Contacts of the helix formed by residues 209 - 233 (chain D) in PDB entry 3OX4
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 THR 209 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C TYR* 4.2 10.2 - - - +
4D SER* 3.8 29.2 - - - +
5D THR 6.1 0.4 - - - +
6D PHE* 5.7 0.7 - - - -
207D ALA 3.6 10.3 - - - +
208D ALA* 1.3 79.9 - - - +
210D PRO* 1.3 75.3 - - - +
211D ILE* 3.1 18.7 + - - +
212D THR* 2.8 23.1 + - + +
213D ASP* 2.9 28.4 + - - -
256D ASN* 5.7 2.9 - - + +
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Residues in contact with PRO 210 (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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218C LYS* 3.3 27.8 - - - +
222C MET* 3.5 41.3 - - + -
245C TYR* 3.9 30.7 - - + -
249C LEU* 4.5 1.8 - - + -
209D THR* 1.3 89.7 - - - +
211D ILE* 1.3 59.9 + - - +
213D ASP* 3.8 5.7 + - + +
214D ALA* 3.3 12.8 + - - +
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Residues in contact with ILE 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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14C MET* 3.6 31.2 - - + -
245C TYR* 3.8 15.7 - - + +
248C PHE* 3.8 22.7 - - + -
249C LEU* 3.8 26.5 - - + -
252C MET* 4.0 19.3 - - + -
6D PHE* 3.6 35.4 - - + -
209D THR* 3.1 5.5 - - - +
210D PRO* 1.3 74.9 - - - +
212D THR* 1.3 65.5 + - - +
213D ASP 3.1 1.1 + - - -
214D ALA* 3.2 3.3 + - - +
215D CYS* 3.1 26.3 + - - -
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Residues in contact with THR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PHE* 4.9 4.7 - - + -
202D ALA* 4.6 2.4 + - - -
208D ALA* 3.5 9.7 - - - +
209D THR* 2.8 39.0 + - + +
211D ILE* 1.3 77.1 - - - +
213D ASP* 1.3 57.1 + - - +
215D CYS* 3.4 1.7 + - - -
216D ALA* 2.8 34.2 + - - +
252D MET 4.1 2.7 - - - +
253D ALA* 3.3 38.4 - - - +
256D ASN* 3.8 21.8 - - + -
257D ALA* 3.8 11.8 - - + +
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Residues in contact with ASP 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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218C LYS* 4.8 9.9 + - - +
203D TYR* 3.4 25.1 + - + +
208D ALA* 3.6 15.8 - - - +
209D THR 2.9 23.3 + - - +
210D PRO* 3.8 8.4 - - + +
212D THR* 1.3 79.6 + - - +
214D ALA* 1.3 63.2 + - - +
216D ALA* 3.8 1.2 - - - +
217D LEU* 3.0 28.5 + - + +
299D ARG* 2.9 32.4 + - - -
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Residues in contact with ALA 214 (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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214C ALA* 4.2 14.4 - - + +
215C CYS* 5.4 0.2 - - - -
218C LYS* 3.6 41.2 - - + +
249C LEU* 4.9 4.9 - - + -
210D PRO 3.3 6.1 + - - +
211D ILE* 3.2 6.5 + - - +
213D ASP* 1.3 78.0 - - - +
215D CYS* 1.3 65.3 + - - +
217D LEU* 3.9 6.0 - - - +
218D LYS* 3.0 24.4 + - - +
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Residues in contact with CYS 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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214C ALA* 5.2 1.8 - - - -
215C CYS* 5.0 9.6 - - - -
249C LEU* 6.0 0.4 - - - -
211D ILE* 3.1 29.6 + - - +
212D THR 3.9 2.2 - - - +
214D ALA* 1.3 76.9 - - - +
216D ALA* 1.3 66.6 + - - +
218D LYS* 3.2 2.0 + - - +
219D ALA* 2.9 25.8 + - - +
249D LEU* 3.6 36.9 - - + +
252D MET* 3.8 39.0 - - + -
253D ALA* 4.3 4.3 - - + +
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ALA* 3.5 37.6 - - - +
203D TYR* 4.1 19.1 - - + +
212D THR 2.8 22.8 + - - +
213D ASP 3.8 3.1 - - - +
215D CYS* 1.3 72.8 - - - +
217D LEU* 1.3 63.9 + - - +
219D ALA* 3.4 2.2 + - - -
220D ALA* 3.1 20.4 + - - +
249D LEU 5.0 0.2 - - - -
253D ALA* 3.9 15.6 - - + +
303D VAL* 6.5 0.2 - - - -
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Residues in contact with LEU 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D TYR* 3.5 48.0 - - + +
213D ASP* 3.0 15.9 + - + +
214D ALA* 3.9 5.8 - - - +
216D ALA* 1.3 77.1 - - - +
218D LYS* 1.3 62.8 + - - +
220D ALA* 3.5 2.0 + - - +
221D SER* 3.1 23.2 + - - -
302D ASP* 4.2 8.7 - - + +
303D VAL* 4.0 30.5 - - + -
306D ALA* 3.6 19.5 - - + +
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Residues in contact with LYS 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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210C PRO* 3.5 24.4 + - - +
213C ASP* 4.6 13.5 + - - +
214C ALA* 3.7 23.5 - - + +
217C LEU* 6.2 1.4 - - - +
214D ALA 3.0 19.0 + - - +
215D CYS 3.7 3.1 - - - +
217D LEU* 1.3 74.2 - - - +
219D ALA* 1.3 66.1 + - - +
221D SER* 3.3 11.0 + - - -
222D MET* 3.0 43.1 + - + +
249D LEU* 3.5 22.9 - - + -
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Residues in contact with ALA 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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199D ALA* 4.2 5.4 - - + -
215D CYS 2.9 16.8 + - - +
216D ALA 3.6 4.7 - - - +
218D LYS* 1.3 77.8 - - - +
220D ALA* 1.3 57.4 + - - +
222D MET* 3.1 3.5 + - - +
223D ILE* 2.8 38.0 + - + +
246D ALA* 3.4 30.7 - - - +
249D LEU* 3.9 4.6 - - + +
250D ALA* 3.6 21.5 - - + +
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Residues in contact with ALA 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D LEU* 4.3 18.2 - - + +
199D ALA* 4.2 5.7 - - + +
216D ALA 3.1 13.5 + - - +
217D LEU* 3.7 7.4 - - - +
218D LYS 3.3 0.2 - - - -
219D ALA* 1.3 78.1 - - - +
221D SER* 1.3 57.5 + - - +
223D ILE* 3.3 2.1 + - - +
224D ALA* 2.9 31.9 + - - +
303D VAL* 3.8 31.0 - - + +
306D ALA* 4.7 0.2 - - + -
307D MET* 3.9 12.3 - - + +
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Residues in contact with SER 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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217D LEU 3.1 11.1 + - - -
218D LYS* 3.5 16.5 + - - +
219D ALA 3.2 0.2 - - - -
220D ALA* 1.3 78.7 - - - +
222D MET* 1.3 63.6 + - - +
224D ALA* 3.6 2.1 + - - +
225D LYS* 3.3 44.5 + - - +
306D ALA* 3.1 29.6 + - - +
307D MET* 4.4 1.5 - - - +
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Residues in contact with MET 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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210C PRO* 3.5 35.0 - - + -
218D LYS* 3.0 28.5 + - + +
219D ALA 3.7 3.6 - - - +
221D SER* 1.3 76.3 - - - +
223D ILE* 1.3 64.9 + - - +
225D LYS* 3.3 4.6 + - + -
226D ASN* 3.0 36.3 + - - +
242D ALA* 3.6 31.6 - - + +
243D MET* 5.1 0.4 - - - -
245D TYR* 3.8 6.1 - - + -
246D ALA* 3.7 15.7 - - + -
249D LEU* 3.7 30.1 - - - -
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Residues in contact with ILE 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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192D GLY 4.2 5.2 - - - +
195D ALA* 3.7 16.6 - - + +
196D LEU* 3.4 52.5 - - + +
199D ALA* 5.3 0.4 - - + -
219D ALA* 2.8 29.2 + - + +
220D ALA* 3.8 3.8 - - - +
222D MET* 1.3 75.4 - - - +
224D ALA* 1.3 66.0 + - - +
226D ASN 3.1 0.2 + - - -
227D LEU* 2.9 51.5 + - + +
243D MET* 4.0 16.2 - - + -
246D ALA* 3.9 16.4 - - + +
330D LEU* 4.8 2.9 - - + +
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Residues in contact with ALA 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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220D ALA 2.9 17.7 + - - +
221D SER 3.8 4.0 - - - +
222D MET 3.3 0.2 - - - -
223D ILE* 1.3 78.3 - - - +
225D LYS* 1.3 62.0 + - + +
226D ASN 3.6 0.3 + - - -
227D LEU 4.9 0.3 + - - -
228D LYS* 5.5 5.2 + - - +
307D MET* 3.4 51.5 - - + +
330D LEU* 5.1 10.7 - - - +
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Residues in contact with LYS 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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221D SER* 3.3 32.9 + - - +
222D MET* 3.3 3.6 + - - +
223D ILE 3.1 0.4 - - - -
224D ALA* 1.3 79.5 - - + +
226D ASN* 1.3 74.3 + - - +
228D LYS* 6.5 0.4 - - - -
229D THR* 4.3 8.5 + - - -
306D ALA 5.5 1.6 - - - -
307D MET 5.6 3.4 - - - +
308D GLY* 6.2 3.6 - - - -
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Residues in contact with ASN 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 MET* 3.0 30.0 + - - +
223D ILE 3.1 0.4 + - - -
225D LYS* 1.3 92.0 - - - +
227D LEU* 1.3 69.0 + - - +
228D LYS 3.3 2.2 - - - -
229D THR* 3.1 10.2 + - - +
230D ALA* 2.9 22.2 + - - +
238D PRO* 4.2 2.3 - - - +
239D ALA* 3.6 30.6 + - - +
242D ALA* 3.3 27.2 - - + +
243D MET* 4.3 6.5 - - - -
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Residues in contact with LEU 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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188D THR* 3.7 28.7 - - + +
189D ALA 4.3 0.7 - - - +
192D GLY* 3.9 30.3 - - - -
193D MET* 4.0 11.4 - - - +
223D ILE* 2.9 33.7 + - + +
226D ASN* 1.3 71.1 - - - +
228D LYS* 1.3 64.0 + - - +
230D ALA* 3.1 3.5 + - - +
231D CYS* 2.9 29.2 + - - -
243D MET* 3.8 14.4 - - + -
330D LEU* 4.5 11.4 - - + -
334D ILE* 3.7 29.4 - - + -
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Residues in contact with LYS 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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185D LYS* 5.1 0.6 - - - +
223D ILE 4.9 0.2 + - - -
224D ALA 5.5 1.4 + - - -
225D LYS 6.5 0.4 - - - -
226D ASN 3.3 1.0 - - - +
227D LEU* 1.3 77.6 - - - +
229D THR* 1.3 64.0 + - - +
231D CYS* 3.1 3.3 + - - +
232D ASP* 3.0 55.9 + - - +
330D LEU* 4.6 13.7 - - + +
333D SER* 2.7 47.6 + - - +
334D ILE* 4.0 14.4 - - + -
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Residues in contact with THR 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 LYS 4.3 9.6 + - - -
226D ASN* 3.1 12.8 + - - +
228D LYS* 1.3 80.5 - - - +
230D ALA* 1.3 57.3 + - - +
232D ASP* 3.3 5.0 + - - +
233D ASN* 2.9 32.3 + - + +
236D ASP* 3.7 20.2 - - + +
239D ALA* 3.7 19.5 - - + -
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D THR* 3.9 20.3 + - + +
226D ASN 2.9 11.7 + - - +
227D LEU* 3.6 8.5 - - - +
229D THR* 1.3 77.5 - - - +
231D CYS* 1.3 61.4 + - - +
233D ASN 4.1 4.7 - - - -
234D GLY* 3.3 25.1 + - - -
236D ASP* 5.3 0.2 - - - -
239D ALA* 3.8 15.2 - - + +
240D ARG* 4.2 17.1 + - - +
243D MET* 4.4 15.5 - - + -
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Residues in contact with CYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LYS* 3.9 36.8 + - + +
188D THR* 3.6 23.1 - - - -
189D ALA* 3.7 24.7 - - - -
227D LEU* 2.9 20.3 + - - -
228D LYS 3.1 7.6 + - - +
230D ALA* 1.3 80.3 - - - +
232D ASP* 1.3 63.4 + - - +
233D ASN* 3.5 0.3 + - - -
234D GLY 4.6 1.9 + - - -
334D ILE* 3.5 29.4 - - + -
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Residues in contact with ASP 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D LYS* 3.9 12.3 + - - +
228D LYS* 3.0 55.6 + - - +
229D THR* 4.1 4.6 - - - +
231D CYS* 1.3 77.0 - - - +
233D ASN* 1.3 62.3 + - + +
234D GLY 4.1 0.2 - - - -
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Residues in contact with ASN 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 THR* 2.9 15.4 + - + +
230D ALA* 3.5 5.3 - - - +
232D ASP* 1.3 81.7 - - + +
234D GLY* 1.3 57.1 + - - +
235D LYS* 2.8 29.2 + - - +
236D ASP* 2.9 39.9 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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