Contacts of the strand formed by residues 80 - 83 (chain D) in PDB entry 2OZB
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 TYR 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D TYR* 4.0 23.9 + - - -
12D PRO* 3.9 20.1 - - + +
54D ILE* 3.2 15.0 - - + +
56D MET* 3.6 27.1 - - + -
70D PRO* 3.7 35.2 + - + +
73D CYS* 3.6 35.7 - - + -
74D GLU 5.6 0.2 - - - -
78D VAL 3.8 2.5 - - - -
79D PRO* 1.3 75.7 - - + +
81D VAL* 1.3 63.7 + - - +
82D PHE* 4.6 2.0 - + - -
123D ILE* 3.4 13.1 - - - +
127D LEU* 5.6 4.1 - - + +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PRO* 3.8 9.6 - - + +
14D ALA* 4.6 1.8 - - + -
18D LEU* 4.4 8.3 - - + -
22D LEU* 3.8 20.0 - - + -
54D ILE 3.2 10.0 + - - +
55D VAL* 3.6 9.8 - - + +
56D MET* 3.0 27.0 + - - +
80D TYR* 1.3 78.0 - - - +
82D PHE* 1.3 71.4 + - - +
123D ILE* 3.5 34.1 - - + -
126D LEU* 3.5 32.8 - - + -
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS 4.2 2.2 - - - -
10D ALA* 3.8 24.7 - - + +
11D TYR 3.5 35.7 - - - -
12D PRO* 2.8 16.4 + - + +
13D LEU* 3.5 13.9 - - + +
14D ALA* 3.0 32.1 + - - +
56D MET* 3.4 46.0 - - + -
58D ALA* 3.9 14.6 - - + -
63D LEU* 4.2 6.1 - - + -
66D ILE* 3.9 14.8 - - + -
67D LEU* 3.9 22.4 - - + -
70D PRO* 4.8 2.7 - - + -
80D TYR* 4.6 6.1 - + - -
81D VAL* 1.3 77.4 - - - +
83D VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.9 5.4 - - - -
19D THR* 4.0 31.6 - - + +
22D LEU* 4.0 19.7 - - + -
23D LEU* 4.7 7.2 - - + -
55D VAL* 3.9 23.1 - - + -
56D MET 2.9 16.8 + - - +
57D ALA* 4.3 3.8 - - - -
58D ALA* 2.7 27.9 + - - +
82D PHE* 1.3 77.3 - - - +
84D ARG* 1.3 61.4 + - - +
85D SER 4.4 7.0 - - - +
89D LEU* 4.3 19.3 - - + -
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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