Contacts of the helix formed by residues 279 - 293 (chain A) in PDB entry 3QRK
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 GLU 279 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A LEU* 4.2 21.3 - - + +
274A LYS 5.4 1.4 - - - +
277A THR* 3.8 22.2 + - + +
278A MET* 1.3 75.3 - - - +
280A VAL* 1.3 62.1 + - - +
281A GLU 3.1 3.1 + - - -
282A GLU* 3.2 22.9 + - + +
283A PHE 3.7 3.6 + - - -
386A ARG* 3.8 26.2 + - - +
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A LEU* 3.6 29.9 - - + +
276A ASP 4.8 3.8 - - - +
277A THR* 3.7 20.9 + - - +
278A MET* 2.9 11.6 - - + +
279A GLU* 1.3 77.6 - - - +
281A GLU* 1.3 67.2 + - + +
283A PHE* 3.5 2.8 + - - +
284A LEU* 3.2 36.8 + - + +
311A PHE* 3.7 28.9 - - + -
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Residues in contact with GLU 281 (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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278A MET 3.7 13.0 + - - +
279A GLU 3.1 1.0 + - - -
280A VAL* 1.3 84.1 - - + +
282A GLU* 1.3 57.3 + - - +
284A LEU* 3.2 10.5 + - - +
285A LYS* 2.9 54.2 + - + +
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Residues in contact with GLU 282 (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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1A 9DP 2.7 54.9 + - - +
279A GLU* 3.2 17.5 + - + +
281A GLU* 1.3 75.9 - - - +
283A PHE* 1.3 65.9 + - - +
285A LYS* 2.9 26.7 + - - +
286A GLU* 2.8 23.7 + - - +
386A ARG* 5.2 8.5 - - - +
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Residues in contact with PHE 283 (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 LYS* 3.2 41.7 - - + -
272A THR 3.7 8.3 - - - -
273A LEU* 3.5 44.0 - - + -
279A GLU 3.7 2.0 + - - -
280A VAL 3.5 10.3 - - - +
282A GLU* 1.3 77.7 - - - +
284A LEU* 1.3 62.8 + - + +
286A GLU* 3.4 8.8 + - - +
287A ALA* 3.1 25.3 + - + +
304A VAL* 6.2 0.2 - - + -
305A CYS 5.2 0.4 - - - -
306A THR* 5.7 2.9 - - + -
311A PHE* 3.4 43.1 - + + -
312A TYR 3.9 3.6 - - - -
313A ILE* 3.5 31.8 - - + +
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Residues in contact with LEU 284 (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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280A VAL* 3.2 33.6 + - + +
281A GLU* 3.2 10.1 + - - +
282A GLU 3.1 0.6 - - - -
283A PHE* 1.3 78.3 - - + +
285A LYS* 1.3 65.2 + - - +
287A ALA* 4.1 7.8 - - + +
288A ALA* 3.2 23.4 + - - +
306A THR* 4.3 18.4 - - + -
311A PHE* 4.2 24.5 - - + -
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Residues in contact with LYS 285 (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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1A 9DP 4.5 7.0 - - + -
281A GLU* 2.9 43.5 + - + +
282A GLU* 2.9 28.3 + - - +
284A LEU* 1.3 74.3 - - - +
286A GLU* 1.3 66.8 + - - +
288A ALA* 3.0 7.6 + - - +
289A VAL* 2.9 29.4 + - + +
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Residues in contact with GLU 286 (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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1A 9DP 2.7 86.0 + - + +
271A LYS* 2.7 34.0 + - - +
282A GLU 2.8 13.2 + - - +
283A PHE* 3.5 12.1 - - - +
285A LYS* 1.3 73.2 - - - +
287A ALA* 1.3 62.0 + - - +
289A VAL* 3.2 3.5 + - - +
290A MET* 3.0 38.9 + - - +
313A ILE* 3.8 7.4 - - + +
381A ASP 4.0 1.0 - - - +
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Residues in contact with ALA 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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283A PHE* 3.1 16.0 + - + +
284A LEU* 4.2 9.6 - - + +
286A GLU* 1.3 79.7 - - - +
288A ALA* 1.3 62.1 + - - +
290A MET* 3.4 5.7 + - - +
291A LYS* 3.1 35.2 + - - +
301A LEU* 3.9 3.9 - - - +
304A VAL* 4.1 18.4 - - + -
313A ILE* 3.9 20.6 - - + +
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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
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284A LEU 3.2 19.4 + - - +
285A LYS* 3.0 7.7 + - - +
287A ALA* 1.3 73.3 - - - +
289A VAL* 1.3 66.5 + - + +
291A LYS* 3.7 15.1 + - + +
292A GLU* 3.3 25.0 + - - +
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Residues in contact with VAL 289 (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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1A 9DP 3.9 39.7 - - + +
285A LYS* 2.9 20.9 + - + +
286A GLU 3.4 6.5 - - - +
288A ALA* 1.3 76.7 - - + +
290A MET* 1.3 58.7 + - - +
292A GLU* 3.1 30.3 + - - +
293A ILE* 3.6 10.4 + - + +
359A PHE* 3.8 27.1 - - + -
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Residues in contact with MET 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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1A 9DP 3.6 61.7 - - + +
235A TRP* 5.6 0.5 - - - -
286A GLU* 3.0 25.3 + - - +
287A ALA 3.4 4.0 + - - +
288A ALA 3.3 0.4 - - - -
289A VAL* 1.3 74.2 - - + +
291A LYS* 1.3 64.5 + - - +
293A ILE* 3.2 26.7 + - - +
299A VAL* 3.9 17.7 - - + +
301A LEU* 4.0 29.0 + - + +
313A ILE* 4.0 10.1 - - + -
315A THR* 3.6 31.2 - - + -
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Residues in contact with LYS 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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233A ASP* 3.9 21.2 + - - -
235A TRP* 3.3 56.4 - - + +
287A ALA* 3.1 22.6 + - - +
288A ALA* 3.9 14.1 - - - +
289A VAL 3.3 0.2 - - - -
290A MET* 1.3 77.6 - - - +
292A GLU* 1.3 64.0 + - - +
293A ILE 3.6 1.4 + - - +
294A LYS* 5.5 5.7 - - - +
301A LEU* 3.4 18.8 - - + +
304A VAL* 5.0 9.6 - - - +
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Residues in contact with GLU 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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288A ALA* 3.3 17.1 - - - +
289A VAL* 3.1 18.3 + - - +
291A LYS* 1.3 81.9 - - - +
293A ILE* 1.3 58.7 + - - +
294A LYS* 3.8 3.8 + - - +
353A TYR* 3.7 3.3 + - - -
357A LYS* 3.1 31.0 + - - +
359A PHE* 4.3 18.2 - - + -
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Residues in contact with ILE 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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1A 9DP 3.8 21.8 - - + -
289A VAL* 3.7 15.5 - - + +
290A MET* 3.2 18.1 + - - +
291A LYS 4.8 0.6 - - - +
292A GLU* 1.3 74.3 - - - +
294A LYS* 1.3 73.3 + - - +
295A HIS 4.2 0.2 - - - -
298A LEU* 3.5 38.4 - - + -
299A VAL 4.4 13.1 - - - +
300A GLN* 4.8 4.7 - - - +
301A LEU 5.2 0.2 + - - -
353A TYR* 3.9 11.7 - - + -
354A LEU* 3.7 24.5 - - + -
357A LYS* 4.1 9.6 - - + -
359A PHE* 3.8 23.6 - - + -
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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