Contacts of the strand formed by residues 115 - 119 (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 ILE 115 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E GLN* 1.3 70.9 + - - +
116E VAL* 1.3 74.1 + - - +
155E CYS* 4.1 14.8 - - - +
158E ARG* 4.0 24.9 - - + +
159E SER* 4.6 8.3 - - - +
162E ALA* 4.4 17.5 - - + -
234E PHE* 4.5 13.2 - - + -
235E ILE 3.9 1.6 - - - +
236E TYR* 3.5 36.3 - - + +
250E LEU* 3.6 12.9 - - + +
255E ASP* 3.3 37.6 + - - +
256E LEU* 4.7 3.4 - - + -
283E ILE* 3.7 13.9 - - + -
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Residues in contact with VAL 116 (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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114E GLN* 3.8 15.5 - - - +
115E ILE* 1.3 79.2 - - - +
117E LEU* 1.3 62.4 + - - +
118E ALA 4.2 1.6 - - - +
234E PHE* 3.4 5.8 - - - -
235E ILE* 2.9 38.8 + - + +
237E LYS* 3.3 32.1 - - + -
240E ALA* 4.1 15.5 - - + -
247E PHE* 3.8 31.4 - - + -
248E VAL 3.6 13.9 - - - +
249E GLU* 5.1 0.7 - - - -
250E LEU* 4.3 8.7 - - - -
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Residues in contact with LEU 117 (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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116E VAL* 1.3 73.5 - - - +
118E ALA* 1.3 59.7 + - - +
119E TYR* 3.9 3.5 - - - -
129E ILE* 4.5 4.9 - - + -
134E TRP* 3.9 25.4 - - + -
138E LEU* 3.6 33.0 - - + -
145E PHE* 5.4 0.2 - - + -
232E TYR* 4.1 22.2 - - + -
233E PHE* 3.7 11.7 - - - -
234E PHE* 3.4 43.3 - - + -
247E PHE* 3.4 0.9 - - - -
248E VAL* 2.9 42.2 + - + +
250E LEU* 4.5 7.7 - - + +
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Residues in contact with ALA 118 (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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116E VAL* 3.8 1.4 + - + -
117E LEU* 1.3 71.4 - - - +
119E TYR* 1.3 71.1 + - - +
232E TYR* 3.2 5.9 - - - -
233E PHE* 2.8 56.1 + - + -
235E ILE* 3.4 18.4 - - + -
240E ALA* 4.2 3.6 - - + -
245E PHE* 4.0 8.7 - - + -
246E ASN 3.2 11.0 - - - +
247E PHE* 3.8 8.7 - - + -
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Residues in contact with TYR 119 (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 2.7 - - - -
118E ALA* 1.3 82.1 - - - +
120E ARG* 1.3 72.5 + - - +
123E SER* 3.6 1.3 - - - +
126E ALA* 3.5 36.7 + - + -
129E ILE* 3.6 19.8 + - + +
225E VAL* 5.0 1.8 - - - -
231E ASP 3.0 21.5 - - - +
232E TYR* 3.1 24.5 - + + -
233E PHE* 3.9 6.6 - - - -
245E PHE* 3.4 11.1 - - - -
246E ASN* 2.6 68.3 + - + -
247E PHE* 3.1 33.1 + - - -
248E VAL* 3.9 7.9 - - + +
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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