Contacts of the helix formed by residues 278 - 286 (chain A) in PDB entry 6B0Z
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 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG* 4.0 17.0 - - - +
130A ILE* 3.9 12.8 - - - +
132A HIS* 4.2 2.3 - - - -
277A GLN* 1.3 75.3 - - - +
279A ASP* 1.3 63.8 + - - +
281A VAL* 3.1 15.7 + - - +
282A ALA 3.2 9.5 + - - -
291A MET* 4.0 8.1 - - - +
502A C81 3.3 42.2 + - - +
504A C81 3.2 21.8 + - - -
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Residues in contact with ASP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.7 25.9 + - - +
277A GLN* 3.4 24.9 + - - +
278A SER* 1.3 73.9 - - - +
280A SER* 1.3 63.3 + - - +
282A ALA* 3.5 0.8 + - - -
283A GLN* 3.0 29.3 + - - +
288A LEU* 3.5 21.3 - - + +
291A MET* 3.8 13.1 - - - -
308A ALA* 4.1 12.5 - - + +
501A NDP 5.8 3.1 - - - -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLN* 3.3 16.5 + - - -
278A SER 3.1 0.8 - - - -
279A ASP* 1.3 84.2 + - - +
281A VAL* 1.3 59.4 + - - +
283A GLN* 3.4 11.1 + - - +
284A GLY 3.1 20.8 + - - -
504A C81 5.9 0.2 - - - -
252C ASP* 3.3 41.4 - - - +
255C VAL* 4.1 14.1 - - - -
256C ALA* 3.8 11.4 - - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 4.1 0.4 - - + -
277A GLN 4.6 0.2 - - - +
278A SER* 3.1 8.8 + - - +
280A SER* 1.3 75.4 - - - +
282A ALA* 1.3 59.2 + - - +
284A GLY 3.2 0.9 + - - -
285A TYR* 2.8 28.1 + - + +
502A C81 3.7 28.5 - - + -
504A C81 3.6 62.6 - - + +
255C VAL* 3.9 9.6 - - + -
259C MET* 3.4 26.6 - - + +
502C C81 4.4 3.6 - - - -
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A SER 3.2 5.8 + - - +
279A ASP 3.7 7.2 - - - +
280A SER 3.4 0.2 - - - -
281A VAL* 1.3 76.5 - - - +
283A GLN* 1.3 50.7 + - - +
285A TYR* 3.2 1.6 + - - -
286A GLY 2.7 31.0 + - - -
287A SER* 2.7 40.7 + - - +
288A LEU* 4.0 7.4 - - + +
291A MET* 3.7 32.5 - - + -
502A C81 3.7 5.9 - - + +
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Residues in contact with GLN 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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279A ASP 3.0 17.5 + - - +
280A SER* 3.6 9.6 - - - +
282A ALA* 1.3 78.0 - - - +
284A GLY* 1.3 62.6 + - - +
286A GLY* 3.2 10.4 + - - +
288A LEU* 3.6 30.0 - - + +
501A NDP 4.0 35.7 + - - +
252C ASP 6.1 0.2 - - - -
253C ASP* 5.9 1.6 + - - +
256C ALA* 4.2 17.7 - - + +
260C LYS* 3.5 16.8 + - + -
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Residues in contact with GLY 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 SER 3.1 12.1 + - - -
281A VAL 3.2 2.9 + - - -
283A GLN* 1.3 76.7 - - - +
285A TYR* 1.3 61.1 + - - +
286A GLY 3.4 0.5 + - - -
256C ALA* 3.8 19.2 - - - +
259C MET* 3.7 31.3 - - - +
260C LYS* 3.7 19.6 + - - +
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Residues in contact with TYR 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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118A PRO* 3.1 32.0 + - - +
119A ARG* 3.1 13.7 + - - -
120A LEU* 3.5 34.8 - - + -
281A VAL* 2.8 21.2 + - + +
282A ALA* 3.7 4.5 - - - +
284A GLY* 1.3 72.6 - - - +
286A GLY* 1.3 59.8 + - - +
287A SER* 3.8 14.1 - - - +
379A CYS* 3.6 29.2 + - - +
502A C81 3.5 31.2 - - - -
121C VAL* 5.8 4.0 - - + -
259C MET* 3.5 8.4 - - + +
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Residues in contact with GLY 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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282A ALA 2.7 11.5 + - - -
283A GLN* 3.2 12.6 + - - -
284A GLY 3.2 0.6 + - - -
285A TYR* 1.3 75.7 - - - +
287A SER* 1.3 55.1 + - - -
288A LEU 3.6 2.7 - - - -
375A ASP* 4.1 29.2 - - - +
376A LEU* 6.1 1.0 - - - +
379A CYS* 5.2 5.0 - - - +
501A NDP 6.4 1.6 - - - -
260C LYS* 4.7 8.1 - - - -
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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
------------------------------------------------------------
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