Contacts of the strand formed by residues 82 - 86 (chain C) in PDB entry 2OC8
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 LEU 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C TRP* 3.5 28.5 - - + -
54C THR 4.1 2.0 - - - +
75C TYR* 5.5 0.8 - - + +
76C THR 3.3 1.0 + - - -
77C ASN* 2.5 49.7 + - + +
80C GLN* 4.1 11.7 - - + +
81C ASP* 1.3 76.5 - - - +
83C VAL* 1.3 61.9 + - - +
153C LEU* 3.7 28.3 - - + -
170C ILE* 3.9 12.6 - - + -
174C ASN* 4.3 3.8 - - + -
175C LEU* 3.6 40.8 - - + +
178C THR* 3.9 16.8 - - + +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 3.5 10.9 - - - -
54C THR* 3.1 53.0 + - + +
55C VAL 4.6 0.7 - - - -
56C TYR* 3.4 40.2 - - + -
59C ALA* 4.0 8.1 - - + -
60C GLY 3.4 9.4 - - - +
73C GLN* 3.5 26.7 - - - +
75C TYR 3.4 6.5 - - - -
76C THR* 4.0 2.7 - - + +
82C LEU* 1.3 78.8 - - - +
84C GLY* 1.3 59.9 + - - +
85C TRP* 4.5 3.4 - - + -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 3.9 14.6 - - - -
52C CYS 3.2 11.7 - - - -
53C TRP* 4.0 5.8 - - - -
73C GLN* 3.4 1.5 - - - +
74C MET* 2.6 32.2 + - - +
75C TYR* 2.8 23.2 + - - +
83C VAL* 1.3 77.5 - - - +
85C TRP* 1.3 58.0 + - - -
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Residues in contact with TRP 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C VAL* 5.6 0.4 - - + -
43C PHE* 5.4 0.2 - + - -
45C ALA* 4.8 3.4 - - + -
51C VAL* 3.2 5.5 - - - +
52C CYS* 2.8 57.3 + - + -
54C THR* 3.4 36.6 - - + -
59C ALA* 3.8 12.1 - - + -
62C ARG 3.1 22.8 + - - -
64C ILE* 3.1 42.3 - - + +
71C VAL 3.4 14.6 - - - -
73C GLN* 3.3 33.3 - - + +
74C MET* 3.9 7.0 - - - +
83C VAL* 4.5 1.1 - - + -
84C GLY* 1.3 76.7 - - - -
86C PRO* 1.3 74.9 - - + +
23D VAL* 3.5 38.4 - - + -
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Residues in contact with PRO 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C GLY 4.0 3.8 - - - +
52C CYS* 4.1 0.6 - - - +
64C ILE* 5.2 3.6 - - - +
71C VAL* 3.5 27.1 - - + -
72C ILE 3.7 3.8 - - - +
74C MET* 3.5 32.1 - - + -
85C TRP* 1.3 96.1 - - + +
87C ALA* 1.3 69.2 + - - +
88C PRO* 3.3 6.4 - - - +
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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