Contacts of the strand formed by residues 86 - 89 (chain J) in PDB entry 2ONK
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 VAL 86 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35J LEU* 4.8 1.1 - - + -
36J LYS 3.0 3.2 + - - +
37J VAL* 3.3 32.5 - - + -
38J PHE 3.1 25.4 + - - -
84J ALA* 3.8 0.9 - - - +
85J ASP* 1.3 90.0 - - + +
87J ILE* 1.3 74.4 + - - +
88J ALA* 4.9 1.6 - - + +
287J ILE* 3.7 32.8 - - + -
288J THR 3.3 6.1 - - - +
290J PRO* 4.3 0.2 - - - -
299J ALA* 4.5 9.4 - - + +
302J PHE* 3.7 29.8 - - + -
303J VAL* 4.8 4.9 - - + -
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Residues in contact with ILE 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38J PHE* 3.2 27.8 - - + +
73J THR* 4.2 18.4 - - + +
74J ILE* 4.2 17.9 - - + -
77J VAL* 4.0 16.4 - - + -
84J ALA* 3.9 11.9 - - + -
86J VAL* 1.3 83.7 - - - +
88J ALA* 1.3 61.9 + - - +
89J THR* 4.4 7.6 - - + -
95J ILE* 4.4 1.0 - - + +
99J MET* 4.4 15.7 - - + -
287J ILE* 3.1 3.6 - - - +
288J THR* 2.8 47.8 + - + +
290J PRO* 4.2 15.7 - - + -
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Residues in contact with ALA 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37J VAL* 5.8 0.2 - - + -
38J PHE 3.2 7.3 + - - -
39J HIS* 3.2 10.7 - - + -
40J ALA 2.8 27.8 + - - -
43J LEU* 3.1 29.8 - - + -
47J MET* 4.7 8.7 - - + -
70J SER* 4.4 0.2 + - - -
73J THR* 4.6 2.6 - - - +
86J VAL* 5.2 1.8 - - + -
87J ILE* 1.3 76.0 - - - +
89J THR* 1.3 62.9 + - - +
110J PHE* 4.3 6.5 - - + -
286J GLY 3.3 8.5 - - - +
287J ILE* 4.4 6.7 - - + -
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Residues in contact with THR 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40J ALA* 4.2 2.5 - - - -
43J LEU* 4.7 0.2 - - - +
70J SER* 3.0 26.7 - - - +
73J THR* 5.4 0.4 - - + -
74J ILE* 4.0 17.9 - - + -
87J ILE* 4.4 4.3 - - + -
88J ALA* 1.3 79.0 - - - +
90J ALA* 1.3 59.0 + - - +
91J ASP 2.6 29.7 + - - +
92J TYR* 3.4 6.8 + - - -
95J ILE* 3.7 24.9 - - + +
285J TYR* 3.1 32.6 - - - +
286J GLY* 2.8 10.6 + - - +
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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