Contacts of the helix formed by residues 372 - 383 (chain A) 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 TYR 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A PRO* 1.3 72.9 - - - +
373A SER* 1.3 61.9 + - - +
375A VAL* 4.4 0.4 - - - -
376A ARG* 2.8 84.8 + - + +
390A THR 4.5 3.8 + - - -
391A LYS* 5.8 0.3 - - - -
392A LEU* 4.8 7.8 + - + +
405A LEU* 3.6 49.1 + - + -
406A SER* 3.5 20.0 - - - +
407A GLU* 3.7 39.4 - - + +
410A MSE 3.6 17.5 - - + +
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Residues in contact with SER 373 (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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371A PRO* 3.3 3.6 - - - +
372A TYR* 1.3 83.3 - - - +
374A GLN* 1.3 76.7 + - - +
376A ARG* 3.7 14.3 + - - +
377A ASP* 3.1 27.5 + - - +
387A LEU* 5.4 1.2 - - - +
407A GLU* 4.6 12.1 + - - +
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Residues in contact with GLN 374 (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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370A LEU* 3.7 28.8 - - + +
371A PRO* 3.1 34.8 + - - +
373A SER* 1.3 86.2 - - - +
375A VAL* 1.3 66.7 + - - +
377A ASP* 3.4 5.9 + - - +
378A MSE 3.0 28.0 + - + +
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Residues in contact with VAL 375 (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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354A LEU* 3.9 16.6 - - + -
366A THR* 5.3 0.2 - - - +
370A LEU* 3.8 28.5 - - + +
371A PRO 3.0 18.2 + - - +
372A TYR 3.2 3.1 + - - +
374A GLN* 1.3 75.2 - - - +
376A ARG* 1.3 66.2 + - - +
378A MSE 3.3 10.0 - - - +
379A VAL* 3.1 20.8 + - + +
392A LEU* 4.4 2.9 - - + -
405A LEU* 4.3 11.0 - - + -
410A MSE 4.1 11.4 - - + -
414A TRP* 4.0 14.6 - - + -
424A LEU* 3.9 27.8 - - + -
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Residues in contact with ARG 376 (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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372A TYR* 2.8 63.9 + - + +
373A SER* 4.0 12.6 + - - +
375A VAL* 1.3 74.6 - - - +
377A ASP* 1.3 56.0 + - - +
379A VAL* 3.3 2.1 + - - +
380A SER* 2.9 30.8 + - - -
387A LEU* 4.0 39.0 + - + +
388A GLU* 5.4 3.6 - - - +
390A THR* 3.6 30.8 + - + +
392A LEU* 4.1 12.1 - - + +
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Residues in contact with ASP 377 (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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373A SER 3.1 20.1 + - - +
374A GLN* 3.7 7.9 - - + +
375A VAL 3.2 0.2 - - - -
376A ARG* 1.3 76.7 - - - +
378A MSE 1.3 58.3 + - - +
380A SER* 3.5 1.9 + - - -
381A LYS* 2.7 66.1 + - - +
387A LEU* 4.0 19.5 - - + +
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Residues in contact with MSE 378 (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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354A LEU* 4.2 13.7 - - + -
364A MSE 3.9 17.7 - - - +
365A LYS 4.2 16.4 - - - +
366A THR* 3.7 23.1 - - - +
367A GLN* 5.7 3.1 - - - +
370A LEU* 3.6 25.4 - - + -
374A GLN* 3.0 14.7 + - + +
375A VAL* 3.3 17.3 - - - +
377A ASP* 1.3 78.2 + - - +
379A VAL* 1.3 57.6 + - - +
381A LYS* 3.5 7.5 + - - +
382A LYS* 3.0 29.8 + - - +
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Residues in contact with VAL 379 (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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354A LEU* 3.8 24.9 - - + -
356A VAL* 3.8 20.6 - - + -
364A MSE 4.5 3.4 - - + -
375A VAL* 3.1 19.6 + - + +
376A ARG 3.8 2.9 - - - +
378A MSE 1.3 74.6 - - - +
380A SER* 1.3 60.0 + - - +
382A LYS* 3.3 4.8 + - - +
383A LEU* 2.9 53.1 + - + +
390A THR* 4.1 9.2 - - + -
392A LEU* 4.0 28.9 - - + -
424A LEU* 4.8 0.9 - - + -
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Residues in contact with SER 380 (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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376A ARG 2.9 17.8 + - - -
377A ASP* 3.6 5.5 + - - -
379A VAL* 1.3 77.4 - - - +
381A LYS* 1.3 58.3 + - - +
384A GLU* 3.0 8.7 + - - -
385A LEU* 2.4 53.9 + - - +
387A LEU* 3.4 23.8 + - - +
390A THR* 3.4 22.3 - - - +
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Residues in contact with LYS 381 (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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377A ASP* 2.7 52.3 + - - +
378A MSE 3.9 6.5 - - - +
380A SER* 1.3 73.2 - - - +
382A LYS* 1.3 68.4 + - - +
384A GLU* 3.2 18.5 + - - +
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Residues in contact with LYS 382 (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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360A TYR* 4.8 0.2 + - - -
362A VAL* 4.1 15.9 - - + -
363A VAL 4.3 11.0 + - - -
364A MSE 4.0 33.6 - - + +
378A MSE 3.0 18.5 + - - +
379A VAL 3.8 3.4 - - - +
381A LYS* 1.3 79.7 - - - +
383A LEU* 1.3 58.3 + - + +
384A GLU* 3.5 5.5 + - - +
298J LEU* 3.7 32.7 - - + +
299J SER* 3.8 12.3 + - - -
301J GLU* 5.7 2.8 + - - +
302J ASP* 2.7 43.3 + - - -
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Residues in contact with LEU 383 (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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356A VAL* 4.4 3.4 - - + -
358A TYR* 3.8 35.8 - - + -
360A TYR* 3.8 40.4 + - + +
362A VAL* 3.9 24.5 - - + -
379A VAL* 2.9 39.7 + - + +
382A LYS* 1.3 75.3 - - + +
384A GLU* 1.3 70.9 + - - +
385A LEU* 3.2 22.0 + - + +
426A CYS* 3.8 15.7 - - + -
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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