Contacts of the helix formed by residues 228 - 239 (chain F) 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 ALA 228 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187F LEU* 3.4 22.9 - - + -
225F PHE 3.6 8.1 + - - +
226F LEU 3.0 1.4 - - - -
227F SER* 1.3 78.1 + - - +
229F ARG* 1.3 63.0 + - - +
230F ASN 3.1 0.9 - - - -
231F LEU* 3.1 24.7 + - + +
232F LEU* 3.2 12.5 + - - +
158G ASP* 5.0 1.3 - - - +
159G LEU* 3.9 11.1 - - + +
160G LYS* 3.7 30.3 - - + +
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Residues in contact with ARG 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LEU* 4.3 0.8 - - - +
187F LEU* 2.5 64.5 + - - +
191F ALA* 4.3 0.4 - - - +
211F LEU* 3.3 34.4 - - - +
215F PHE* 2.8 28.7 - - + -
226F LEU* 3.0 13.2 - - - +
227F SER* 2.9 1.9 + - - +
228F ALA* 1.3 77.3 - - - +
230F ASN* 1.3 52.3 + - - +
232F LEU* 3.0 10.5 + - - +
233F LEU* 2.7 42.6 + - + +
239G LEU* 2.9 43.6 - - + +
240G ASP* 3.5 24.7 - - - +
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Residues in contact with ASN 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F SER* 2.8 29.5 + - - +
228F ALA 3.1 0.2 - - - -
229F ARG* 1.3 78.1 - - - +
231F LEU* 1.3 56.4 + - + +
233F LEU* 2.9 12.2 + - - +
234F LYS* 2.6 53.5 + - + +
240G ASP* 4.5 9.4 - - - +
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Residues in contact with LEU 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227F SER 5.1 0.4 - - - +
228F ALA* 3.1 13.4 + - + +
230F ASN* 1.3 81.6 - - + +
232F LEU* 1.3 59.4 + - + +
234F LYS* 3.9 21.8 - - + +
235F VAL* 2.9 39.0 + - + +
159G LEU* 3.3 33.0 - - + +
160G LYS* 3.6 22.9 - - + +
163G GLY* 3.8 23.1 - - - +
164G VAL* 5.1 0.4 - - + +
167G GLU* 4.9 7.2 - - - +
188G ILE* 6.0 3.4 - - + -
192G MET* 6.4 1.1 - - - -
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Residues in contact with LEU 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187F LEU* 4.3 4.7 - - + -
188F ILE* 3.8 33.0 - - + -
228F ALA 3.2 8.6 + - - +
229F ARG* 3.0 31.7 + - - +
231F LEU* 1.3 79.7 - - + +
233F LEU* 1.3 65.7 + - + +
235F VAL* 3.7 3.6 + - - +
236F SER* 3.2 22.5 + - - -
159G LEU* 4.2 16.8 - - + -
188G ILE* 4.1 18.2 - - + -
232G LEU* 4.2 13.9 - - + +
235G VAL* 3.5 30.5 - - + -
236G SER* 4.1 4.3 - - - -
239G LEU* 4.0 3.8 - - + -
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Residues in contact with LEU 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229F ARG* 2.7 32.8 + - + +
230F ASN* 3.4 10.5 - - - +
232F LEU* 1.3 73.7 - - + +
234F LYS* 1.3 64.4 + - + +
236F SER* 2.4 20.8 + - - +
237F LYS* 3.0 25.5 + - - +
236G SER* 3.2 42.6 - - - +
239G LEU* 3.7 7.6 - - + +
240G ASP* 3.5 36.6 - - + +
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Residues in contact with LYS 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230F ASN* 2.6 38.2 + - - +
231F LEU* 3.9 18.7 - - + +
233F LEU* 1.3 71.5 - - + +
235F VAL* 1.3 57.9 + - - +
237F LYS* 3.2 18.7 + - + +
238F ILE* 3.0 36.4 + - + +
167G GLU* 4.7 13.3 + - - +
192G MET* 4.2 14.6 - - + -
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Residues in contact with VAL 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F LEU* 2.9 28.5 + - + +
232F LEU* 3.8 6.5 - - - +
234F LYS* 1.3 74.9 - - - +
236F SER* 1.3 65.5 + - - +
238F ILE* 3.2 1.6 + - - -
239F LEU* 3.0 46.3 + - + +
188G ILE* 3.7 35.9 - - + -
191G ALA* 4.6 1.1 - - + -
192G MET* 3.5 27.4 - - + -
232G LEU* 3.8 22.2 - - + -
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Residues in contact with SER 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232F LEU 3.2 5.9 + - - -
233F LEU* 2.4 26.3 + - - +
235F VAL* 1.3 79.5 - - - +
237F LYS* 1.3 57.9 + - - +
239F LEU* 2.5 27.9 - - - +
240F ASP 4.2 1.6 - - - +
232G LEU* 4.1 6.0 - - - +
233G LEU* 3.6 23.2 - - - +
236G SER* 3.3 34.0 - - - -
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Residues in contact with LYS 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233F LEU* 3.0 27.9 + - - +
234F LYS* 3.3 17.2 - - + +
235F VAL 3.1 0.4 - - - -
236F SER* 1.3 81.2 + - - +
238F ILE* 1.3 65.3 + - + +
239F LEU 2.9 6.2 + - - +
240F ASP 4.1 5.2 - - - +
212G LYS* 6.1 0.2 - - - -
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Residues in contact with ILE 238 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234F LYS* 3.0 17.1 + - + +
235F VAL 3.2 4.0 + - - +
237F LYS* 1.3 76.3 - - + +
239F LEU* 1.3 68.4 + - + +
240F ASP 4.3 0.2 + - - -
170G ARG* 5.9 0.9 - - - +
191G ALA 3.7 20.4 - - - +
192G MET* 3.1 31.2 - - + -
212G LYS* 4.4 18.6 - - - +
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Residues in contact with LEU 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235F VAL* 3.0 31.6 + - + +
236F SER* 2.5 24.3 - - - +
237F LYS 3.9 0.2 - - - -
238F ILE* 1.3 86.4 - - + +
240F ASP* 1.3 75.8 + - + +
191G ALA* 3.3 31.4 - - + -
211G LEU* 3.4 22.7 - - + -
212G LYS* 5.9 1.8 - - + +
215G PHE* 4.1 8.7 - - + -
229G ARG* 3.1 45.1 - - + +
232G LEU* 4.2 3.4 - - + -
233G LEU* 4.0 4.9 - - + +
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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