Contacts of the helix formed by residues 281 - 292 (chain J) in PDB entry 6O81
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 CYS 281 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30J VAL 5.9 3.4 - - - +
277J PRO 4.3 4.6 + - - +
278J TYR* 3.9 24.1 - - + +
279J ASP 3.5 1.6 - - - -
280J ALA* 1.3 77.0 - - - +
282J TRP* 1.3 64.8 + - - +
283J ASN 3.4 0.2 - - - -
284J ALA* 3.6 17.4 + - - +
285J CYS* 4.3 4.5 + - - +
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Residues in contact with TRP 282 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J TYR 4.7 2.4 + - - -
279J ASP 4.8 4.9 + - - +
280J ALA* 3.3 1.2 - - - +
281J CYS* 1.3 81.0 - - - +
283J ASN* 1.3 58.6 + - - +
284J ALA 3.3 1.2 + - - -
285J CYS* 4.1 4.2 + - - +
286J ARG* 4.0 15.9 + - - +
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Residues in contact with ASN 283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279J ASP 5.5 0.4 + - - +
280J ALA* 3.7 15.2 + - + +
281J CYS 3.4 0.2 - - - -
282J TRP* 1.3 76.8 - - - +
284J ALA* 1.3 58.4 + - - +
285J CYS 3.6 0.2 - - - -
286J ARG* 4.6 6.5 - - - -
287J GLY* 3.1 24.0 + - - -
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Residues in contact with ALA 284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30J VAL 5.7 4.7 - - - +
109J ILE* 5.4 17.4 - - + +
274J ASN* 5.4 7.0 - - + -
280J ALA 3.6 11.1 + - - +
281J CYS* 3.6 15.7 + - - +
282J TRP 3.3 1.2 - - - -
283J ASN* 1.3 76.3 - - - +
285J CYS* 1.3 62.1 + - - +
287J GLY 3.4 1.2 + - - -
288J ASP* 2.9 31.1 + - - +
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Residues in contact with CYS 285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J GLY* 6.0 1.3 - - - -
32J ASN* 4.6 24.0 - - + +
281J CYS 4.3 4.2 + - - +
282J TRP 4.1 5.6 + - - +
284J ALA* 1.3 76.5 - - - +
286J ARG* 1.3 60.3 + - - +
288J ASP* 3.7 5.0 - - - -
289J ARG* 2.9 33.0 + - - +
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Residues in contact with ARG 286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282J TRP 4.0 15.3 + - - +
283J ASN* 4.5 5.6 - - - +
284J ALA 3.4 0.2 - - - -
285J CYS* 1.3 78.2 - - - +
287J GLY* 1.3 60.8 + - - +
288J ASP 3.4 0.2 - - - -
289J ARG* 4.0 9.4 + - - +
290J TRP* 4.2 12.6 + - - +
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Residues in contact with GLY 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J ILE* 5.3 10.3 - - - +
283J ASN 3.1 19.6 + - - -
284J ALA 3.7 0.9 - - - -
286J ARG* 1.3 79.2 - - - +
288J ASP* 1.3 58.2 + - - +
290J TRP* 4.0 1.8 + - - +
291J GLU* 3.3 29.1 + - - +
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Residues in contact with ASP 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32J ASN* 5.5 7.4 - - + -
38J TYR* 3.7 29.7 + - + +
109J ILE* 5.7 8.3 - - + -
284J ALA 2.9 18.9 + - - +
285J CYS* 4.0 4.9 - - - +
287J GLY* 1.3 74.9 - - - +
289J ARG* 1.3 63.6 + - - +
290J TRP 3.3 2.0 - - - -
291J GLU* 4.2 0.9 - - - -
292J ASP* 3.3 27.7 + - - +
293J LEU 4.9 0.3 + - - -
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Residues in contact with ARG 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285J CYS 2.9 17.3 + - - +
286J ARG* 4.5 7.0 - - - +
287J GLY 3.4 0.6 - - - -
288J ASP* 1.3 76.9 - - - +
290J TRP* 1.3 58.2 + - + +
291J GLU 3.8 0.2 - - - -
292J ASP 5.0 0.4 - - - -
293J LEU* 5.2 7.4 - - - +
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Residues in contact with TRP 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286J ARG 4.2 10.7 + - - +
287J GLY 4.0 3.4 + - - +
289J ARG* 1.3 79.8 - - - +
291J GLU* 1.3 58.6 + - - +
292J ASP 3.8 0.7 - - - -
293J LEU* 4.7 9.1 + - - +
294J SER 5.6 0.3 + - - -
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Residues in contact with GLU 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J ILE* 6.3 2.0 - - + -
111J ASP* 4.6 21.1 - - + -
287J GLY 3.3 19.4 + - - +
288J ASP* 5.2 0.2 - - - -
290J TRP* 1.3 78.9 - - + +
292J ASP* 1.3 60.6 + - - +
293J LEU 3.2 2.6 + - - -
294J SER* 3.8 12.8 + - - -
295J ARG* 4.0 8.5 + - - +
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Residues in contact with ASP 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J TRP* 5.5 5.3 - - + -
38J TYR* 3.7 33.7 - - + +
288J ASP* 3.3 20.8 + - - +
291J GLU* 1.3 76.1 - - - +
293J LEU* 1.3 62.9 + - - +
294J SER 3.4 1.1 - - - -
295J ARG* 3.4 25.4 + - + +
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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