Contacts of the helix formed by residues 84 - 91 (chain E) in PDB entry 1GZ0
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 ASP 84 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78E ARG* 3.9 27.7 + - - +
79E GLN 4.3 2.9 - - - +
80E TYR* 3.7 16.3 - - + -
81E GLN* 2.5 49.2 + - - +
83E ASN* 1.3 79.6 - - - +
85E LEU* 1.3 63.7 + - - +
86E PRO* 3.4 1.8 - - - -
87E ASP* 3.5 13.5 + - + +
88E LEU* 3.3 19.9 + - - +
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E GLN 3.3 2.4 + - - -
82E GLU* 3.2 17.6 + - + +
84E ASP* 1.3 78.3 - - - +
86E PRO* 1.3 63.1 - - + +
88E LEU* 3.1 18.1 - - + +
89E ILE* 3.0 44.6 + - + +
97E LEU* 5.8 2.0 - - + -
123E ALA* 5.4 1.1 - - + -
125E ILE* 4.1 21.5 - - + -
152E ILE* 4.0 31.2 - - + -
154E VAL* 4.1 15.9 - - + -
160E THR* 3.6 21.3 - - + +
163E MSE 3.5 22.0 - - + -
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Residues in contact with PRO 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E GLU 3.8 4.5 - - - +
83E ASN* 3.6 13.2 - - - +
84E ASP 3.5 3.4 - - - -
85E LEU* 1.3 92.6 - - + +
87E ASP* 1.3 65.6 + - - +
89E ILE* 3.6 9.5 + - + +
90E ALA* 3.0 25.3 + - - +
163E MSE 4.4 22.2 - - + -
167E GLU* 5.2 5.0 - - + +
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Residues in contact with ASP 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E ARG* 5.4 8.4 + - - +
83E ASN 4.9 3.2 - - - +
84E ASP* 3.5 18.6 + - + +
85E LEU 3.4 0.8 - - - -
86E PRO* 1.3 76.2 - - - +
88E LEU* 1.3 68.3 + - - +
90E ALA* 3.2 6.4 + - - +
91E SER* 3.1 24.5 + - - -
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Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E TYR* 3.4 35.4 - - + +
84E ASP 3.3 10.1 + - - +
85E LEU* 3.1 18.2 - - + +
87E ASP* 1.3 78.7 - - - +
89E ILE* 1.3 63.3 + - + +
91E SER* 2.7 27.8 + - - +
92E LEU* 3.2 25.4 - - + +
97E LEU* 5.4 2.2 - - + -
122E HIS* 4.7 7.9 - - + +
123E ALA* 3.7 30.1 - - + -
150E PRO* 5.2 3.4 - - + -
152E ILE* 4.0 17.7 - - + -
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Residues in contact with ILE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E LEU* 3.0 24.8 + - + +
86E PRO* 3.9 5.2 - - + +
88E LEU* 1.3 74.1 - - + +
90E ALA* 1.3 58.1 + - - +
91E SER 2.9 10.7 + - - -
92E LEU* 3.0 30.5 + - + +
95E PRO* 4.2 5.6 - - + +
97E LEU* 5.0 8.5 - - + -
163E MSE 3.7 23.3 - - + -
164E LEU* 3.3 33.7 - - + -
167E GLU* 4.4 15.3 - - + +
169E ILE* 3.8 22.9 - - + -
190E ARG* 4.1 16.1 + - - +
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Residues in contact with ALA 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E PRO 3.0 20.3 + - - +
87E ASP* 3.2 6.3 + - - +
89E ILE* 1.3 76.5 - - - +
91E SER* 1.3 57.2 + - - +
92E LEU 3.3 4.2 + - - +
167E GLU* 5.0 9.0 - - - +
190E ARG* 6.1 0.9 - - - +
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Residues in contact with SER 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ASP 3.1 9.9 + - - -
88E LEU* 2.7 21.5 + - - +
89E ILE 2.9 1.8 - - - -
90E ALA* 1.3 77.5 - - - +
92E LEU* 1.3 70.4 + - - +
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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