Contacts of the helix formed by residues 285 - 293 (chain B) in PDB entry 3QNQ
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 THR 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B TRP* 3.7 13.0 - - - -
266B LEU 4.2 0.7 - - - -
267B MET* 3.7 31.4 - - - +
270B ASN* 4.0 21.5 - - + +
282B ASN* 4.6 0.7 - - + -
283B THR 3.1 5.7 + - - +
284B ILE* 1.3 79.6 - - - +
286B ALA* 1.3 64.7 + - - +
287B GLN* 3.3 15.2 + - - -
288B PHE* 3.3 12.3 + - - +
289B PHE* 3.3 23.4 - - - -
375B PRO* 3.7 28.0 - - + +
377B GLY* 5.7 0.6 - - - -
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Residues in contact with ALA 286 (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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260B SER* 6.4 1.6 - - - -
263B TRP* 3.2 32.3 + - + +
264B LEU* 4.8 4.9 - - + +
267B MET* 4.9 2.7 - - + -
285B THR* 1.3 76.1 - - - +
287B GLN* 1.3 77.1 + - - +
288B PHE 2.9 9.9 + - - -
289B PHE* 3.4 8.6 + - - -
290B ASP* 3.3 26.9 + - - +
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Residues in contact with GLN 287 (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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267B MET* 3.5 20.9 - - - +
285B THR* 3.3 13.4 + - - +
286B ALA* 1.3 87.2 - - - +
288B PHE* 1.3 66.0 + - - +
290B ASP* 3.8 14.6 + - + +
291B LEU* 3.1 31.4 - - + +
292B TRP* 3.2 12.6 - - + -
375B PRO* 5.2 4.8 - - + +
377B GLY* 4.8 2.3 - - - +
378B ALA 4.0 6.1 - - - +
379B ALA* 3.4 31.6 - - - +
380B VAL* 3.4 32.6 + - + +
393B GLY* 5.8 1.3 - - - +
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Residues in contact with PHE 288 (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 ALA* 4.3 0.2 - - + -
283B THR* 3.6 10.3 - - + +
284B ILE* 3.8 24.0 - - + -
285B THR* 3.3 29.1 + - - +
286B ALA 2.9 1.0 + - - -
287B GLN* 1.3 80.8 - - - +
289B PHE* 1.3 92.3 + + - +
292B TRP* 3.1 35.8 + + + +
293B ILE* 3.5 18.0 - - + +
360B THR* 4.1 16.2 - - + -
363B SER* 3.9 14.1 - - - -
364B TYR* 3.8 24.7 - - + -
367B MET* 3.6 33.7 - - + -
375B PRO* 4.8 1.1 - - - -
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Residues in contact with PHE 289 (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 ALA* 3.6 45.8 - - + -
237B ALA* 5.0 1.1 - - + -
238B VAL* 3.6 21.5 - - + -
263B TRP* 3.6 47.1 - + - -
284B ILE* 4.3 5.4 - - + -
285B THR 3.3 22.9 - - - -
286B ALA 3.7 5.6 - - - +
288B PHE* 1.3 96.6 - + - +
290B ASP* 1.3 63.5 + - - +
291B LEU 2.9 1.7 + - - -
293B ILE* 3.0 15.5 + - + -
294B TYR* 2.9 51.5 + + + -
360B THR* 4.9 0.7 - - - -
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Residues in contact with ASP 290 (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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286B ALA* 3.3 20.8 + - - +
287B GLN* 3.8 14.0 + - + +
288B PHE 3.4 0.2 - - - -
289B PHE* 1.3 79.8 - - - +
291B LEU* 1.3 70.5 + - + +
294B TYR* 3.4 30.5 - - - +
331B ASN* 4.1 7.8 - - - +
380B VAL 4.9 1.9 - - - +
381B THR 4.8 0.2 - - - -
382B TRP* 3.2 36.5 + - - +
1G NAG 2.6 27.3 + - - -
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Residues in contact with LEU 291 (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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287B GLN* 3.1 32.0 + - + +
289B PHE 3.1 0.4 - - - -
290B ASP* 1.3 89.2 - - + +
292B TRP* 1.3 77.3 + - + +
293B ILE 3.7 0.4 - - - -
294B TYR 5.3 0.2 - - - -
295B MET* 3.9 10.6 - - - +
331B ASN* 5.5 1.8 - - - +
380B VAL* 3.2 33.4 - - + +
381B THR 3.9 21.3 - - - +
382B TRP* 4.9 2.0 - - - +
384B THR* 4.8 2.2 - - - +
386B ILE* 5.2 0.3 - - - +
389B SER* 3.3 34.6 + - - +
393B GLY* 4.1 4.3 - - - -
404B GLN* 2.7 30.5 + - - +
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Residues in contact with TRP 292 (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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287B GLN 3.2 30.7 - - - -
288B PHE* 3.1 25.1 + + + +
291B LEU* 1.3 85.5 - - + +
293B ILE* 1.3 67.9 + - + +
295B MET* 4.4 7.4 - - - +
359B LEU* 4.2 2.9 - - - +
363B SER* 3.4 17.4 + - - +
367B MET* 5.1 5.6 - - + -
372B VAL* 5.6 0.9 - - + -
373B ALA 5.6 3.1 - - - -
375B PRO* 4.5 17.9 - - + -
390B GLY* 3.4 26.9 - - - -
393B GLY* 3.8 29.4 - - - -
394B SER* 3.6 11.2 - - - -
400B GLY* 3.1 22.1 + - - -
403B LEU* 3.4 30.3 - - + +
404B GLN* 3.6 21.3 - - + +
407B ASN* 3.3 23.9 + - - +
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Residues in contact with ILE 293 (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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238B VAL* 4.3 2.9 - - + -
288B PHE* 3.5 40.2 - - + +
289B PHE* 3.0 16.8 + - + +
291B LEU 3.7 0.6 - - - -
292B TRP* 1.3 93.8 - - + +
294B TYR* 1.3 76.3 + - + +
295B MET* 2.7 20.4 + - - +
299B GLY 4.0 8.5 - - - +
300B ALA* 4.4 1.2 - - - -
356B PRO* 4.0 26.9 - - + +
359B LEU* 4.0 21.1 - - - +
360B THR* 3.4 30.5 - - - +
363B SER* 4.3 0.2 - - - +
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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