Contacts of the helix formed by residues 279 - 283 (chain A) in PDB entry 3QJQ
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 VAL 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A HIS* 3.6 36.1 - - + +
275A LEU* 4.0 14.1 - - + +
276A SER 3.6 9.4 - - - +
277A THR 3.0 3.4 + - - -
278A PRO* 1.3 84.5 - - + +
280A GLY* 1.3 58.9 + - - +
281A PHE 3.3 2.9 - - - -
282A HIS* 3.1 33.1 + - - +
298A HIS* 3.4 8.2 - - - +
301A LEU* 3.6 32.5 - - + +
302A THR* 3.1 24.7 + - + +
305A VAL* 5.3 2.7 - - + -
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Residues in contact with GLY 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A TRP* 3.7 24.1 - - - +
233A HIS* 4.8 2.6 - - - +
234A PRO* 5.9 0.2 - - - +
277A THR 4.4 1.4 + - - -
279A VAL* 1.3 71.7 - - - +
281A PHE* 1.3 52.7 + - - +
282A HIS 2.6 17.6 + - - -
283A HIS* 2.7 30.7 + - - +
284A GLN* 3.5 2.8 + - - +
298A HIS* 3.5 0.8 - - - -
542A TYR* 2.9 23.2 + - - -
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Residues in contact with PHE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A THR* 4.2 7.9 - - + -
279A VAL 4.0 0.2 - - - -
280A GLY* 1.3 72.3 - - - +
282A HIS* 1.3 58.8 + - - +
283A HIS 3.3 1.1 - - - -
284A GLN* 3.6 28.7 - - + +
285A PHE* 3.4 29.9 + - - -
290A ILE* 4.2 21.5 - - + -
294A TRP* 3.6 26.9 - - + -
295A LYS* 4.5 10.7 - - + +
298A HIS* 3.1 47.8 - + + -
541A ALA 4.4 2.5 - - - -
542A TYR* 3.5 25.8 - + - -
545A THR* 3.5 38.6 - - + -
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A HIS* 2.9 25.4 - + + -
279A VAL* 3.1 18.6 + - + +
280A GLY 2.6 6.9 + - - -
281A PHE* 1.3 77.1 - - - +
283A HIS* 1.3 68.5 + + - -
285A PHE* 2.9 38.4 - - + +
298A HIS* 5.4 1.1 - - + +
302A THR* 3.4 23.5 + - + +
372A ASP* 4.6 1.7 - - - +
376A HIS* 5.8 0.2 + - - -
563A CMO 2.8 11.1 + - - -
801A HAS 3.0 45.3 + + + +
803A CU1 2.1 30.2 - - - -
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Residues in contact with HIS 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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225A ARG* 3.9 12.0 + - - -
229A TRP* 3.3 64.9 + + + +
232A GLY 3.8 2.2 - - - -
233A HIS* 3.4 7.8 - - + +
280A GLY* 2.7 23.1 + - - +
282A HIS* 1.3 93.2 + + - +
284A GLN* 1.3 58.5 + - - +
285A PHE 3.5 1.4 + - - -
286A ALA 4.9 0.5 + - - -
287A ASP* 4.5 1.0 - - - +
376A HIS* 4.0 19.3 - - - -
563A CMO 3.7 7.9 - - - -
801A HAS 4.5 26.4 + + + +
803A CU1 2.2 31.0 - - - -
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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
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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