Contacts of the helix formed by residues 76 - 82 (chain B) in PDB entry 2GZD
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 ILE 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.5 31.4 - - + -
67B THR* 4.7 2.7 - - - +
71B GLU* 4.5 6.5 - - - +
74B ARG* 3.8 29.6 - - + +
75B ALA* 1.3 77.4 - - - +
77B THR* 1.3 69.5 - - - +
79B ALA* 3.1 7.3 + - - +
80B TYR* 3.0 29.0 + - + +
482D ASP* 3.1 41.2 + - - +
485D LEU* 3.3 23.1 - - + -
486D VAL* 3.6 8.5 - - + +
489D MSE 3.7 11.0 - - - +
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Residues in contact with THR 77 (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 GLU* 3.8 21.1 - - + +
72B ARG 4.1 3.6 - - - +
73B TYR* 3.8 24.5 - - + -
74B ARG* 2.8 43.8 + - + +
76B ILE* 1.3 78.9 - - - +
78B SER* 1.3 67.3 + - - +
80B TYR* 3.3 11.3 + - - +
81B TYR* 3.2 27.3 + - - -
108B GLU* 5.2 0.4 - - - -
112B HIS* 4.0 16.5 + - + -
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Residues in contact with SER 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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73B TYR* 4.9 14.8 - - - -
74B ARG 4.6 1.2 + - - -
75B ALA 4.4 5.9 + - - -
76B ILE 3.4 0.6 - - - -
77B THR* 1.3 84.2 + - - +
79B ALA* 1.3 57.7 + - - +
81B TYR* 3.8 3.2 + - - +
82B ARG* 3.1 47.1 + - - +
112B HIS* 5.1 12.2 - - - +
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Residues in contact with ALA 79 (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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13B LYS* 3.2 16.1 + - - -
75B ALA 4.8 4.2 + - - +
76B ILE* 3.1 9.3 + - - +
78B SER* 1.3 75.5 + - - +
80B TYR* 1.3 64.8 + - - +
81B TYR 3.5 0.2 - - - -
82B ARG* 3.6 31.8 + - - +
486D VAL* 5.4 11.9 - - + +
489D MSE 3.4 30.8 - - + +
490D GLU* 5.6 3.4 - - + +
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Residues in contact with TYR 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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13B LYS* 3.1 12.9 + - - +
15B VAL* 3.1 47.1 - - + +
16B LEU 2.8 27.1 + - - -
17B ILE* 4.1 9.2 - - + -
46B VAL* 3.9 23.3 - - + -
65B TRP* 3.2 33.6 + + + -
66B ASP* 3.6 7.3 - - - -
67B THR* 3.6 30.2 + - + -
71B GLU* 4.1 14.1 - - - -
76B ILE* 3.0 19.3 + - + +
77B THR* 3.3 9.8 + - - +
79B ALA* 1.3 78.6 - - - +
81B TYR* 1.3 69.0 + + - +
489D MSE 3.5 7.8 - - + +
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Residues in contact with TYR 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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15B VAL* 4.1 13.2 - - + -
17B ILE* 3.4 31.6 - - + +
71B GLU* 4.1 13.8 + - - -
77B THR* 3.2 27.1 + - - +
78B SER 4.4 1.3 - - - +
80B TYR* 1.3 81.6 - + - +
82B ARG* 1.3 68.2 + - - +
83B GLY 3.0 1.0 + - - -
84B ALA* 3.0 21.7 + - + +
105B TRP* 4.5 0.9 - - - -
108B GLU* 3.1 39.7 + - + +
109B LEU* 3.6 28.7 - - + -
112B HIS* 3.4 43.3 - - + +
113B ALA* 4.1 14.4 - - + -
114B ASP 5.2 1.6 + - - -
117B ILE* 5.2 1.1 - - + -
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Residues in contact with ARG 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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13B LYS* 2.9 25.3 + - - +
78B SER* 3.1 41.5 + - - +
79B ALA* 3.7 32.0 - - - +
80B TYR 3.4 1.8 - - - -
81B TYR* 1.3 74.9 - - - +
83B GLY* 1.3 61.5 + - - +
84B ALA 3.1 0.7 + - - -
112B HIS 5.1 2.0 + - - -
490D GLU* 4.7 20.0 + - - +
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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