Contacts of the strand formed by residues 283 - 288 (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 ILE 283 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112J LYS* 3.0 28.6 - - - +
113J ASN* 3.2 51.1 + - + +
114J GLN* 4.0 2.7 - - - +
115J ILE* 3.7 37.9 - - + +
158J ARG* 3.4 40.8 - - - +
236J TYR* 4.0 5.2 - - + -
256J LEU* 3.1 19.6 + - + +
257J SER* 4.8 1.0 - - - +
281J LYS 4.6 0.2 - - - +
282J PRO* 1.3 69.1 - - - +
284J VAL* 1.3 62.7 + - - +
285J TYR* 3.7 10.3 - - + -
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Residues in contact with VAL 284 (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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90J ALA 3.4 6.4 - - - +
91J ASP* 3.6 1.2 + - - -
92J TYR* 3.0 43.9 + - + -
109J MET* 3.2 41.3 - - + -
111J ALA 3.2 7.9 - - - +
112J LYS* 4.4 11.2 - - + -
158J ARG* 3.8 4.2 - - - +
282J PRO* 3.1 18.7 + - + +
283J ILE* 1.3 80.6 - - - +
285J TYR* 1.3 62.1 + - - +
323J LEU* 4.6 9.6 - - + -
327J ARG* 5.1 9.4 - - - +
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Residues in contact with TYR 285 (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* 4.9 0.4 - - + -
42J SER* 2.7 31.5 + - - -
43J LEU* 3.4 32.3 - - + -
89J THR 3.1 20.0 - - - +
90J ALA* 3.7 19.1 - - + -
92J TYR* 4.1 0.9 - - - -
109J MET* 3.3 5.7 - - - -
110J PHE* 2.9 40.3 + - + -
111J ALA* 2.6 23.2 + - + +
113J ASN* 2.8 45.9 + - + -
236J TYR* 3.8 8.5 - - - -
283J ILE* 3.7 10.1 - - + -
284J VAL* 1.3 72.5 - - - +
286J GLY* 1.3 58.3 + - - +
320J GLN* 3.5 17.0 - - - -
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Residues in contact with GLY 286 (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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88J ALA* 3.3 0.2 - - - -
89J THR* 2.8 30.0 + - - -
92J TYR* 3.5 29.1 - - - +
95J ILE* 4.1 5.2 - - - -
107J THR* 4.0 4.0 - - - -
108J ILE 3.4 8.5 - - - -
110J PHE* 3.2 10.1 - - - -
284J VAL 3.7 0.2 + - - -
285J TYR* 1.3 73.0 - - - +
287J ILE* 1.3 60.4 + - - -
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Residues in contact with ILE 287 (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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47J MET* 5.4 1.1 - - + -
86J VAL* 3.7 24.9 - - + -
87J ILE 3.1 14.1 - - - +
88J ALA* 4.1 5.8 - - + +
95J ILE* 4.0 1.5 - - - +
106J TRP* 4.1 1.4 - - - -
107J THR* 3.7 3.1 - - - +
108J ILE* 3.1 47.7 + - + +
110J PHE* 3.4 19.3 - - + -
286J GLY* 1.3 74.1 - - - -
288J THR* 1.3 80.0 + - - +
302J PHE* 4.7 1.3 - - + -
303J VAL* 4.4 21.8 - - + -
306J VAL* 3.8 35.2 - - + -
307J ILE* 5.6 0.7 - - + -
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Residues in contact with THR 288 (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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86J VAL* 3.3 5.9 - - - +
87J ILE* 2.8 48.5 + - + +
95J ILE* 3.3 33.9 - - + -
99J MET* 4.6 9.4 - - + -
104J ALA* 4.3 8.5 - - + +
106J TRP* 2.9 34.4 + - - -
287J ILE* 1.3 81.0 - - - +
289J ILE* 1.3 80.2 + - - +
290J PRO* 3.7 0.7 - - - +
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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