Contacts of the helix formed by residues 82 - 89 (chain E) in PDB entry 2GOO
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 GLY 82 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D ASN* 3.1 23.2 + - - +
62D ILE* 3.6 13.7 - - - +
80E TYR 3.3 1.0 + - - -
81E GLU* 1.3 72.8 - - - +
83E SER* 1.3 62.4 + - - +
84E ASP* 3.3 4.0 - - - -
85E PHE* 3.3 17.3 + - - +
86E GLN* 3.2 24.5 + - - +
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Residues in contact with SER 83 (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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58E HIS* 2.9 34.3 + - - -
78E MET* 3.6 16.6 - - - -
79E LYS 3.4 14.6 + - - -
80E TYR* 2.7 26.0 + - - -
81E GLU 3.3 1.4 + - - -
82E GLY* 1.3 75.6 - - - +
84E ASP* 1.3 65.2 + - - +
87E CYS* 2.8 35.6 + - - +
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Residues in contact with ASP 84 (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* 5.1 10.7 + - - -
82E GLY* 3.3 1.1 - - - -
83E SER* 1.3 80.0 + - - +
85E PHE* 1.3 71.5 + - + +
87E CYS* 4.4 2.3 - - - +
88E LYS* 3.1 26.2 + - - +
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Residues in contact with PHE 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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59D ASN* 4.1 23.8 - - + -
62D ILE* 3.9 16.8 - - + -
63D VAL* 4.1 27.1 - - + -
66D LEU* 3.7 17.2 - - + +
82E GLY* 3.3 17.2 + - - +
83E SER 3.3 0.2 - - - -
84E ASP* 1.3 85.1 - - + +
86E GLN* 1.3 57.4 + - - +
88E LYS* 3.4 5.0 + - - +
89E ASP* 2.9 27.7 + - - -
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Residues in contact with GLN 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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49D PHE* 3.3 36.7 - - + -
50D PRO* 3.4 9.2 - - + +
51D LEU* 2.6 50.8 + - - +
62D ILE* 3.5 36.0 - - + +
65D THR* 5.7 0.7 - - - +
78E MET* 3.7 37.9 - - + +
81E GLU 5.5 0.6 + - - -
82E GLY 3.2 13.1 + - - +
83E SER 3.3 0.2 + - - -
85E PHE* 1.3 73.2 - - - +
87E CYS* 1.3 64.5 + - - +
89E ASP 3.5 2.1 + - - -
99E ILE* 3.4 10.0 - - - +
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Residues in contact with CYS 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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58E HIS* 4.4 12.3 - - - -
78E MET* 3.6 13.0 - - - -
83E SER* 2.8 24.6 + - - +
84E ASP* 4.4 2.2 - - - +
86E GLN* 1.3 70.3 - - - +
88E LYS* 1.3 66.6 + - - +
99E ILE* 3.9 16.9 - - - +
100E GLU* 5.8 0.2 - - - -
101E CYS* 2.1 52.9 - - + +
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Residues in contact with LYS 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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84E ASP 3.1 20.7 + - - +
85E PHE* 3.7 5.8 - - - +
86E GLN 3.3 0.2 - - - -
87E CYS* 1.3 80.1 - - - +
89E ASP* 1.3 77.6 + - - +
91E PRO* 5.6 2.7 - - + +
99E ILE* 5.1 0.2 - - - +
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Residues in contact with ASP 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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49D PHE* 3.5 10.3 - - + -
66D LEU* 3.4 12.3 - - - +
85E PHE 2.9 16.4 + - - -
86E GLN 3.5 2.9 + - - -
87E CYS 3.4 1.2 - - - -
88E LYS* 1.3 96.6 - - - +
90E SER* 1.3 83.8 + - - +
91E PRO* 3.8 6.6 - - - +
97E ARG* 2.7 59.3 + - - +
98E THR* 5.1 0.2 - - - -
99E ILE* 3.9 20.1 + - + +
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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