Contacts of the helix formed by residues 285 - 293 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263C TRP* 3.7 5.8 - - - +
266C LEU* 3.7 8.5 - - + +
267C MET* 3.5 36.3 - - - +
270C ASN* 3.9 23.3 - - + +
282C ASN* 4.2 4.5 - - + +
283C THR 3.2 5.0 + - - +
284C ILE* 1.3 79.3 - - - +
286C ALA* 1.3 69.5 + - - +
287C GLN* 3.8 7.7 + - - +
288C PHE* 2.7 21.2 + - - +
289C PHE* 3.8 8.4 + - - -
375C PRO* 3.1 27.9 - - + +
377C GLY* 5.8 0.2 - - - -
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C SER* 6.0 2.7 - - - -
263C TRP* 2.9 40.7 + - + +
264C LEU* 4.7 7.6 - - + -
267C MET* 4.7 4.3 - - + -
285C THR* 1.3 71.7 - - - +
287C GLN* 1.3 79.1 + - - +
288C PHE 3.0 1.4 + - - -
289C PHE* 3.3 17.7 + - - -
290C ASP* 3.4 20.0 + - - +
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Residues in contact with GLN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C MET* 3.9 18.8 - - + +
285C THR* 3.2 10.7 - - - +
286C ALA* 1.3 90.1 - - - +
288C PHE* 1.3 62.8 + - - +
290C ASP* 4.0 9.1 + - - +
291C LEU* 3.0 47.8 + - + +
292C TRP* 3.7 3.0 - - - -
375C PRO* 4.4 10.8 - - + -
377C GLY* 5.3 0.7 - - - -
378C ALA 3.4 16.4 - - - +
379C ALA* 3.1 13.9 - - - +
380C VAL 3.1 43.0 + - - +
393C GLY 5.5 0.7 - - - +
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Residues in contact with PHE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ALA* 4.6 0.4 - - + -
283C THR* 3.7 12.3 - - + +
284C ILE* 3.3 31.2 - - + -
285C THR* 2.7 34.9 + - - +
287C GLN* 1.3 74.2 - - - +
289C PHE* 1.3 94.9 + + - +
292C TRP* 3.1 29.8 + + + +
293C ILE* 3.8 17.0 + - + +
360C THR* 4.1 14.4 - - + -
363C SER* 3.7 23.1 - - - -
364C TYR* 4.0 19.7 - - + -
367C MET* 4.1 20.6 - - + -
375C PRO* 4.4 2.8 - - + +
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Residues in contact with PHE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C ALA* 3.7 26.5 - - + -
238C VAL* 3.4 31.4 - - + -
263C TRP* 3.2 58.3 - + - -
284C ILE* 3.8 21.3 - - + -
285C THR 3.9 5.6 - - - -
286C ALA 3.3 11.6 + - - +
288C PHE* 1.3 86.7 - + - +
290C ASP* 1.3 67.9 + - - +
291C LEU 2.9 0.2 + - - -
293C ILE* 2.8 31.1 + - + -
294C TYR* 3.0 32.3 + - + -
360C THR* 4.7 2.5 - - - -
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Residues in contact with ASP 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286C ALA* 3.4 19.9 + - - +
287C GLN* 4.0 10.4 + - - +
289C PHE* 1.3 74.9 - - - +
291C LEU* 1.3 68.5 + - + +
294C TYR* 3.3 35.0 - - - +
295C MET* 4.9 0.2 - - - -
331C ASN* 3.8 9.0 - - - +
380C VAL 4.9 2.5 - - - +
381C THR 4.6 0.5 - - - -
382C TRP* 3.1 42.9 + - - +
1I NAG 2.9 23.7 + - - -
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C GLN* 3.0 39.0 + - + +
290C ASP* 1.3 86.4 - - + +
292C TRP* 1.3 73.5 + - + +
295C MET* 3.5 10.5 - - - +
331C ASN* 5.5 1.3 - - - +
380C VAL* 3.3 35.9 - - + +
381C THR 3.8 16.2 - - - +
382C TRP* 4.9 2.0 - - - -
384C THR* 5.0 3.1 - - - +
386C ILE* 5.0 0.2 - - - +
389C SER* 3.0 26.8 + - - +
393C GLY* 4.1 16.8 - - - -
404C GLN* 2.8 26.5 + - - +
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Residues in contact with TRP 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C GLN 3.7 13.9 - - - -
288C PHE* 3.1 32.3 + + + +
291C LEU* 1.3 90.7 - - + +
293C ILE* 1.3 72.2 + - + +
295C MET* 3.3 19.5 - - - +
359C LEU* 3.9 5.2 - - - +
363C SER* 4.1 9.6 - - - +
367C MET* 5.3 4.3 - - - -
372C VAL* 5.4 0.9 - - + -
373C ALA 4.9 5.2 - - - -
375C PRO* 4.3 22.2 - - + -
389C SER 5.0 0.2 - - - -
390C GLY* 3.5 16.6 - - - -
393C GLY* 3.7 22.0 - - - -
394C SER* 3.2 27.6 - - - -
400C GLY* 3.3 22.1 + - - -
403C LEU* 3.3 31.9 - - + +
404C GLN* 3.4 22.2 - - + +
407C ASN* 3.4 12.2 + - - +
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Residues in contact with ILE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C VAL* 4.4 3.8 - - + -
288C PHE* 3.9 34.3 - - + +
289C PHE* 2.8 14.8 + - + +
292C TRP* 1.3 85.8 - - - +
294C TYR* 1.3 76.7 + - + +
295C MET* 2.6 23.4 + - - +
299C GLY 4.1 7.7 - - - +
300C ALA* 4.4 1.7 - - - +
356C PRO* 4.0 23.3 - - + +
359C LEU* 3.8 25.7 - - - +
360C THR* 3.0 37.2 - - - +
363C SER* 3.9 4.7 - - - +
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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