Contacts of the helix formed by residues 80 - 87 (chain E) in PDB entry 2JE0
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 LEU 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57E ILE* 3.7 24.9 - - + -
76E VAL* 4.4 11.2 - - + -
78E GLY* 4.2 13.7 - - - +
79E GLY* 1.3 73.6 - - - +
81E GLU* 1.3 61.4 + - - +
82E VAL 3.0 6.9 + - - -
83E LEU* 3.2 30.3 + - + +
84E ALA 4.3 1.2 + - - -
95E LEU* 4.0 28.9 - - + -
100E ILE* 4.3 4.7 - - + -
105E THR* 3.4 32.1 + - + +
106E ILE* 4.1 17.7 - - + -
108E PRO* 3.9 11.8 - - + +
109E LEU* 4.1 18.6 - - + +
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Residues in contact with GLU 81 (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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79E GLY* 3.3 25.5 + - - -
80E LEU* 1.3 79.4 + - - +
82E VAL* 1.3 66.4 + - + +
83E LEU 3.2 0.7 + - - -
84E ALA* 3.6 14.1 + - - +
85E GLU* 3.6 27.2 + - - +
108E PRO* 3.6 30.0 - - + +
111E LYS* 6.6 0.2 - - + -
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Residues in contact with VAL 82 (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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57E ILE* 3.5 26.0 - - + +
58E ALA* 4.1 26.2 - - + +
60E LEU* 4.1 12.6 - - + +
79E GLY* 3.4 18.6 - - - +
81E GLU* 1.3 85.1 - - + +
83E LEU* 1.3 57.5 + - - +
85E GLU* 3.3 14.5 + - - +
86E LYS* 3.0 44.3 + - + +
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Residues in contact with LEU 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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57E ILE* 3.9 20.0 - - + -
60E LEU* 3.9 8.3 - - + -
69E LEU* 3.5 28.0 - - + -
71E LEU* 5.6 0.4 - - + -
80E LEU* 3.5 24.7 - - + +
81E GLU 3.2 1.0 - - - -
82E VAL* 1.3 77.0 - - - +
84E ALA* 1.3 57.4 + - - +
87E CYS* 2.9 52.2 + - - +
90E LEU* 4.6 1.1 - - + -
93E LEU* 3.7 34.3 - - + -
109E LEU* 3.8 13.7 - - + -
112E LEU* 3.8 17.0 - - + -
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Residues in contact with ALA 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 LEU 4.3 1.0 + - - -
81E GLU* 3.6 9.2 + - - +
82E VAL 3.5 0.6 - - - -
83E LEU* 1.3 78.1 - - - +
85E GLU* 1.3 61.3 + - + +
88E PRO* 3.5 20.8 - - - +
108E PRO 4.7 5.2 - - - +
111E LYS* 3.7 45.3 - - + +
112E LEU* 3.7 14.1 - - + +
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Residues in contact with GLU 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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62E LYS* 5.3 4.5 - - - +
81E GLU* 3.6 27.9 + - - +
82E VAL* 3.3 17.8 + - - +
83E LEU 3.2 0.2 - - - -
84E ALA* 1.3 81.0 - - + +
86E LYS* 1.3 74.8 + - + +
88E PRO* 4.4 5.8 - - - +
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Residues in contact with LYS 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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60E LEU* 3.4 35.1 + - + +
61E PRO* 3.5 12.3 - - - +
62E LYS* 3.6 26.2 - - + +
63E LEU 2.8 29.9 + - - +
64E ASN 4.3 0.2 + - - -
82E VAL* 3.0 26.5 + - + +
85E GLU* 1.3 90.9 - - + +
87E CYS* 1.3 60.1 + - - +
88E PRO* 3.6 6.1 - - - +
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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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60E LEU* 3.7 26.9 - - - -
63E LEU* 3.5 19.3 - - + +
66E LEU* 4.0 29.4 - - + +
83E LEU* 2.9 35.7 + - - +
86E LYS* 1.3 78.0 - - - +
88E PRO* 1.4 64.9 - - - +
89E ASN 3.1 4.5 + - - -
90E LEU* 3.3 23.6 + - + +
112E LEU* 3.6 1.7 - - - +
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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