Contacts of the helix formed by residues 247 - 275 (chain B) 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 GLU 247 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ALA* 2.7 7.3 + - - -
246B GLY* 1.3 67.7 + - - -
248B LYS* 1.3 51.2 + - - +
249B MET* 2.4 48.4 + - + +
250B SER* 4.3 0.5 + - - -
251B LEU* 4.4 5.2 + - - +
318C SER 5.4 0.2 - - - +
320C HIS* 2.4 60.9 + - + +
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Residues in contact with LYS 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 2.7 56.8 + - - +
241B LEU* 3.2 36.0 - - + +
242B PRO* 3.6 22.7 - - + -
245B ALA 2.3 29.7 + - - +
246B GLY 2.5 5.2 + - - +
247B GLU* 1.3 66.6 - - - +
249B MET* 1.3 62.5 + - - +
250B SER 2.7 1.2 + - - -
251B LEU* 2.9 16.1 + - - -
252B SER* 2.5 68.3 + - - +
305B HIS* 3.9 14.8 - - + +
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Residues in contact with MET 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 4.5 24.7 - - + +
242A LYS* 5.7 2.9 - - + -
245A LEU* 3.6 4.0 - - + +
246B GLY 2.8 10.4 + - - +
247B GLU* 2.4 44.4 - - + +
248B LYS* 1.3 76.3 - - - +
250B SER* 1.3 98.3 + - - +
252B SER* 2.2 22.6 + - - -
253B ILE* 4.9 0.2 - - - +
305B HIS* 5.7 2.2 - - - -
312B HIS* 3.2 45.7 - - + +
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Residues in contact with SER 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 5.4 0.4 - - - -
244A THR* 6.4 0.9 - - - -
245A LEU* 3.0 43.3 - - - +
248B LYS 2.7 1.0 + - - -
249B MET* 1.3 106.3 - - - +
251B LEU* 1.3 63.0 + - - +
252B SER 2.7 15.6 + - - -
253B ILE 2.7 13.7 + - - -
254B SER 3.3 2.1 + - - -
258C SER* 4.4 11.9 + - - -
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Residues in contact with LEU 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B LEU* 3.2 42.8 - - + -
245B ALA* 5.2 2.0 - - + +
247B GLU 4.7 3.4 - - - +
248B LYS* 3.5 18.8 - - - +
249B MET* 4.3 0.4 - - - -
250B SER* 1.3 82.7 + - - +
252B SER* 1.3 66.3 + - - +
254B SER* 2.7 29.4 + - - -
255B ALA* 3.1 8.5 + - + -
257C MET* 5.8 5.6 - - + -
258C SER* 4.5 16.2 - - - +
261C ILE* 3.1 46.4 - - + -
310C LEU* 5.6 2.5 - - + -
314C PHE* 5.7 2.0 - - + -
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.6 1.2 - - - +
248B LYS* 2.5 56.0 + - - +
249B MET* 2.2 33.3 + - - -
250B SER 2.7 0.6 + - - -
251B LEU* 1.3 75.1 - - - +
253B ILE* 1.3 60.9 + - - +
255B ALA* 2.9 27.8 + - - +
256B LEU* 3.2 8.2 + - - +
302B LEU* 4.9 2.2 - - - +
305B HIS* 4.3 17.2 - - - -
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 5.4 1.8 - - + -
235A LEU* 5.2 8.1 - - + -
242A LYS* 4.4 11.2 - - - +
245A LEU* 3.2 47.6 - - + +
246A SER* 6.1 1.6 - - - -
248A SER* 3.3 22.4 - - - +
249A VAL* 5.0 14.1 - - + +
250B SER 2.7 6.3 + - - -
252B SER* 1.3 77.8 + - - +
254B SER* 1.3 60.8 + - - +
256B LEU* 3.2 4.1 + - + +
257B LEU* 2.9 26.6 + - + +
302B LEU* 3.2 49.6 - - + -
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 4.7 3.1 - - - +
248A SER* 5.1 4.0 - - - -
250B SER 3.3 4.4 + - - -
251B LEU* 2.7 23.4 + - - -
253B ILE* 1.3 81.6 - - - +
255B ALA* 1.3 54.3 + - - +
257B LEU* 3.5 6.8 + - - +
258B ALA 3.0 14.4 + - - -
258C SER* 5.9 2.2 - - - -
261C ILE* 3.5 18.7 - - - +
262C CYS* 5.7 3.8 - - - -
265C LEU* 2.3 39.6 - - - +
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 6.0 4.4 - - + +
238B VAL* 3.2 31.6 - - + -
251B LEU* 3.1 9.8 + - + +
252B SER* 2.9 17.2 + - - +
254B SER* 1.3 81.7 + - - +
256B LEU* 1.3 48.8 + - - +
258B ALA* 3.2 4.0 - - - +
259B LEU* 2.3 39.3 + - + +
261C ILE* 6.0 0.4 - - + -
265C LEU* 3.7 13.5 - - + +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 4.8 15.9 - - + -
239B PHE* 5.1 0.4 - - + -
252B SER 3.2 7.8 + - - +
253B ILE* 3.2 6.7 + - + +
255B ALA* 1.3 78.0 - - - +
257B LEU* 1.3 61.2 + - + +
259B LEU* 3.7 20.0 - - + -
260B THR* 2.5 43.3 + - - +
298B SER* 2.8 58.8 - - - +
299B VAL* 4.2 2.5 - - + +
301B VAL* 4.8 1.3 - - + -
302B LEU* 3.3 38.8 - - + -
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Residues in contact with LEU 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 5.1 2.0 - - + -
248A SER* 2.8 52.5 - - - +
249A VAL* 3.2 24.7 - - + -
251A LEU* 5.6 0.2 - - + -
252A SER* 2.5 31.9 - - - +
256A PHE* 3.7 6.9 - - + -
253B ILE* 2.9 19.6 + - + +
254B SER* 3.6 8.7 - - - +
256B LEU* 1.3 74.9 - - + +
258B ALA* 1.4 56.7 + - - +
260B THR* 4.7 2.7 - - - -
261B VAL* 2.8 36.3 + - - +
265C LEU* 5.0 1.3 - - + -
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B LEU* 6.2 0.2 - - + -
254B SER 3.0 1.2 + - - -
255B ALA 3.2 1.6 - - - +
257B LEU* 1.4 82.0 - - - +
259B LEU* 1.3 60.2 + - - +
261B VAL* 4.7 1.8 - - - -
262B PHE* 2.5 49.6 + - + -
265C LEU* 2.6 57.8 - - + +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 3.2 35.0 - - + +
234B LEU* 4.9 11.4 - - + +
235B ALA* 4.3 19.3 - - + +
238B VAL* 5.4 3.6 - - + -
239B PHE* 5.1 0.2 - - + -
255B ALA* 2.3 31.7 + - + +
256B LEU* 2.9 25.7 + - + +
258B ALA* 1.3 68.4 - - - +
260B THR* 1.3 63.3 + - - +
262B PHE* 3.6 8.5 - - + +
263B LEU* 3.1 43.7 + - + +
294B SER* 5.2 8.7 - - - +
295B VAL* 6.4 0.7 - - - -
298B SER* 4.9 8.5 - - - +
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Residues in contact with THR 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 5.7 11.0 - - + -
256A PHE* 3.3 25.8 - - + -
256B LEU* 2.5 35.8 + - - +
257B LEU* 4.7 1.1 - - - -
259B LEU* 1.3 72.3 - - - +
261B VAL* 1.3 67.1 + - - +
263B LEU* 3.3 5.8 + - + +
264B LEU* 2.9 40.8 + - + +
295B VAL* 6.0 8.2 - - + +
298B SER* 5.2 4.0 + - - -
299B VAL* 5.6 5.4 - - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A SER* 5.8 0.2 - - - -
255A VAL* 5.1 5.4 - - + -
256A PHE* 3.0 32.8 - - + -
259A VAL* 6.6 0.2 - - + -
257B LEU 2.8 19.3 + - - +
258B ALA* 3.7 1.1 - - - +
260B THR* 1.3 70.5 - - - +
262B PHE* 1.3 84.4 + - + +
264B LEU* 2.9 6.8 + - + +
265B LEU* 2.8 51.6 + - + +
269C VAL* 4.9 6.1 - - + -
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Residues in contact with PHE 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ILE* 4.7 20.0 - - + -
234B LEU* 4.9 11.2 - - + -
258B ALA* 2.5 43.1 - - + +
259B LEU* 3.6 7.9 - - - +
261B VAL* 1.3 92.1 - - + +
263B LEU* 1.3 58.6 + - - +
265B LEU* 3.3 13.5 + - - +
266B LEU* 3.0 31.6 + - + +
265C LEU* 3.2 24.7 - - + -
268C ALA* 3.4 22.0 - - + -
269C VAL* 3.4 19.5 - - + -
272C LEU* 3.6 26.9 - - + -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B CYS* 6.4 2.2 - - - -
231B ILE* 4.0 14.8 - - + -
259B LEU* 3.1 42.8 + - + +
260B THR* 3.9 5.6 - - + +
262B PHE* 1.3 77.9 - - + +
264B LEU* 1.3 63.7 + - + +
266B LEU* 3.3 24.6 - - + +
267B ALA* 2.9 23.2 + - - +
291B VAL* 3.3 38.8 - - + +
294B SER* 5.0 10.5 - - - -
295B VAL* 5.4 12.3 - - + -
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO* 6.1 4.0 - - + -
224A LEU* 5.7 8.1 - - + -
256A PHE* 3.2 49.6 - - + -
260A ILE* 6.4 2.0 - - + -
260B THR* 2.9 30.7 + - + +
261B VAL* 3.5 4.9 - - + +
263B LEU* 1.3 77.5 - - + +
265B LEU* 1.3 63.2 + - - +
267B ALA* 2.8 31.5 + - + +
268B ASP* 2.9 12.6 + - - +
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Residues in contact with LEU 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL* 2.8 33.3 + - + +
262B PHE* 3.5 18.6 - - + +
264B LEU* 1.3 76.7 - - - +
266B LEU* 1.3 55.7 + - + +
268B ASP* 2.7 45.3 + - + +
269B LYS* 3.0 7.8 + - - +
269C VAL* 4.7 8.1 - - + -
272C LEU* 3.5 33.7 - - + -
273C LEU* 4.6 29.4 - - + -
276C GLN* 6.5 0.2 - - + -
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 5.9 2.5 - - + -
224B THR* 6.1 0.7 - - + -
227B PRO* 4.1 32.8 - - + -
231B ILE* 5.3 4.9 - - + -
262B PHE* 3.0 20.0 + - + +
263B LEU* 3.3 34.1 - - + +
264B LEU 3.1 0.2 - - - -
265B LEU* 1.3 77.7 - - + +
267B ALA* 1.3 55.7 - - - +
269B LYS* 3.1 34.8 - - + +
270B VAL* 2.8 35.5 + - + +
276C GLN* 4.5 14.6 - - - +
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASN* 5.8 4.0 - - - +
263B LEU 2.9 11.6 + - - +
264B LEU* 2.8 29.1 + - + +
266B LEU* 1.3 76.6 - - - +
268B ASP* 1.3 49.8 + - - +
270B VAL* 4.1 5.4 - - - +
271B PRO* 2.5 34.0 - - - +
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 4.8 11.5 - - - +
263A LEU* 3.0 37.9 - - - +
264B LEU* 2.9 10.4 + - - +
265B LEU* 2.7 34.8 + - + +
267B ALA* 1.3 75.9 - - - +
269B LYS* 1.3 58.3 + - - +
271B PRO* 2.9 18.8 - - - +
272B GLU* 3.9 10.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TYR* 5.2 10.7 + - - +
224B THR* 3.8 25.9 + - - +
265B LEU 3.0 5.2 + - - +
266B LEU* 3.1 40.8 - - + +
268B ASP* 1.3 75.7 - - - +
270B VAL* 1.3 94.4 + - + +
272B GLU* 3.5 3.6 + - - +
273B THR* 2.7 51.8 + - + +
276C GLN* 4.8 13.0 - - + +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B LEU* 2.8 27.6 + - + +
267B ALA* 4.1 4.5 - - - +
269B LYS* 1.3 98.1 - - - +
271B PRO* 1.3 66.6 - - + +
273B THR* 2.8 18.1 + - - +
274B SER* 3.1 15.0 + - - -
284B LEU* 3.7 41.7 - - + -
287B ILE* 6.0 3.8 - - + -
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Residues in contact with PRO 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A TYR* 6.4 2.2 - - + -
267B ALA 2.5 31.6 - - - +
268B ASP* 2.9 16.8 - - - +
270B VAL* 1.3 87.9 - - + +
272B GLU* 1.3 57.0 + - + +
274B SER* 3.3 7.7 + - - +
275B LEU* 2.6 44.2 + - + +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASP 3.9 13.7 - - - +
269B LYS* 4.2 4.1 - - - +
271B PRO* 1.3 83.8 - - + +
273B THR* 1.3 60.1 + - + +
275B LEU* 2.9 37.7 - - + +
276B SER* 4.7 1.2 + - - -
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 6.3 3.8 - - + -
269B LYS* 2.7 40.4 + - + +
270B VAL* 2.8 18.0 + - - +
272B GLU* 1.3 79.8 - - + +
274B SER* 1.3 62.9 + - - +
275B LEU 3.0 1.9 + - - -
276B SER* 3.6 8.5 + - - -
277B VAL* 3.8 15.5 - - - +
----------------------------------------------------------
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Residues in contact with SER 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.1 16.2 + - - -
271B PRO* 3.3 13.2 + - - +
273B THR* 1.3 72.7 + - - +
275B LEU* 1.3 54.9 + - - +
276B SER 2.5 20.5 + - - -
277B VAL* 2.8 3.5 + - - +
278B PRO* 2.6 51.2 - - - +
284B LEU* 5.5 7.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 2.2 44.7 + - - +
271B PRO* 2.6 35.6 + - + +
272B GLU* 2.9 41.7 - - + +
273B THR 3.0 0.2 - - - -
274B SER* 1.3 76.0 + - - +
276B SER* 1.3 53.3 + - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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