Contacts of the helix formed by residues 438 - 445 (chain A) in PDB entry 2OR4
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 ASN 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A TRP* 2.9 62.5 + - + +
435A ALA 3.5 1.8 - - - -
437A GLU* 1.3 90.3 + - - +
439A SER* 1.4 65.0 + - - +
440A ARG 3.2 2.9 - - - -
441A LEU* 3.0 39.8 + - + +
442A LEU* 3.0 24.3 + - + +
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Residues in contact with SER 439 (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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435A ALA 2.8 16.6 + - - -
436A GLU* 3.7 9.3 + - - -
437A GLU 3.5 2.4 + - - -
438A ASN* 1.4 76.4 - - - +
440A ARG* 1.3 81.8 + - - +
442A LEU* 3.8 6.4 - - - +
443A GLN* 2.9 27.2 + - - -
528A LEU* 4.3 22.2 - - - +
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Residues in contact with ARG 440 (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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272A TYR* 6.3 0.8 - - - -
436A GLU 4.7 5.7 + - - -
437A GLU 5.1 5.2 + - - -
438A ASN 3.2 1.0 - - - -
439A SER* 1.3 101.8 + - - +
441A LEU* 1.3 68.0 + - + +
443A GLN* 4.3 0.4 - - - +
444A GLU* 3.3 32.1 + - + +
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Residues in contact with LEU 441 (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 TYR* 4.3 18.6 - - + +
438A ASN* 3.0 33.7 + - + +
440A ARG* 1.3 84.1 - - + +
442A LEU* 1.3 58.4 + - + +
444A GLU 3.5 0.2 + - - -
445A ARG* 3.0 73.6 + - - +
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Residues in contact with LEU 442 (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 TYR* 4.8 11.7 - - + -
373A ILE* 3.6 31.0 - - + -
417A LEU* 5.4 0.2 - - + -
434A TRP* 3.9 22.0 - - + -
435A ALA* 3.7 30.3 - - - +
438A ASN* 3.0 25.2 + - + +
439A SER 3.8 3.4 - - - +
441A LEU* 1.3 78.1 - - + +
443A GLN* 1.3 60.7 + - - +
446A GLY* 2.7 32.2 + - - +
524A PHE* 3.9 7.4 - - + -
528A LEU* 3.9 16.8 - - + -
530A ILE* 3.7 19.4 - - + +
673A ARG* 3.9 1.2 + - - -
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Residues in contact with GLN 443 (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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439A SER 2.9 16.2 + - - -
440A ARG* 4.3 0.9 - - - +
442A LEU* 1.3 78.7 - - - +
444A GLU* 1.3 64.6 + - - +
528A LEU* 5.2 7.3 - - - +
530A ILE* 5.2 2.2 - - - -
670A PHE* 3.4 7.1 - - - -
673A ARG* 2.8 39.0 + - - +
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Residues in contact with GLU 444 (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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370A ARG* 3.6 9.9 + - - -
440A ARG* 3.3 20.3 + - + +
442A LEU 3.2 0.2 - - - -
443A GLN* 1.3 86.5 - - - +
445A ARG* 1.3 68.7 + - + +
446A GLY 3.9 0.2 - - - -
669A MET* 3.4 20.0 - - - +
670A PHE* 3.5 21.7 - - + -
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Residues in contact with ARG 445 (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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369A ASP* 3.2 34.2 - - + +
370A ARG* 3.5 14.9 - - - +
371A TYR* 2.9 73.5 + - + -
441A LEU* 3.0 45.5 + - - +
444A GLU* 1.3 90.1 - - + +
446A GLY* 1.3 61.7 + - - +
447A VAL 3.3 0.7 + - - -
669A MET* 4.0 4.9 - - - -
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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