Contacts of the strand formed by residues 81 - 88 (chain B) in PDB entry 2OT7
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 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLY* 3.4 2.6 - - - -
78B GLN 3.0 31.1 + - - +
79B SER* 3.9 5.4 - - - +
80B GLY* 1.3 87.4 - - - +
82B PHE* 1.3 61.8 + - - +
226B PHE* 3.3 61.9 - - + +
227B PHE* 4.4 13.0 - - + -
244B LEU 3.8 1.1 - - - -
245B ILE* 4.2 15.9 - - + -
249B MET* 3.8 18.2 - - + -
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Residues in contact with PHE 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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75B VAL* 3.6 18.6 - - + -
76B THR 3.3 4.7 - - - +
77B GLY* 3.5 33.2 - - - -
78B GLN* 3.6 4.9 - - - -
79B SER 4.9 0.4 - - - -
80B GLY* 3.5 33.7 - - - -
81B LEU* 1.3 77.7 - - - +
83B THR* 1.3 62.9 + - - +
122B TRP* 3.9 29.2 - + - -
125B LEU* 3.8 21.5 - - + -
126B THR* 3.9 20.6 - - + -
227B PHE* 4.1 10.0 - - - -
243B THR* 3.7 5.0 - - - -
244B LEU* 3.0 43.5 + - + +
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Residues in contact with THR 83 (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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74B LEU 3.7 0.7 - - - +
75B VAL* 3.4 4.3 - - - -
76B THR* 2.8 46.3 + - - +
82B PHE* 1.3 75.3 + - - +
84B GLN* 1.3 62.5 + - - +
85B TYR* 3.7 29.3 - - + +
227B PHE* 3.9 18.5 - - - -
242B MET* 3.2 33.2 + - + +
243B THR* 5.6 1.1 + - - +
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.3 38.9 - - + +
74B LEU 3.4 4.7 - - - +
75B VAL* 3.8 22.5 - - + +
82B PHE 4.3 0.2 - - - -
83B THR* 1.3 72.8 - - - +
85B TYR* 1.3 63.5 + - - +
86B ASN* 3.6 21.1 + - - +
184B SER* 3.4 31.6 + - - -
185B PHE* 5.0 0.2 - - - +
186B ALA 4.6 2.6 - - - +
241B LYS 4.4 7.7 + - - -
242B MET* 2.8 44.4 + - - +
244B LEU* 4.1 19.9 - - + +
11D THR 5.4 2.8 + - - -
13D GLY 3.5 2.1 - - - +
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Residues in contact with TYR 85 (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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72B GLN 3.4 2.6 - - - +
73B GLN* 3.7 0.7 - - - -
74B LEU* 2.8 49.5 + - + +
76B THR* 3.5 29.3 - - + +
83B THR* 3.7 25.1 - - + +
84B GLN* 1.3 75.0 - - - +
86B ASN* 1.3 60.9 + - - +
87B ILE* 3.7 9.6 + - + +
242B MET* 3.8 13.5 - - + -
13D GLY 3.7 3.1 - - - -
14D ALY 3.6 29.8 - - + -
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Residues in contact with ASN 86 (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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71B ILE* 3.1 29.8 - - + +
72B GLN 3.6 3.1 - - - -
73B GLN* 3.1 33.6 + - - +
84B GLN* 3.6 22.9 + - - +
85B TYR* 1.3 73.0 - - - +
87B ILE* 1.3 63.7 + - - +
88B GLN 3.9 2.0 + - - -
241B LYS 4.2 3.0 + - - -
11D THR* 4.6 1.7 + - - -
12D GLY* 3.7 14.5 - - - +
13D GLY* 3.1 41.6 + - - +
14D ALY 3.7 15.8 - - - +
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Residues in contact with ILE 87 (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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71B ILE* 4.1 1.3 - - - -
72B GLN* 2.8 46.1 + - + +
74B LEU* 3.4 30.7 - - + -
85B TYR* 4.0 11.4 - - + +
86B ASN* 1.3 73.6 - - - +
88B GLN* 1.3 67.3 + - - +
89B LYS* 3.3 19.0 + - + +
14D ALY 3.4 49.8 - - + +
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Residues in contact with GLN 88 (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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68B PRO 4.9 2.6 + - - -
69B ALA* 3.9 30.9 - - + +
70B PRO 3.4 6.5 - - - +
71B ILE* 4.0 8.0 - - + +
86B ASN 3.9 1.8 + - - -
87B ILE* 1.3 70.7 - - - +
89B LYS* 1.3 76.1 + - - +
14D ALY 3.0 39.6 + - + +
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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