Contacts of the helix formed by residues 77 - 85 (chain B) in PDB entry 1WG8
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 HIS 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B ASN* 2.9 21.0 + - + +
76B ARG* 1.3 110.2 + - + +
78B LEU* 1.3 56.3 + - - +
79B LYS 3.5 1.8 - - - -
80B ARG* 3.3 38.6 + - - +
81B HIS* 2.8 54.0 + + + +
214B GLU* 5.7 0.4 - - - -
218B GLN* 3.8 2.0 - - - -
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Residues in contact with LEU 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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27B VAL* 3.9 23.1 - - + -
50B LEU* 4.0 18.4 - - + -
75B PHE 3.2 15.8 + - - +
77B HIS* 1.3 76.2 - - - +
79B LYS* 1.3 59.1 + - - +
81B HIS* 3.8 1.4 - - - +
82B LEU* 2.9 52.2 + - + +
93B ILE* 4.4 5.4 - - + -
215B PHE* 3.9 23.8 - - + -
218B GLN* 3.2 11.5 + - + +
219B ALA* 3.8 33.9 - - + +
222B VAL* 4.0 15.7 - - + -
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 1.3 79.5 - - - +
80B ARG* 1.3 57.6 + - - +
82B LEU* 3.5 5.6 + - - +
83B ALA* 3.0 30.2 + - + +
87B VAL 4.9 0.2 - - - +
89B ARG* 5.4 5.8 - - - +
218B GLN* 3.1 24.8 + - + +
221B GLU* 2.8 37.7 - - - +
222B VAL* 4.1 21.1 - - + -
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Residues in contact with ARG 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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77B HIS* 3.3 50.1 + - + +
78B LEU 3.3 0.6 - - - -
79B LYS* 1.3 79.3 - - - +
81B HIS* 1.3 84.4 + - - +
83B ALA* 3.3 8.0 + - - +
84B ALA* 3.1 23.1 + - - +
218B GLN* 4.7 0.4 + - - -
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Residues in contact with HIS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.6 16.4 - - + -
71B VAL* 4.5 23.3 - - + +
72B GLN 5.3 2.2 - - - -
73B GLY* 4.0 24.7 - - - -
74B ASN 4.0 11.0 + - - -
77B HIS* 2.8 39.6 + + + +
78B LEU* 4.0 2.9 - - - +
80B ARG* 1.3 108.2 + - - +
82B LEU* 1.3 62.8 + - - +
84B ALA* 3.3 16.5 + - - +
85B LEU* 3.3 19.2 + - - +
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Residues in contact with LEU 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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27B VAL* 3.8 22.2 - - + -
48B ILE* 4.0 32.3 - - + -
50B LEU* 5.8 2.2 - - + -
78B LEU* 2.9 44.3 + - + +
79B LYS* 3.8 3.6 - - - +
81B HIS* 1.3 75.8 - - - +
83B ALA* 1.3 59.3 + - - +
85B LEU* 2.9 18.9 + - + +
87B VAL* 2.9 39.1 + - + +
88B GLU 5.7 0.4 - - - +
90B VAL* 4.1 15.0 - - + -
222B VAL* 4.1 30.7 - - + -
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Residues in contact with ALA 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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79B LYS* 3.0 24.9 + - + +
80B ARG* 3.6 6.7 - - - +
82B LEU* 1.3 76.0 - - - +
84B ALA* 1.3 58.5 + - - +
86B GLY* 2.9 19.1 + - - -
87B VAL 3.4 12.1 + - - +
88B GLU* 6.1 0.7 - - - -
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Residues in contact with ALA 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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80B ARG* 3.1 13.9 + - - +
81B HIS* 3.4 15.0 - - - +
82B LEU 3.1 0.4 - - - -
83B ALA* 1.3 75.6 - - - +
85B LEU* 1.3 63.8 + - + +
86B GLY 3.3 1.3 + - - -
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Residues in contact with LEU 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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48B ILE* 3.7 28.7 - - + -
50B LEU* 5.9 0.2 - - + -
69B THR* 4.0 20.4 - - + -
71B VAL* 3.7 29.2 - - + -
81B HIS 3.3 14.1 + - - +
82B LEU* 2.9 11.0 + - - +
84B ALA* 1.3 82.6 - - + +
86B GLY* 1.3 61.5 + - - +
87B VAL* 4.0 12.7 - - + +
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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