Contacts of the helix formed by residues 210 - 235 (chain F) in PDB entry 6NHW
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 SER 210 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209F GLY* 1.4 75.1 - - - -
211F LEU* 1.4 62.6 + - - +
212F SER* 3.1 13.8 + - - -
213F GLY* 3.1 19.8 + - - -
214F ILE* 3.7 14.4 - - - +
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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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210F SER* 1.4 70.7 - - - +
212F SER* 1.4 62.0 + - - +
213F GLY 3.3 0.2 - - - -
214F ILE* 3.4 32.2 + - + +
215F ILE* 3.8 8.4 + - - +
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Residues in contact with SER 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F SER* 3.1 10.1 + - - -
211F LEU* 1.4 78.3 + - - +
213F GLY* 1.3 59.9 + - - +
215F ILE* 3.5 21.5 - - - +
216F ILE* 4.5 3.8 - - - +
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Residues in contact with GLY 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210F SER* 3.1 13.2 + - - -
212F SER* 1.3 78.8 - - - +
214F ILE* 1.3 61.9 + - - +
215F ILE 3.6 0.2 - - - -
216F ILE* 3.2 25.6 - - - +
217F GLY* 3.4 7.6 + - - -
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Residues in contact with ILE 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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210F SER 3.7 17.7 - - - +
211F LEU* 3.4 25.0 + - + +
213F GLY* 1.3 77.9 - - - +
215F ILE* 1.4 58.5 + - - +
217F GLY* 3.1 2.4 + - - +
218F VAL* 3.0 37.8 + - + +
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Residues in contact with ILE 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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215D ILE* 4.7 9.9 - - + +
216E ILE* 6.4 2.0 - - + -
219E THR* 5.7 4.2 - - + +
211F LEU* 3.8 6.7 + - - +
212F SER* 3.5 19.5 - - - +
214F ILE* 1.4 75.9 - - - +
216F ILE* 1.4 73.7 + - + +
218F VAL* 3.3 21.7 - - + +
219F THR* 3.6 11.9 - - + +
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Residues in contact with ILE 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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214D ILE* 6.2 4.0 - - + -
215D ILE* 4.1 29.4 - - + -
218D VAL* 6.5 1.3 - - + -
212F SER 4.5 5.6 - - - +
213F GLY* 3.2 22.9 - - - +
215F ILE* 1.4 81.5 - - + +
217F GLY* 1.4 61.1 + - - +
219F THR* 2.8 22.9 + - - +
220F VAL* 3.5 12.9 - - + +
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Residues in contact with GLY 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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213F GLY 3.4 8.2 + - - -
214F ILE* 3.1 8.4 + - - -
216F ILE* 1.4 82.5 - - - +
218F VAL* 1.4 62.2 + - - +
220F VAL* 3.3 11.3 - - - +
221F ALA* 3.3 23.8 + - - +
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Residues in contact with VAL 218 (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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219E THR* 4.6 19.4 - - + +
220E VAL* 5.2 10.3 - - + -
223E VAL* 4.0 29.1 - - + +
214F ILE* 3.0 23.2 + - + +
215F ILE* 3.3 24.5 - - + +
217F GLY* 1.4 72.4 - - - +
219F THR* 1.4 68.1 + - + +
221F ALA* 3.6 17.2 + - + +
222F ALA* 3.8 4.9 + - - +
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Residues in contact with THR 219 (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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215D ILE* 4.3 17.0 - - + +
218D VAL* 3.6 29.1 - - - +
219D THR* 4.0 17.2 - - + +
222D ALA* 5.3 1.0 - - - +
219E THR* 4.0 33.9 - - + +
215F ILE* 3.6 15.7 - - + +
216F ILE* 2.8 23.4 + - - +
218F VAL* 1.4 78.0 - - - +
220F VAL* 1.4 62.5 + - - +
222F ALA* 3.8 12.1 + - - +
223F VAL* 3.8 8.5 - - - +
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Residues in contact with VAL 220 (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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218D VAL* 3.7 17.0 - - + -
216F ILE* 3.5 15.5 - - + +
217F GLY* 3.3 20.6 - - - +
219F THR* 1.4 78.5 + - - +
221F ALA* 1.4 64.4 + - - +
222F ALA 3.3 0.2 - - - -
223F VAL* 3.2 16.8 + - + +
224F VAL* 3.3 27.7 + - + +
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Residues in contact with ALA 221 (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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223E VAL* 6.1 1.3 - - + -
217F GLY 3.3 19.6 + - - +
218F VAL* 3.6 11.7 - - + +
219F THR 3.4 0.4 - - - -
220F VAL* 1.4 78.5 - - - +
222F ALA* 1.4 56.2 + - - +
224F VAL* 3.6 6.3 + - - +
225F LEU* 3.1 30.4 + - - +
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Residues in contact with ALA 222 (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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222D ALA* 4.2 18.8 - - + -
219E THR 5.8 0.2 - - - +
222E ALA* 4.5 13.9 - - + -
223E VAL* 4.6 13.4 - - + +
226E ILE* 4.0 14.0 - - + +
218F VAL 3.8 6.0 + - - +
219F THR* 3.8 11.1 + - - +
220F VAL 3.3 0.6 - - - -
221F ALA* 1.4 78.5 - - - +
223F VAL* 1.4 61.3 + - - +
225F LEU* 3.6 13.6 + - - +
226F ILE* 3.4 23.9 + - - +
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Residues in contact with VAL 223 (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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218D VAL* 3.9 26.0 - - + +
221D ALA* 4.5 9.0 - - + -
222D ALA* 4.4 15.7 - - + +
225D LEU* 4.9 13.8 - - + +
219F THR 3.8 15.9 - - - +
220F VAL* 3.2 10.0 + - + +
222F ALA* 1.4 75.6 - - - +
224F VAL* 1.4 67.7 + - + +
226F ILE* 3.4 20.1 + - - +
227F VAL* 3.6 17.4 + - + +
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Residues in contact with VAL 224 (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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220F VAL* 3.3 29.9 + - + +
221F ALA* 4.1 6.1 - - - +
223F VAL* 1.4 77.5 - - + +
225F LEU* 1.4 61.2 + - - +
227F VAL* 3.3 13.0 + - + +
228F ALA* 3.2 21.5 + - + +
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Residues in contact with LEU 225 (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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223E VAL* 5.6 8.1 - - + +
226E ILE* 3.8 39.3 - - + -
227E VAL* 6.3 2.2 - - + -
230E PHE* 5.8 7.6 - - + -
221F ALA 3.1 19.1 + - - +
222F ALA* 3.7 9.6 - - - +
223F VAL 3.3 0.4 - - - -
224F VAL* 1.4 76.8 - - - +
226F ILE* 1.4 59.8 + - - +
228F ALA* 3.5 22.9 + - + +
229F VAL* 3.7 10.0 + - - +
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Residues in contact with ILE 226 (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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222D ALA* 4.3 13.5 - - + +
225D LEU* 4.0 44.4 - - + +
226D ILE* 4.9 7.2 - - + -
229D VAL* 6.2 4.0 - - + -
226E ILE* 4.2 19.5 - - + -
222F ALA 3.4 18.6 - - - +
223F VAL* 3.4 8.9 + - - +
224F VAL 3.3 0.6 - - - -
225F LEU* 1.4 72.2 - - - +
227F VAL* 1.4 66.0 + - + +
229F VAL* 3.3 23.9 - - + +
230F PHE* 3.4 12.6 + - + +
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Residues in contact with VAL 227 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223F VAL* 3.6 19.7 - - + +
224F VAL* 3.3 14.3 + - + +
226F ILE* 1.4 77.7 - - + +
228F ALA* 1.4 61.6 + - - +
230F PHE* 3.4 8.2 + - + +
231F VAL* 3.1 30.7 + - + +
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Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224F VAL* 3.2 13.2 + - + +
225F LEU* 3.5 20.6 - - + +
226F ILE 3.3 0.2 - - - -
227F VAL* 1.4 76.1 - - - +
229F VAL* 1.4 58.5 + - - +
231F VAL* 3.3 12.8 - - - +
232F CYS* 3.0 27.4 - - - -
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Residues in contact with VAL 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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230E PHE* 5.1 20.0 - - + -
225F LEU 3.7 9.3 + - - +
226F ILE* 3.3 22.4 - - + +
228F ALA* 1.4 78.1 - - - +
230F PHE* 1.4 63.4 + - + +
232F CYS* 3.6 9.5 + - + +
233F LYS* 3.5 19.2 + - - +
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Residues in contact with PHE 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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226F ILE* 3.4 16.6 + - + +
227F VAL* 3.4 10.5 + - + +
228F ALA 3.4 0.4 - - - -
229F VAL* 1.4 80.0 - - + +
231F VAL* 1.4 68.1 + - + +
233F LYS* 3.4 19.8 + - + +
234F SER* 3.8 5.0 + - - -
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Residues in contact with VAL 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 VAL* 3.1 21.6 + - + +
228F ALA* 3.3 18.4 - - - +
230F PHE* 1.4 77.5 - - + +
232F CYS* 1.4 73.3 + - - +
234F SER* 3.2 24.5 + - - -
235F LEU* 3.4 13.8 - - + +
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Residues in contact with CYS 232 (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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228F ALA 3.0 23.1 - - - -
229F VAL* 3.7 12.6 - - + +
230F PHE 3.4 0.4 - - - -
231F VAL* 1.4 80.1 - - - +
233F LYS* 1.4 61.4 + - - +
234F SER 3.6 0.2 + - - -
235F LEU* 3.6 27.6 + - - +
236F LEU* 4.4 7.8 - - - +
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Residues in contact with LYS 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 VAL 3.5 10.1 + - - +
230F PHE* 3.4 16.3 + - + +
231F VAL 3.2 0.6 - - - -
232F CYS* 1.4 74.7 - - - +
234F SER* 1.4 64.4 + - - +
235F LEU 3.2 1.1 - - - -
236F LEU* 3.3 42.6 + - + +
237F TRP* 4.0 8.5 - - - +
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Residues in contact with SER 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 PHE 3.8 4.2 + - - -
231F VAL* 3.2 20.2 + - - -
233F LYS* 1.4 73.1 - - - +
235F LEU* 1.4 63.8 + - - +
236F LEU 3.1 5.6 - - - -
237F TRP* 3.2 51.6 + - - +
238F LYS* 4.7 0.7 + - - +
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Residues in contact with LEU 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 VAL* 3.4 25.4 - - + +
232F CYS* 3.7 17.0 - - - +
233F LYS 3.2 0.6 - - - -
234F SER* 1.4 78.2 - - - +
236F LEU* 1.4 60.6 + - + +
237F TRP 3.3 2.5 - - - -
238F LYS* 3.3 48.3 - - - +
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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