Contacts of the helix formed by residues 367 - 379 (chain B) in PDB entry 2OR0
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 PRO 367 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A ARG* 4.3 19.3 - - + +
321B ILE* 3.7 17.5 - - + -
325B TRP* 3.7 20.2 - - + -
365B HIS 3.3 6.1 - - - +
366B VAL* 1.4 87.9 - - + +
368B GLY* 1.3 69.3 + - - +
369B PRO* 3.6 0.9 - - - -
370B THR* 3.4 3.9 + - - -
371B ASN* 2.9 32.0 + - - +
608B ACT 3.3 35.7 - - + -
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Residues in contact with GLY 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 3.7 31.1 - - - +
366B VAL* 4.5 0.8 - - - +
367B PRO* 1.3 84.5 - - - +
369B PRO* 1.3 71.6 - - - +
371B ASN* 3.7 5.1 - - - +
372B HIS* 3.0 25.1 + - - +
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Residues in contact with PRO 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASP* 5.4 4.3 - - - +
272A TYR* 3.8 29.1 - - + +
366B VAL* 4.1 21.5 - - + +
367B PRO 3.9 0.9 - - - -
368B GLY* 1.3 88.8 - - - +
370B THR* 1.3 52.6 + - - +
372B HIS* 3.5 1.0 - - - +
373B ALA* 2.7 37.7 + - - +
386B MSE 5.7 2.0 - - - +
387B MSE 4.1 28.8 - - + +
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Residues in contact with THR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA 4.0 5.8 - - - +
317B ARG* 3.6 48.8 + - + +
318B ARG* 3.8 11.2 - - - +
321B ILE* 3.7 20.2 - - + +
366B VAL 4.4 3.3 + - - -
367B PRO 3.4 3.9 + - - -
368B GLY 3.3 0.8 - - - -
369B PRO* 1.3 75.1 - - - +
371B ASN* 1.3 61.0 + - - +
373B ALA* 4.4 4.9 - - - +
374B SER* 2.9 32.5 + - - -
389B ALA 5.1 4.9 + - - -
391B ILE* 5.0 11.8 - - + +
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Residues in contact with ASN 371 (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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318B ARG* 3.3 36.6 + - - +
321B ILE* 5.6 3.8 - - - +
322B ALA* 5.9 2.2 - - - +
367B PRO* 2.9 36.1 + - - +
368B GLY* 3.7 5.3 - - - +
370B THR* 1.3 76.0 - - - +
372B HIS* 1.3 62.1 + - - +
374B SER* 3.2 4.6 + - - -
375B ALA* 3.0 26.2 + - - +
608B ACT 4.3 8.7 - - - +
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Residues in contact with HIS 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 2.6 35.5 + + + +
368B GLY 3.0 17.6 + - - +
369B PRO 3.5 3.8 - - - +
371B ASN* 1.3 76.9 - - - +
373B ALA* 1.3 59.4 + - - +
375B ALA* 3.3 5.2 + - - +
376B LEU* 2.8 45.3 + - + +
387B MSE 5.2 8.7 - - + +
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Residues in contact with ALA 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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314B ALA* 5.2 0.9 - - - -
369B PRO 2.7 22.1 + - - +
370B THR* 4.0 5.4 - - - +
372B HIS* 1.3 76.0 - - - +
374B SER* 1.3 61.0 + - - +
376B LEU* 3.3 9.8 + - - +
377B THR* 3.1 28.2 + - - +
383B PRO* 3.7 15.4 - - + +
387B MSE 3.4 30.9 - - + +
391B ILE* 4.5 9.0 - - + -
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ALA* 3.7 35.8 - - - +
315B ILE* 4.3 2.9 - - - -
318B ARG* 3.0 35.2 + - - +
370B THR 2.9 26.3 + - - -
371B ASN 3.2 4.5 + - - -
373B ALA* 1.3 69.7 - - - +
375B ALA* 1.3 66.1 + - - +
377B THR* 2.9 22.8 + - - -
378B GLN* 3.2 12.6 + - - +
391B ILE* 5.6 0.2 - - - +
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Residues in contact with ALA 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ARG* 3.8 8.9 - - - +
371B ASN 3.0 19.0 + - - +
372B HIS* 3.7 4.3 - - - +
374B SER* 1.3 77.9 + - - +
376B LEU* 1.3 57.7 + - - +
378B GLN* 3.0 9.0 + - - +
379B LEU* 2.9 40.6 + - + +
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Residues in contact with LEU 376 (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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372B HIS* 2.8 35.3 + - + +
373B ALA* 3.4 6.7 - - - +
374B SER 3.2 0.2 - - - -
375B ALA* 1.3 75.6 - - - +
377B THR* 1.3 59.7 + - - +
379B LEU* 3.1 21.0 + - + +
381B GLY* 3.0 41.3 + - - +
382B GLU 4.2 5.6 - - - +
383B PRO* 3.9 28.3 - - + -
387B MSE 6.4 0.2 - - + -
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Residues in contact with THR 377 (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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310B PHE* 3.9 18.8 - - + -
311B GLU* 3.2 39.0 + - - +
314B ALA* 4.8 3.7 - - + +
315B ILE* 5.3 0.3 - - - +
373B ALA 3.1 17.5 + - - +
374B SER* 2.9 16.4 + - - -
376B LEU* 1.3 74.4 - - - +
378B GLN* 1.3 57.7 + - - +
380B GLY* 3.1 17.3 + - - -
381B GLY 3.6 11.1 - - - +
382B GLU* 4.4 4.9 - - - +
383B PRO* 3.5 25.1 - - + -
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Residues in contact with GLN 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLU* 3.6 19.9 + - - +
315B ILE* 4.2 12.0 - - + +
318B ARG* 2.6 45.2 + - - +
374B SER 3.4 8.5 - - - +
375B ALA* 3.0 11.6 + - - +
377B THR* 1.3 81.7 + - - +
379B LEU* 1.3 61.7 + - + +
380B GLY* 3.1 4.9 + - - -
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Residues in contact with LEU 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ALA* 2.9 28.6 + - + +
376B LEU* 3.1 19.7 + - + +
378B GLN* 1.3 78.9 - - + +
380B GLY* 1.3 60.2 + - - +
381B GLY 3.3 2.1 + - - +
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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