Contacts of the helix formed by residues 228 - 239 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F LEU* 3.9 9.8 - - + +
160F LYS* 3.4 38.8 - - + +
187G LEU* 3.3 23.1 - - + -
225G PHE 3.6 3.2 + - - +
226G LEU 3.0 1.2 - - - -
227G SER* 1.3 79.6 + - - +
229G ARG* 1.3 64.2 - - - +
230G ASN 3.1 0.7 - - - -
231G LEU* 3.1 23.0 + - + +
232G LEU* 3.2 12.1 + - - +
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Residues in contact with ARG 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239F LEU* 3.1 37.2 - - + +
240F ASP* 3.6 22.7 - - + +
30G LEU* 4.3 1.0 - - - +
187G LEU* 2.5 62.0 + - - +
211G LEU* 3.3 35.2 - - - +
215G PHE* 2.8 32.3 - - + -
226G LEU* 3.1 13.6 + - - +
227G SER* 2.9 2.3 + - - +
228G ALA* 1.3 77.5 - - - +
230G ASN* 1.3 54.5 + - - +
232G LEU* 3.0 10.2 + - - +
233G LEU* 2.7 46.4 + - + +
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Residues in contact with ASN 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240F ASP* 5.5 1.0 - - - +
227G SER* 2.8 28.7 + - - +
229G ARG* 1.3 80.0 - - - +
231G LEU* 1.3 57.3 + - + +
233G LEU* 2.9 13.4 + - - +
234G LYS* 2.6 55.3 + - - +
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Residues in contact with LEU 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU* 3.6 20.0 - - + +
160F LYS* 3.9 7.4 - - + +
162F LYS* 5.4 0.2 - - + -
163F GLY* 3.2 41.1 - - - +
164F VAL* 4.7 0.7 - - + +
166F MET* 6.6 0.2 - - - -
167F GLU* 4.5 12.3 - - - +
170F ARG* 6.2 1.3 - - - +
188F ILE* 5.7 6.7 - - + -
192F MET* 5.7 8.5 - - + -
227G SER 5.1 0.7 - - - +
228G ALA* 3.1 17.0 + - + +
230G ASN* 1.3 80.4 - - + +
232G LEU* 1.3 58.7 + - + +
234G LYS* 3.9 20.9 - - + +
235G VAL* 2.9 39.1 + - + +
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Residues in contact with LEU 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU* 4.3 11.4 - - + -
188F ILE* 4.1 17.7 - - + -
232F LEU* 4.2 13.7 - - + +
235F VAL* 3.8 24.7 - - + -
236F SER* 4.1 5.3 - - - -
239F LEU* 4.2 2.9 - - + -
187G LEU* 4.3 10.3 - - + -
188G ILE* 3.8 33.0 - - + -
228G ALA 3.2 8.5 + - - +
229G ARG* 3.0 36.9 + - - +
231G LEU* 1.3 80.8 - - + +
233G LEU* 1.3 65.8 + - + +
235G VAL* 3.8 4.0 - - - +
236G SER* 3.2 22.7 + - - -
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Residues in contact with LEU 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F SER* 3.6 38.6 - - - +
239F LEU* 4.0 9.2 - - + +
240F ASP* 3.9 28.7 - - + +
229G ARG* 2.7 36.4 + - + +
230G ASN* 3.4 11.4 - - - +
232G LEU* 1.3 72.1 - - + +
234G LYS* 1.3 65.5 + - + +
235G VAL 3.2 0.2 - - - -
236G SER* 2.4 20.7 + - - +
237G LYS* 3.0 25.4 + - - +
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Residues in contact with LYS 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F GLU* 4.6 14.8 + - - -
170F ARG* 5.8 6.2 - - - +
192F MET* 4.1 18.4 - - + -
230G ASN* 2.6 35.9 + - - +
231G LEU* 3.9 19.1 - - + +
233G LEU* 1.3 71.6 - - + +
235G VAL* 1.3 57.4 + - - +
237G LYS* 3.2 18.4 + - + +
238G ILE* 3.0 34.9 + - + +
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Residues in contact with VAL 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188F ILE* 3.8 34.8 - - + -
191F ALA* 4.5 1.8 - - + -
192F MET* 3.4 26.9 - - + -
232F LEU* 3.5 24.5 - - + -
231G LEU 2.9 26.3 + - - +
232G LEU* 3.8 6.3 - - - +
234G LYS* 1.3 74.9 - - - +
236G SER* 1.3 66.2 + - - +
238G ILE* 3.2 2.9 + - - +
239G LEU* 3.1 45.0 + - + +
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Residues in contact with SER 236 (chain G).
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* 4.1 6.0 + - - -
233F LEU* 3.2 24.8 - - - +
236F SER* 3.3 32.0 - - - -
232G LEU 3.2 5.7 + - - -
233G LEU* 2.4 30.5 + - - +
235G VAL* 1.3 79.6 - - - +
237G LYS* 1.3 58.1 + - - +
239G LEU* 2.5 26.8 - - - +
240G ASP 4.2 1.4 - - - +
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Residues in contact with LYS 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F LYS* 5.8 0.7 - - - -
233G LEU* 3.0 26.6 + - - +
234G LYS* 3.3 17.4 - - + +
235G VAL 3.1 0.2 - - - -
236G SER* 1.3 82.1 - - - +
238G ILE* 1.3 65.9 + - + +
239G LEU 2.9 5.9 + - - +
240G ASP 4.1 4.9 - - - +
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Residues in contact with ILE 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F ALA* 4.0 20.0 - - + +
192F MET* 3.4 27.6 - - + -
211F LEU* 5.8 3.0 - - + +
212F LYS* 4.1 26.8 - - + +
234G LYS* 3.0 15.7 + - + +
235G VAL* 3.2 6.0 + - - +
237G LYS* 1.3 76.1 - - + +
239G LEU* 1.3 69.7 + - + +
240G ASP 4.3 0.2 + - - -
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Residues in contact with LEU 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F ALA* 3.9 9.4 - - + -
211F LEU* 3.6 20.4 - - + -
212F LYS* 6.2 0.2 - - - -
215F PHE* 3.4 32.1 - - + -
229F ARG* 2.9 45.1 - - + +
232F LEU* 4.0 3.6 - - + -
233F LEU* 3.7 5.0 - - + +
235G VAL* 3.1 35.9 + - + +
236G SER* 2.5 25.5 - - - +
237G LYS 3.1 0.4 - - - -
238G ILE* 1.3 86.1 - - + +
240G ASP* 1.3 72.6 + - - +
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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