Contacts of the helix formed by residues 377 - 383 (chain A) in PDB entry 2OMU
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 VAL 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355A ILE* 4.7 2.0 - - + -
369A PHE* 4.2 2.5 - - + -
374A VAL* 4.0 11.7 - - + -
375A SER 3.4 2.3 + - - +
376A ASP* 1.3 76.5 + - - +
378A SER* 1.3 64.1 + - - +
379A SER 3.2 2.9 - - - -
380A LEU* 3.0 44.3 + - + +
396A ILE* 3.7 41.3 - - + -
398A ASP 4.0 20.4 - - - +
401A PRO* 3.5 17.9 - - + +
402A LEU* 4.3 20.3 - - + +
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Residues in contact with SER 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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376A ASP* 2.8 29.1 + - - -
377A VAL* 1.3 76.7 - - - +
379A SER* 1.3 63.3 + - - +
380A LEU 3.3 0.5 + - - -
381A ALA* 3.4 21.3 + - - +
382A ASN* 4.5 2.1 + - - -
401A PRO* 3.7 19.1 - - - +
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ILE* 3.6 18.9 + - - +
356A SER* 3.5 36.2 - - - -
358A VAL* 4.4 0.7 - - - +
359A SER* 3.8 21.9 - - - -
376A ASP 4.8 1.4 + - - -
377A VAL 4.6 0.3 - - - -
378A SER* 1.3 81.9 + - - +
380A LEU* 1.3 64.7 + - - +
381A ALA 3.2 0.2 - - - -
382A ASN* 2.9 31.9 + - - +
383A LEU* 4.6 1.4 + - - +
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Residues in contact with LEU 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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355A ILE* 4.1 14.1 - - + -
358A VAL* 3.6 29.8 - - + -
367A LEU* 4.0 13.7 - - + -
369A PHE* 3.7 29.6 - - + -
377A VAL* 3.0 34.1 + - + +
379A SER* 1.3 72.5 - - - +
381A ALA* 1.3 61.1 + - - +
382A ASN 3.1 5.6 - - - -
383A LEU* 3.1 27.1 + - + +
389A LEU* 3.9 16.6 - - + -
391A ALA* 5.8 0.2 - - + -
401A PRO 4.9 0.7 - - - -
402A LEU* 4.0 18.4 - - + -
405A LEU* 3.7 14.7 - - + +
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Residues in contact with ALA 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 VAL 4.1 0.8 + - - -
378A SER 3.4 15.5 + - - +
379A SER 3.2 0.6 - - - -
380A LEU* 1.3 76.7 - - - +
382A ASN* 1.3 63.6 + - - +
383A LEU 3.5 0.5 + - - -
384A THR* 3.8 14.7 - - - +
401A PRO* 3.4 27.2 + - + +
405A LEU* 3.9 11.3 - - - +
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Residues in contact with ASN 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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359A SER* 3.5 32.8 - - - +
362A THR* 3.7 21.3 - - + +
378A SER 4.5 2.0 + - - -
379A SER* 2.9 32.2 + - - +
380A LEU 3.1 0.8 - - - -
381A ALA* 1.3 77.6 - - - +
383A LEU* 1.3 56.4 + - - +
384A THR* 3.1 18.9 + - - +
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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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358A VAL* 3.3 23.1 - - + +
359A SER* 4.2 6.3 - - - +
361A LEU 3.3 28.7 - - - +
362A THR 5.0 5.2 - - - -
364A LEU* 3.8 16.8 - - + +
367A LEU* 3.8 29.4 - - + -
379A SER 4.7 1.3 - - - +
380A LEU* 3.1 30.9 + - + +
381A ALA 3.3 0.2 - - - -
382A ASN* 1.3 78.0 - - - +
384A THR* 1.3 58.7 + - - +
385A ASN 3.2 4.0 - - - -
386A ILE* 3.1 46.0 + - + +
389A LEU* 5.8 0.9 - - + -
405A LEU* 3.4 5.8 - - - +
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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