Contacts of the helix formed by residues 77 - 89 (chain B) in PDB entry 1O0W
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 GLU 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS* 5.2 1.1 - - - +
75B GLU 3.6 3.2 + - - +
76B ALA* 1.3 75.9 - - - +
78B VAL* 1.3 61.4 + - - +
79B GLY* 4.1 6.8 - - - +
80B ASP* 2.9 41.5 + - - +
81B LEU* 3.2 8.7 + - - +
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Residues in contact with VAL 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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51A GLU* 3.7 37.2 - - + +
52A LYS* 3.9 21.3 - - + +
55A PHE* 4.2 26.5 - - + -
76B ALA 3.6 0.2 + - - -
77B GLU* 1.3 72.0 - - - +
79B GLY* 1.3 56.7 + - - +
81B LEU* 3.2 10.4 + - + +
82B ALA* 3.0 28.4 + - + +
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.0 6.7 - - - +
78B VAL* 1.3 80.0 - - - +
80B ASP* 1.3 61.1 + - - +
82B ALA* 3.5 6.5 + - - +
83B ARG* 3.1 23.0 + - - +
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Residues in contact with ASP 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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76B ALA* 4.4 4.7 - - + -
77B GLU* 2.9 40.5 + - - +
79B GLY* 1.3 74.0 - - - +
81B LEU* 1.3 61.3 + - - +
83B ARG* 3.2 23.6 + - - +
84B VAL* 2.9 36.3 + - - +
161B MET* 4.2 19.3 - - - -
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Residues in contact with LEU 81 (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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52A LYS* 3.9 30.1 - - + -
55A PHE* 3.8 40.8 - - + -
69B LEU* 3.5 39.2 - - + +
70B TYR* 5.1 3.4 - - - -
73B TYR 4.1 2.9 - - - +
76B ALA* 3.6 25.6 - - + -
77B GLU 3.2 11.5 + - - +
78B VAL* 3.2 9.8 + - - +
80B ASP* 1.3 77.0 - - - +
82B ALA* 1.3 55.9 + - - +
84B VAL* 4.7 1.6 - - - -
85B LYS* 2.9 30.5 + - - +
161B MET* 4.2 8.3 - - + -
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Residues in contact with ALA 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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55A PHE* 4.1 13.8 - - + -
78B VAL* 3.0 17.6 + - + +
79B GLY* 3.9 7.2 - - - +
81B LEU* 1.3 73.8 - - - +
83B ARG* 1.3 64.3 + - - +
85B LYS* 3.5 9.3 + - - +
86B SER* 3.1 27.5 + - - -
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Residues in contact with ARG 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 GLY 3.1 16.7 + - - +
80B ASP* 3.2 25.1 + - - +
82B ALA* 1.3 73.5 - - - +
84B VAL* 1.3 85.9 + - - +
86B SER* 3.4 6.2 + - - -
87B ALA* 3.2 21.3 + - + +
160B ILE* 3.3 28.0 + - + +
161B MET* 3.7 24.9 + - - -
163B GLY* 5.1 3.8 - - - +
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Residues in contact with VAL 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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69B LEU* 3.6 26.0 - - + -
80B ASP 2.9 20.9 + - - +
81B LEU 3.9 3.1 - - - +
83B ARG* 1.3 94.3 - - - +
85B LYS* 1.3 60.2 - - - +
87B ALA* 3.3 1.2 + - - +
88B ALA* 2.8 28.1 + - + +
157B ILE* 4.1 23.8 - - + +
160B ILE* 3.9 18.2 - - + -
161B MET* 3.6 28.9 - - + +
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Residues in contact with LYS 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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55A PHE* 4.3 9.4 - - + -
58A ASP* 5.6 3.8 + - - -
62B GLU* 3.8 24.3 + - + +
65B VAL* 4.2 13.3 - - + +
66B CYS* 3.5 31.2 - - - -
69B LEU* 3.7 13.6 - - + +
81B LEU 2.9 18.6 + - - +
82B ALA* 3.7 10.8 - - - +
83B ARG 3.2 0.2 - - - -
84B VAL* 1.3 75.5 - - - +
86B SER* 1.3 78.9 + - - +
88B ALA* 3.2 2.3 + - - +
89B ALA* 3.0 24.5 + - + +
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Residues in contact with SER 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 3.1 16.3 + - - -
83B ARG* 3.8 5.8 - - - -
84B VAL 3.3 0.2 - - - -
85B LYS* 1.3 86.5 - - - +
87B ALA* 1.3 61.6 + - - +
89B ALA* 3.6 4.0 + - - +
90B SER* 3.2 22.3 + - - -
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Residues in contact with ALA 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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83B ARG* 3.2 9.5 + - + +
84B VAL 3.7 1.8 - - - +
85B LYS 3.2 0.4 - - - -
86B SER* 1.3 80.9 - - - +
88B ALA* 1.3 61.6 + - - +
90B SER* 2.7 28.0 + - - -
93B VAL* 3.4 8.2 - - + +
160B ILE* 3.6 35.0 - - + -
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Residues in contact with ALA 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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65B VAL* 3.7 28.7 - - + -
84B VAL 2.8 21.7 + - - +
85B LYS 3.8 0.2 - - - +
87B ALA* 1.3 74.5 - - - +
89B ALA* 1.3 56.7 + - - +
90B SER 3.3 0.2 - - - -
93B VAL* 3.4 23.9 - - - +
94B LEU* 4.3 1.4 - - - +
153B PHE* 3.9 15.7 - - + -
156B TYR* 5.8 1.8 - - + -
157B ILE* 3.9 20.4 - - + -
160B ILE* 3.7 12.3 - - + +
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Residues in contact with ALA 89 (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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58B ASP* 5.7 0.5 - - - +
61B LEU* 3.7 20.7 - - + +
62B GLU* 3.6 30.3 - - - +
65B VAL* 5.0 5.4 - - + -
85B LYS* 3.0 16.6 + - + +
86B SER* 3.8 4.0 - - - +
88B ALA* 1.3 75.2 - - - +
90B SER* 1.3 63.9 + - - +
91B GLU 3.9 0.3 + - - -
94B LEU* 3.5 15.4 - - - +
130B GLU* 4.8 2.1 - - - +
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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