Contacts of the helix formed by residues 286 - 296 (chain A) in PDB entry 7A62
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 286 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284A GLY* 3.5 3.4 - - - -
285A GLY* 1.3 84.6 - - - +
287A HIS* 1.3 68.4 + - - -
288A ALA 3.1 5.2 + - - -
289A ALA* 3.4 4.6 + - - +
290A GLN* 3.2 17.2 + - - +
401B LYS* 5.2 9.0 - - - +
402B GLU* 5.8 1.0 - - - +
403B GLY* 3.5 28.5 - - - -
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Residues in contact with HIS 287 (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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286A GLY* 1.3 72.1 - - - -
288A ALA* 1.3 56.9 + - - +
290A GLN* 4.0 15.2 - - - +
291A PHE* 3.1 27.7 + - - +
387A PHE* 4.7 3.3 - - + -
402B GLU* 5.0 3.4 - - - -
403B GLY* 3.0 35.9 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLN* 5.5 2.7 - - - +
286A GLY 3.1 1.4 - - - -
287A HIS* 1.3 76.9 - - - +
289A ALA* 1.3 65.4 + - - +
291A PHE* 3.3 1.9 + - - +
292A LEU* 2.9 32.8 + - + +
387A PHE* 3.8 24.9 - - + -
390A THR* 4.2 24.2 - - + -
391A VAL* 4.5 7.4 - - + -
403B GLY* 4.4 2.7 + - - +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLN 3.3 26.5 + - - +
282A THR* 3.7 18.9 - - - +
283A ALA 3.9 6.7 - - - +
284A GLY 3.8 20.4 - - - +
286A GLY* 3.4 7.4 + - - +
288A ALA* 1.3 78.7 - - - +
290A GLN* 1.3 57.2 + - + +
292A LEU* 3.8 1.6 - - - +
293A GLN* 2.8 36.2 + - - +
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Residues in contact with GLN 290 (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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284A GLY 5.6 0.9 - - - +
285A GLY* 4.0 19.0 + - - +
286A GLY 3.2 14.8 + - - +
287A HIS* 4.2 15.5 - - - +
289A ALA* 1.3 78.3 - - + +
291A PHE* 1.3 58.7 + - - +
293A GLN* 3.9 5.9 - - - +
294A ASP* 2.8 32.4 + - - +
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Residues in contact with PHE 291 (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 ALA* 6.2 0.9 - - + -
263A SER* 5.4 0.4 - - - -
265A GLY* 5.2 1.3 - - - -
287A HIS 3.1 21.3 + - - +
288A ALA 3.8 2.2 - - - +
290A GLN* 1.3 75.9 - - - +
292A LEU* 1.3 65.9 + - + +
294A ASP* 3.2 8.2 + - - +
295A MET* 3.0 62.2 + - + +
387A PHE* 3.4 34.5 - + + -
502A HEM 3.6 43.5 - - + -
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Residues in contact with LEU 292 (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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265A GLY 5.9 0.4 - - - +
271A GLN* 3.0 43.7 + - + +
274A ASP* 5.4 1.6 - - - +
281A GLN* 3.6 33.7 - - + +
282A THR* 5.1 6.3 - - - +
288A ALA* 2.9 25.3 + - + +
289A ALA* 3.9 3.1 - - - +
291A PHE* 1.3 79.5 - - + +
293A GLN* 1.3 62.4 + - - +
295A MET* 3.2 12.6 + - + +
296A ARG* 3.6 2.9 + - - +
343A ARG* 5.6 0.4 - - - +
387A PHE* 4.1 18.8 - - + -
391A VAL* 4.0 20.4 - - + -
502A HEM 4.2 26.5 - - + +
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Residues in contact with GLN 293 (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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282A THR* 3.5 41.8 + - + +
284A GLY 5.5 1.2 - - - +
289A ALA* 2.8 18.6 + - - +
290A GLN* 3.9 5.1 - - - +
292A LEU* 1.3 74.2 - - - +
294A ASP* 1.3 65.3 + - - +
296A ARG* 3.3 26.4 + - - +
297A ARG* 4.1 4.5 + - - +
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Residues in contact with ASP 294 (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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238A LYS* 3.7 20.0 + - - +
260A ALA* 5.3 1.2 - - - +
290A GLN 2.8 18.8 + - - +
291A PHE* 3.6 9.8 - - - +
293A GLN* 1.3 78.6 - - - +
295A MET* 1.3 74.8 + - + +
297A ARG* 2.8 58.6 + - - +
298A TYR* 3.5 8.2 + - - -
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Residues in contact with MET 295 (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 ALA* 4.2 15.7 - - + -
261A GLY 5.9 0.2 - - - +
263A SER* 4.3 7.4 - - - -
265A GLY 3.7 18.6 - - - +
266A GLN* 3.7 29.0 - - - +
271A GLN* 4.5 7.0 - - - +
291A PHE* 3.0 54.0 + - + +
292A LEU* 3.6 11.7 - - + +
293A GLN 3.2 1.2 - - - -
294A ASP* 1.3 88.1 - - - +
296A ARG* 1.3 62.3 + - - +
298A TYR* 2.9 39.8 + - + +
299A MET* 3.6 13.1 - - + +
502A HEM 6.2 0.2 - - + -
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Residues in contact with ARG 296 (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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271A GLN* 2.6 31.4 + - - +
275A VAL* 3.7 26.7 - - - +
282A THR* 3.6 22.6 + - - +
292A LEU 3.9 4.2 + - - +
293A GLN* 3.7 18.9 - - - +
294A ASP 3.2 1.4 - - - -
295A MET* 1.3 77.1 - - - +
297A ARG* 1.3 63.1 + - - +
298A TYR 3.0 0.9 + - - -
299A MET* 3.1 27.5 + - + +
304A ARG* 3.1 35.4 - - + +
307A LEU* 3.9 27.6 - - - +
308A CYS* 4.3 13.6 - - - -
311A GLU* 3.2 22.4 + - - -
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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