Contacts of the strand formed by residues 108 - 113 (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 108 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106J TRP* 3.2 31.4 - - + -
107J THR* 1.3 81.2 - - - +
109J MET* 1.3 73.1 + - - +
110J PHE 3.4 0.3 + - - -
286J GLY* 3.4 2.7 - - - -
287J ILE* 3.1 39.8 + - + +
303J VAL* 4.3 8.1 - - + -
307J ILE* 4.2 25.1 - - + -
326J PRO* 4.2 2.9 - - + -
327J ARG 2.8 19.1 - - - +
328J ALA* 4.2 8.5 - - + -
332J VAL* 4.6 3.6 - - + -
335J LEU* 3.7 27.8 - - + -
338J MET 6.3 0.7 - - - -
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Residues in contact with MET 109 (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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342E SER 4.6 7.0 - - - +
92J TYR* 4.1 37.0 - - + +
107J THR* 4.6 5.8 - - - +
108J ILE* 1.3 78.5 - - - +
110J PHE* 1.3 59.8 + - - +
284J VAL* 3.2 25.1 - - + -
285J TYR 3.3 5.6 - - - -
286J GLY* 4.4 0.4 - - - -
323J LEU* 3.1 24.6 - - + +
326J PRO* 3.4 8.5 - - - +
327J ARG* 2.7 69.8 + - + +
328J ALA* 4.5 8.5 - - - +
329J ASP* 5.0 4.5 - - + +
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Residues in contact with PHE 110 (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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43J LEU* 3.5 42.6 - - + -
47J MET* 5.9 0.7 - - + -
50J PHE* 5.2 3.1 - + - -
88J ALA* 4.3 2.2 - - + -
108J ILE 3.7 1.6 - - - +
109J MET* 1.3 74.4 - - - +
111J ALA* 1.3 74.9 + - + +
285J TYR* 2.9 21.3 + - + -
286J GLY 3.2 25.6 - - - -
287J ILE* 3.4 28.9 - - + -
306J VAL* 3.8 24.2 - - + +
307J ILE* 4.2 22.7 - - + -
315J LEU* 3.9 15.7 - - + +
322J PRO* 3.7 5.9 - - - +
323J LEU* 3.1 23.2 + - - +
326J PRO* 5.2 0.7 - - - -
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Residues in contact with ALA 111 (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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110J PHE* 1.3 97.5 - - + +
112J LYS* 1.3 64.3 + - - +
284J VAL* 3.2 8.0 - - - +
285J TYR* 2.6 33.8 + - + -
315J LEU* 4.2 7.4 - - + -
320J GLN* 3.4 25.8 - - - +
321J GLU 3.8 6.1 - - - +
323J LEU* 3.5 12.2 - - - +
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Residues in contact with LYS 112 (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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260E ASP* 5.7 6.5 + - - +
111J ALA* 1.3 79.9 - - - +
113J ASN* 1.3 67.2 + - - +
257J SER 6.1 0.9 - - - +
259J PRO* 6.2 6.3 - - + -
283J ILE* 3.0 14.6 - - - +
284J VAL* 4.4 5.2 - - + +
285J TYR* 4.3 1.3 - - - -
320J GLN* 3.6 17.0 + - - +
321J GLU* 2.9 38.6 + - + +
322J PRO 3.8 18.9 + - - -
323J LEU* 3.8 26.5 - - + +
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Residues in contact with ASN 113 (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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112J LYS* 1.3 75.3 - - - +
114J GLN* 1.3 72.5 + - - +
236J TYR* 3.4 21.1 - - + +
237J LYS* 4.6 0.2 - - - +
238J SER* 3.1 41.9 + - - -
257J SER* 3.6 15.2 - - - -
283J ILE* 3.2 41.5 + - + +
285J TYR* 2.8 28.7 + - + -
320J GLN* 3.5 11.4 - - - +
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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