Contacts of the helix formed by residues 242 - 271 (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 LYS 242 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D LEU* 3.2 37.1 - - + +
239D SER* 2.7 41.4 + - - +
240D GLY* 2.5 7.8 + - - -
241D GLU* 1.4 77.0 - - - +
243D MET* 1.3 54.5 + - - +
244D THR* 3.2 4.7 - - - -
245D LEU* 2.8 54.4 - - + +
246D SER* 2.8 15.6 + - - -
251E CYS* 4.9 8.3 - - - -
252E THR* 5.8 0.4 - - + -
304E LEU* 3.0 33.1 - - + +
307E SER 3.0 14.5 + - - +
308E LEU* 3.5 6.9 - - - +
314E HIS* 4.6 6.5 - - + -
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Residues in contact with MET 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D GLY* 2.4 27.3 + - - +
241D GLU* 2.8 40.8 - - - +
242D LYS* 1.3 74.5 - - - +
244D THR* 1.3 76.7 + - + +
246D SER* 2.7 28.5 - - - -
247D ILE 2.9 6.8 + - - -
299D HIS* 4.4 18.8 - - + +
300D HIS* 3.6 29.3 - - + +
305D THR 5.1 4.7 - - - +
306D HIS* 4.0 35.7 - - + +
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Residues in contact with THR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C LYS* 5.7 2.0 - - - -
259C THR* 2.2 46.0 + - - -
241D GLU 5.1 0.9 - - - +
242D LYS* 4.3 7.2 - - - -
243D MET* 1.3 89.5 - - + +
245D LEU* 1.3 74.9 + - + +
246D SER 3.0 1.3 - - - -
247D ILE* 2.7 26.1 + - - +
248D SER* 2.8 13.0 + - - -
300D HIS* 5.0 1.6 - - - -
252E THR* 5.8 6.7 - - + +
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Residues in contact with LEU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D LEU* 5.1 2.7 - - + -
242D LYS* 2.8 54.3 - - + +
244D THR* 1.3 84.9 - - + +
246D SER* 1.3 60.9 + - - +
248D SER* 2.5 28.7 + - - -
249D VAL* 3.0 15.4 - - + +
251E CYS* 4.5 1.6 - - - +
252E THR* 4.0 23.8 - - - +
255E ILE* 2.9 56.8 - - + -
304E LEU* 4.5 8.1 - - + -
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Residues in contact with SER 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 4.6 10.9 + - - +
235D LEU* 5.4 10.3 - - - -
242D LYS 2.8 10.4 + - - -
243D MET* 2.7 21.5 - - - -
245D LEU* 1.3 78.2 - - - +
247D ILE* 1.3 60.6 + - - +
249D VAL* 3.0 18.2 + - - +
250D LEU* 3.0 34.5 + - - +
296D ILE* 3.5 13.4 - - - +
299D HIS* 3.9 13.8 + - - -
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Residues in contact with ILE 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C LYS* 5.2 4.9 - - - -
259C THR* 2.8 38.4 - - + +
262C CYS* 3.1 24.7 - - - -
263C VAL* 3.9 18.4 - - + -
243D MET 2.9 6.2 + - - +
244D THR* 2.7 15.5 + - - +
246D SER* 1.3 70.9 - - - +
248D SER* 1.3 64.5 + - - +
250D LEU* 2.8 17.9 + - + +
251D LEU* 3.0 14.2 + - + +
296D ILE* 4.4 18.2 - - + -
300D HIS* 3.9 24.2 + - + +
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Residues in contact with SER 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C THR* 5.4 0.4 - - - -
262C CYS* 4.6 10.5 - - - -
244D THR 2.8 13.1 + - - -
245D LEU* 2.5 21.7 + - - -
247D ILE* 1.3 80.4 - - - +
249D VAL* 1.3 64.8 + - - +
251D LEU* 3.4 6.5 + - - +
252D SER 2.9 15.8 + - - -
255E ILE* 3.8 9.4 - - - +
256E SER* 5.5 1.8 + - - -
259E LEU* 2.8 27.3 - - - +
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Residues in contact with VAL 249 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 3.2 41.3 - - + +
232D VAL* 6.2 3.1 - - + -
235D LEU* 6.1 1.8 - - + -
245D LEU* 3.0 33.9 - - + +
246D SER* 3.0 9.0 + - - +
248D SER* 1.3 80.3 - - - +
250D LEU* 1.3 58.9 + - + +
252D SER* 3.1 5.5 + - - +
253D LEU* 2.5 37.1 + - - +
255E ILE* 3.8 8.3 - - + -
258E LEU* 4.3 2.2 - - + -
259E LEU* 3.2 16.6 - - + -
304E LEU* 5.9 2.5 - - + -
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Residues in contact with LEU 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 4.3 13.7 - - + -
246D SER* 3.0 38.5 + - - +
247D ILE* 2.8 11.2 + - + +
249D VAL* 1.3 76.9 - - + +
251D LEU* 1.3 54.8 + - + +
252D SER 3.0 0.9 - - - -
253D LEU* 2.6 54.2 - - + +
254D THR* 2.6 23.1 + - - +
292D THR* 2.5 44.4 - - + +
296D ILE* 3.0 30.5 - - + -
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Residues in contact with LEU 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C LEU* 5.5 3.1 - - + -
262C CYS* 2.8 55.9 - - + +
263C VAL* 3.0 34.1 - - + +
266C ALA* 3.1 23.8 - - + -
270C PHE* 3.5 6.2 - - + -
247D ILE* 3.0 18.6 + - + +
248D SER* 3.6 7.2 - - - +
250D LEU* 1.3 74.4 - - + +
252D SER* 1.4 62.8 + - - +
254D THR* 2.8 22.9 - - + +
255D VAL* 3.0 13.6 + - - +
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Residues in contact with SER 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D LEU* 4.8 3.1 - - - +
248D SER 2.9 5.9 + - - -
249D VAL* 3.1 11.8 + - - +
250D LEU 3.0 0.2 - - - -
251D LEU* 1.4 71.6 - - - +
253D LEU* 1.3 66.0 + - - -
255D VAL* 2.8 13.9 - - - +
256D PHE* 2.8 48.5 + - - -
259E LEU* 2.8 51.4 - - - +
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Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D PHE* 5.6 9.9 - - + +
228D LEU* 5.9 7.9 - - + -
229D THR* 4.6 20.6 - - + +
232D VAL* 4.9 4.9 - - + -
249D VAL* 2.5 13.5 + - + +
250D LEU* 2.6 57.2 - - + +
252D SER* 1.3 77.7 + - - +
254D THR* 1.3 95.0 + - - +
256D PHE* 2.9 9.3 + - - +
257D LEU* 2.8 37.1 + - + +
288D SER* 4.8 6.5 - - - +
289D ILE* 5.7 5.4 - - + -
292D THR* 5.2 3.4 - - + -
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Residues in contact with THR 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C PHE* 3.3 23.0 - - + -
250D LEU 2.6 25.5 + - - +
251D LEU* 2.8 16.6 - - + +
253D LEU* 1.3 94.9 - - - +
255D VAL* 1.3 62.5 + - - +
257D LEU* 3.3 6.0 + - - +
258D LEU* 2.6 66.5 + - - +
289D ILE* 4.7 8.4 - - - +
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Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C VAL* 4.7 9.4 - - + -
270C PHE* 3.3 32.5 - - + -
251D LEU 3.0 12.7 + - - +
252D SER* 2.8 22.9 - - - +
254D THR* 1.3 81.5 - - - +
256D PHE* 1.3 63.0 + - + +
258D LEU* 4.2 6.3 - - + -
259D VAL* 2.3 55.4 + - + +
263E ILE* 5.2 10.1 - - + -
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Residues in contact with PHE 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D SER* 2.8 46.1 + - - -
253D LEU* 3.1 11.2 - - - +
255D VAL* 1.3 83.2 - - + +
257D LEU* 1.3 58.2 + - - +
259D VAL* 3.2 10.2 - - - +
260D ILE* 2.7 30.0 + - + +
259E LEU* 3.6 9.6 - - + -
262E THR* 3.2 38.8 - - + -
263E ILE* 3.1 45.8 - - + -
266E PHE* 5.2 17.3 - + + -
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Residues in contact with LEU 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D PHE* 4.5 15.9 - - + -
253D LEU* 2.8 32.1 + - + +
254D THR* 3.5 8.3 - - - +
256D PHE* 1.3 70.6 - - + +
258D LEU* 1.3 78.5 - - + +
259D VAL 2.8 1.3 - - - -
260D ILE* 2.6 39.3 + - + +
261D VAL* 2.7 24.7 + - + +
285D VAL* 4.2 36.6 - - + +
288D SER* 5.4 7.4 - - - +
289D ILE* 4.8 15.7 - - + -
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Residues in contact with LEU 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C PRO* 5.8 8.3 - - + -
239C ILE* 5.6 7.2 - - + -
270C PHE* 4.6 24.7 - - + +
277C ARG* 6.0 4.9 - - - +
254D THR* 2.6 57.9 + - - +
255D VAL* 3.7 6.7 - - + +
257D LEU* 1.3 85.3 - - + +
259D VAL* 1.3 62.3 + - + +
261D VAL* 3.3 9.0 + - - +
262D GLU* 3.2 23.1 + - - +
289D ILE* 4.6 9.6 - - + -
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Residues in contact with VAL 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ARG* 5.3 0.2 - - - +
255D VAL* 2.3 49.7 + - + +
256D PHE* 3.2 9.9 - - - +
258D LEU* 1.3 78.4 - - + +
260D ILE* 1.3 62.4 + - - +
262D GLU* 2.5 55.8 + - - +
263D LEU* 3.4 12.1 + - + +
266E PHE* 4.5 17.0 - - + -
270E GLN* 4.6 10.5 - - - +
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Residues in contact with ILE 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D ASN 6.1 0.2 - - - +
218D VAL* 5.9 7.9 - - + +
221D PRO* 3.8 35.2 - - + -
225D PHE* 4.5 12.6 - - + -
256D PHE* 2.7 24.8 + - + +
257D LEU* 2.6 35.4 + - + +
259D VAL* 1.3 71.6 - - - +
261D VAL* 1.3 59.0 + - + +
263D LEU* 3.1 27.3 + - + +
264D ILE* 2.9 33.6 + - + +
281D THR* 6.5 0.7 - - + -
266E PHE* 5.6 4.5 - - + -
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Residues in contact with VAL 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ASN* 4.4 18.2 - - + +
257D LEU* 2.7 21.8 + - + +
258D LEU* 3.7 11.0 - - - +
259D VAL 3.2 0.2 - - - -
260D ILE* 1.3 74.2 - - + +
262D GLU* 1.3 51.0 + - + +
264D ILE* 2.9 19.5 - - + -
265D PRO* 2.1 54.3 - - + +
278D MET* 5.0 13.5 - - + -
281D THR* 6.3 0.7 - - - -
282D MET* 5.5 7.0 - - + -
285D VAL* 5.6 8.7 - - + -
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Residues in contact with GLU 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ARG* 2.5 39.8 + - - +
258D LEU* 3.2 11.9 + - - +
259D VAL* 2.5 54.4 + - - +
260D ILE 3.1 0.6 - - - -
261D VAL* 1.3 77.9 - - - +
263D LEU* 1.3 64.0 + - + +
265D PRO* 3.5 6.3 - - - +
266D SER* 3.1 21.3 + - - -
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Residues in contact with LEU 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PHE* 5.6 3.4 - - + -
217D ASN* 5.8 7.0 - - - +
259D VAL 3.6 13.7 - - - +
260D ILE* 3.3 20.2 - - + +
262D GLU* 1.3 78.2 - - + +
264D ILE* 1.3 52.8 + - + +
266D SER* 3.1 7.3 + - - -
267D THR* 2.5 42.0 + - + +
266E PHE* 2.9 48.0 - - + -
270E GLN* 4.3 13.9 - - + +
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Residues in contact with ILE 264 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PHE* 4.6 15.7 - - + -
218D VAL* 6.2 4.0 - - + -
260D ILE* 2.9 22.0 - - + +
261D VAL* 2.9 40.8 - - + +
263D LEU* 1.3 74.5 - - + +
265D PRO* 1.3 68.2 - - + +
267D THR* 2.7 11.4 - - - +
268D SER* 2.5 46.2 + - - -
273D LEU* 6.3 0.9 - - + -
278D MET* 3.6 38.1 - - + -
281D THR* 5.5 6.7 - - + -
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Residues in contact with PRO 265 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ASN* 5.9 1.8 - - - +
261D VAL* 2.1 42.4 - - + +
262D GLU* 3.7 8.1 - - - +
263D LEU 3.5 0.2 - - - -
264D ILE* 1.3 87.6 - - + +
266D SER* 1.3 62.0 + - - +
268D SER* 4.5 4.7 - - - -
269D SER* 3.0 31.0 + - - +
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Residues in contact with SER 266 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D GLU 3.1 13.0 + - - -
263D LEU* 3.1 11.0 + - - -
265D PRO* 1.3 76.5 - - - +
267D THR* 1.3 52.5 + - - +
269D SER* 3.5 2.0 - - - -
270D ALA* 2.7 41.5 + - - +
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Residues in contact with THR 267 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D PHE* 3.1 40.2 - - + -
263D LEU* 2.5 32.8 + - + +
264D ILE* 2.7 25.4 - - - +
266D SER* 1.3 73.1 + - - +
268D SER* 1.3 51.7 + - - +
270D ALA* 2.8 8.4 + - - -
271D VAL* 2.4 51.9 + - - +
----------------------------------------------------------
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Residues in contact with SER 268 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D VAL* 4.5 0.2 - - - +
214D PHE* 5.7 1.8 - - - -
264D ILE* 2.5 34.7 + - - -
265D PRO* 4.3 3.6 - - - -
267D THR* 1.3 73.5 + - - +
269D SER* 1.3 60.1 + - - +
271D VAL* 2.4 32.3 - - - +
272D PRO* 3.4 6.1 - - - +
273D LEU* 2.8 34.9 - - - +
278D MET* 6.2 0.9 - - - -
----------------------------------------------------------
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Residues in contact with SER 269 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D VAL* 3.1 17.8 - - - +
265D PRO* 3.0 22.5 + - - +
266D SER 3.5 1.1 - - - -
268D SER* 1.3 78.7 + - - +
270D ALA* 1.3 56.3 + - - +
271D VAL 3.4 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ALA 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D VAL* 2.7 27.3 - - - +
266D SER* 2.7 25.8 + - - +
267D THR* 2.8 9.4 + - - +
269D SER* 1.3 75.0 - - - +
271D VAL* 1.3 56.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D GLU* 4.1 17.5 - - + +
46D VAL* 4.3 3.8 - - + -
135D PHE* 4.8 13.4 - - + -
209D ARG* 6.3 0.2 - - - +
214D PHE* 6.0 4.9 - - + -
267D THR* 2.4 31.9 + - - +
268D SER* 2.4 24.2 - - - +
269D SER 3.4 0.4 - - - -
270D ALA* 1.3 78.7 - - + +
272D PRO* 1.3 71.2 - - + +
273D LEU* 4.0 3.6 + - + +
----------------------------------------------------------
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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
------------------------------------------------------------
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