Contacts of the helix formed by residues 228 - 239 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A LEU* 3.3 23.3 - - + -
225A PHE 3.6 3.4 + - - +
226A LEU 3.0 0.8 - - - -
227A SER* 1.3 78.1 + - - +
229A ARG* 1.3 64.8 + - - +
230A ASN 3.1 0.4 - - - -
231A LEU* 3.1 21.3 + - + +
232A LEU* 3.2 12.8 + - - +
158B ASP* 4.9 0.2 - - - +
159B LEU* 3.7 9.3 - - + +
160B LYS* 3.2 40.6 - - + +
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.3 0.6 - - - +
187A LEU* 2.5 64.5 + - - +
211A LEU* 3.3 34.9 - - - +
215A PHE* 2.8 31.5 - - + -
226A LEU* 3.0 13.0 - - - +
227A SER* 2.9 1.9 - - - +
228A ALA* 1.3 78.2 - - - +
230A ASN* 1.3 56.0 + - - +
232A LEU* 3.0 11.0 + - - +
233A LEU* 2.7 44.7 + - + +
239B LEU* 3.3 34.3 - - + +
240B ASP* 3.7 23.3 - - - +
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Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A SER* 2.8 29.6 + - - +
229A ARG* 1.3 80.2 - - - +
231A LEU* 1.3 55.8 + - + +
233A LEU* 2.9 13.3 + - - +
234A LYS* 2.6 55.8 + - + +
240B ASP* 5.1 2.6 - - - +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A SER 5.1 0.2 - - - +
228A ALA* 3.1 12.5 + - + +
230A ASN* 1.3 80.0 - - + +
232A LEU* 1.3 59.6 + - + +
234A LYS* 3.9 20.0 - - + +
235A VAL* 2.9 39.2 + - + +
159B LEU* 3.5 21.8 - - + +
160B LYS* 3.6 14.1 - - + +
163B GLY* 3.2 41.7 - - - +
164B VAL* 4.6 0.9 - - + +
167B GLU* 4.4 13.2 - - - +
188B ILE* 5.9 4.9 - - + -
192B MET* 6.0 5.8 - - + -
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Residues in contact with LEU 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 4.3 4.7 - - + -
188A ILE* 3.8 32.8 - - + -
228A ALA 3.2 8.5 + - - +
229A ARG* 3.0 37.5 + - - +
231A LEU* 1.3 79.9 - - + +
233A LEU* 1.3 66.2 + - + +
235A VAL* 3.8 4.1 - - + +
236A SER* 3.2 22.5 + - - -
159B LEU* 4.0 18.2 - - + -
188B ILE* 3.9 17.9 - - + -
232B LEU* 4.2 14.3 - - + +
235B VAL* 3.9 23.3 - - + -
236B SER* 4.3 5.0 - - - -
239B LEU* 4.4 3.4 - - + -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ARG* 2.7 33.6 + - + +
230A ASN* 3.4 11.4 - - - +
232A LEU* 1.3 74.5 - - + +
234A LYS* 1.3 64.8 + - + +
236A SER* 2.4 20.9 + - - +
237A LYS* 3.0 25.1 + - - +
236B SER* 3.6 38.4 - - - +
239B LEU* 3.8 10.1 - - + +
240B ASP* 3.8 34.5 - - + +
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASN* 2.6 37.5 + - + +
231A LEU* 3.9 16.7 - - + +
233A LEU* 1.3 73.6 - - + +
235A VAL* 1.3 57.9 + - - +
237A LYS* 3.2 18.7 + - + +
238A ILE* 3.0 37.4 + - + +
167B GLU* 4.6 14.6 + - - -
170B ARG* 6.2 1.1 - - - +
192B MET* 4.2 13.5 - - + -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 2.9 26.5 + - + +
232A LEU* 3.8 7.4 - - - +
233A LEU 3.2 0.2 - - - -
234A LYS* 1.3 74.3 - - - +
236A SER* 1.3 65.7 + - - +
238A ILE* 3.2 1.7 + - - -
239A LEU* 3.0 46.1 + - + +
188B ILE* 3.9 22.9 - - + +
191B ALA* 4.5 5.2 - - + -
192B MET* 3.2 37.9 - - + -
232B LEU* 4.0 21.5 - - + -
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU 3.2 6.2 + - - -
233A LEU* 2.4 29.5 + - - +
235A VAL* 1.3 80.3 - - - +
237A LYS* 1.3 58.7 + - - +
239A LEU* 2.5 27.3 - - - +
240A ASP 4.2 1.6 - - - +
232B LEU* 4.3 5.6 - - - -
233B LEU* 3.7 21.4 - - - +
236B SER* 3.4 32.4 - - - -
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.0 27.1 + - - +
234A LYS* 3.3 17.6 - - + +
235A VAL 3.1 0.2 - - - -
236A SER* 1.3 82.2 + - - +
238A ILE* 1.3 65.8 + - + +
239A LEU 2.9 5.4 + - - +
240A ASP 4.1 5.4 - - - +
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Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LYS* 3.0 17.8 + - + +
235A VAL 3.2 4.7 + - - +
237A LYS* 1.3 76.0 - - + +
239A LEU* 1.3 70.5 + - + +
191B ALA* 4.1 17.5 - - - +
192B MET* 3.5 28.3 - - + -
212B LYS* 4.2 20.7 - - - +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A VAL* 3.0 39.0 + - + +
236A SER* 2.5 26.8 - - - +
237A LYS 2.9 0.2 + - - -
238A ILE* 1.3 89.7 - - + +
240A ASP* 1.3 75.0 + - + +
191B ALA* 3.5 12.1 - - + -
211B LEU* 3.7 29.4 - - + -
212B LYS* 5.9 2.9 - - + +
215B PHE* 4.0 15.3 - - + -
229B ARG* 3.3 38.4 - - + +
232B LEU* 4.4 3.1 - - + -
233B LEU* 3.9 5.6 - - + +
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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