Contacts of the helix formed by residues 210 - 237 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER* 5.2 1.8 - - - -
213A GLY* 6.4 0.9 - - - -
215B ILE* 5.2 9.4 - - - +
207D MET* 5.2 1.9 - - - -
208D PRO* 4.9 6.0 - - - +
209D GLY* 1.4 74.8 - - - +
211D LEU* 1.4 67.4 + - - +
212D SER 3.2 0.7 - - - -
213D GLY* 3.2 17.4 + - - +
214D ILE* 3.7 13.3 + - - +
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D MET* 5.6 12.3 - - + +
209D GLY* 3.0 7.1 - - - +
210D SER* 1.4 90.3 - - - +
212D SER* 1.4 60.5 + - - +
214D ILE* 3.4 36.4 - - + +
215D ILE* 3.6 9.7 - - - +
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Residues in contact with SER 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A GLY 4.6 3.6 + - - -
210A SER* 3.7 24.2 + - - -
213A GLY* 5.4 0.2 - - - -
209D GLY 3.2 14.1 + - - -
210D SER 3.2 0.8 - - - -
211D LEU* 1.4 79.6 - - - +
213D GLY* 1.4 59.2 + - - +
215D ILE* 3.2 23.0 - - - +
216D ILE* 3.6 18.7 - - - +
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Residues in contact with GLY 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER* 4.6 0.8 + - - -
213A GLY* 3.7 29.9 - - - -
216A ILE* 3.6 20.1 - - - +
217A GLY 5.0 0.2 + - - -
209D GLY 4.5 0.2 + - - -
210D SER* 3.2 12.8 + - - -
212D SER* 1.4 77.9 - - - +
214D ILE* 1.4 60.7 + - - +
216D ILE* 3.1 21.8 - - - +
217D GLY* 3.8 2.6 + - - -
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Residues in contact with ILE 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 4.9 13.9 - - + -
210D SER* 3.7 11.3 + - - +
211D LEU* 3.4 34.3 - - + +
213D GLY* 1.4 72.9 - - - +
215D ILE* 1.4 69.4 + - + +
217D GLY* 3.2 13.2 + - - -
218D VAL* 3.5 15.0 + - - +
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Residues in contact with ILE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU 3.6 12.8 - - - +
212D SER* 3.2 26.7 - - - +
214D ILE* 1.4 82.2 - - + +
216D ILE* 1.4 67.3 + - + +
218D VAL* 3.5 22.9 - - + +
219D THR* 4.0 8.2 - - + +
219E THR* 6.2 1.3 - - + -
215F ILE* 4.7 13.5 - - + +
216F ILE* 4.1 42.0 - - + +
219F THR* 4.3 20.3 + - + +
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Residues in contact with ILE 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A SER 5.6 1.8 - - - +
213A GLY* 3.7 31.0 - - - +
214A ILE* 3.8 18.4 - - + +
217A GLY* 5.6 3.4 - - - -
212D SER* 3.6 16.4 - - - +
213D GLY* 3.1 22.0 - - - +
215D ILE* 1.4 84.5 - - + +
217D GLY* 1.4 60.3 + - - +
219D THR* 2.6 32.9 + - - -
220D VAL* 3.8 6.2 - - - +
215E ILE* 5.3 15.0 - - + -
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Residues in contact with GLY 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ILE* 6.2 0.4 - - - -
217A GLY* 4.1 24.0 - - - -
220A VAL* 4.2 14.8 - - - +
213D GLY 3.8 1.9 + - - -
214D ILE 3.2 10.0 + - - -
216D ILE* 1.4 80.9 - - - +
218D VAL* 1.4 61.6 + - - +
219D THR 3.3 0.2 - - - -
220D VAL* 3.4 16.6 + - - +
221D ALA* 3.5 11.6 + - - +
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Residues in contact with VAL 218 (chain D).
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 3.5 15.9 + - - +
215D ILE* 3.5 16.8 - - + +
216D ILE 3.3 0.4 - - - -
217D GLY* 1.4 77.2 - - - +
219D THR* 1.4 61.1 + - - +
221D ALA* 3.4 20.4 + - - +
222D ALA* 3.7 4.9 + - - +
216F ILE* 6.5 0.9 - - + -
219F THR* 3.6 37.3 - - - +
220F VAL* 3.6 17.5 - - + +
223F VAL* 3.9 12.3 - - + +
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Residues in contact with THR 219 (chain D).
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* 4.0 12.6 - - + +
216D ILE* 2.6 25.9 + - - +
218D VAL* 1.4 77.2 - - - +
220D VAL* 1.4 70.7 + - - +
221D ALA 3.4 0.5 + - - -
222D ALA* 3.4 15.0 + - - +
223D VAL* 3.7 17.0 + - - +
218E VAL* 4.5 25.1 - - + +
219E THR* 4.2 19.3 - - + +
222E ALA* 5.6 0.7 - - - +
219F THR* 4.0 24.2 - - + +
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Residues in contact with VAL 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A GLY* 4.2 19.3 - - - +
218A VAL* 5.8 0.9 - - - -
220A VAL* 5.1 2.0 - - + -
221A ALA* 4.1 29.8 - - + +
216D ILE 3.8 9.6 - - - +
217D GLY* 3.4 12.1 + - - +
218D VAL 3.4 0.2 - - - -
219D THR* 1.4 89.9 + - - +
221D ALA* 1.4 61.2 + - - +
223D VAL* 3.4 23.4 - - + +
224D VAL* 3.5 12.5 - - + +
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Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL* 4.2 18.1 - - + +
224A VAL* 5.5 5.9 - - + +
217D GLY 3.5 8.9 + - - +
218D VAL* 3.4 14.1 + - - +
219D THR 3.3 0.6 - - - -
220D VAL* 1.4 78.2 - - - +
222D ALA* 1.3 60.0 + - - +
224D VAL* 3.3 18.1 - - - +
225D LEU* 3.3 23.5 - - + +
223F VAL* 4.5 14.6 - - + -
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Residues in contact with ALA 222 (chain D).
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 4.1 + - - +
219D THR* 3.4 11.2 + - - +
220D VAL 3.4 0.4 - - - -
221D ALA* 1.3 77.3 - - - +
223D VAL* 1.4 63.7 + - - +
225D LEU* 3.5 18.9 + - - +
226D ILE* 3.5 19.3 + - + +
222E ALA* 4.1 20.9 - - + -
226E ILE* 6.3 0.4 - - + -
219F THR 5.3 0.9 - - - +
222F ALA* 4.2 19.1 - - + -
223F VAL* 4.4 12.7 - - + +
226F ILE* 4.3 6.6 - - + +
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Residues in contact with VAL 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D THR 3.7 10.7 + - - +
220D VAL* 3.4 24.0 - - + +
222D ALA* 1.4 75.5 - - - +
224D VAL* 1.4 66.0 - - + +
226D ILE* 3.5 21.6 + - + +
227D VAL* 3.7 15.2 - - - +
218E VAL* 4.7 18.2 - - + +
221E ALA* 6.4 1.3 - - + -
222E ALA* 4.6 17.9 - - + +
225E LEU* 6.5 0.7 - - + -
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Residues in contact with VAL 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL 5.5 0.2 - - - +
221A ALA* 4.4 28.0 - - + +
224A VAL* 4.2 29.1 - - + +
225A LEU* 5.0 13.7 - - + +
220D VAL* 3.5 12.8 - - + +
221D ALA* 3.3 23.6 - - - +
223D VAL* 1.4 80.5 - - + +
225D LEU* 1.4 62.3 + - - +
227D VAL* 3.3 20.1 + - + +
228D ALA* 3.6 9.5 + - - +
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Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 3.6 27.6 - - + -
221D ALA* 3.3 22.4 - - + +
222D ALA* 3.5 7.6 + - - +
223D VAL 3.4 0.4 - - - -
224D VAL* 1.4 77.0 - - - +
226D ILE* 1.4 61.9 + - - +
228D ALA* 3.4 22.8 + - + +
229D VAL* 3.7 12.0 + - - +
223F VAL* 4.9 15.5 - - + +
226F ILE* 4.0 38.8 - - + +
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Residues in contact with ILE 226 (chain D).
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* 3.5 17.3 - - + +
223D VAL* 3.5 15.5 + - + +
224D VAL 3.3 0.8 - - - -
225D LEU* 1.4 76.3 - - - +
227D VAL* 1.4 63.8 + - + +
229D VAL* 3.2 25.9 - - + +
230D PHE* 3.4 11.3 + - + +
222E ALA* 4.5 16.4 - - + +
225E LEU* 4.0 50.5 - - + -
226E ILE* 4.6 13.2 - - + -
229E VAL* 6.2 1.8 - - + -
226F ILE* 4.9 10.1 - - + -
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D VAL 3.7 16.4 - - - +
224D VAL* 3.3 13.0 + - + +
225D LEU 3.3 0.4 - - - -
226D ILE* 1.4 78.8 - - + +
228D ALA* 1.4 62.1 + - - +
230D PHE* 3.4 10.8 + - + +
231D VAL* 3.3 34.4 + - + +
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Residues in contact with ALA 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A VAL* 6.3 2.0 - - + -
228A ALA* 4.6 20.6 - - + -
224D VAL 3.6 6.0 + - - +
225D LEU* 3.4 20.2 + - + +
227D VAL* 1.4 78.2 - - - +
229D VAL* 1.4 61.2 + - + +
231D VAL* 3.3 13.9 - - - +
232D CYS* 3.0 25.4 - - - -
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LEU 3.7 8.2 + - - +
226D ILE* 3.2 28.5 - - + +
228D ALA* 1.4 75.4 - - + +
230D PHE* 1.4 63.6 + - - +
232D CYS* 3.5 10.1 + - - +
233D LYS* 3.4 36.6 + - - +
226F ILE* 6.2 3.6 - - + -
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Residues in contact with PHE 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ILE* 3.6 12.1 - - + +
227D VAL* 3.4 15.7 + - + +
228D ALA 3.4 0.8 - - - -
229D VAL* 1.4 83.0 - - + +
231D VAL* 1.4 68.1 + - + +
233D LYS* 3.4 23.7 + - + +
234D SER* 3.5 23.7 + - - -
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA* 6.3 2.5 - - + -
232A CYS* 6.1 4.7 - - - -
230C PHE* 5.3 13.5 - - + -
227D VAL* 3.3 23.7 + - + +
228D ALA* 3.3 19.5 - - - +
230D PHE* 1.4 80.0 - - + +
232D CYS* 1.4 67.4 + - - +
234D SER* 3.2 11.3 + - - -
235D LEU* 3.0 29.4 + - - +
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Residues in contact with CYS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A VAL* 5.1 15.7 - - - -
232A CYS* 5.7 8.3 - - - -
235A LEU* 5.3 13.9 - - + -
228D ALA 3.0 24.5 - - - -
229D VAL* 3.6 11.4 - - - +
230D PHE 3.4 0.6 - - - -
231D VAL* 1.4 81.1 - - - +
233D LYS* 1.4 56.3 + - + +
235D LEU* 3.5 10.6 - - - +
236D LEU* 3.1 26.0 + - - +
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Residues in contact with LYS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D VAL* 3.6 25.4 - - - +
230D PHE* 3.4 19.4 + - + +
231D VAL 3.2 0.4 - - - -
232D CYS* 1.4 74.0 - - + +
234D SER* 1.4 55.6 + - - +
235D LEU 3.2 1.3 - - - -
236D LEU* 3.1 10.0 + - + +
237D TRP* 2.8 35.5 + - - +
229E VAL* 5.6 10.0 - - - +
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Residues in contact with SER 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 3.5 22.9 + - - -
231D VAL* 3.2 14.0 + - - -
233D LYS* 1.4 77.4 - - - +
235D LEU* 1.4 60.5 + - - +
237D TRP* 3.6 23.2 + - - +
238D LYS* 4.5 6.2 + - - +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D VAL 3.0 13.6 + - - +
232D CYS* 3.5 15.5 - - - +
234D SER* 1.4 78.1 - - - +
236D LEU* 1.4 55.0 + - - +
238D LYS* 3.4 41.1 - - + +
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D CYS 3.1 15.1 + - - +
233D LYS* 3.1 10.4 + - + +
235D LEU* 1.4 72.4 - - - +
237D TRP* 1.4 57.1 + - - +
238D LYS* 2.9 12.9 + - - +
239D LYS* 3.4 12.5 + - - -
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Residues in contact with TRP 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D LYS 2.8 19.4 + - - +
234D SER* 3.6 18.4 - - - +
235D LEU 3.4 1.0 - - - -
236D LEU* 1.4 70.9 - - - +
238D LYS* 1.4 63.0 + - + +
239D LYS* 3.2 6.6 + - - +
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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