Contacts of the helix formed by residues 219 - 227 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222I LEU 3.3 20.9 - - - +
223I SER 3.5 25.8 - - - +
225I GLY* 4.6 2.1 + - - -
41J GLY* 3.1 41.7 - - - +
42J SER* 3.9 4.3 - - - +
44J THR* 4.3 7.6 - - - -
45J GLU* 5.0 1.6 - - - +
217J MET* 2.6 21.2 + - + -
218J GLU* 1.3 80.1 - - - +
220J GLU* 1.3 58.4 + - - +
222J ILE* 3.0 37.0 + - + +
223J HIS 4.2 1.0 + - - -
239J VAL* 3.8 40.6 - - + -
242J GLN* 4.9 2.5 - - - +
243J HIS* 4.5 8.5 - - + -
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Residues in contact with GLU 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208H TYR* 6.0 0.9 - - - -
222I LEU* 3.5 43.9 - - + +
215J ARG* 3.4 36.6 - - + +
216J SER* 3.4 13.5 + - - -
217J MET* 2.6 50.0 + - + +
219J MET* 1.3 68.7 - - - +
221J LEU* 1.3 59.8 + - - +
222J ILE 2.9 6.6 + - - -
223J HIS* 3.5 33.0 + - + -
224J LEU* 3.7 5.0 - - - +
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Residues in contact with LEU 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J GLY* 3.9 9.6 - - - +
147J PHE* 3.6 44.4 - - - +
148J SER* 3.7 6.1 - - - +
213J MET 4.3 8.7 - - - +
214J ILE* 4.6 0.7 - - - -
215J ARG* 4.4 17.0 - - + +
217J MET 4.6 0.4 - - - +
218J GLU* 2.9 27.8 + - + +
220J GLU* 1.3 79.2 - - - +
222J ILE* 1.3 59.1 + - - +
224J LEU* 3.5 9.5 + - + +
225J VAL* 2.9 29.9 + - - +
230J LEU* 4.5 6.0 - - + +
233J PHE* 3.5 20.4 - - + -
234J PHE 3.6 18.8 - - - +
235J ILE* 5.2 0.2 - - + -
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Residues in contact with ILE 222 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223I SER 4.3 3.6 - - - +
224I GLU 3.7 18.2 - - - +
225I GLY* 3.9 3.4 - - - -
218J GLU 4.3 3.1 - - - +
219J MET* 3.0 43.2 + - + +
220J GLU 2.9 2.6 - - - -
221J LEU* 1.3 75.9 - - - +
223J HIS* 1.3 66.0 + - - +
225J VAL* 3.0 17.0 + - - +
226J GLU* 3.0 34.9 + - + +
233J PHE* 4.3 13.5 - - + -
239J VAL* 4.2 9.0 - - + -
243J HIS* 3.6 37.0 - - + +
245J PHE* 4.1 10.3 - - + -
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Residues in contact with HIS 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H LEU* 5.1 1.3 - - + -
221I TYR* 2.8 69.4 + + + -
222I LEU* 4.5 4.5 - - + -
225I GLY* 4.0 2.9 - - - -
226I LEU* 3.5 14.6 - - + +
215J ARG* 3.9 18.7 + - - -
219J MET 4.2 0.2 + - - -
220J GLU* 3.5 22.3 + - + -
222J ILE* 1.3 77.6 - - - +
224J LEU* 1.3 103.3 + - + +
226J GLU* 3.0 11.8 + - - -
227J SER* 2.8 37.3 + - - -
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Residues in contact with LEU 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H VAL* 4.5 12.6 - - + -
213J MET* 4.0 35.2 - - + -
214J ILE 4.8 0.2 - - - +
215J ARG* 3.5 46.2 - - + +
220J GLU 3.7 6.1 - - - +
221J LEU* 3.5 12.3 + - + +
222J ILE 3.2 0.8 - - - -
223J HIS* 1.3 109.5 - - + +
225J VAL* 1.3 59.4 + - - +
227J SER* 3.9 4.8 + - - +
228J GLY 3.6 0.9 + - - -
229J GLU* 2.9 30.2 + - + -
230J LEU* 3.3 20.4 + - + -
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Residues in contact with VAL 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J TYR* 5.0 1.3 - - - -
120J ARG* 2.6 54.4 + - + +
221J LEU 2.9 19.1 - - - +
222J ILE 3.0 6.6 + - - +
224J LEU* 1.3 76.7 - - - +
226J GLU* 1.3 65.7 + - - +
228J GLY 3.0 7.1 + - - -
230J LEU* 4.2 15.7 - - + +
231J ASP 5.4 1.1 - - - +
232J TYR 5.6 0.2 - - - -
233J PHE* 3.6 36.1 - - + -
245J PHE* 3.5 27.4 - - + -
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Residues in contact with GLU 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H SER* 3.1 12.5 + - - -
224I GLU 4.6 2.8 - - - +
225I GLY* 3.4 2.1 - - - -
226I LEU* 2.6 41.7 + - + -
227I SER* 3.0 30.8 + - - +
120J ARG* 4.9 7.4 - - - +
222J ILE* 3.1 30.7 - - + +
223J HIS* 3.6 4.3 - - - +
225J VAL* 1.3 72.6 - - - +
227J SER* 1.3 57.8 + - - +
228J GLY* 2.9 9.3 + - - -
243J HIS* 5.3 3.1 - - - -
245J PHE* 4.6 11.0 - - + -
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Residues in contact with SER 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H LEU* 3.2 35.7 - - - +
111H GLY* 4.5 1.8 - - - -
112H SER 2.9 12.3 + - - -
113H SER* 3.1 14.6 + - - -
125H VAL* 4.9 0.9 - - - +
226I LEU* 4.2 10.5 - - - +
223J HIS* 2.8 25.3 + - - -
224J LEU* 3.9 4.5 + - - +
226J GLU* 1.3 69.1 - - - +
228J GLY* 1.3 55.7 + - - +
229J GLU* 2.5 42.0 + - - +
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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