Contacts of the helix formed by residues 372 - 383 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371C PRO* 1.3 71.8 - - - +
373C SER* 1.3 68.9 + - - +
375C VAL* 3.1 2.8 + - - +
376C ARG* 2.9 52.7 + - + +
390C THR 4.5 10.2 + - - -
391C LYS* 5.8 0.2 - - - -
392C LEU* 4.8 7.6 + - + +
405C LEU* 3.3 37.3 + - + -
406C SER* 3.5 19.5 - - - +
407C GLU* 3.4 51.6 - - + +
410C MSE 3.0 32.0 - - + +
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Residues in contact with SER 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C PRO* 3.3 7.8 - - - +
372C TYR* 1.3 80.8 - - - +
374C GLN* 1.3 69.1 + - - +
376C ARG* 3.1 52.0 - - - +
377C ASP* 3.1 10.4 + - - +
407C GLU* 4.8 8.8 + - - -
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Residues in contact with GLN 374 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370C LEU* 3.5 33.0 - - + +
371C PRO* 3.2 29.1 + - + +
373C SER* 1.3 86.6 + - - +
375C VAL* 1.3 64.1 + - - +
377C ASP* 3.4 6.7 + - - +
378C MSE 3.1 26.2 + - - +
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Residues in contact with VAL 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU* 3.9 23.8 - - + -
366C THR* 5.5 0.4 - - - +
370C LEU* 4.3 11.2 - - + +
371C PRO 3.3 7.2 + - - +
372C TYR 3.1 1.0 + - - -
374C GLN* 1.3 75.1 - - - +
376C ARG* 1.3 68.5 + - - +
377C ASP 3.1 0.5 + - - -
378C MSE 3.1 12.7 + - - +
379C VAL* 3.1 22.9 + - + +
392C LEU* 4.6 0.9 - - + -
405C LEU* 4.4 3.6 - - + -
410C MSE 3.2 36.8 - - + -
414C TRP* 4.1 22.7 - - + -
422C LEU* 5.9 1.1 - - + -
424C LEU* 3.9 18.4 - - + -
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Residues in contact with ARG 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C TYR* 2.9 44.9 + - + +
373C SER* 3.1 39.6 + - - +
375C VAL* 1.3 77.0 - - - +
377C ASP* 1.3 88.1 + - - +
379C VAL* 3.4 1.6 + - - +
380C SER* 2.8 31.7 + - - -
387C LEU* 3.4 38.4 - - - +
390C THR* 4.0 9.7 - - + +
392C LEU* 3.9 17.9 - - + +
410C MSE 4.9 0.4 - - - +
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Residues in contact with ASP 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C SER 3.1 21.1 + - - +
374C GLN* 3.5 9.0 - - - +
375C VAL 3.1 1.0 - - - -
376C ARG* 1.3 95.9 + - - +
378C MSE 1.3 62.9 + - - +
380C SER* 3.4 5.0 - - - -
381C LYS* 3.1 41.3 + - - +
387C LEU* 4.3 8.3 - - - +
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Residues in contact with MSE 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C LEU* 4.3 8.3 - - + -
364C MSE 3.5 30.1 - - + +
365C LYS 3.2 28.3 - - - +
366C THR* 3.6 24.0 - - - +
370C LEU* 4.3 15.3 - - - -
374C GLN 3.1 12.0 + - - +
375C VAL* 3.2 17.5 - - - +
377C ASP* 1.3 77.4 - - - +
379C VAL* 1.3 64.3 + - - +
381C LYS* 3.3 6.1 + - - +
382C LYS* 3.1 23.9 + - - +
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Residues in contact with VAL 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C LEU* 3.9 16.8 - - + -
356C VAL* 3.9 34.5 - - + -
364C MSE 4.0 9.6 - - + -
375C VAL* 3.1 18.8 + - + +
376C ARG 3.9 3.1 - - - +
378C MSE 1.3 76.5 - - - +
380C SER* 1.3 63.7 + - - +
382C LYS* 3.4 0.5 + - - +
383C LEU* 3.2 46.3 + - + +
390C THR* 4.4 5.8 - - + -
392C LEU* 4.0 27.8 - - + -
424C LEU* 4.7 1.8 - - + -
426C CYS* 4.6 0.4 - - - -
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Residues in contact with SER 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C ARG 2.8 18.9 + - - -
377C ASP* 3.4 7.1 + - - -
379C VAL* 1.3 78.8 - - - +
381C LYS* 1.3 61.8 + - - +
383C LEU 4.0 0.2 - - - -
384C GLU* 3.3 2.6 + - - -
385C LEU* 2.6 53.0 + - - +
387C LEU* 3.5 26.7 + - - +
390C THR* 3.6 20.1 + - - +
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Residues in contact with LYS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C ASP* 3.1 36.3 + - - +
378C MSE 3.8 5.8 - - - +
379C VAL 3.2 0.2 - - - -
380C SER* 1.3 77.3 - - - +
382C LYS* 1.3 65.3 + - - +
383C LEU 3.2 0.7 - - - -
384C GLU* 3.3 16.2 + - - +
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Residues in contact with LYS 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360C TYR* 5.0 0.2 + - - -
362C VAL* 4.0 28.5 - - + -
363C VAL 4.0 14.4 + - - -
364C MSE 4.1 27.5 - - + +
378C MSE 3.1 16.4 + - - +
379C VAL 3.8 4.0 - - - +
381C LYS* 1.3 78.7 - - - +
383C LEU* 1.3 59.9 + - + +
384C GLU* 3.3 5.9 + - - +
298L LEU* 3.7 27.7 - - + +
299L SER* 4.1 7.3 + - - -
301L GLU* 5.4 4.8 + - - -
302L ASP* 2.5 41.4 + - - -
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Residues in contact with LEU 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C VAL* 4.3 7.4 - - + -
358C TYR* 3.9 34.0 - - + -
360C TYR* 3.8 39.7 + - + +
362C VAL* 3.9 22.2 - - + -
379C VAL* 3.2 36.9 + - + +
380C SER 4.5 0.2 - - - +
382C LYS* 1.3 79.9 - - + +
384C GLU* 1.3 75.6 + - - +
385C LEU* 3.5 22.0 + - + +
426C CYS* 4.2 11.7 - - - -
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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