Contacts of the helix formed by residues 219 - 227 (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 MET 219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D LEU 3.2 23.2 - - - +
223D SER 3.4 25.4 - - - +
225D GLY* 4.7 1.9 + - - -
41E GLY* 2.9 46.7 - - - +
42E SER* 3.7 14.8 - - - +
44E THR* 4.1 9.4 - - + -
45E GLU* 4.9 0.7 - - - +
217E MET* 2.7 15.5 + - + -
218E GLU* 1.3 83.6 - - - +
220E GLU* 1.3 55.0 + - - +
222E ILE* 3.0 36.0 + - + +
223E HIS 4.2 0.7 + - - -
239E VAL* 3.8 31.4 - - + -
242E GLN* 4.9 2.2 - - - +
243E HIS* 4.5 8.3 - - + -
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Residues in contact with GLU 220 (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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208C TYR* 5.9 2.4 - - - -
218D TYR* 5.9 0.2 - - - -
222D LEU* 3.3 48.0 - - + +
215E ARG* 3.4 36.0 - - + +
216E SER* 3.4 13.6 + - - -
217E MET* 2.6 48.8 + - + +
219E MET* 1.3 68.8 - - - +
221E LEU* 1.3 60.5 + - - +
222E ILE* 2.9 6.7 + - - -
223E HIS* 3.5 32.2 + - + -
224E LEU* 3.7 4.5 - - - +
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Residues in contact with LEU 221 (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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146E GLY* 3.9 9.2 - - - +
147E PHE* 3.6 46.2 - - - +
148E SER 3.7 5.4 - - - +
213E MET 4.3 7.9 - - - +
214E ILE* 4.6 0.9 - - - -
215E ARG* 4.4 17.3 - - + +
217E MET 4.6 0.7 - - - +
218E GLU* 2.9 28.3 + - + +
220E GLU* 1.3 80.5 - - - +
222E ILE* 1.3 57.3 + - - +
224E LEU* 3.5 10.0 + - + +
225E VAL* 2.9 30.5 + - - +
230E LEU* 4.5 5.3 - - + +
233E PHE* 3.5 20.4 - - + -
234E PHE 3.6 19.1 - - - +
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Residues in contact with ILE 222 (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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223D SER 4.2 4.7 - - - +
224D GLU 3.8 17.7 - - - +
225D GLY* 3.9 2.9 - - - -
218E GLU 4.3 2.7 - - - +
219E MET* 3.0 44.1 + - + +
220E GLU 2.9 2.2 - - - -
221E LEU* 1.3 76.0 - - - +
223E HIS* 1.3 65.1 + - - +
225E VAL* 2.9 17.9 + - - +
226E GLU* 3.0 34.1 + - + +
233E PHE* 4.3 13.5 - - + -
239E VAL* 4.2 8.1 - - + -
243E HIS* 3.6 36.8 - - + +
245E PHE* 4.2 10.5 - - + -
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Residues in contact with HIS 223 (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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107C LEU* 5.0 2.5 - - + -
205C VAL 5.0 0.4 + - - -
221D TYR* 2.8 67.7 + + + -
222D LEU* 4.6 3.8 - - + -
225D GLY* 4.1 3.1 - - - -
226D LEU* 3.5 16.7 - - + +
215E ARG* 3.9 17.6 + - - -
219E MET 4.2 0.2 + - - -
220E GLU* 3.5 23.0 + - + -
222E ILE* 1.3 79.2 - - - +
224E LEU* 1.3 102.5 + - + +
226E GLU* 3.9 11.2 - - - -
227E SER* 2.8 37.4 + - - +
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Residues in contact with LEU 224 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C VAL* 4.5 13.0 - - + -
213E MET* 4.0 35.0 - - + -
214E ILE 4.8 0.7 - - - +
215E ARG* 3.5 44.2 - - + +
220E GLU 3.7 5.8 - - - +
221E LEU* 3.6 12.6 - - + +
222E ILE 3.2 0.6 - - - -
223E HIS* 1.3 110.1 - - + +
225E VAL* 1.3 59.4 + - - +
227E SER* 4.0 5.1 + - - +
228E GLY 3.7 0.5 + - - -
229E GLU* 2.9 30.6 + - + +
230E LEU* 3.3 20.8 + - + -
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Residues in contact with VAL 225 (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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119E TYR* 5.0 1.6 - - - -
120E ARG* 2.5 54.5 + - + +
221E LEU 2.9 17.9 - - - +
222E ILE 2.9 7.3 + - - +
224E LEU* 1.3 76.9 - - - +
226E GLU* 1.3 66.1 + - - +
228E GLY 3.0 6.8 + - - -
230E LEU* 4.2 15.9 - - + +
231E ASP 5.4 0.9 - - - +
232E TYR 5.6 0.2 - - - -
233E PHE* 3.6 36.8 - - + -
245E PHE* 3.5 27.8 - - + -
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Residues in contact with GLU 226 (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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113C SER* 3.2 10.2 + - - -
224D GLU 4.6 3.1 - - - +
225D GLY* 3.5 2.7 - - - -
226D LEU* 2.8 38.6 + - + -
227D SER* 3.3 27.6 + - - +
120E ARG* 4.9 7.8 - - - +
222E ILE* 3.1 29.4 - - + +
223E HIS* 3.6 5.4 - - - +
225E VAL* 1.3 73.1 - - - +
227E SER* 1.3 57.5 + - - +
228E GLY* 2.9 10.1 + - - -
243E HIS* 5.3 3.1 - - - -
245E PHE* 4.6 10.8 - - + -
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Residues in contact with SER 227 (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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107C LEU* 3.6 30.4 - - - +
111C GLY* 4.5 3.4 - - - -
112C SER 3.1 11.4 + - - -
113C SER* 3.1 17.2 + - - -
125C VAL* 5.0 0.9 - - - +
226D LEU* 4.4 11.2 - - - +
223E HIS* 2.8 26.3 + - - -
224E LEU* 4.0 4.0 + - - +
226E GLU* 1.3 70.3 - - - +
228E GLY* 1.3 56.4 + - - +
229E GLU* 2.5 39.8 + - - +
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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