Contacts of the helix formed by residues 82 - 89 (chain B) in PDB entry 1KNY
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 GLU 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LYS* 2.4 35.9 + - - +
56B VAL* 3.5 23.3 - - + +
57B MET 3.2 7.1 + - - -
80B TYR 3.6 1.6 + - - -
81B SER* 1.3 73.0 - - - +
83B GLU* 1.3 63.0 + - - +
85B LEU* 4.1 5.8 - - - +
86B LEU* 2.8 47.8 + - + +
115B TYR* 3.4 27.2 - - + +
118B LYS* 3.8 30.4 + - + +
119B VAL* 5.8 3.1 - - + -
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Residues in contact with GLU 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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60B GLU* 5.3 9.2 - - - +
81B SER* 3.1 6.8 - - - +
82B GLU* 1.3 80.8 - - - +
84B ILE* 1.3 67.7 + - + +
86B LEU* 3.6 5.5 - - - +
87B ASP* 3.0 33.4 + - - +
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Residues in contact with ILE 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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60B GLU 4.0 9.2 - - - +
61B GLU 5.0 0.9 - - - -
62B ALA 2.8 31.9 - - - +
63B GLU* 3.8 31.9 - - + +
80B TYR* 4.8 5.6 - - + -
81B SER* 2.8 22.0 + - - +
83B GLU* 1.3 81.8 - - + +
85B LEU* 1.3 64.6 + - - +
87B ASP* 3.2 8.1 - - - +
88B TYR* 3.1 22.0 + - + +
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Residues in contact with LEU 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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54B MET* 5.0 7.0 - - - -
56B VAL* 3.6 31.4 - - + -
80B TYR* 3.4 43.5 - - + -
81B SER 3.1 4.2 + - - +
82B GLU* 4.6 7.6 - - - +
84B ILE* 1.3 78.6 - - - +
86B LEU* 1.3 70.9 + - - +
88B TYR* 2.9 9.2 + - + +
89B ALA* 2.8 18.5 + - - +
103B PHE* 3.2 35.9 - - + -
116B LEU* 5.8 0.2 - - + -
119B VAL* 4.0 22.2 - - + -
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Residues in contact with LEU 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 GLU* 2.8 44.0 + - + +
83B GLU* 3.6 5.4 - - - +
85B LEU* 1.3 77.9 - - - +
87B ASP* 1.3 59.3 + - - +
89B ALA* 2.9 23.7 + - - +
90B SER* 3.2 8.7 + - - -
118B LYS* 3.7 20.6 - - + +
119B VAL* 3.4 37.0 - - + +
122B THR* 3.2 37.0 - - + +
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Residues in contact with ASP 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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83B GLU* 3.0 24.8 + - - +
84B ILE* 3.2 11.7 - - - +
86B LEU* 1.3 80.1 - - - +
88B TYR* 1.3 59.1 + - + +
90B SER* 2.9 19.1 + - - -
91B GLN* 3.5 25.6 + - - +
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Residues in contact with TYR 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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80B TYR* 4.5 23.8 - + + -
84B ILE* 3.4 12.1 - - + +
85B LEU* 2.9 9.1 + - + +
87B ASP* 1.3 79.3 - - - +
89B ALA* 1.3 60.4 + - - +
90B SER 3.2 0.9 - - - -
91B GLN* 3.4 27.2 + - + +
99B THR* 4.6 9.9 - - - +
100B HIS* 2.8 44.9 + + - -
102B GLN* 4.0 16.1 + - - -
103B PHE* 3.2 35.0 - + - -
557B APC 5.6 0.9 - - - -
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Residues in contact with ALA 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 LEU 2.8 11.0 + - - +
86B LEU* 2.9 15.9 + - - +
88B TYR* 1.3 81.4 - - - +
90B SER* 1.3 53.1 - - - +
91B GLN 3.3 0.6 + - - -
96B TRP* 4.6 0.3 + - - -
100B HIS* 3.1 22.6 - - - -
103B PHE* 4.2 20.4 - - + -
119B VAL* 3.8 24.5 - - + +
122B THR* 4.3 3.1 - - + -
123B ALA* 3.5 23.9 - - - +
126B VAL* 4.2 1.2 - - - +
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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