Contacts of the helix formed by residues 80 - 90 (chain B) in PDB entry 5UQ3
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 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B LYS 3.9 3.8 + - - +
77B LEU* 3.1 23.0 + - - +
78B PHE 3.2 1.5 - - - +
79B ASP* 1.3 82.9 - - - +
81B ASP* 1.3 80.5 + - - +
82B LEU 3.4 3.5 + - - -
83B ILE* 3.8 9.7 - - + +
84B GLN* 3.2 23.1 + - - +
120B ARG* 2.4 52.2 + - - +
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Residues in contact with ASP 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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79B ASP 3.9 0.4 + - - -
80B ASP* 1.3 82.1 + - - +
82B LEU* 1.3 80.1 + - + +
83B ILE 3.1 1.1 - - - -
84B GLN* 2.9 6.0 + - - +
85B ASP* 2.9 46.2 + - - +
120B ARG* 4.9 3.4 - - - +
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Residues in contact with LEU 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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80B ASP* 3.4 2.0 + - - -
81B ASP* 1.3 92.9 - - + +
83B ILE* 1.3 58.9 + - + +
85B ASP* 4.7 2.2 - - + +
86B PHE* 2.9 29.5 + - - +
120B ARG* 3.7 36.8 - - - +
124B PHE* 4.8 4.9 - - + -
147B TRP* 3.2 44.0 - - + +
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Residues in contact with ILE 83 (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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77B LEU* 3.1 34.3 - - + +
78B PHE* 3.9 21.3 - - + -
80B ASP* 3.8 15.3 - - + +
81B ASP 3.1 0.6 - - - -
82B LEU* 1.3 74.6 - - + +
84B GLN* 1.3 60.5 + - - +
86B PHE* 3.0 5.2 + - - +
87B LEU* 2.9 49.8 + - + +
120B ARG* 4.6 17.0 - - + -
123B PHE* 3.6 32.5 - - + -
124B PHE* 3.8 18.4 - - + -
193B TYR* 5.6 0.2 - - - +
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Residues in contact with GLN 84 (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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78B PHE 4.5 10.5 + - - +
79B ASP 5.5 1.1 - - - +
80B ASP 3.2 17.2 + - - +
81B ASP* 2.9 6.5 + - - +
83B ILE* 1.3 79.0 - - - +
85B ASP* 1.3 62.4 + - - +
87B LEU* 3.2 9.1 + - - +
88B TRP* 2.9 27.1 + - - +
193B TYR* 5.3 4.5 - - - +
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Residues in contact with ASP 85 (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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81B ASP* 2.9 33.8 + - - +
82B LEU* 4.7 1.9 - - + +
84B GLN* 1.3 80.6 - - - +
86B PHE* 1.3 56.8 + - - +
88B TRP* 3.6 9.6 - - - +
89B MET* 2.9 23.2 + - - +
147B TRP* 3.2 29.4 - - + -
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Residues in contact with PHE 86 (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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82B LEU 2.9 21.0 + - - +
83B ILE* 3.0 6.9 + - - +
85B ASP* 1.3 77.9 - - - +
87B LEU* 1.3 74.2 + - + +
89B MET* 3.4 6.8 - - - +
90B ASP* 3.2 18.9 + - + +
95B ILE* 3.7 29.6 - - + -
96B ALA* 4.5 11.4 - - + -
123B PHE* 4.7 3.1 - + - -
124B PHE* 3.7 21.8 - + + -
127B LEU* 3.6 32.8 - - + -
143B GLU 4.8 0.7 - - - -
144B ILE* 4.3 26.0 - - + -
147B TRP* 3.4 39.2 - + + -
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Residues in contact with LEU 87 (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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78B PHE* 4.6 11.9 - - + -
83B ILE* 2.9 41.3 + - + +
84B GLN* 3.6 9.0 - - - +
86B PHE* 1.3 86.6 - - + +
88B TRP* 1.3 59.7 + - - +
90B ASP* 2.8 28.4 + - + +
96B ALA* 3.8 21.8 - - + -
101B LEU* 4.0 11.4 - - + -
123B PHE* 5.2 2.9 - - + -
193B TYR* 4.6 15.5 - - + +
197B ARG* 3.0 49.0 + - - +
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Residues in contact with TRP 88 (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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84B GLN 2.9 16.7 + - - +
85B ASP* 3.6 10.5 - - - +
86B PHE 3.3 0.2 - - - -
87B LEU* 1.3 74.6 - - - +
89B MET* 1.3 64.2 + - - +
90B ASP 3.7 5.2 - - - +
91B CYS* 4.9 4.5 - - - -
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Residues in contact with MET 89 (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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85B ASP 2.9 14.1 + - - +
86B PHE* 3.4 14.4 - - - +
87B LEU 3.2 0.2 - - - -
88B TRP* 1.3 78.2 - - - +
90B ASP* 1.3 62.1 + - - +
91B CYS* 3.3 15.6 + - - -
95B ILE* 5.1 7.9 - - + -
143B GLU* 4.1 36.8 - - + +
147B TRP* 2.8 43.7 - - + +
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Residues in contact with ASP 90 (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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86B PHE* 3.2 11.0 + - + +
87B LEU* 2.8 29.8 + - + +
88B TRP* 3.7 3.7 - - - +
89B MET* 1.3 78.8 - - - +
91B CYS* 1.3 62.8 + - - +
93B CYS* 3.2 9.8 - - - -
94B LYS* 3.2 20.4 + - - +
95B ILE* 3.3 25.8 + - + +
96B ALA* 2.9 38.6 + - + +
197B ARG* 3.3 13.9 + - - +
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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