Contacts of the helix formed by residues 281 - 287 (chain B) in PDB entry 2QU7
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 SER 281 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A TRP* 3.9 6.5 + - - -
76B PRO* 6.1 1.8 - - - -
80B GLU* 5.1 5.2 - - - -
252B HIS* 3.9 24.0 - - - -
280B ASP* 1.3 82.0 - - - +
282B TYR* 1.3 68.3 + - - +
283B TRP* 2.9 27.5 + - - +
284B ASN* 3.0 26.3 + - - +
285B GLU* 4.1 4.2 + - - +
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Residues in contact with TYR 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASN* 3.6 33.8 + - - -
229A ILE* 4.0 21.1 - - + -
256A LEU* 4.0 17.5 - - + +
260A GLN* 3.8 28.2 + - - +
281B SER* 1.3 75.2 + - - +
283B TRP* 1.3 59.2 + - - +
285B GLU* 3.4 36.2 + - - +
286B ILE* 3.8 10.0 + - - +
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Residues in contact with TRP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A HIS* 3.5 37.8 + + - -
255A LEU* 4.6 5.6 - - + -
256A LEU* 3.6 40.4 - - + +
259A LEU* 3.3 34.5 - - + -
283A TRP* 3.2 70.0 - + + -
284A ASN* 4.7 1.1 - - - -
287A TYR* 3.7 23.3 - + - -
291A LEU* 4.0 11.4 - - + -
281B SER* 2.9 9.1 + - - -
282B TYR* 1.3 75.4 - - + +
284B ASN* 1.3 57.0 + - - -
285B GLU 3.3 0.2 - - - -
286B ILE* 3.4 19.0 + - + +
287B TYR* 2.9 30.7 + - - +
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Residues in contact with ASN 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TRP* 3.6 12.8 - - - -
252B HIS* 5.1 1.1 + - - -
255B LEU* 4.3 6.4 - - - +
279B ASP 3.5 8.5 + - - -
280B ASP* 2.7 26.7 + - - +
281B SER* 3.0 26.5 + - - +
283B TRP* 1.3 76.0 - - - +
285B GLU* 1.3 61.2 + - - +
286B ILE 3.5 0.5 + - - -
287B TYR* 3.7 2.9 + - - +
290B LYS* 3.4 5.5 - - - +
291B LEU* 3.0 58.0 + - + +
293B VAL* 3.7 9.7 - - - +
330B ARG* 3.6 17.3 - - - +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A GLN* 5.0 5.2 + - - +
263A LYS* 3.9 2.4 - - - +
281B SER 4.1 2.4 + - - +
282B TYR* 3.4 30.3 + - - +
283B TRP 3.3 0.6 - - - -
284B ASN* 1.3 77.2 - - - +
286B ILE* 1.3 64.3 + - + +
287B TYR 3.5 0.2 - - - -
290B LYS* 3.4 31.4 - - + +
330B ARG* 3.6 37.6 + - - +
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Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU* 3.8 16.4 - - + -
259A LEU* 3.6 27.8 - - + +
260A GLN* 3.8 33.0 - - + +
263A LYS* 3.3 28.3 + - + -
287A TYR* 3.1 29.7 + - + +
282B TYR 3.8 11.2 - - - +
283B TRP* 3.6 34.5 - - + +
285B GLU* 1.3 82.1 - - + +
287B TYR* 1.3 66.9 + - - +
288B THR* 3.7 1.0 + - - -
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Residues in contact with TYR 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LYS* 3.3 8.3 + - - -
283A TRP* 4.0 19.3 - + - -
286A ILE* 3.0 58.7 + - + +
287A TYR* 4.3 13.9 - + - -
288A THR 5.9 0.2 - - - -
259B LEU* 3.9 33.3 + - + +
263B LYS* 4.3 5.8 - - - +
269B ILE* 4.5 7.5 - - + +
283B TRP 2.9 14.8 + - - +
284B ASN 3.9 2.2 - - - +
285B GLU 3.5 1.2 - - - -
286B ILE* 1.3 81.5 - - - +
288B THR* 1.3 78.1 + - - +
289B PRO 3.0 36.2 - - - +
290B LYS* 3.1 7.1 + - - +
291B LEU* 3.7 23.8 - - + -
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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