Contacts of the helix formed by residues 82 - 88 (chain B) in PDB entry 2O1S
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 ALA 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B TRP* 4.4 13.5 - - + -
79B GLY* 3.0 20.8 + - - +
80B HIS 3.5 0.8 - - - -
81B GLN* 1.3 76.7 - - - +
83B TYR* 1.3 61.0 + - - +
84B PRO* 3.4 2.9 - - - -
85B HIS* 3.3 18.7 + - + +
86B LYS* 2.9 33.8 + - + +
108B PRO* 3.8 23.8 - - + -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.3 20.2 - - + -
53B GLY* 5.8 4.5 - - - -
80B HIS* 3.7 23.1 - - - -
81B GLN* 3.4 1.1 - - - -
82B ALA* 1.3 74.7 - - - +
84B PRO* 1.3 75.7 - - + +
86B LYS* 2.9 21.8 + - + +
87B ILE* 2.7 24.1 + - + +
106B PRO* 4.1 24.1 + - + +
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Residues in contact with PRO 84 (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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35B LEU* 4.3 16.4 - - + -
39B LEU* 4.5 10.7 - - + -
53B GLY 3.8 17.3 - - - +
56B THR* 3.3 25.1 - - - +
57B VAL* 4.5 11.9 - - + +
60B THR* 3.6 20.9 - - + +
81B GLN 4.1 4.7 - - - +
82B ALA 3.6 0.4 - - - -
83B TYR* 1.3 94.3 - - + +
85B HIS* 1.3 62.3 + - - +
87B ILE* 3.2 18.3 + - + +
88B LEU* 3.3 20.8 + - - +
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Residues in contact with HIS 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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60B THR* 3.5 12.5 - - + +
64B HIS* 2.7 41.3 + + - -
74B LEU* 4.8 5.2 - - + -
76B TRP* 3.3 43.6 + + + +
82B ALA* 3.3 17.9 + - + +
83B TYR 3.1 0.6 - - - -
84B PRO* 1.3 82.8 - - - +
86B LYS* 1.3 62.9 + - + +
88B LEU* 3.7 2.9 + - - +
89B THR* 2.9 38.0 + - - -
108B PRO* 5.0 0.2 - - + -
115B TYR* 3.0 29.3 + - + -
116B ASP* 3.3 20.8 + - - -
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Residues in contact with LYS 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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82B ALA* 2.9 18.5 + - + +
83B TYR* 2.9 15.3 + - + +
85B HIS* 1.3 83.5 - - + +
87B ILE* 1.3 69.1 + - + +
89B THR* 3.1 22.4 + - + +
105B HIS 3.6 19.1 + - - +
106B PRO 4.5 2.9 - - - +
107B PHE* 3.4 33.9 + - - +
108B PRO* 3.6 14.8 - - - +
109B TRP 4.2 0.2 - - - +
112B GLU* 2.9 35.3 + - - +
116B ASP* 3.7 7.7 + - - +
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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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11B LEU* 4.1 22.7 - - + -
14B VAL 5.3 3.9 - - - +
15B ASP* 5.5 1.4 - - - +
35B LEU* 3.6 27.4 - - + -
38B TYR* 4.0 24.5 - - + -
39B LEU* 3.6 18.6 - - + -
83B TYR* 2.7 41.8 + - + +
84B PRO* 3.2 7.1 + - + +
86B LYS* 1.3 76.0 - - + +
88B LEU* 1.3 64.6 + - + +
89B THR 2.8 16.8 + - - +
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Residues in contact with LEU 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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11B LEU* 5.1 4.0 - - + -
14B VAL* 4.0 27.4 - - + -
15B ASP 5.3 1.1 - - - -
16B SER* 3.8 5.9 + - - -
17B THR* 3.4 34.7 + - + +
20B LEU* 4.0 24.9 - - + -
31B LEU* 4.8 11.4 - - + -
35B LEU* 4.3 16.8 - - + -
60B THR* 3.8 27.6 - - + -
61B VAL* 4.2 16.6 - - + -
64B HIS* 4.2 7.2 - - + -
84B PRO 3.3 9.9 + - - +
85B HIS 4.1 3.6 - - - +
87B ILE* 1.3 80.3 - - + +
89B THR* 1.3 60.7 + - - +
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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