Contacts of the helix formed by residues 76 - 82 (chain B) 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 GLY 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407A TRP* 3.7 12.8 - - - -
75B PHE* 1.3 70.5 - - - +
77B VAL* 1.3 63.9 + - - -
78B GLY 3.2 0.6 + - - -
79B GLU* 2.8 17.4 + - - +
80B LEU* 3.0 29.5 + - - +
116B HIS 3.9 2.7 - - - -
126B PHE* 3.6 28.3 - - - -
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Residues in contact with VAL 77 (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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84A ASN* 3.5 12.7 - - - +
407A TRP* 3.1 50.6 - - + +
409A SER* 3.8 12.1 - - - -
600A TPP 3.4 32.5 - - + +
74B THR* 3.6 15.7 - - + -
75B PHE 2.9 6.9 + - - +
76B GLY* 1.3 71.2 - - - +
78B GLY* 1.3 61.5 + - - +
81B SER* 2.9 25.5 + - - -
116B HIS* 3.4 21.7 - - + +
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Residues in contact with GLY 78 (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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52B GLU* 3.3 35.8 - - - +
73B THR* 3.6 13.2 - - - +
74B THR* 3.0 19.5 + - - -
77B VAL* 1.3 81.1 - - - +
79B GLU* 1.3 64.8 + - - +
81B SER* 3.2 11.1 + - - -
82B ALA 3.4 3.6 + - - -
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Residues in contact with GLU 79 (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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73B THR* 3.3 12.8 + - - +
74B THR 3.1 5.5 + - - +
75B PHE* 3.5 19.6 - - - -
76B GLY* 2.8 31.4 + - - +
78B GLY* 1.3 75.6 - - - +
80B LEU* 1.3 66.5 + - + +
82B ALA* 3.1 13.3 + - - +
83B MET* 3.3 16.7 + - + +
98B HIS* 3.7 23.3 - - + -
100B VAL* 3.7 9.1 - - + +
126B PHE* 3.3 29.2 - - + +
130B SER* 5.5 0.2 - - - -
164B TYR* 2.6 32.4 + - + -
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Residues in contact with LEU 80 (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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80A LEU 4.2 3.5 - - - +
81A SER 5.5 0.5 - - - +
83A MET* 4.1 14.7 - - + +
84A ASN* 3.9 16.8 + - + +
87A ALA* 3.4 32.5 - - + -
407A TRP* 4.0 6.3 - - + -
76B GLY 3.0 18.4 + - - +
79B GLU* 1.3 78.8 - - + +
81B SER* 1.3 62.3 + - - +
83B MET* 3.2 39.5 + - + +
126B PHE* 4.0 35.9 - - + -
129B MET* 3.7 30.3 - - + -
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Residues in contact with SER 81 (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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53A LEU* 5.0 10.7 - - - +
57A TYR* 4.7 1.9 + - - -
80A LEU 5.9 0.2 - - - -
81A SER* 5.5 7.8 - - - +
84A ASN* 3.1 21.9 + - - +
600A TPP 4.3 2.9 - - - +
51B ASN* 6.3 0.2 - - - -
52B GLU* 3.7 21.0 + - - -
53B LEU* 3.5 29.0 - - - +
77B VAL 2.9 19.0 + - - -
78B GLY 3.2 11.3 + - - -
79B GLU 3.2 0.6 - - - -
80B LEU* 1.3 78.1 - - - +
82B ALA* 1.3 58.2 + - - +
83B MET 3.5 0.4 + - - -
84B ASN* 5.0 1.2 + - - +
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Residues in contact with ALA 82 (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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52B GLU* 3.8 20.0 - - + +
53B LEU* 4.5 0.2 - - - +
56B SER* 3.9 8.3 - - - -
71B LEU* 3.9 24.9 - - + -
73B THR* 4.5 1.1 - - + -
78B GLY 3.4 8.0 + - - +
79B GLU 3.1 9.9 + - - +
80B LEU 3.0 0.8 - - - -
81B SER* 1.3 78.8 - - - +
83B MET* 1.3 63.8 + - - +
84B ASN 3.3 2.9 - - - -
85B GLY* 2.9 13.9 + - - -
86B ILE* 3.1 14.1 + - + +
98B HIS* 4.3 6.5 - - + -
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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