Contacts of the helix formed by residues 272 - 280 (chain A) 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 LYS 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLN* 6.0 3.6 - - - +
214A ILE* 4.3 12.3 - - + +
215A ASP* 2.8 39.0 + - - +
218A PHE* 3.5 47.8 - - + -
219A GLU* 5.6 3.8 - - - -
226A GLU 4.8 1.0 + - - -
271A THR* 1.3 73.6 - - - +
273A ASP* 1.3 65.9 + - - +
275A PHE* 3.5 2.6 - - - +
276A LEU* 3.1 24.0 + - + +
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Residues in contact with ASP 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A PRO* 3.3 26.4 - - + +
261A SER* 5.4 3.3 + - - -
271A THR* 3.7 11.9 + - - +
272A LYS* 1.3 81.0 - - - +
274A GLY* 1.3 53.6 + - - +
276A LEU* 3.1 7.4 + - - +
277A MET* 2.8 43.4 + - + +
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Residues in contact with GLY 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A TYR* 3.3 25.8 - - - +
259A GLU* 3.5 18.1 + - - -
260A PRO* 3.6 3.8 - - - +
270A MET* 3.7 11.5 - - - +
271A THR 3.4 4.0 + - - -
273A ASP* 1.3 79.4 - - - +
275A PHE* 1.3 56.0 + - - +
277A MET* 3.7 0.8 - - - +
278A TYR* 2.9 30.5 + - - +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 3.7 15.9 - - + -
217A ALA* 3.8 15.3 - - + -
218A PHE* 3.3 58.8 - + + -
221A ALA* 4.8 1.3 - - + -
228A LEU* 4.0 15.9 - - + -
236A PHE* 3.4 44.2 - + - -
270A MET* 3.6 11.8 - - - +
271A THR 3.0 18.2 + - - +
272A LYS 3.5 3.8 - - - +
273A ASP 3.1 0.2 - - - -
274A GLY* 1.3 77.9 - - - +
276A LEU* 1.3 57.1 + - - +
278A TYR* 3.5 5.8 + + - -
279A LEU* 3.0 52.9 + - + +
730A TYR* 5.8 0.4 - + - -
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A THR* 3.9 30.7 - - + -
211A ARG* 3.3 32.1 - - + +
214A ILE* 3.4 33.0 - - + -
272A LYS 3.1 14.3 + - - +
273A ASP* 3.6 4.3 - - - +
275A PHE* 1.3 77.8 - - - +
277A MET* 1.3 70.6 + - + +
278A TYR 3.2 0.2 - - - -
279A LEU* 3.7 6.4 - - - -
280A LEU* 3.0 42.2 + - + +
732A HIS* 4.5 1.3 - - + -
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Residues in contact with MET 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A TYR* 3.6 27.8 - - + +
260A PRO* 3.6 34.5 - - + -
273A ASP* 2.8 23.6 + - + +
274A GLY 3.9 0.4 - - - +
276A LEU* 1.3 80.2 - - + +
278A TYR* 1.3 62.5 + - - +
280A LEU* 3.4 6.2 + - - +
281A SER* 3.0 23.8 + - - -
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Residues in contact with TYR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 6.0 1.3 - - + -
236A PHE* 4.1 14.1 - + - -
237A LEU* 3.9 7.7 - - + +
241A GLN* 3.0 30.5 + - - +
243A GLU* 5.3 1.6 + - - +
254A LEU* 3.4 44.2 - - + -
258A TYR* 3.5 21.5 - + + +
270A MET* 4.6 9.2 - - + -
274A GLY 2.9 19.1 + - - +
275A PHE* 3.6 12.8 - + - -
277A MET* 1.3 77.2 - - - +
279A LEU* 1.3 81.1 + - + +
281A SER* 2.6 25.2 + - - -
283A ASP* 3.8 22.0 - - + -
284A GLY* 3.2 11.3 + - - -
731A ARG* 3.7 8.7 + - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 3.9 20.2 - - + -
217A ALA* 5.9 0.2 - - + -
236A PHE* 4.5 4.9 - - + -
241A GLN* 4.0 4.0 - - - +
275A PHE* 3.0 52.6 + - + +
276A LEU* 3.2 6.0 + - - +
278A TYR* 1.3 97.4 - - + +
280A LEU* 1.3 53.6 + - - +
281A SER 3.4 0.2 - - - -
284A GLY* 3.7 15.2 - - - +
730A TYR* 3.4 33.7 - - + +
731A ARG 4.5 0.2 - - - -
732A HIS* 2.6 39.7 + - + +
749A PHE* 4.0 13.9 - - + -
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ARG* 4.2 6.7 - - - +
276A LEU* 3.0 41.2 + - + +
277A MET* 3.8 5.2 - - - +
279A LEU* 1.3 74.8 - - - +
281A SER* 1.3 64.5 + - - +
639A GLN* 5.2 1.8 - - + -
732A HIS* 3.2 41.3 - - + +
734A HIS* 3.1 23.8 + - - +
747A THR* 4.4 13.2 - - + +
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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