Contacts of the helix formed by residues 212 - 240 (chain D) in PDB entry 2BG9
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 LEU 212 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D PHE* 5.8 5.4 - - + -
210D ILE 4.4 5.4 - - - +
211D PRO* 1.2 82.6 - - + +
213D TYR* 1.3 56.4 + - - +
214D PHE 3.5 1.1 - - - -
215D VAL* 3.2 26.9 - - + +
216D VAL* 2.4 42.7 + - + +
432D GLU* 5.6 6.1 - - - +
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Residues in contact with TYR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D GLU* 4.8 7.0 - - - -
211D PRO* 3.4 31.9 - - + +
212D LEU* 1.3 79.7 - - - +
214D PHE* 1.3 56.3 + - - +
215D VAL 3.0 1.0 + - - -
216D VAL* 3.1 17.2 + - - +
217D ASN* 2.8 20.6 + - - +
281E LEU* 3.9 33.3 - - + +
286E LEU* 5.0 12.3 - - + -
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Residues in contact with PHE 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D PHE* 6.1 5.8 - + - -
210D ILE* 5.8 7.0 - - + -
211D PRO* 5.4 5.7 - - + +
213D TYR* 1.3 78.2 - - - +
215D VAL* 1.3 56.0 + - + +
217D ASN* 2.6 31.4 - - - +
218D VAL* 2.7 49.1 + - + +
263D LEU* 5.2 3.6 - - + -
264D ILE* 4.3 21.1 - - + -
267D THR* 3.1 47.3 - - + -
268D SER* 5.1 2.5 - - - -
271D VAL* 6.0 4.0 - - + -
273D LEU* 5.1 16.4 - - + -
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Residues in contact with VAL 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D PHE* 5.5 9.6 - - + -
210D ILE* 4.9 9.4 - - + -
211D PRO 4.3 5.4 - - - +
212D LEU* 3.2 38.6 - - + +
214D PHE* 1.3 79.4 - - + +
216D VAL* 1.3 65.1 + - + +
218D VAL* 3.2 10.0 + - - +
219D ILE* 2.9 38.8 - - + +
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D LEU* 2.4 39.9 - - + +
213D TYR* 3.1 12.1 - - - +
215D VAL* 1.3 75.9 - - + +
217D ASN* 1.3 51.5 + - - +
219D ILE* 3.8 6.0 - - + +
220D ILE* 2.5 54.4 + - + +
290E MET* 6.5 1.1 - - + -
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Residues in contact with ASN 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D TYR 2.8 7.6 + - - +
214D PHE* 2.6 51.3 + - - +
216D VAL* 1.3 79.8 - - - +
218D VAL* 1.3 57.3 + - - +
220D ILE* 4.3 6.5 - - + -
221D PRO* 2.6 31.8 - - - +
263D LEU* 5.8 7.5 - - - +
266E PHE* 6.1 2.8 - - - -
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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
----------------------------------------------------------
214D PHE* 2.7 58.6 + - + +
215D VAL* 3.2 7.7 + - - +
217D ASN* 1.3 78.9 - - - +
219D ILE* 1.3 65.7 + - + +
221D PRO* 3.1 17.9 - - - +
222D CYS* 3.5 11.2 - - + +
225D PHE* 5.9 0.2 - - - -
260D ILE* 5.9 8.4 - - + +
264D ILE* 6.2 3.1 - - + -
281D THR* 4.0 28.0 - - + -
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Residues in contact with ILE 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D VAL* 2.9 26.5 - - + +
216D VAL* 3.8 12.1 - - + +
218D VAL* 1.3 82.9 - - + +
220D ILE* 1.3 69.5 + - + +
222D CYS* 3.4 9.0 - - + +
223D LEU* 2.9 38.7 + - + +
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Residues in contact with ILE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D VAL* 2.5 45.9 + - + +
217D ASN* 4.3 5.2 - - + -
219D ILE* 1.3 84.5 - - + +
221D PRO* 1.3 67.7 - - + +
223D LEU* 3.9 3.1 - - - +
224D LEU* 2.7 39.5 + - + +
290E MET* 5.8 9.0 - - + -
294E LEU* 3.5 40.4 - - + -
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Residues in contact with PRO 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D ASN* 2.6 31.2 - - - +
218D VAL* 3.1 15.7 - - - +
220D ILE* 1.3 92.7 - - + +
222D CYS* 1.3 48.6 + - - +
224D LEU* 4.0 10.1 - - + -
225D PHE* 2.5 45.8 + - + +
260D ILE* 3.8 31.4 - - + -
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Residues in contact with CYS 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 3.5 13.9 - - + +
219D ILE* 3.3 14.3 + - + +
220D ILE 3.0 0.2 - - - -
221D PRO* 1.3 79.8 - - - +
223D LEU* 1.3 55.2 + - - +
225D PHE* 2.4 64.6 - - + -
226D SER* 2.7 16.9 + - - -
281D THR* 6.2 3.8 - - - -
284D PHE* 6.0 9.2 - - - -
285D VAL* 5.3 0.9 - - - -
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Residues in contact with LEU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ILE* 2.9 25.5 + - + +
220D ILE* 3.9 2.9 - - - +
222D CYS* 1.3 75.4 - - - +
224D LEU* 1.3 62.1 + - + +
226D SER* 3.1 9.6 + - - -
227D PHE* 2.7 39.1 + - + +
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Residues in contact with LEU 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D ILE* 2.7 32.0 + - + +
221D PRO* 4.0 9.0 - - + +
223D LEU* 1.3 80.7 - - + +
225D PHE* 1.3 54.8 + - - +
227D PHE* 2.9 24.9 + - + +
228D LEU* 3.0 29.5 - - + +
262E THR* 5.5 7.6 - - + +
265E LEU* 5.7 0.2 - - + -
294E LEU* 5.0 12.6 - - + -
297E VAL* 3.4 40.8 - - + -
298E THR* 5.6 2.5 - - - +
301E VAL* 4.7 14.8 - - + -
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Residues in contact with PHE 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL 5.9 0.2 - - - -
221D PRO* 2.5 25.5 + - + +
222D CYS* 2.4 59.5 - - + -
224D LEU* 1.3 72.6 - - - +
226D SER* 1.3 66.6 + - - +
227D PHE 3.1 0.2 - - - -
228D LEU* 3.6 8.5 + - - +
229D THR* 2.9 34.6 + - + +
253D LEU* 5.6 10.1 - - + +
257D LEU* 4.5 18.6 - - + -
260D ILE* 4.5 14.4 - - + -
284D PHE 5.9 0.9 - - - -
285D VAL* 3.1 37.2 - - + -
288D SER* 5.2 10.5 - - - -
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Residues in contact with SER 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D CYS* 2.7 18.3 + - - -
223D LEU* 3.1 11.4 + - - -
225D PHE* 1.3 82.5 - - - +
227D PHE* 1.3 56.1 + - - +
229D THR* 2.5 25.9 + - - +
230D VAL* 2.6 23.7 + - - +
417D ILE* 4.0 24.9 - - - +
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Residues in contact with PHE 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D LEU* 2.7 17.8 + - + +
224D LEU* 2.9 20.6 + - + +
226D SER* 1.3 79.9 - - - +
228D LEU* 1.3 52.5 + - + +
230D VAL* 2.7 19.3 - - + +
231D LEU* 2.5 67.9 + - + -
298E THR* 5.3 2.0 - - + -
301E VAL* 3.9 41.7 - - + -
302E ILE* 4.5 6.7 - - + -
305E ASN* 4.3 12.8 - - + -
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Residues in contact with LEU 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D LEU* 3.0 33.1 + - + +
225D PHE* 4.1 8.7 - - - +
227D PHE* 1.3 79.1 - - + +
229D THR* 1.3 53.7 - - - +
231D LEU* 3.2 19.7 - - + +
232D VAL* 2.5 35.6 + - - +
249D VAL* 3.2 36.0 - - + +
252D SER* 4.8 5.2 - - - +
253D LEU* 5.9 8.1 - - + -
258E LEU* 3.3 21.8 - - + -
301E VAL* 3.6 24.0 - - + -
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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
----------------------------------------------------------
225D PHE* 2.9 24.7 + - + +
226D SER* 2.5 37.4 + - - +
228D LEU* 1.3 74.1 - - - +
230D VAL* 1.3 55.0 + - - +
232D VAL* 2.5 35.8 - - + +
233D PHE* 2.7 39.6 + - - -
253D LEU* 4.6 11.0 - - + -
288D SER* 3.1 28.9 - - - +
292D THR* 6.5 0.9 - - - -
417D ILE* 4.8 2.7 - - + +
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Residues in contact with VAL 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D SER 2.6 18.5 + - - +
227D PHE* 2.7 39.5 + - + +
229D THR* 1.3 76.5 + - - +
231D LEU* 1.3 58.0 + - + +
233D PHE* 3.0 14.3 + - + -
234D TYR* 2.8 65.3 + - + +
414D PHE* 5.5 11.7 - - + -
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Residues in contact with LEU 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D PHE* 2.5 53.4 + - + +
228D LEU* 3.2 26.7 - - + +
230D VAL* 1.3 74.9 - - + +
232D VAL* 1.3 64.4 + - - +
233D PHE 2.9 0.5 + - - -
234D TYR* 3.1 3.3 + - + +
235D LEU* 2.7 44.5 + - + +
258E LEU* 5.9 0.9 - - + -
301E VAL* 4.1 11.9 - - + +
304E LEU* 4.2 18.8 - - + -
305E ASN* 4.4 6.5 - - + +
308E LEU* 3.3 33.0 - - + -
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Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 2.5 33.0 + - + +
229D THR* 2.5 32.1 + - + +
231D LEU* 1.3 74.1 - - - +
233D PHE* 1.3 62.8 + - + +
235D LEU* 4.5 3.9 - - - +
236D PRO* 3.2 19.1 - - - +
246D SER* 4.6 6.7 - - - +
249D VAL* 6.2 3.4 - - + -
250D LEU* 4.3 22.9 - - + -
253D LEU* 4.9 4.0 - - + -
292D THR* 4.9 2.5 - - - +
295D VAL* 4.0 27.1 - - + -
296D ILE* 4.4 13.5 - - + -
299D HIS* 3.6 9.9 + - - +
409D ILE* 5.2 0.3 - - - +
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Residues in contact with PHE 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D THR* 2.7 48.4 + - - -
230D VAL* 3.4 14.8 - - + +
231D LEU 2.9 0.4 + - - -
232D VAL* 1.3 77.9 - - + +
234D TYR* 1.3 60.3 + - - +
236D PRO* 2.8 24.1 - - - +
237D THR 4.5 0.7 + - - -
291D VAL* 3.7 13.9 - - + -
295D VAL* 3.9 8.1 - - + -
406D ILE* 4.7 1.6 - - - +
409D ILE* 3.1 34.9 - - + +
410D LEU* 3.1 34.4 - - + +
413D VAL* 3.3 44.2 - - + -
414D PHE* 5.4 3.1 - - + -
417D ILE* 3.4 19.7 - - + -
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Residues in contact with TYR 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230D VAL* 2.8 62.0 + - + +
231D LEU* 4.1 4.5 - - + +
233D PHE* 1.3 72.4 - + - +
235D LEU* 1.3 69.0 + - + +
237D THR* 2.9 20.4 + - + +
238D ASP* 3.1 12.6 + - + +
410D LEU* 3.2 36.8 - - + -
414D PHE* 3.6 30.3 - + + -
308E LEU* 4.5 10.8 - - + -
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231D LEU* 2.7 45.0 + - + +
232D VAL* 4.5 3.1 - - - +
234D TYR* 1.3 71.5 - - - +
236D PRO* 1.3 62.5 - - + +
237D THR 2.7 2.8 + - - -
239D SER 2.3 39.5 + - - +
242D LYS* 3.2 35.2 - - + +
245D LEU* 5.1 6.3 - - + -
246D SER* 5.4 8.3 - - - -
249D VAL* 6.1 1.6 - - + -
299D HIS* 5.4 1.3 - - + -
304E LEU* 3.9 15.0 - - + -
308E LEU* 2.9 45.3 - - + -
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Residues in contact with PRO 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL 3.2 15.0 - - - +
233D PHE* 2.8 25.1 - - - +
235D LEU* 1.3 84.9 - - + +
237D THR* 1.3 56.6 + - - +
240D GLY* 3.2 25.0 + - - -
299D HIS* 2.8 39.3 - - + +
403D ALA* 5.8 2.9 - - - +
406D ILE* 3.1 31.2 - - + +
409D ILE* 5.4 2.9 - - + -
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Residues in contact with THR 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D TYR* 2.9 16.9 + - + +
235D LEU 2.7 5.3 + - - -
236D PRO* 1.3 77.3 - - - +
238D ASP* 1.3 69.8 + - + +
240D GLY 4.8 0.4 + - - -
403D ALA* 4.5 5.7 + - - +
406D ILE* 2.5 33.7 - - - +
407D ASP* 4.3 5.5 + - - +
410D LEU* 4.5 7.3 - - - +
311E PRO 4.6 7.6 - - - +
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Residues in contact with ASP 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D TYR* 3.1 7.0 + - + +
235D LEU 3.0 1.2 + - - -
237D THR* 1.3 82.5 - - + +
239D SER* 1.3 66.4 + - - +
241D GLU* 4.4 1.1 - - - +
305E ASN* 5.6 0.9 - - - +
308E LEU* 2.5 49.4 - - + +
309E ARG* 2.4 34.4 - - - +
310E THR 3.3 17.1 + - - +
311E PRO* 4.4 6.3 - - - +
314E HIS* 3.4 2.8 - - - -
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Residues in contact with SER 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D LEU 2.3 26.2 + - - +
237D THR 3.5 0.4 - - - -
238D ASP* 1.3 85.2 + - - +
240D GLY* 1.3 59.2 + - - +
241D GLU* 2.8 16.4 - - - -
242D LYS* 2.7 55.4 - - - +
308E LEU* 2.8 11.1 + - - -
314E HIS* 2.7 33.4 + - - -
----------------------------------------------------------
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Residues in contact with GLY 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D LEU* 2.8 5.2 + - - -
236D PRO* 3.2 34.3 + - - +
237D THR 4.8 0.2 - - - -
239D SER* 1.3 68.1 - - - +
241D GLU* 1.3 54.1 + - - +
242D LYS 2.5 10.6 + - - -
243D MET* 2.4 42.0 + - - +
299D HIS* 5.0 1.8 - - - -
----------------------------------------------------------
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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