Contacts of the strand formed by residues 86 - 89 (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 VAL 86 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35E LEU* 4.6 1.3 - - + -
36E LYS 2.9 2.2 + - - -
37E VAL* 3.4 32.7 - - + -
38E PHE 3.1 23.9 + - - -
84E ALA* 3.8 2.1 - - - +
85E ASP* 1.3 90.2 - - + +
87E ILE* 1.3 75.3 + - - +
88E ALA* 5.2 1.3 - - + -
287E ILE* 3.9 28.3 - - + -
288E THR 3.4 11.0 - - - +
299E ALA* 4.5 9.9 - - + +
302E PHE* 3.8 28.3 - - + -
303E VAL* 4.9 5.6 - - + -
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Residues in contact with ILE 87 (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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38E PHE* 3.2 24.5 - - + -
73E THR* 4.2 12.3 - - + +
74E ILE* 4.1 24.9 - - + -
77E VAL* 3.7 29.8 - - + -
84E ALA* 3.9 4.0 - - + -
86E VAL* 1.3 83.6 - - - +
88E ALA* 1.3 62.4 + - - +
89E THR* 4.4 7.6 - - + -
95E ILE* 4.4 0.8 - - + +
99E MET* 4.4 12.8 - - + -
287E ILE* 3.2 3.6 - - - +
288E THR* 2.9 47.4 + - + +
290E PRO* 4.2 15.3 - - + -
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Residues in contact with ALA 88 (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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37E VAL* 5.6 0.7 - - + -
38E PHE 3.1 7.3 + - - -
39E HIS* 3.2 11.8 - - + -
40E ALA 2.9 26.4 + - - -
43E LEU* 3.3 27.4 - - + -
47E MET* 4.8 8.5 - - + -
70E SER* 4.5 0.2 + - - -
73E THR* 4.4 2.6 - - - +
86E VAL* 5.2 2.5 - - + -
87E ILE* 1.3 75.5 - - - +
89E THR* 1.3 64.8 + - - +
110E PHE* 4.3 7.0 - - + -
286E GLY 3.4 7.6 - - - +
287E ILE* 4.5 7.9 - - + -
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Residues in contact with THR 89 (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* 4.3 2.9 - - - -
43E LEU* 4.7 0.2 - - - +
70E SER* 3.1 18.6 - - - +
73E THR* 5.4 0.7 - - + -
74E ILE* 3.9 23.8 - - + -
87E ILE* 4.4 3.4 - - + -
88E ALA* 1.3 78.8 - - - +
90E ALA* 1.3 59.3 + - - +
91E ASP 2.6 31.4 + - - +
92E TYR* 3.4 7.1 + - - -
95E ILE* 3.7 25.3 - - + +
285E TYR* 3.1 31.2 - - - +
286E GLY* 2.9 10.6 + - - +
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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