Contacts of the helix formed by residues 230 - 239 (chain B) in PDB entry 1QAS
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 VAL 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229B SER* 1.3 70.6 - - - +
231B GLU* 1.3 71.6 + - + +
233B LEU* 3.4 5.0 + - - +
234B VAL* 3.0 34.2 + - + +
248B PRO* 4.0 25.4 - - + +
251B ALA* 3.8 20.3 - - + +
252B LEU* 3.5 28.3 - - + -
255B ILE* 3.7 13.4 - - + +
268B ARG* 3.0 35.3 + - + +
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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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229B SER* 2.9 16.8 + - - +
230B VAL* 1.3 97.2 + - + +
232B ARG* 1.3 60.6 + - + +
234B VAL* 3.6 14.1 + - - +
235B THR* 3.2 15.8 + - - -
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Residues in contact with ARG 232 (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 GLU 4.7 8.5 + - - -
221B ALA* 3.3 34.2 + - - +
222B ALA 4.1 17.7 + - - +
223B GLY* 4.8 3.2 - - - +
228B LEU* 4.2 8.3 - - + +
229B SER* 2.8 33.3 + - - +
231B GLU* 1.3 71.6 - - + +
233B LEU* 1.3 65.9 + - - +
235B THR* 3.1 35.1 + - - +
236B PHE* 3.2 11.8 + - - +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 4.4 23.0 - - + +
229B SER 2.9 14.8 + - - +
230B VAL* 3.8 5.4 - - - +
232B ARG* 1.3 72.2 - - - +
234B VAL* 1.3 60.0 + - - +
235B THR 3.0 2.0 - - - -
236B PHE* 3.0 29.2 + - + +
237B LEU* 2.8 50.7 + - + +
251B ALA* 4.0 27.1 - - + +
254B LEU* 4.7 5.6 - - + -
255B ILE* 4.3 11.4 - - + -
270B MET* 4.0 28.9 - - + -
275B PHE* 5.3 1.1 - - + -
278B TYR* 5.5 3.4 - - + -
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Residues in contact with VAL 234 (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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230B VAL* 3.0 24.5 + - + +
231B GLU* 3.7 9.6 - - - +
232B ARG 3.3 0.2 - - - -
233B LEU* 1.3 76.6 - - - +
235B THR* 1.3 59.9 + - - +
237B LEU* 3.9 9.3 - - - +
238B GLN* 2.9 44.5 + - - +
245B GLU* 5.1 2.9 - - + +
247B GLY* 3.4 40.4 - - - +
248B PRO* 3.9 10.1 - - + -
251B ALA* 3.6 9.4 - - + -
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Residues in contact with THR 235 (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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231B GLU 3.2 13.9 + - - -
232B ARG* 3.1 28.9 + - - +
233B LEU 3.0 0.4 - - - -
234B VAL* 1.3 79.0 - - - +
236B PHE* 1.3 57.0 + - - +
238B GLN* 3.5 14.2 + - + +
239B HIS* 2.7 49.7 + - + +
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Residues in contact with PHE 236 (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 ALA 4.9 2.9 - - - -
221B ALA* 4.0 24.9 - - + -
228B LEU* 5.5 0.4 - - + -
232B ARG 3.2 10.8 + - - +
233B LEU* 3.0 30.5 + - + +
235B THR* 1.3 74.7 - - - +
237B LEU* 1.3 63.5 + - + +
240B GLN* 2.6 62.0 + - + -
241B GLN* 3.0 38.5 + - + -
275B PHE* 3.8 33.4 - + - -
278B TYR* 4.1 12.6 - + - -
279B LEU* 4.7 4.5 - - + -
730B TYR* 4.0 17.5 - + - -
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Residues in contact with LEU 237 (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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233B LEU* 2.8 46.5 + - + +
234B VAL* 3.9 6.7 - - - +
235B THR 3.4 0.2 - - - -
236B PHE* 1.3 76.5 - - + +
238B GLN* 1.3 56.5 + - - +
241B GLN* 3.3 11.9 - - + +
242B ARG 3.1 6.6 + - - -
243B GLU* 2.8 37.9 + - + +
245B GLU* 4.0 13.2 - - + -
247B GLY 4.8 2.0 - - - +
250B LEU* 4.0 14.1 - - + -
251B ALA* 3.9 27.6 - - + +
254B LEU* 4.1 12.8 - - + -
278B TYR* 3.8 23.1 - - + +
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Residues in contact with GLN 238 (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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234B VAL* 2.9 41.9 - - - +
235B THR* 3.5 15.3 + - - +
237B LEU* 1.3 76.3 - - - +
239B HIS* 1.3 68.6 + - + +
242B ARG* 2.9 31.3 + - - -
243B GLU 4.1 13.0 - - - +
245B GLU* 4.5 7.5 - - + +
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Residues in contact with HIS 239 (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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235B THR* 2.7 35.2 + - + +
238B GLN* 1.3 75.2 - - + +
240B GLN* 1.3 91.2 + - + +
242B ARG* 2.7 44.9 + - - +
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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