Contacts of the helix formed by residues 379 - 392 (chain A) in PDB entry 2OIV
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 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A SER* 3.1 11.6 + - - +
378A ALA* 1.3 78.8 - - - +
380A PRO* 1.3 71.0 - - - +
381A ASP* 2.7 41.7 + - - +
382A GLN* 3.2 30.2 + - + +
383A GLN* 3.1 21.7 + - - +
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Residues in contact with PRO 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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377A SER 5.5 0.2 - - - +
378A ALA 3.4 9.6 - - - +
379A ASP* 1.3 92.2 - - - +
381A ASP* 1.3 64.5 + - - +
383A GLN* 3.8 9.0 - - + +
384A ALA* 3.0 30.5 + - - +
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Residues in contact with ASP 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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379A ASP* 2.7 20.1 + - - +
380A PRO* 1.3 80.8 - - - +
382A GLN* 1.3 58.3 + - + +
384A ALA* 3.9 5.9 - - - +
385A ARG* 3.1 29.3 + - - +
388A ARG* 5.6 0.3 + - - -
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Residues in contact with GLN 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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374A MET* 3.5 37.5 - - - +
377A SER* 3.3 29.3 + - - +
379A ASP* 3.2 25.9 + - + +
381A ASP* 1.3 74.1 - - - +
383A GLN* 1.3 66.0 + - - +
385A ARG* 3.5 3.8 + - - +
386A ALA* 3.0 23.6 + - - +
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Residues in contact with GLN 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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374A MET 3.3 12.3 + - - +
375A LEU* 2.6 28.1 + - - +
376A SER* 4.0 1.6 - - - +
377A SER 3.6 17.4 + - - +
379A ASP 3.1 13.1 + - - +
380A PRO* 3.8 8.1 - - + +
382A GLN* 1.3 80.8 - - - +
384A ALA* 1.3 55.8 + - - +
386A ALA* 3.2 4.7 + - - +
387A GLN* 2.9 47.9 + - - +
448A HIS* 3.1 31.8 + - - -
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Residues in contact with ALA 384 (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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380A PRO 3.0 19.1 + - - +
381A ASP* 4.0 6.3 - - - +
383A GLN* 1.3 75.2 - - - +
385A ARG* 1.3 58.8 + - - +
387A GLN* 3.2 16.7 + - - +
388A ARG* 2.9 43.6 + - - +
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Residues in contact with ARG 385 (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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374A MET* 5.4 7.6 - - + -
381A ASP 3.1 18.5 + - - +
382A GLN* 3.9 4.9 - - - +
384A ALA* 1.3 78.4 - - - +
386A ALA* 1.3 57.4 + - - +
388A ARG* 3.0 54.4 + - - +
389A LEU* 2.9 64.5 + - + +
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Residues in contact with ALA 386 (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 VAL* 3.6 34.8 - - + +
374A MET* 3.7 6.2 - - + -
375A LEU* 3.6 24.0 - - + +
382A GLN 3.0 14.8 + - - +
383A GLN 3.2 9.6 + - - +
385A ARG* 1.3 74.9 - - - +
387A GLN* 1.3 53.7 + - - +
389A LEU* 3.3 1.3 + - - -
390A LEU* 2.8 40.7 + - - +
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Residues in contact with GLN 387 (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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375A LEU* 4.0 11.7 - - + -
383A GLN* 2.9 35.9 + - + +
384A ALA* 3.5 17.8 + - - +
386A ALA* 1.3 73.4 - - - +
388A ARG* 1.3 57.2 + - - +
390A LEU* 5.1 0.2 - - - -
391A ALA* 2.6 43.7 + - + +
392A GLY 3.3 1.0 + - - -
448A HIS* 3.0 38.8 + - - +
449A LEU* 5.7 0.2 - - - -
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Residues in contact with ARG 388 (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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381A ASP 5.6 0.4 + - - -
384A ALA* 2.9 20.0 + - - +
385A ARG* 3.0 68.0 - - - +
387A GLN* 1.3 75.5 - - - +
389A LEU* 1.3 60.3 + - + +
392A GLY* 2.9 32.2 + - - +
394A ASP* 4.8 0.7 - - - +
395A ILE* 3.6 6.2 - - - +
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Residues in contact with LEU 389 (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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365A HIS* 4.0 7.0 + - - +
371A VAL* 3.9 33.2 - - + -
374A MET* 5.5 2.5 - - + -
385A ARG* 2.9 61.3 + - + +
386A ALA 3.8 3.6 - - - +
388A ARG* 1.3 77.8 - - + +
390A LEU* 1.3 64.6 - - + +
395A ILE* 3.1 26.8 - - + +
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Residues in contact with LEU 390 (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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365A HIS* 3.9 13.9 - - + +
367A ALA* 3.5 26.9 - - + -
368A ASP 5.0 0.7 - - - +
371A VAL* 3.9 19.1 - - + -
372A VAL* 4.0 17.7 - - + +
375A LEU* 3.8 27.6 - - + -
386A ALA 2.8 16.7 + - - +
389A LEU* 1.3 86.9 - - + +
391A ALA* 1.3 58.8 + - - +
392A GLY 3.8 0.9 - - - -
395A ILE* 3.7 5.8 - - - +
399A VAL* 4.5 6.4 - - + +
401A LEU* 3.9 17.5 - - + -
417A ARG* 2.9 28.8 + - - -
449A LEU* 3.7 14.1 - - + +
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Residues in contact with ALA 391 (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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387A GLN* 2.6 22.4 + - + +
390A LEU* 1.3 75.6 - - - +
392A GLY* 1.3 67.7 + - - +
393A ASP* 5.4 1.2 - - - +
417A ARG* 3.6 16.8 - - - +
449A LEU* 3.9 28.3 - - + +
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Residues in contact with GLY 392 (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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387A GLN 3.3 1.8 + - - -
388A ARG* 2.9 27.6 + - - -
391A ALA* 1.3 84.1 - - - +
393A ASP* 1.3 60.1 + - - -
394A ASP* 3.2 6.3 - - - -
395A ILE* 3.2 24.9 + - - +
417A ARG* 4.9 1.6 + - - -
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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