Contacts of the helix formed by residues 372 - 383 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B PRO* 1.3 71.2 - - - +
373B SER* 1.3 66.9 + - - +
375B VAL* 3.8 0.3 - - - +
376B ARG* 2.7 75.1 + - + +
390B THR 4.7 0.3 + - - -
392B LEU* 5.2 5.4 + - + -
405B LEU* 3.3 46.4 + - + -
406B SER* 3.7 33.4 - - - +
407B GLU* 4.0 17.3 - - + +
410B MSE 3.5 22.0 - - + +
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Residues in contact with SER 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B PRO* 3.0 11.1 + - - +
372B TYR* 1.3 85.5 - - - +
374B GLN* 1.3 66.7 + - - +
376B ARG* 3.7 5.4 - - - +
377B ASP* 3.3 27.1 + - - +
387B LEU* 5.6 0.3 - - - +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B LEU* 3.7 23.7 - - + +
371B PRO* 3.0 38.1 + - + +
373B SER* 1.3 79.4 - - - +
375B VAL* 1.3 64.4 + - - +
377B ASP* 3.4 8.1 + - - +
378B MSE 3.2 29.3 + - + +
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 4.0 17.7 - - + -
366B THR* 5.8 0.7 - - - +
370B LEU* 3.9 15.5 - - + +
371B PRO 3.2 14.9 + - - +
372B TYR 3.8 5.2 - - - +
374B GLN* 1.3 74.3 - - - +
376B ARG* 1.3 66.2 - - - +
377B ASP 3.1 1.2 + - - -
378B MSE 3.2 12.0 + - - +
379B VAL* 3.1 28.1 + - + +
392B LEU* 4.8 0.7 - - + -
405B LEU* 4.6 9.0 - - + -
410B MSE 3.8 18.8 - - + -
414B TRP* 4.0 16.8 - - + -
424B LEU* 3.9 28.0 - - + -
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Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 2.7 62.2 + - + +
373B SER* 3.7 7.2 - - - +
375B VAL* 1.3 76.7 - - - +
377B ASP* 1.3 56.0 + - - +
379B VAL 3.6 0.2 + - - -
380B SER* 3.1 30.1 + - - -
387B LEU* 2.7 46.2 + - + +
388B GLU* 4.2 9.3 + - - +
390B THR* 2.8 34.7 + - + +
391B LYS* 4.0 7.5 - - - +
392B LEU* 4.0 19.3 - - + +
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Residues in contact with ASP 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B SER* 3.3 18.7 + - - +
374B GLN* 3.7 9.2 - - - +
375B VAL 3.0 1.2 - - - -
376B ARG* 1.3 78.2 - - - +
378B MSE 1.3 64.0 + - - +
380B SER* 3.6 4.8 + - - -
381B LYS* 3.1 31.1 + - - +
387B LEU* 4.4 21.5 - - - +
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Residues in contact with MSE 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 4.6 6.5 - - + -
364B MSE 3.8 27.7 - - + +
365B LYS 3.2 27.6 - - - +
366B THR* 3.8 23.3 - - - +
370B LEU* 4.5 12.8 - - - -
374B GLN* 3.2 17.0 + - + +
375B VAL* 3.2 12.9 + - - +
377B ASP* 1.3 77.7 - - + +
379B VAL* 1.3 58.9 + - + +
381B LYS* 3.3 12.6 + - - +
382B LYS* 3.0 30.1 + - - +
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU* 3.9 24.2 - - + -
356B VAL* 4.0 19.1 - - + -
364B MSE 4.2 4.3 - - + -
375B VAL* 3.1 20.5 + - + +
376B ARG 3.9 4.3 - - - +
378B MSE 1.3 74.5 - - - +
380B SER* 1.3 65.1 + - - +
382B LYS* 3.3 4.6 + - - +
383B LEU* 3.0 45.9 + - + +
390B THR* 4.0 16.2 - - + -
392B LEU* 4.0 23.6 - - + -
424B LEU* 4.9 0.9 - - + -
426B CYS* 4.8 0.2 - - - -
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B ARG 3.1 19.2 + - - -
377B ASP* 3.7 6.1 - - - -
379B VAL* 1.3 78.3 - - - +
381B LYS* 1.3 55.7 + - - -
383B LEU* 5.1 1.6 - - - -
384B GLU* 2.9 24.1 + - - -
385B LEU* 2.4 37.5 + - - +
386B ARG* 4.3 0.2 - - - -
387B LEU* 3.7 21.9 + - - +
390B THR* 3.4 19.6 + - - +
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Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ASP* 3.1 23.7 + - - +
378B MSE 3.6 10.3 - - - +
379B VAL 3.2 0.2 - - - -
380B SER* 1.3 74.5 - - - +
382B LYS* 1.3 65.5 + - - +
384B GLU* 3.5 16.7 + - - +
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B VAL* 4.0 26.2 - - + -
363B VAL 4.2 12.3 + - - -
364B MSE 4.1 25.7 - - + +
378B MSE 3.0 18.1 + - - +
379B VAL 3.7 4.3 - - - +
381B LYS* 1.3 79.1 - - - +
383B LEU* 1.3 59.3 + - + +
384B GLU* 3.3 6.5 + - - +
298K LEU* 3.7 30.3 - - + +
299K SER* 3.6 13.5 + - - -
301K GLU* 5.4 4.0 + - - +
302K ASP* 2.7 41.2 + - - -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B VAL* 4.3 4.0 - - + -
358B TYR* 3.9 31.5 - - + -
360B TYR* 3.8 41.4 + - + +
362B VAL* 3.9 24.5 - - + -
379B VAL* 3.0 35.8 + - + +
380B SER* 4.5 0.7 - - - +
382B LYS* 1.3 75.5 - - + +
384B GLU* 1.3 68.9 + - - +
385B LEU* 3.4 23.6 + - + +
390B THR* 6.0 0.2 - - + -
426B CYS* 4.0 17.5 - - + -
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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