Contacts of the helix formed by residues 273 - 280 (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 ASP 273 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B GLU* 4.7 0.3 - - - +
260B PRO* 3.5 21.3 - - + +
261B SER* 5.2 3.1 - - - -
271B THR* 3.2 19.0 + - - +
272B LYS* 1.3 84.5 + - - +
274B GLY* 1.3 56.8 + - - +
276B LEU* 4.1 3.8 - - - +
277B MET* 3.2 38.2 + - + +
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Residues in contact with GLY 274 (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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258B TYR* 3.8 10.1 - - - +
259B GLU* 3.6 12.1 - - - -
260B PRO* 3.6 19.7 - - - +
270B MET* 3.1 24.6 - - - +
271B THR* 3.3 7.3 + - - -
273B ASP* 1.3 77.5 - - - +
275B PHE* 1.3 58.8 + - - +
277B MET* 4.0 2.7 - - - -
278B TYR* 3.3 15.8 + - - +
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Residues in contact with PHE 275 (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 ILE* 4.0 15.5 - - + -
217B ALA* 4.1 12.8 - - + -
218B PHE* 3.3 45.5 - + + -
221B ALA* 5.0 1.8 - - + -
228B LEU* 3.5 26.2 - - + -
233B LEU* 5.3 0.7 - - + -
236B PHE* 3.8 42.2 - + - -
270B MET* 3.8 11.9 - - - -
271B THR 3.2 18.5 + - - +
272B LYS 3.5 5.6 - - - +
273B ASP 3.2 0.4 - - - -
274B GLY* 1.3 77.7 - - - +
276B LEU* 1.3 63.4 + - - +
278B TYR* 3.7 6.7 + + - +
279B LEU* 3.2 47.8 + - + +
730B TYR* 6.1 0.2 - + - -
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Residues in contact with LEU 276 (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 THR* 4.9 17.7 - - + +
211B ARG* 3.4 35.4 - - + +
214B ILE* 3.7 30.7 - - + -
272B LYS* 3.0 17.0 + - + +
273B ASP* 4.1 4.3 - - - +
275B PHE* 1.3 76.1 - - - +
277B MET* 1.3 54.9 + - + +
279B LEU* 2.9 9.4 + - - +
280B LEU* 2.8 50.6 + - + +
732B HIS* 4.2 3.4 - - + -
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Residues in contact with MET 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TYR* 3.5 33.1 - - + +
260B PRO* 4.0 23.1 - - + -
273B ASP* 3.2 25.2 + - + +
274B GLY* 4.1 1.8 - - - -
276B LEU* 1.3 80.0 - - + +
278B TYR* 1.3 60.9 + - - +
280B LEU* 3.3 7.9 + - + +
281B SER* 3.0 25.1 + - - -
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Residues in contact with TYR 278 (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* 5.5 2.9 - - + -
236B PHE* 4.1 15.0 - + - -
237B LEU* 3.8 13.6 - - + +
241B GLN* 3.3 28.6 + - - +
243B GLU* 4.4 3.5 + - - -
254B LEU* 3.7 28.0 - - + -
258B TYR* 3.5 21.0 - + + +
270B MET* 4.1 11.7 - - + -
274B GLY 3.3 19.1 + - - +
275B PHE* 3.8 13.0 - + - +
276B LEU 3.3 0.4 - - - -
277B MET* 1.3 78.3 - - - +
279B LEU* 1.3 81.3 + - + +
281B SER* 2.7 18.6 + - - -
283B ASP* 3.7 31.0 - - + -
284B GLY* 3.1 8.9 + - - -
731B ARG* 3.9 10.7 + - - -
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Residues in contact with LEU 279 (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 ILE* 4.3 17.5 - - + -
217B ALA* 5.7 0.2 - - + -
236B PHE* 4.7 3.4 - - + -
241B GLN* 3.9 11.0 - - - +
275B PHE* 3.2 48.5 + - + +
276B LEU* 2.9 8.8 + - - +
278B TYR* 1.3 95.7 - - + +
280B LEU* 1.3 56.5 + - - +
281B SER 3.3 0.2 - - - -
284B GLY* 3.2 24.8 - - - +
730B TYR* 3.3 38.4 - - + +
732B HIS* 3.0 27.0 + - + +
749B PHE* 4.4 9.2 - - + -
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Residues in contact with LEU 280 (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 ARG* 4.2 7.4 - - - +
276B LEU* 2.8 41.4 + - + +
277B MET* 3.3 7.4 + - + +
279B LEU* 1.3 74.1 - - - +
281B SER* 1.3 61.6 + - - +
639B GLN* 5.3 1.3 - - + -
732B HIS* 3.2 38.4 - - + +
734B HIS* 3.0 25.9 + - - +
747B THR* 4.3 15.5 - - + +
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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