Contacts of the helix formed by residues 210 - 217 (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 LYS 210 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195F ASP* 3.4 24.1 + - - +
196F GLU* 5.0 5.2 - - + +
197F VAL* 4.7 1.3 - - - +
209F GLY* 1.3 78.2 - - - +
211F LEU* 1.3 69.3 + - - +
212F LYS* 3.3 4.7 - - + +
213F GLU* 2.9 35.5 + - + +
214F LEU* 2.9 20.8 + - - +
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Residues in contact with LEU 211 (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* 4.5 1.6 - - + -
190F ALA* 4.2 3.4 - - + +
191F ALA* 3.5 34.3 - - - +
197F VAL* 4.0 23.5 - - + +
210F LYS* 1.3 71.1 - - - +
212F LYS* 1.3 68.0 + - + +
214F LEU* 2.7 25.8 + - + +
215F PHE* 3.0 29.9 + - + -
226F LEU* 4.1 17.7 - - + -
229F ARG* 3.3 33.2 - - - +
238G ILE* 5.8 2.2 - - + -
239G LEU* 3.6 12.3 - - + -
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Residues in contact with LYS 212 (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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210F LYS* 3.3 4.5 - - + +
211F LEU* 1.3 78.9 - - + +
213F GLU* 1.3 66.4 + - + +
215F PHE* 3.2 21.1 + - + +
216F SER* 3.4 13.5 + - - -
237G LYS 5.8 0.4 - - - -
238G ILE* 4.1 25.6 - - + +
240G ASP 6.2 1.6 - - - +
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Residues in contact with GLU 213 (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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209F GLY* 4.9 5.3 - - - -
210F LYS* 2.9 41.0 + - + +
212F LYS* 1.3 79.7 - - + +
214F LEU* 1.3 64.5 + - + +
216F SER* 3.1 19.9 + - - -
217F ALA* 3.2 15.6 + - - +
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Residues in contact with LEU 214 (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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197F VAL* 3.7 42.8 - - + +
199F VAL* 4.1 10.8 - - + -
207F GLU* 4.1 33.2 - - + +
208F LYS 4.3 14.6 - - - +
209F GLY* 4.8 0.9 - - - -
210F LYS 2.9 18.8 + - - +
211F LEU* 2.7 22.3 + - + +
213F GLU* 1.3 74.7 - - + +
215F PHE* 1.3 61.6 + - - +
217F ALA* 3.7 12.1 - - - +
218F LYS* 4.7 1.4 - - - -
222F VAL* 4.6 14.1 - - + +
223F ALA* 5.2 3.1 - - - -
226F LEU* 3.4 18.6 - - + +
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Residues in contact with PHE 215 (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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211F LEU* 3.0 34.4 + - + -
212F LYS* 3.2 12.8 + - + +
214F LEU* 1.3 75.1 - - - +
216F SER* 1.3 69.2 + - - +
217F ALA 3.0 1.6 + - - -
218F LYS* 2.8 36.8 + - - +
223F ALA* 6.0 1.3 - - - +
226F LEU* 3.3 33.4 - - + -
229F ARG* 2.8 52.5 - - + -
238G ILE 5.4 0.7 - - - -
239G LEU* 3.4 23.6 - - + -
240G ASP* 3.6 26.0 - - - +
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Residues in contact with SER 216 (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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212F LYS 3.4 8.9 + - - -
213F GLU* 3.1 13.9 + - - -
215F PHE* 1.3 77.6 - - - +
217F ALA* 1.3 59.9 + - - +
218F LYS* 2.6 23.6 + - - +
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Residues in contact with ALA 217 (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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207F GLU* 4.6 5.4 - - - +
213F GLU* 3.2 15.0 + - + +
214F LEU* 3.7 9.6 - - - +
215F PHE 3.0 4.3 + - - -
216F SER* 1.3 76.0 + - - +
218F LYS* 1.3 58.9 + - - +
219F ASN* 3.0 27.1 + - - +
222F VAL* 6.0 0.3 - - - +
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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