Contacts of the helix formed by residues 300 - 309 (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 ASP 300 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264J THR* 5.5 0.9 - - - +
265J PRO 5.2 1.3 - - - +
266J LEU* 3.6 26.9 - - + +
267J LEU* 2.9 30.5 + - - +
268J LYS 4.5 1.0 + - - -
299J SER* 1.3 74.2 - - - +
301J GLU* 1.3 61.6 + - - +
303J VAL* 3.2 11.7 + - - +
304J ALA* 3.1 21.5 + - - +
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Residues in contact with GLU 301 (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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364A MSE 5.8 2.4 - - - +
365A LYS* 4.1 40.1 + - + +
382A LYS* 5.7 2.3 + - - +
299J SER* 3.2 9.0 + - - +
300J ASP* 1.3 77.3 - - - +
302J ASP* 1.3 67.5 + - - +
304J ALA* 3.3 9.3 + - + +
305J LEU* 3.1 21.0 + - - +
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Residues in contact with ASP 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A VAL* 5.7 0.3 - - - +
363A VAL 3.8 14.0 - - - +
364A MSE 5.5 0.5 - - - -
382A LYS* 2.7 40.0 + - - -
287J TYR* 4.3 5.1 - - + +
295J VAL* 6.3 1.3 - - - -
296J ARG 3.9 6.5 - - - +
297J LEU* 3.6 22.4 - - + +
298J LEU* 2.9 22.6 + - - +
299J SER* 3.2 13.9 + - - +
301J GLU* 1.3 76.8 - - - +
303J VAL* 1.3 66.2 + - - +
305J LEU* 3.2 11.4 + - - +
306J MSE 3.0 18.2 + - - -
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Residues in contact with VAL 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J THR* 4.5 2.7 - - + -
265J PRO* 3.2 40.4 - - + +
267J LEU* 4.1 33.9 - - + +
270J LEU* 4.1 8.7 - - + -
297J LEU* 3.8 16.2 - - + -
299J SER 3.3 12.1 + - - +
300J ASP* 3.2 9.3 + - - +
302J ASP* 1.3 75.7 - - - +
304J ALA* 1.3 57.7 + - - +
306J MSE 3.1 20.1 + - + +
307J VAL* 3.0 25.3 + - - +
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Residues in contact with ALA 304 (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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264J THR* 4.0 22.4 - - + -
300J ASP 3.1 12.7 + - - +
301J GLU* 3.6 12.1 - - + +
302J ASP 3.2 0.4 - - - -
303J VAL* 1.3 72.9 - - - +
305J LEU* 1.3 60.2 + - - +
307J VAL* 3.3 2.6 + - - +
308J ARG* 2.9 30.1 + - - +
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Residues in contact with LEU 305 (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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353A THR* 4.8 11.4 - - + -
363A VAL* 4.0 34.3 - - + +
364A MSE 5.5 0.9 - - - -
365A LYS* 5.2 19.5 - - + -
287J TYR* 4.0 14.1 - - + +
301J GLU 3.1 12.5 + - - +
302J ASP* 3.3 13.7 - - - +
304J ALA* 1.3 74.6 - - - +
306J MSE 1.3 65.8 + - - +
308J ARG* 3.3 15.7 + - + +
309J GLN* 2.9 30.2 + - + +
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Residues in contact with MSE 306 (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* 4.2 11.0 - - + -
287J TYR* 3.7 46.8 - - + -
297J LEU* 4.2 15.0 - - + -
302J ASP 3.0 9.5 + - - +
303J VAL* 3.1 37.9 + - + +
305J LEU* 1.3 75.6 - - - +
307J VAL* 1.3 66.7 + - + +
309J GLN* 3.3 11.8 + - - +
310J ALA* 3.2 19.9 + - - +
322J TRP* 3.4 51.5 - - + +
323J LYS 4.3 8.5 - - - +
324J LEU* 4.5 5.6 - - + -
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Residues in contact with VAL 307 (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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262J SER 5.1 7.2 - - - +
263J SER 4.6 4.5 - - - +
264J THR* 4.2 21.3 - - + +
265J PRO* 4.3 14.8 - - + -
303J VAL 3.0 14.9 + - - +
304J ALA* 3.8 6.5 - - - +
305J LEU 3.2 0.2 - - - -
306J MSE 1.3 83.6 - - + +
308J ARG* 1.3 63.8 + - - +
310J ALA* 3.1 19.5 - - + +
321J PRO* 5.9 1.7 - - + +
322J TRP* 3.6 40.2 - - + +
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Residues in contact with ARG 308 (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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304J ALA 2.9 18.5 + - - +
305J LEU* 3.6 16.7 - - + +
307J VAL* 1.3 78.8 - - - +
309J GLN* 1.3 60.3 + - - +
310J ALA 3.3 3.3 + - - +
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Residues in contact with GLN 309 (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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287J TYR* 3.6 17.1 - - + -
288J ARG 3.0 25.1 + - - -
289J ASP* 3.4 27.3 - - - +
290J ALA* 3.8 9.0 + - + +
305J LEU* 2.9 21.6 + - + +
306J MSE 3.4 17.9 - - + +
308J ARG* 1.3 75.9 - - - +
310J ALA* 1.3 67.7 + - - +
311J ARG* 3.2 29.7 + - - +
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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