Contacts of the strand formed by residues 232 - 236 (chain E) 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 TYR 232 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E LEU* 4.1 13.7 - - + -
118E ALA 3.2 8.5 - - - +
119E TYR* 3.1 43.5 - + + -
123E SER* 4.5 2.0 - - - -
124E ARG 2.9 27.9 + - - -
125E TYR 3.6 15.1 + - - -
126E ALA* 3.6 4.9 + - - -
129E ILE* 3.5 26.6 - - + +
137E ILE* 3.7 17.5 - - + +
138E LEU* 3.2 31.2 - - + -
143E VAL* 3.7 8.5 - - + -
144E ARG 3.0 2.6 + - - -
145E PHE* 2.8 31.6 - - + -
146E GLY 2.8 4.2 + - - -
230E LEU* 3.6 5.0 - - - +
231E ASP* 1.3 88.3 - - + +
233E PHE* 1.3 66.2 + - - +
248E VAL* 5.8 0.2 - - + -
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Residues in contact with PHE 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LEU* 3.9 4.9 - - - -
118E ALA* 2.8 62.6 + - + -
119E TYR 3.9 0.4 - - - -
146E GLY 3.4 13.7 - - - +
218E GLU 4.7 0.2 - - - -
221E LEU* 3.5 32.8 - - + -
222E ILE* 4.3 13.9 - - + -
225E VAL* 3.6 29.2 - - + -
230E LEU* 4.5 2.5 - - + -
232E TYR* 1.3 78.2 - - - +
234E PHE* 1.3 61.3 - - - +
235E ILE* 3.2 41.7 + - + +
239E VAL* 5.8 0.7 - - + -
245E PHE* 3.8 40.6 - + - -
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Residues in contact with PHE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ILE* 4.5 14.1 - - + -
116E VAL 3.4 10.8 - - - +
117E LEU* 3.4 28.9 - - + -
134E TRP* 3.7 26.7 - + - -
138E LEU* 3.7 7.0 - - + -
145E PHE* 3.9 20.0 - + - -
146E GLY 3.1 17.4 + - - +
147E PHE* 4.3 7.9 - - + -
148E SER 5.1 0.2 + - - -
155E CYS* 3.8 7.5 - - - -
159E SER* 3.3 33.8 + - - +
162E ALA* 5.5 1.6 - - + -
163E ILE* 3.5 39.0 - - + -
221E LEU* 3.6 15.4 - - - +
233E PHE* 1.3 67.9 - - - +
235E ILE* 1.3 59.9 + - - +
250E LEU* 4.6 8.3 - - + -
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Residues in contact with ILE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ILE* 4.7 2.2 - - - -
116E VAL* 2.9 28.4 + - + +
118E ALA* 3.4 34.3 - - + +
155E CYS* 4.0 5.8 - - - -
218E GLU* 3.4 44.4 - - + +
219E MET* 4.5 0.2 - - - -
222E ILE* 5.8 0.2 - - + -
233E PHE* 3.4 25.6 - - + +
234E PHE* 1.3 75.0 - - - +
236E TYR* 1.3 85.6 + - + +
239E VAL* 3.8 32.1 - - + -
240E ALA* 4.3 4.5 - - + +
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Residues in contact with TYR 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E SER* 3.6 27.4 - - - -
90E ALA* 3.2 2.4 - - + +
113E ASN* 3.3 31.0 - - + +
114E GLN 3.0 9.4 - - - -
115E ILE* 3.5 23.3 - - + -
155E CYS* 3.2 19.2 + - + -
158E ARG* 2.9 32.0 + - - -
218E GLU* 3.0 27.1 - - + -
235E ILE* 1.3 85.6 - - + +
237E LYS* 1.3 62.9 + - - +
238E SER* 4.0 3.8 - - - +
239E VAL* 4.2 8.5 - - + +
240E ALA* 3.1 19.8 + - - +
283E ILE* 4.0 9.0 - - + -
285E TYR* 3.8 7.6 - - - -
701E WO4 2.4 18.7 + - - -
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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