Contacts of the strand formed by residues 108 - 113 (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 108 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E TRP* 3.3 32.1 - - + -
107E THR* 1.3 79.9 - - - +
109E MET* 1.3 74.6 + - - +
110E PHE 3.5 0.2 + - - -
286E GLY* 3.4 2.4 - - - -
287E ILE* 3.1 37.9 + - + +
303E VAL* 4.2 8.1 - - + -
307E ILE* 4.2 16.4 - - + -
327E ARG 2.9 15.3 - - - +
328E ALA* 4.3 8.1 - - + -
332E VAL* 4.5 3.8 - - + -
335E LEU* 3.5 23.3 - - + -
339E VAL* 3.7 27.8 - - + -
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Residues in contact with MET 109 (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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92E TYR* 4.0 37.5 - - + +
107E THR* 4.6 6.5 - - - +
108E ILE* 1.3 79.3 - - - +
110E PHE* 1.3 60.7 - - - +
284E VAL* 3.2 25.1 - - + -
285E TYR 3.3 5.4 - - - -
286E GLY* 4.4 0.2 - - - -
323E LEU* 3.1 24.4 - - + +
326E PRO* 3.4 8.8 - - - +
327E ARG* 2.7 70.9 + - + +
328E ALA* 4.5 5.2 - - - +
329E ASP* 5.0 5.2 - - + +
342E SER* 4.5 10.3 - - - +
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Residues in contact with PHE 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.5 39.3 - - + -
47E MET* 5.8 1.6 - - + -
50E PHE* 5.1 3.4 - + - -
88E ALA* 4.3 3.1 - - + -
108E ILE 3.7 4.0 - - - +
109E MET* 1.3 75.0 - - - +
111E ALA* 1.3 77.1 + - + +
285E TYR* 2.9 17.7 + - + -
286E GLY 3.2 25.4 - - - -
287E ILE* 3.4 31.2 - - + -
306E VAL* 3.7 24.8 - - + +
307E ILE* 4.2 22.4 - - + -
315E LEU* 3.9 15.9 - - + +
322E PRO* 3.8 5.7 - - - +
323E LEU* 3.2 23.0 + - - +
326E PRO* 5.2 0.7 - - - -
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Residues in contact with ALA 111 (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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110E PHE* 1.3 97.9 - - + +
112E LYS* 1.3 63.5 + - - +
284E VAL* 3.2 7.6 - - - +
285E TYR* 2.6 33.7 + - + +
315E LEU* 4.1 8.7 - - + -
320E GLN* 3.3 24.7 - - - +
321E GLU 3.7 5.6 - - - +
323E LEU* 3.6 12.6 - - - +
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Residues in contact with LYS 112 (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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111E ALA* 1.3 78.8 - - - +
113E ASN* 1.3 67.4 + - - +
257E SER 6.2 0.2 - - - +
259E PRO* 6.3 4.7 - - + -
283E ILE 3.0 14.8 - - - +
284E VAL* 4.5 4.7 - - + -
285E TYR* 4.2 2.9 - - - -
320E GLN* 3.5 22.5 + - - +
321E GLU* 2.9 34.6 + - + +
322E PRO 3.7 20.2 + - - -
323E LEU* 3.8 26.9 - - + +
259J PRO 5.7 2.6 + - - -
260J ASP* 5.9 4.6 - - - +
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Residues in contact with ASN 113 (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* 5.2 0.2 - - - -
112E LYS* 1.3 75.9 - - - +
114E GLN* 1.3 73.1 + - - +
236E TYR* 3.3 20.0 - - + +
237E LYS* 4.6 0.2 - - - +
238E SER* 3.0 42.6 + - - -
257E SER* 3.7 14.1 - - - -
283E ILE* 3.2 41.2 + - + +
285E TYR* 2.8 30.6 + - + -
320E GLN* 3.4 10.9 - - - +
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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