Contacts of the helix formed by residues 78 - 89 (chain E) in PDB entry 5UQ9
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 78 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E LYS 3.6 1.0 + - - -
77E ALA* 1.3 76.1 - - - +
79E GLN* 1.3 64.9 + - - -
80E ALA 3.2 1.7 + - - -
81E VAL* 3.5 7.1 + - - +
82E ASP* 3.3 17.4 - - - +
104E SER* 4.7 0.4 + - - -
108E ASP* 5.3 5.6 + - - -
112E ARG* 3.3 13.2 + - - +
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Residues in contact with GLN 79 (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 GLY* 1.3 69.7 - - - -
80E ALA* 1.3 65.4 + - - +
81E VAL 3.3 0.3 + - - -
82E ASP* 3.3 17.8 + - - +
83E ASP* 3.0 52.8 + - - +
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Residues in contact with ALA 80 (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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34E ARG* 3.6 37.1 + - - +
75E VAL* 4.2 7.4 - - + -
76E LYS* 3.4 24.5 - - + +
78E GLY* 3.2 1.4 - - - -
79E GLN* 1.3 78.1 - - - +
81E VAL* 1.3 59.7 + - - +
83E ASP* 3.5 7.3 + - - +
84E PHE* 3.3 20.1 + - - +
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Residues in contact with VAL 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LEU* 4.5 11.1 - - + +
75E VAL* 3.8 19.1 - - + +
76E LYS 3.7 17.5 - - - +
77E ALA* 4.1 12.8 - - - -
78E GLY 3.5 1.7 + - - +
79E GLN 3.2 0.6 - - - -
80E ALA* 1.3 75.9 - - - +
82E ASP* 1.3 65.0 + - - +
84E PHE* 3.2 6.8 + - - +
85E ILE* 3.1 33.9 + - + +
100E ASP* 3.9 21.5 - - + +
104E SER* 4.3 3.8 - - - +
112E ARG* 3.1 38.6 - - - +
123E PHE* 5.4 0.2 - - + -
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Residues in contact with ASP 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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78E GLY 3.3 7.4 - - - +
79E GLN* 3.3 21.7 + - - +
81E VAL* 1.3 76.7 - - - +
83E ASP* 1.3 63.4 + - - +
85E ILE* 3.3 11.0 + - - +
86E GLU* 3.1 30.6 + - + +
111E ARG* 3.0 35.1 + - - -
112E ARG* 2.8 38.2 + - - +
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Residues in contact with ASP 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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34E ARG* 5.3 6.9 + - - +
79E GLN* 3.0 44.1 + - - +
80E ALA* 3.7 9.8 - - - +
82E ASP* 1.3 77.5 - - - +
84E PHE* 1.3 56.6 + - - +
86E GLU* 3.3 8.6 + - - +
87E LYS* 3.0 38.7 + - + +
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Residues in contact with PHE 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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9E ILE* 3.5 30.3 - - + -
32E PHE* 4.4 4.5 - + - -
34E ARG* 3.3 55.4 - - + -
58E LEU* 4.1 25.6 - - + -
73E LEU* 4.3 19.5 - - + -
75E VAL* 3.6 27.1 - - + -
80E ALA 3.3 4.9 + - - +
81E VAL* 3.2 9.4 + - - +
83E ASP* 1.3 76.0 - - + +
85E ILE* 1.3 59.4 + - - +
87E LYS* 3.4 24.5 + - + +
88E LEU* 2.9 35.6 + - + +
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Residues in contact with ILE 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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73E LEU* 4.5 12.3 - - + -
81E VAL* 3.1 18.6 + - + +
82E ASP* 3.6 13.2 - - - +
83E ASP 3.2 0.2 - - - -
84E PHE* 1.3 77.0 - - - +
86E GLU* 1.3 62.0 + - + +
88E LEU* 3.2 3.5 + - - +
89E VAL* 2.9 39.5 + - + +
98E ILE* 5.0 7.0 - - + -
112E ARG* 3.8 37.7 - - + -
116E LEU* 3.8 34.5 - - + -
119E LYS* 6.2 0.2 - - - +
123E PHE* 4.2 15.7 - - + -
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Residues in contact with GLU 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 ASP* 3.1 21.6 + - + +
83E ASP* 3.8 7.6 - - - +
85E ILE* 1.3 78.4 - - + +
87E LYS* 1.3 57.9 + - + +
89E VAL* 4.8 3.1 - - - +
90E PRO* 3.2 22.3 - - - +
119E LYS* 6.0 4.5 - - - +
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Residues in contact with LYS 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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32E PHE* 5.8 1.6 - - - -
34E ARG* 5.5 7.9 - - - +
58E LEU* 3.6 26.0 - - + +
83E ASP* 3.0 28.3 + - + +
84E PHE* 3.8 27.0 - - + +
85E ILE 3.2 0.2 - - - -
86E GLU* 1.3 78.7 - - + +
88E LEU* 1.3 60.6 + - - +
90E PRO* 4.1 6.2 - - - +
91E LEU* 3.6 21.8 - - - +
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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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9E ILE* 4.2 3.1 - - + -
58E LEU* 4.0 19.1 - - + -
61E MET* 3.9 16.2 - - + -
62E VAL* 4.1 11.9 - - + -
71E ILE* 3.7 44.6 - - + -
73E LEU* 4.2 18.6 - - + -
84E PHE* 2.9 19.3 + - + +
85E ILE 3.2 2.9 + - - +
87E LYS* 1.3 79.9 - - - +
89E VAL* 1.3 66.1 + - - +
90E PRO 3.4 0.9 - - - -
91E LEU* 2.8 17.1 + - + +
92E LEU* 3.1 17.8 + - + +
98E ILE* 4.3 21.3 - - + -
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Residues in contact with VAL 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E ILE* 2.9 25.0 + - + +
86E GLU* 4.8 2.5 - - - +
88E LEU* 1.3 74.9 - - - +
90E PRO* 1.3 69.6 - - + +
92E LEU* 3.1 27.7 + - - +
98E ILE* 5.0 6.1 - - + -
116E LEU* 3.6 29.6 - - + -
119E LYS* 4.0 29.2 - - + +
121E ILE* 4.4 17.9 - - + +
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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