220B ARG* 1.3 59.7 + - - +
221B TYR 2.7 18.7 - - - +
223B ASP* 3.4 13.8 - - - +
243B GLU* 5.4 1.0 + - - -
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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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187B GLN* 4.9 11.7 - - - +
190B VAL* 3.5 20.4 - - + +
191B GLU* 2.6 46.0 + - - +
194B TYR* 3.0 58.9 + - + +
195B GLN* 4.5 1.0 + - - -
216B ALA 2.8 19.4 + - - +
217B ILE 3.5 2.9 - - - +
219B ARG* 1.3 78.3 - - - +
221B TYR* 1.3 65.4 + - + +
222B GLY* 3.7 1.0 + - - -
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Residues in contact with TYR 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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190B VAL* 6.1 0.7 - - + -
193B ILE* 3.6 21.6 + - + +
194B TYR* 3.6 43.7 + + + -
197B ARG* 4.3 13.4 - - - -
198B ALA 4.4 2.1 + - - -
217B ILE* 3.2 32.1 + - + +
218B ALA 3.4 5.8 - - - +
219B ARG 2.7 16.9 - - - +
220B ARG* 1.3 82.8 - - + +
222B GLY* 1.3 54.5 + - - +
223B ASP* 2.7 21.3 + - - +
224B GLY 4.6 7.6 - - - +
225B ARG 5.3 0.9 - - - -
226B ARG* 3.9 29.2 - - + -
227B PRO* 3.4 34.0 - - + +
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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