Contacts of the helix formed by residues 186 - 194 (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 ASP 186 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30F LEU* 3.5 7.8 - - - +
162F LYS* 2.8 28.5 + - - +
184F THR* 3.1 16.4 - - + +
185F HIS* 1.3 87.7 - - + +
187F LEU* 1.3 64.9 + - - +
188F ILE* 3.0 25.1 + - - +
189F GLU* 3.1 26.2 + - - +
190F ALA 3.3 7.3 + - - -
159G LEU* 3.5 27.7 - - - +
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Residues in contact with LEU 187 (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* 3.5 26.6 - - + +
185F HIS 3.9 2.5 + - - +
186F ASP* 1.3 72.5 + - - +
188F ILE* 1.3 57.6 + - - +
190F ALA* 2.6 24.5 + - - +
191F ALA* 2.7 13.2 + - - +
225F PHE* 4.2 8.7 - - + +
226F LEU* 3.7 16.4 - - + +
228F ALA* 3.4 34.8 - - + +
229F ARG* 2.5 61.0 - - - +
232F LEU* 4.3 4.5 - - + -
158G ASP* 6.0 1.1 - - - +
159G LEU* 4.3 10.4 - - + +
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Residues in contact with ILE 188 (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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159F LEU* 4.0 24.9 - - + -
162F LYS* 4.7 8.7 - - + +
166F MET* 4.6 9.9 - - - -
186F ASP* 3.0 23.5 - - - +
187F LEU* 1.3 78.4 - - - +
189F GLU* 1.3 54.8 + - - +
191F ALA* 4.0 1.0 - - - +
192F MET* 3.0 34.1 + - + +
229F ARG* 4.2 0.4 - - - +
232F LEU* 3.8 35.7 - - + -
159G LEU* 4.4 2.2 - - + -
188G ILE* 4.5 5.8 - - + -
231G LEU* 5.3 6.7 - - + +
232G LEU* 4.1 12.1 - - + -
235G VAL* 3.8 26.9 - - + -
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Residues in contact with GLU 189 (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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28F VAL* 4.8 3.0 - - + +
153F PRO* 5.1 0.2 - - - +
154F LEU* 3.1 31.3 + - - +
155F SER* 4.9 1.0 + - - -
162F LYS* 3.4 20.3 - - - -
166F MET* 3.0 20.9 - - + -
182F HIS* 3.0 27.3 + - + +
184F THR* 3.2 31.2 + - - +
185F HIS* 5.7 0.3 - - - -
186F ASP* 3.1 20.2 + - - +
187F LEU 2.7 4.4 + - - -
188F ILE* 1.3 73.4 - - - +
190F ALA* 1.3 65.1 + - - +
193F LEU* 3.0 33.4 + - + +
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Residues in contact with ALA 190 (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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28F VAL* 3.7 21.5 - - + +
30F LEU* 3.8 35.9 - - + -
186F ASP 3.3 2.0 + - - -
187F LEU 2.6 13.5 + - - +
189F GLU* 1.3 75.0 - - - +
191F ALA* 1.3 62.7 + - - +
194F ALA* 3.0 31.0 + - - +
197F VAL* 4.2 11.1 - - + +
211F LEU* 4.2 7.5 - - + +
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Residues in contact with ALA 191 (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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187F LEU 2.7 18.6 + - - +
188F ILE* 4.0 5.4 - - - +
190F ALA* 1.3 73.2 - - - +
192F MET* 1.3 62.9 + - + +
194F ALA 5.2 1.9 + - - +
211F LEU* 3.5 22.5 - - + +
229F ARG* 4.3 0.2 - - - +
235G VAL* 4.5 5.4 - - + -
238G ILE* 4.0 25.8 - - + +
239G LEU* 3.9 27.1 - - + -
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Residues in contact with MET 192 (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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166F MET* 3.6 28.0 - - + -
170F ARG* 3.2 45.4 + - - +
188F ILE* 3.0 25.8 + - + +
190F ALA 3.2 0.4 - - - -
191F ALA* 1.3 81.5 - - + +
193F LEU* 1.3 59.1 + - + +
231G LEU* 5.2 9.9 - - + +
234G LYS* 4.1 15.5 - - + -
235G VAL* 3.4 39.7 - - + +
238G ILE* 3.4 33.0 - - + -
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Residues in contact with LEU 193 (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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26F TYR* 3.4 45.0 - - + +
28F VAL* 4.6 1.1 - - + -
154F LEU* 4.8 0.2 - - + -
166F MET* 3.2 59.0 - - + +
169F LEU* 3.9 19.3 - - + -
170F ARG* 3.7 19.4 - - + +
182F HIS* 4.1 14.1 - - + +
189F GLU 3.0 13.5 + - - +
190F ALA 3.2 0.2 + - - -
191F ALA 3.5 0.2 - - - -
192F MET* 1.3 80.7 - - - +
194F ALA* 1.3 68.9 + - - +
195F ASP* 3.6 10.6 + - - +
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Residues in contact with ALA 194 (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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26F TYR 3.4 6.7 - - - -
28F VAL* 3.5 17.2 - - + +
190F ALA 3.0 12.5 + - - +
191F ALA 5.4 1.9 - - - +
193F LEU* 1.3 81.3 - - - +
195F ASP* 1.3 60.3 + - - +
196F GLU 2.9 23.1 - - - +
197F VAL* 3.3 23.6 - - + -
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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