Contacts of the helix formed by residues 267 - 279 (chain J) in PDB entry 1OEY
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 LEU 267 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265J PRO 4.0 1.0 + - - -
266J LEU* 1.3 70.6 - - - +
268J LYS* 1.3 63.1 + - - +
270J LEU* 3.0 6.5 + - + +
271J LEU* 3.0 35.9 + - + +
285J LEU* 4.1 23.1 - - + -
297J LEU* 4.3 15.5 - - + +
298J LEU* 3.5 37.2 - - - +
299J SER* 3.5 8.5 - - - +
300J ASP* 2.9 17.8 + - - +
303J VAL* 4.1 26.4 - - + +
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Residues in contact with LYS 268 (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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266J LEU* 3.3 7.9 - - + +
267J LEU* 1.3 78.9 - - - +
269J ASP* 1.3 61.3 + - - +
271J LEU* 3.5 15.1 + - + +
272J GLU* 3.1 35.2 + - - +
300J ASP* 4.5 1.2 + - - +
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Residues in contact with ASP 269 (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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265J PRO* 5.1 5.2 - - + -
266J LEU* 3.2 37.9 + - - +
267J LEU 3.2 1.0 - - - -
268J LYS* 1.3 78.2 - - - +
270J LEU* 1.3 61.9 + - - +
272J GLU* 3.3 26.4 - - + +
273J LEU* 3.0 27.2 + - - +
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Residues in contact with LEU 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240J LEU* 4.4 14.1 - - + -
265J PRO* 3.8 31.6 - - + -
266J LEU 3.2 10.7 + - - +
267J LEU* 3.0 8.5 + - - +
269J ASP* 1.3 73.3 - - - +
271J LEU* 1.3 60.8 + - - +
273J LEU* 3.4 11.2 + - + +
274J THR* 2.9 33.6 + - - +
285J LEU* 3.6 15.9 - - + -
297J LEU* 4.7 1.6 - - + -
303J VAL* 4.1 23.3 - - + -
306J MSE 4.2 14.4 - - + -
322J TRP* 4.2 15.3 - - + -
324J LEU* 4.4 16.6 - - + -
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Residues in contact with LEU 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267J LEU* 3.0 32.4 + - + +
268J LYS* 3.7 16.4 - - + +
269J ASP 3.3 0.2 - - - -
270J LEU* 1.3 76.4 - - - +
272J GLU* 1.3 56.7 + - - +
274J THR* 2.8 15.4 + - - -
275J ARG* 3.0 17.8 + - - +
280J ARG 5.4 0.2 - - - +
281J GLU* 5.9 2.6 - - - +
283J ILE* 3.8 31.6 - - + +
285J LEU* 3.9 17.3 - - + +
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Residues in contact with GLU 272 (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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268J LYS* 3.1 23.2 + - + +
269J ASP* 3.3 39.6 - - - +
270J LEU 3.2 0.4 - - - -
271J LEU* 1.3 72.2 - - - +
273J LEU* 1.3 60.4 + - - +
275J ARG* 3.5 12.1 + - - +
276J ARG* 3.0 29.8 + - - +
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Residues in contact with LEU 273 (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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240J LEU* 4.3 21.1 - - + -
242J VAL* 5.0 0.2 - - + -
255J ILE* 4.0 34.3 - - + -
256J ALA 5.2 0.9 - - - +
257J VAL* 4.0 28.0 - - + -
269J ASP 3.0 17.5 + - - +
270J LEU* 3.5 11.4 - - + +
272J GLU* 1.3 78.7 - - - +
274J THR* 1.3 77.9 + - + +
276J ARG* 3.4 5.4 + - - +
277J GLU* 3.1 30.6 + - + +
324J LEU* 4.7 3.4 - - + -
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Residues in contact with THR 274 (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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270J LEU 2.9 16.7 + - - +
271J LEU* 2.8 24.8 + - - -
273J LEU* 1.3 87.4 - - + +
275J ARG* 1.3 56.1 + - - +
277J GLU 3.3 0.2 + - - -
278J PHE* 2.8 40.9 + - - +
280J ARG 4.4 3.0 - - - +
283J ILE* 3.8 17.8 - - - +
285J LEU* 3.7 16.3 - - + +
324J LEU* 4.0 6.1 - - + -
326J ILE* 3.5 32.3 - - + -
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Residues in contact with ARG 275 (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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271J LEU 3.0 16.2 + - - +
272J GLU* 3.8 11.0 + - - +
274J THR* 1.3 76.3 + - - +
276J ARG* 1.3 73.4 + - - +
279J GLN* 2.9 30.5 + - - +
280J ARG 3.7 19.6 + - - +
281J GLU* 3.5 41.6 + - + -
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Residues in contact with ARG 276 (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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272J GLU 3.0 18.7 + - - +
273J LEU* 3.8 7.0 - - - +
274J THR 3.4 0.2 - - - -
275J ARG* 1.3 90.1 - - - +
277J GLU* 1.3 70.4 + - + +
279J GLN* 4.3 9.0 + - - +
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Residues in contact with GLU 277 (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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253J LYS* 2.6 50.0 + - - +
255J ILE* 3.7 37.5 - - + +
273J LEU* 3.1 18.8 + - + +
276J ARG* 1.3 91.1 - - + +
278J PHE* 1.3 80.6 + - + +
279J GLN* 4.8 3.0 - - - +
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Residues in contact with PHE 278 (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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242J VAL* 3.5 25.6 - - + -
244J TYR* 3.6 55.1 + + + -
253J LYS* 3.6 26.5 - - + -
255J ILE* 4.0 13.7 - - + -
274J THR* 2.8 22.6 + - - +
277J GLU* 1.3 78.2 - - + +
279J GLN* 1.3 74.3 + - - +
280J ARG* 3.2 17.6 + - + +
326J ILE* 3.6 28.9 - - + -
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Residues in contact with GLN 279 (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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275J ARG* 2.9 26.2 + - - +
276J ARG 4.3 10.5 + - - +
277J GLU 4.8 2.7 - - - +
278J PHE* 1.3 82.3 - - - +
280J ARG* 1.3 59.6 + - - +
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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