Contacts of the strand formed by residues 283 - 288 (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 283 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E LYS* 3.0 25.6 - - - +
113E ASN* 3.2 50.5 + - + +
114E GLN* 4.0 3.4 - - - +
115E ILE* 3.7 37.0 - - + +
158E ARG* 3.4 42.6 - - - +
236E TYR* 4.0 3.1 - - + -
256E LEU* 3.1 21.7 + - + +
257E SER* 4.8 1.0 - - - +
281E LYS 4.6 0.2 - - - +
282E PRO* 1.3 69.5 - - - +
284E VAL* 1.3 62.3 + - - +
285E TYR* 3.7 9.6 - - + -
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Residues in contact with VAL 284 (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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90E ALA 3.4 5.5 - - - +
91E ASP* 3.7 0.9 + - - -
92E TYR* 3.0 42.8 + - + -
109E MET* 3.2 42.8 - - + -
111E ALA 3.2 7.9 - - - +
112E LYS* 4.5 10.3 - - + -
158E ARG* 3.8 3.8 - - - +
282E PRO* 3.1 19.8 + - + +
283E ILE* 1.3 80.6 - - - +
285E TYR* 1.3 62.1 + - - +
323E LEU* 4.6 10.5 - - + -
327E ARG* 5.1 9.4 - - - +
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Residues in contact with TYR 285 (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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40E ALA* 5.0 0.2 - - + -
42E SER* 2.9 26.4 + - - -
43E LEU* 3.4 41.3 - - + -
89E THR 3.1 20.6 - - - +
90E ALA* 3.7 19.7 - - + -
92E TYR* 4.1 0.4 - - - -
109E MET* 3.3 5.4 - - - -
110E PHE* 2.9 39.7 + - + -
111E ALA* 2.6 23.6 + - + +
113E ASN* 2.8 47.5 + - + -
236E TYR* 3.8 7.6 - - - -
283E ILE* 3.7 10.3 - - + -
284E VAL* 1.3 73.8 - - - +
286E GLY* 1.3 58.3 + - - +
320E GLN* 3.5 11.0 - - - -
701E WO4 4.9 0.4 - - - -
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Residues in contact with GLY 286 (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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88E ALA* 3.4 0.2 - - - -
89E THR 2.9 29.9 + - - -
92E TYR* 3.5 29.6 - - - +
95E ILE* 4.1 4.9 - - - -
107E THR* 4.0 3.8 - - - -
108E ILE 3.4 8.1 - - - -
110E PHE* 3.2 10.9 - - - -
284E VAL 3.7 0.2 + - - -
285E TYR* 1.3 73.4 - - - +
287E ILE* 1.3 60.4 + - - -
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Residues in contact with ILE 287 (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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47E MET* 5.6 1.1 - - + -
86E VAL* 3.9 23.3 - - + -
87E ILE 3.2 13.7 - - - +
88E ALA* 4.5 5.6 - - + -
95E ILE* 4.0 1.2 - - - +
106E TRP* 4.1 1.2 - - - -
107E THR* 3.6 2.8 - - - +
108E ILE* 3.1 52.8 + - + +
110E PHE* 3.4 19.5 - - + -
286E GLY* 1.3 75.0 - - - -
288E THR* 1.3 80.4 + - - +
302E PHE* 4.7 1.3 - - + -
303E VAL* 4.3 22.2 - - + -
306E VAL* 3.8 36.6 - - + -
307E ILE* 5.6 0.7 - - + -
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Residues in contact with THR 288 (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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86E VAL* 3.4 5.7 - - - +
87E ILE* 2.9 47.5 + - + +
95E ILE* 3.3 35.0 - - + -
99E MET* 4.6 9.6 - - + -
104E ALA* 4.3 7.6 - - - +
106E TRP* 2.9 33.9 + - - -
287E ILE* 1.3 82.1 - - - +
289E ILE* 1.3 80.6 + - - +
290E PRO* 3.7 1.0 - - - +
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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