Contacts of the helix formed by residues 285 - 293 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263D TRP* 3.5 16.0 - - - -
266D LEU 4.0 3.1 - - - +
267D MET* 3.8 27.4 - - - +
270D ASN* 3.9 25.6 - - + +
282D ASN 4.2 2.2 - - - +
283D THR 3.3 5.0 + - - +
284D ILE* 1.3 81.4 - - - +
286D ALA* 1.3 68.7 + - - +
287D GLN* 3.4 17.6 + - - -
288D PHE* 3.5 10.9 + - - +
289D PHE* 3.5 20.6 - - - -
375D PRO* 3.6 19.5 - - + +
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263D TRP* 3.2 23.7 + - + +
264D LEU* 4.7 14.6 - - + -
267D MET* 4.4 2.0 - - + +
285D THR* 1.3 79.7 - - - +
287D GLN* 1.3 76.6 - - - +
288D PHE 2.9 7.2 + - - -
289D PHE* 3.3 17.4 + - - +
290D ASP* 3.6 15.3 + - - +
379D ALA* 5.5 0.2 - - + -
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Residues in contact with GLN 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D MET* 3.0 35.2 - - - +
285D THR* 3.4 13.1 + - - +
286D ALA* 1.3 81.7 - - - +
288D PHE* 1.3 67.7 + - - +
289D PHE 3.2 0.4 - - - -
290D ASP* 3.8 15.7 - - + +
291D LEU* 3.1 37.9 + - + +
292D TRP* 3.1 17.4 - - + -
375D PRO* 4.8 8.9 - - + +
377D GLY 5.1 0.4 - - - -
378D ALA 3.9 15.8 + - - +
379D ALA* 3.3 26.2 - - - +
380D VAL 4.1 8.3 - - - +
393D GLY 5.3 1.8 - - - +
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Residues in contact with PHE 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D THR* 3.9 10.8 - - + +
284D ILE* 3.6 28.9 - - + -
285D THR* 3.5 30.0 + - - +
286D ALA 2.9 1.0 + - - -
287D GLN* 1.3 79.8 - - - +
289D PHE* 1.3 95.7 + + - +
292D TRP* 3.2 33.0 - + + +
293D ILE* 3.3 20.5 - - + +
360D THR* 3.9 19.3 - - + -
363D SER* 4.1 8.3 - - - -
364D TYR* 3.9 28.5 - - - -
367D MET* 3.9 31.0 - - + -
375D PRO* 4.7 2.4 - - - +
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ALA* 3.5 34.1 - - + -
238D VAL* 3.4 34.5 - - + -
263D TRP* 3.4 48.0 - + - -
284D ILE* 4.3 3.4 - - + -
285D THR 3.5 12.6 - - - -
286D ALA 3.4 12.8 - - - +
287D GLN 3.2 0.2 - - - -
288D PHE* 1.3 90.6 - + - +
290D ASP* 1.3 67.8 + - - +
291D LEU 2.9 0.7 + - - -
293D ILE* 2.8 32.2 + - + -
294D TYR* 3.0 33.7 + + + -
360D THR* 5.0 0.2 - - + -
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Residues in contact with ASP 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D ALA* 3.6 15.7 + - - +
287D GLN* 3.8 17.8 + - + +
288D PHE 3.6 0.2 - - - -
289D PHE* 1.3 74.4 - - - +
291D LEU* 1.3 68.5 + - + +
294D TYR* 3.3 35.9 - - - +
295D MET* 4.9 0.5 - - - -
331D ASN* 4.7 4.3 - - - +
380D VAL 5.2 2.0 - - - +
382D TRP* 3.4 39.8 + - + +
1K NAG 2.8 26.2 + - - -
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Residues in contact with LEU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D GLN* 3.1 35.2 + - + +
289D PHE 2.9 2.2 + - - -
290D ASP* 1.3 87.2 - - + +
292D TRP* 1.3 72.9 + - + +
295D MET* 4.6 8.0 - - - +
331D ASN* 5.9 0.4 - - - +
380D VAL* 3.7 21.1 - - + +
381D THR 3.9 21.1 - - - +
382D TRP* 4.7 2.5 - - - +
384D THR* 4.9 1.8 - - - +
386D ILE* 5.2 1.0 - - - +
389D SER* 3.0 40.6 + - - +
393D GLY* 3.8 13.5 - - - -
404D GLN* 2.8 30.3 + - - +
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Residues in contact with TRP 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D GLN 3.1 31.6 - - - -
288D PHE* 3.2 27.7 + + + +
289D PHE 3.0 1.4 + - - -
290D ASP 3.9 0.2 + - - -
291D LEU* 1.3 90.6 - - + +
293D ILE* 1.3 71.1 + - + +
295D MET* 4.0 12.3 - - - +
359D LEU* 3.6 17.8 - - - +
363D SER* 4.2 10.2 + - - +
367D MET* 5.3 7.0 - - + -
372D VAL* 5.7 1.3 - - + -
373D ALA 5.5 3.6 - - - -
374D ARG 5.4 0.7 - - - -
375D PRO* 4.5 15.7 - - + -
390D GLY* 3.7 25.4 - - - -
393D GLY* 4.0 27.1 - - - -
394D SER* 4.3 9.9 - - - -
400D GLY* 3.4 21.5 + - - -
403D LEU* 3.5 32.7 - - + +
404D GLN* 3.7 19.5 - - + +
407D ASN* 3.8 10.3 + - - +
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Residues in contact with ILE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 4.1 10.3 - - + -
288D PHE* 3.3 48.5 - - + +
289D PHE* 2.8 21.2 + - + +
292D TRP* 1.3 79.7 - - + +
294D TYR* 1.3 64.9 + - + +
295D MET* 2.5 23.9 + - - +
299D GLY 4.3 6.8 - - - +
300D ALA* 4.6 2.8 + - - -
356D PRO* 4.1 25.3 - - + +
359D LEU* 4.0 16.6 - - + +
360D THR* 3.7 36.1 - - - +
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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