Contacts of the helix formed by residues 476 - 480 (chain A) in PDB entry 1OVM
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 GLN 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469A ARG* 4.7 0.5 + - - -
473A GLY* 2.9 31.2 + - - +
474A ALA 3.4 0.2 - - - -
475A GLU* 1.3 83.5 - - - +
477A ARG* 1.3 65.6 + - - +
478A TYR* 3.1 29.8 - - + +
479A ASN* 3.0 19.8 + - - +
480A ASP* 4.0 7.1 - - - +
36B ASP* 2.9 29.9 + - - +
39B ILE* 4.4 18.9 - - - +
40B ASP* 5.4 3.6 + - - -
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Residues in contact with ARG 477 (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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475A GLU 3.7 2.4 + - - -
476A GLN* 1.3 73.7 + - - +
478A TYR* 1.3 57.8 + - - +
479A ASN 3.1 0.2 - - - -
480A ASP* 3.1 39.5 + - + +
39B ILE* 4.0 23.3 - - + +
45B CYS* 4.2 10.8 - - - +
46B TRP* 3.2 57.6 + - - +
47B VAL* 5.3 0.6 - - - +
48B GLY 5.5 0.6 - - - +
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Residues in contact with TYR 478 (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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465A TYR* 3.8 4.3 - - - -
472A HIS* 3.2 20.5 + - - -
473A GLY* 3.5 1.4 - - - -
476A GLN* 3.4 22.9 - - + +
477A ARG* 1.3 76.3 - - - +
479A ASN* 1.3 87.8 + - - +
480A ASP 3.3 4.7 - - - +
27B PRO* 3.5 27.3 - - + +
32B LEU* 3.6 21.9 + - + -
35B LEU* 3.6 40.8 - - + -
36B ASP* 3.0 24.5 + - - -
39B ILE* 3.4 25.2 - - + +
46B TRP* 3.7 30.6 + - + +
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Residues in contact with ASN 479 (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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464A GLY* 3.6 0.2 - - - -
465A TYR* 3.2 33.5 + - - +
468A GLU* 3.1 28.4 - - - +
469A ARG* 3.2 34.6 + - + +
472A HIS 3.2 17.2 + - - -
473A GLY 2.8 27.3 + - - -
476A GLN 3.0 9.9 + - - +
478A TYR* 1.3 95.5 - - - +
480A ASP* 1.3 64.8 + - - +
27B PRO* 4.7 2.9 - - - +
32B LEU* 5.0 0.5 - - - +
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Residues in contact with ASP 480 (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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463A GLU 4.7 1.8 - - - +
465A TYR* 4.3 2.1 + - - -
469A ARG* 3.0 31.1 + - - +
475A GLU 5.9 0.2 - - - -
476A GLN 4.0 3.3 - - - +
477A ARG* 3.1 33.1 + - + +
478A TYR 4.1 5.9 - - - +
479A ASN* 1.3 80.4 - - - +
481A ILE* 1.3 71.9 + - - +
532A LYS* 4.8 5.3 + - - -
450B ARG* 5.2 3.4 + - - -
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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