Contacts of the helix formed by residues 285 - 303 (chain B) in PDB entry 2QA5
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 GLN 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B TYR* 2.8 28.5 + - - +
214B PRO* 3.9 19.9 - - + +
282B THR 4.8 2.4 + - - +
283B HIS* 4.3 12.6 - - + -
284B MSE 1.3 77.6 - - - +
286B ASP* 1.3 54.2 + - - +
287B LEU* 2.9 7.2 - - - +
288B GLN* 3.3 36.4 + - - +
289B GLU* 3.4 27.2 + - - +
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Residues in contact with ASP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 3.9 17.3 - - + -
147B HIS* 3.9 12.4 - - - +
148B CYS* 3.5 25.7 - - - +
176B ASN* 3.6 7.9 + - - +
178B VAL* 5.6 2.1 - - - +
211B TYR* 3.5 29.5 + - - -
279B MSE 5.7 2.4 - - - +
280B LEU* 5.5 2.5 - - - +
283B HIS* 2.8 26.8 - - - +
284B MSE 3.1 0.2 - - - -
285B GLN* 1.3 80.4 - - - +
287B LEU* 1.3 64.3 + - - +
288B GLN 3.2 0.2 - - - -
289B GLU* 3.8 6.5 - - - -
290B VAL* 3.1 27.7 + - - +
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PHE* 6.4 2.2 - - + -
37B GLU* 4.4 15.0 - - + +
38B PHE* 4.0 13.0 - - + -
143B ASP* 5.7 2.7 - - - +
147B HIS* 3.2 40.9 + - + +
284B MSE 3.4 21.9 + - + +
285B GLN* 4.5 0.9 - - - -
286B ASP* 1.3 79.4 - - - +
288B GLN* 1.3 60.2 + - + +
290B VAL* 4.0 3.8 - - - +
291B THR* 3.0 32.3 + - - +
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN* 3.3 28.8 + - - +
286B ASP 3.2 0.2 - - - -
287B LEU* 1.3 76.8 - - + +
289B GLU* 1.3 59.9 + - - +
290B VAL 3.2 1.8 - - - -
291B THR* 4.0 8.1 - - + -
292B GLN* 2.8 60.2 + - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ASN* 3.7 23.7 - - - +
211B TYR* 3.9 13.7 - - + -
212B HIS* 4.8 9.4 - - - +
214B PRO* 6.0 1.9 - - + +
285B GLN* 3.4 28.5 + - - +
286B ASP* 3.5 4.2 + - - +
288B GLN* 1.3 77.2 - - - +
290B VAL* 1.3 57.5 + - - +
292B GLN* 4.3 6.4 - - - +
293B ASP* 3.1 51.3 + - - +
294B LEU* 4.4 1.2 - - - +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 5.0 5.1 - - + -
145B ARG* 4.6 13.0 - - + +
146B VAL 3.4 17.3 - - - +
147B HIS* 3.1 50.9 - - + +
175B VAL* 4.0 7.2 - - + -
176B ASN* 3.1 16.8 - - - +
286B ASP 3.1 10.6 + - - +
287B LEU 4.0 1.6 - - - +
289B GLU* 1.3 76.3 - - - +
291B THR* 1.3 72.1 + - - +
294B LEU* 3.4 19.9 + - + +
295B HIS* 3.2 20.1 + - - +
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ASP* 5.1 1.4 + - - -
145B ARG* 3.3 31.5 + - - +
147B HIS* 5.7 2.3 - - - -
287B LEU* 3.0 22.2 + - - +
288B GLN* 3.1 7.1 + - + +
290B VAL* 1.3 83.3 - - - +
292B GLN* 1.3 81.0 + - + +
295B HIS* 3.3 20.4 - - - +
296B TYR* 3.8 3.1 + - - +
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Residues in contact with GLN 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B GLN* 2.8 51.6 + - - +
289B GLU* 4.1 5.2 + - - +
291B THR* 1.3 81.9 - - + +
293B ASP* 1.3 61.1 + - + +
296B TYR* 3.1 27.7 - - - +
297B GLU* 5.3 0.5 - - - +
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 5.3 2.6 - - - +
289B GLU* 3.1 31.3 + - - +
292B GLN* 1.3 79.9 - - + +
294B LEU* 1.3 76.3 + - + +
296B TYR 4.5 0.2 - - - -
297B GLU* 3.2 41.9 - - - +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 4.4 19.9 - - + -
172B HIS 4.1 5.2 - - - +
173B ASN* 3.3 45.4 - - + +
175B VAL* 3.6 21.3 - - - +
176B ASN* 3.2 27.1 - - - +
289B GLU* 4.4 2.9 - - - +
290B VAL* 3.4 25.2 + - + +
293B ASP* 1.3 92.5 - - + +
295B HIS* 1.3 63.7 + - - +
296B TYR 3.5 0.2 - - - -
297B GLU* 3.6 4.5 + - - +
298B ASN* 3.3 18.0 + - - +
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Residues in contact with HIS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 3.9 40.6 + - + +
129B TYR* 3.5 29.6 - + - -
130B LEU* 4.2 14.6 - - + -
133B GLU* 4.1 7.9 + - - -
145B ARG* 3.2 35.4 + - - +
290B VAL 3.2 10.1 + - - +
291B THR 3.3 13.7 - - - +
294B LEU* 1.3 71.7 - - - +
296B TYR* 1.3 67.8 + - + +
297B GLU 3.2 1.6 - - - -
298B ASN* 3.3 3.8 + - - +
299B PHE* 2.8 33.7 + - + +
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B THR 3.8 4.6 + - - +
292B GLN* 3.1 24.3 + - - +
294B LEU 3.5 0.4 - - - -
295B HIS* 1.3 81.5 - - + +
297B GLU* 1.3 53.5 + - + +
299B PHE* 2.7 14.9 + - + +
300B ARG* 2.4 54.6 + - + +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ASN* 5.8 1.9 - - - +
292B GLN 5.3 0.4 - - - +
293B ASP* 3.2 33.3 + - - +
294B LEU* 3.6 6.0 + - - +
295B HIS 3.2 0.4 - - - -
296B TYR* 1.3 79.2 - - + +
298B ASN* 1.3 49.6 + - - +
300B ARG* 4.2 18.1 - - - +
301B SER* 2.7 36.0 + - - -
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Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 3.5 20.1 + - - +
126B PHE* 3.2 48.4 - - + +
127B GLU* 4.0 2.8 + - - +
130B LEU* 5.0 4.5 - - - +
294B LEU 3.3 7.7 + - - +
295B HIS* 3.3 9.1 + - - +
297B GLU* 1.3 73.4 - - - +
299B PHE* 1.3 59.0 + - - +
301B SER* 4.0 5.2 - - - -
302B GLU* 2.9 49.1 + - - +
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Residues in contact with PHE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 2.7 41.5 - - + -
133B GLU* 4.6 17.7 - - - -
134B SER* 6.3 2.9 - - - -
295B HIS* 2.8 23.3 + - - +
296B TYR* 2.7 23.7 + - + +
298B ASN* 1.3 68.2 + - - +
300B ARG* 1.4 75.3 + - + -
303B ARG* 3.0 39.9 + - + +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B TYR* 2.4 43.1 + - + +
297B GLU* 4.2 17.3 - - - +
299B PHE* 1.4 78.8 - - + +
301B SER* 1.4 57.7 + - - +
303B ARG* 3.9 1.6 - - - +
304B LEU* 2.9 39.5 + - + +
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU 2.7 24.7 + - - -
298B ASN* 3.6 8.1 - - - -
299B PHE 3.1 1.4 - - - -
300B ARG* 1.4 75.2 - - - +
302B GLU* 1.3 63.5 + - - -
304B LEU* 3.4 21.0 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU* 2.7 46.0 - - - +
130B LEU* 4.2 15.1 - - + +
298B ASN* 2.9 34.3 + - - +
299B PHE 4.9 0.2 - - - +
301B SER* 1.3 69.9 - - - +
303B ARG* 1.3 59.3 + - - +
304B LEU 2.8 17.1 + - - -
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Residues in contact with ARG 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LEU* 4.9 6.7 - - + +
299B PHE* 3.0 38.1 + - + +
300B ARG* 4.4 1.8 - - - +
302B GLU* 1.3 74.7 - - - +
304B LEU* 1.3 69.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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