Contacts of the strand formed by residues 115 - 119 (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 115 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114J GLN* 1.3 70.7 + - - +
116J VAL* 1.3 76.0 + - - +
155J CYS* 4.0 13.9 - - - +
158J ARG* 4.0 26.2 - - + +
159J SER* 4.6 8.3 - - - +
162J ALA* 4.4 18.4 - - + -
234J PHE* 4.5 12.8 - - + -
235J ILE 4.0 2.0 - - - +
236J TYR* 3.6 35.4 - - + -
250J LEU* 3.6 11.7 - - + +
255J ASP* 3.2 38.3 + - - +
256J LEU* 4.5 3.6 - - + -
283J ILE* 3.7 13.9 - - + -
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Residues in contact with VAL 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114J GLN* 3.8 15.9 - - - +
115J ILE* 1.3 79.9 - - - +
117J LEU* 1.3 64.1 + - - +
118J ALA 4.2 1.1 - - - +
234J PHE* 3.4 7.9 - - - -
235J ILE* 3.0 38.4 + - + +
237J LYS* 3.4 37.9 - - + -
240J ALA* 4.2 7.2 - - + -
247J PHE* 3.9 32.8 - - + -
248J VAL 3.6 13.9 - - - +
249J GLU* 5.1 0.7 - - - -
250J LEU* 4.2 8.1 - - - +
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Residues in contact with LEU 117 (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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116J VAL* 1.3 73.7 - - - +
118J ALA* 1.3 60.6 + - - +
119J TYR* 3.9 3.6 - - - -
129J ILE* 4.5 7.0 - - + -
134J TRP* 4.0 24.9 - - + -
138J LEU* 3.6 35.4 - - + -
232J TYR* 4.1 18.8 - - + -
233J PHE 3.9 10.1 - - - -
234J PHE* 3.3 44.6 - - + -
247J PHE* 3.5 0.3 - - - -
248J VAL* 2.8 41.1 + - + +
250J LEU* 4.4 7.7 - - + +
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Residues in contact with ALA 118 (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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116J VAL* 3.8 0.8 + - + -
117J LEU* 1.3 72.0 - - - +
119J TYR* 1.3 71.1 + - - +
232J TYR* 3.2 5.2 - - - -
233J PHE* 2.8 56.9 + - + -
235J ILE* 3.4 17.9 - - + -
240J ALA* 4.2 3.4 - - + -
245J PHE* 4.1 7.4 - - + -
246J ASN 3.3 11.2 - - - +
247J PHE* 3.8 9.4 - - + -
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Residues in contact with TYR 119 (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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117J LEU 3.9 2.5 - - - -
118J ALA* 1.3 79.3 - - - +
120J ARG* 1.3 75.0 - - - +
123J SER* 3.6 1.3 - - - +
126J ALA* 3.5 36.4 + - + -
129J ILE* 3.6 19.4 + - + +
225J VAL* 5.1 1.3 - - - -
231J ASP 3.0 24.5 - - - +
232J TYR* 3.0 24.9 - + + -
233J PHE* 4.0 6.2 - - - -
245J PHE* 3.4 9.6 - - - -
246J ASN* 2.7 67.6 + - + -
247J PHE* 3.2 32.5 + - - -
248J VAL* 3.9 8.7 - - + +
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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