Contacts of the helix formed by residues 279 - 307 (chain B) in PDB entry 2BKU
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 ASN 279 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 3.3 30.5 - - - +
277B SER* 3.1 18.5 + - - +
278B PRO* 1.3 80.1 - - - +
280B ASP* 1.3 79.6 + - - +
281B LYS* 3.1 17.2 + - - +
282B VAL* 3.3 8.9 + - + +
283B ALA* 3.2 17.8 + - - +
335B ARG* 3.9 0.7 - - - -
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Residues in contact with ASP 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B PRO 3.4 6.6 - - - +
279B ASN* 1.3 75.0 + - - +
281B LYS* 1.3 58.7 + - - +
283B ALA* 3.8 0.6 - - - +
284B SER* 2.9 35.0 + - - -
335B ARG* 3.0 32.8 + - - +
346B ASN* 5.6 3.7 - - + +
347B VAL* 3.7 29.4 - - + +
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Residues in contact with LYS 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 4.7 20.2 - - - +
238B ILE* 4.1 23.1 - - + -
279B ASN* 3.1 11.8 + - - +
280B ASP* 1.3 77.4 - - - +
282B VAL* 1.3 61.8 + - - +
284B SER* 3.5 7.4 - - - -
285B MET* 3.1 35.1 + - + +
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Residues in contact with VAL 282 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 3.4 16.2 - - + -
241B GLN* 3.3 32.3 - - - +
245B PHE* 5.6 2.7 - - + -
274B THR* 3.6 23.8 - - + +
277B SER* 3.5 30.1 - - - +
279B ASN* 3.3 13.3 + - + +
280B ASP 3.2 0.8 - - - -
281B LYS* 1.3 76.0 - - - +
283B ALA* 1.3 63.6 + - - +
285B MET* 3.2 17.2 + - + +
286B THR* 2.9 22.1 + - + +
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B THR 3.6 11.7 - - - +
275B MET* 3.8 21.2 - - - +
277B SER 4.2 7.2 - - - +
279B ASN 3.2 14.1 + - - +
280B ASP 4.0 0.9 - - - +
282B VAL* 1.3 78.7 - - - +
284B SER* 1.3 62.6 + - - +
286B THR* 3.3 4.8 + - - +
287B VAL* 3.0 28.5 + - - +
332B LEU* 4.2 9.2 - - + -
335B ARG* 4.3 3.1 - - - +
347B VAL* 3.9 16.2 - - + -
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Residues in contact with SER 284 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ASN* 5.6 9.2 - - - -
280B ASP 2.9 22.9 + - - -
281B LYS* 3.5 11.4 - - - -
282B VAL 3.2 0.2 - - - -
283B ALA* 1.3 75.5 - - - +
285B MET* 1.3 63.4 + - - +
287B VAL* 3.0 16.8 + - - +
288B GLU* 3.1 17.4 + - - +
345B TRP* 5.9 0.5 + - - -
346B ASN 4.5 1.4 - - - -
347B VAL* 3.3 30.7 + - - +
350B SER* 4.5 8.0 - - - -
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B ILE* 3.6 39.5 - - + +
241B GLN* 3.6 11.7 - - + +
242B ALA* 3.4 38.4 - - + +
245B PHE* 3.6 34.4 - - + +
249B CYS* 5.1 1.4 - - - -
281B LYS* 3.1 32.6 + - + +
282B VAL* 3.2 12.8 + - - +
284B SER* 1.3 78.6 - - - +
286B THR* 1.3 60.6 + - - +
288B GLU* 3.5 9.0 - - - +
289B PHE 3.3 14.7 + - - -
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Residues in contact with THR 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 3.9 20.9 - - + -
271B THR* 3.2 22.0 + - - -
274B THR* 3.0 42.4 - - - +
275B MET* 3.7 13.6 - - - +
282B VAL 2.9 19.5 - - - +
283B ALA 3.6 5.8 - - - +
285B MET* 1.3 72.7 - - - +
287B VAL* 1.3 65.3 + - - +
289B PHE* 3.3 3.3 + - - +
290B TRP* 3.2 25.1 + - - -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B MET* 4.6 8.1 - - + -
283B ALA 3.0 22.2 + - - +
284B SER* 3.0 9.2 + - - +
286B THR* 1.3 73.1 - - - +
288B GLU* 1.3 61.1 + - - +
290B TRP* 3.1 8.3 + - - +
291B SER* 2.9 26.1 + - - +
329B LEU* 3.9 12.6 - - + -
332B LEU* 3.5 28.7 - - + -
347B VAL* 4.6 4.5 - - + -
350B SER* 3.4 36.3 - - - +
351B ALA* 4.9 0.7 - - - -
354B CYS* 3.5 16.6 - - + -
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Residues in contact with GLU 288 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 2.8 62.5 + - - +
141A LYS* 4.2 16.0 + - + +
249B CYS* 4.2 10.5 - - - -
284B SER 3.1 10.1 + - - +
285B MET* 3.5 12.6 - - - +
287B VAL* 1.3 74.5 - - - +
289B PHE* 1.3 66.1 + - - +
291B SER* 3.0 6.9 + - - -
292B THR* 2.8 29.7 + - - +
350B SER* 3.1 24.8 + - - -
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PHE* 4.3 7.9 - + + -
248B LEU* 3.9 48.2 - - + -
249B CYS* 3.7 16.7 - - - -
252B MET* 3.7 31.9 - - + -
263B MET* 3.9 17.3 - - + -
267B LEU* 4.4 11.9 - - + -
271B THR* 3.9 26.9 - - + -
285B MET 3.3 9.4 + - - +
286B THR* 3.3 13.4 + - - +
287B VAL 3.3 0.2 - - - -
288B GLU* 1.3 79.1 - - - +
290B TRP* 1.3 68.4 + + - +
292B THR* 3.4 4.2 + - - -
293B ILE* 3.0 42.6 + - + +
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Residues in contact with TRP 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B MET* 3.8 24.9 - - + -
268B TYR* 4.9 6.3 - + - -
271B THR* 3.1 31.5 + - - -
272B ILE* 5.0 3.4 - - + -
275B MET* 3.4 25.2 - - + +
286B THR 3.2 19.8 + - - +
287B VAL 3.1 9.6 + - - +
289B PHE* 1.3 82.6 - + - +
291B SER* 1.3 60.4 + - - +
293B ILE* 3.5 27.4 - - + +
294B CYS* 3.1 31.4 + - - -
317B PHE 3.8 17.3 - - - -
318B ALA* 4.0 3.4 - - + -
321B SER* 3.1 32.1 - - - -
325B VAL* 3.9 17.4 - - + +
354B CYS* 4.1 12.3 - - - -
358B PHE* 4.2 17.9 - + + -
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.9 18.2 + - - -
287B VAL* 2.9 12.2 + - - +
288B GLU* 3.0 12.5 + - - -
290B TRP* 1.3 73.9 - - - +
292B THR* 1.3 54.6 + - - +
294B CYS* 3.1 5.0 + - - +
295B GLU* 2.8 40.1 + - - +
350B SER 4.7 1.0 + - - -
353B ALA* 4.7 0.3 - - - +
354B CYS* 3.2 34.6 + - - +
357B LEU* 3.6 19.0 - - - +
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 5.1 0.8 + - - +
141A LYS* 5.0 6.6 + - - +
249B CYS* 3.4 33.7 - - + +
252B MET* 4.5 6.5 - - + -
253B SER* 3.2 32.3 - - - +
288B GLU* 2.8 17.4 + - - +
289B PHE 3.4 7.9 - - - -
291B SER* 1.3 73.5 - - - +
293B ILE* 1.3 63.2 + - - +
295B GLU* 3.0 19.6 + - - +
296B GLU* 2.9 26.2 + - + +
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 3.7 31.4 - - + -
256B TYR* 4.9 1.6 - - + -
263B MET* 3.9 13.2 - - + -
289B PHE* 3.0 45.1 + - + +
290B TRP* 3.5 37.5 - - + +
291B SER 3.2 0.2 - - - -
292B THR* 1.3 76.3 - - - +
294B CYS* 1.3 62.9 + - - +
296B GLU* 3.4 2.8 + - - +
297B GLU* 3.1 35.4 + - - +
317B PHE* 3.8 24.9 - - + -
318B ALA* 4.2 3.8 - - + +
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Residues in contact with CYS 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B TRP 3.1 17.8 + - - -
291B SER* 3.5 7.2 - - - +
293B ILE* 1.3 74.0 - - - +
295B GLU* 1.3 61.5 + - - +
297B GLU* 3.3 1.4 + - - +
298B ILE* 2.8 35.9 + - - +
318B ALA* 4.0 6.3 - - - -
354B CYS 4.6 0.2 - - - -
357B LEU* 3.7 23.1 - - + +
358B PHE* 3.6 47.6 - - - -
361B ASN* 3.6 18.3 + - - +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.6 8.5 - - - +
140A ARG* 3.2 32.1 + - - -
141A LYS* 3.0 25.2 + - - -
291B SER 2.8 18.4 + - - +
292B THR* 3.4 17.9 - - - +
294B CYS* 1.3 74.5 - - - +
296B GLU* 1.3 60.2 + - + +
298B ILE* 3.3 7.2 + - - +
299B ASP* 3.0 37.6 + - - +
357B LEU* 3.9 18.7 - - + +
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B MET* 4.4 2.7 - - + +
253B SER* 3.0 48.7 - - - +
254B LYS* 5.6 0.5 + - - -
256B TYR* 4.5 15.9 - - + -
292B THR* 2.9 19.3 + - + +
293B ILE* 4.2 2.9 - - - +
295B GLU* 1.3 80.1 - - + +
297B GLU* 1.3 58.7 + - - +
299B ASP* 3.6 13.3 + - - +
300B ILE* 3.0 35.6 + - + +
309D GLN* 3.7 17.9 - - - +
311D PRO* 3.3 25.9 - - - +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 2.9 31.5 + - + +
293B ILE* 3.1 22.3 + - - +
295B GLU 3.2 0.2 - - - -
296B GLU* 1.3 75.8 - - - +
298B ILE* 1.3 63.8 + - - +
300B ILE* 3.4 9.2 + - - +
301B ALA* 3.2 20.1 + - - +
314B SER* 3.8 17.4 - - - +
316B ASN* 3.4 3.1 + - - -
317B PHE* 2.6 35.5 + - - +
318B ALA* 3.4 15.4 + - - +
319B LEU 4.8 0.3 + - - -
361B ASN* 2.9 35.4 + - - +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B CYS 2.8 21.2 + - - +
295B GLU* 3.3 5.1 + - - +
297B GLU* 1.3 73.5 - - - +
299B ASP* 1.3 72.2 + - - +
301B ALA* 3.1 17.6 + - + +
302B TYR* 3.2 28.5 + - + -
357B LEU* 3.6 45.5 - - + +
360B GLN* 3.9 20.0 - - + +
361B ASN* 3.6 20.6 - - + +
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Residues in contact with ASP 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.0 20.8 + - - +
296B GLU* 3.9 14.5 - - - +
298B ILE* 1.3 80.9 - - - +
300B ILE* 1.3 60.6 + - + +
302B TYR* 3.4 11.1 + - - +
303B GLU* 3.0 30.1 + - - +
307D PHE* 5.0 3.0 - - + -
309D GLN* 3.5 33.1 - - - +
311D PRO* 5.8 3.6 - - + -
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 3.8 37.7 - - + -
296B GLU* 3.0 26.3 + - + +
297B GLU* 3.5 8.3 - - - +
298B ILE 3.2 0.2 - - - -
299B ASP* 1.3 74.3 - - - +
301B ALA* 1.3 59.1 + - - +
303B GLU* 3.0 8.1 + - - +
304B LEU* 2.9 43.7 + - + +
312B LEU* 3.9 29.4 - - + -
313B GLN 4.4 0.2 - - - -
314B SER* 4.0 28.0 - - - +
311D PRO* 4.0 16.4 - - + -
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU 3.2 11.9 + - - +
298B ILE* 3.1 14.6 + - - +
300B ILE* 1.3 78.0 - - - +
302B TYR* 1.3 62.3 + - + +
304B LEU* 3.6 8.4 + - - +
305B ALA* 3.1 23.0 + - - +
361B ASN* 6.0 0.7 - - - +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ILE* 3.2 28.3 + - + -
299B ASP* 3.6 12.3 - - - +
301B ALA* 1.3 81.5 - - + +
303B GLU* 1.3 62.6 + - - +
305B ALA* 3.2 8.6 + - + +
306B GLN* 3.2 22.9 + - - +
307D PHE* 3.9 18.0 - + + -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP 3.0 15.9 + - - +
300B ILE* 3.0 10.5 + - - +
302B TYR* 1.3 78.0 - - - +
304B LEU* 1.3 58.2 + - + +
306B GLN 3.4 1.9 + - - -
307B PHE* 2.9 33.1 + - - +
310B SER* 5.3 0.9 - - - +
312B LEU* 3.7 16.0 - - + +
303D GLU* 3.0 30.8 - - + +
307D PHE* 3.7 34.0 - - + +
309D GLN* 4.4 2.6 - - - +
310D SER* 2.6 44.9 + - - -
311D PRO* 4.0 4.7 - - - +
312D LEU* 4.2 1.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ILE* 2.9 32.2 + - + +
301B ALA* 4.0 7.4 - - - +
303B GLU* 1.3 75.6 - - + +
305B ALA* 1.3 65.7 + - - +
307B PHE 3.8 4.3 - - - +
308B PRO* 3.1 35.5 - - + +
310B SER* 4.1 20.9 - - - +
312B LEU* 3.4 27.4 - - + +
313B GLN* 5.1 6.3 - - + -
314B SER* 5.2 3.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ALA 3.1 15.2 + - - +
302B TYR* 3.2 13.9 + - + +
304B LEU* 1.3 78.1 - - - +
306B GLN* 1.3 58.0 + - + +
308B PRO* 4.4 5.0 - - - +
----------------------------------------------------------
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B TYR 3.2 13.6 + - - +
304B LEU 3.2 0.2 - - - -
305B ALA* 1.3 76.4 - - + +
307B PHE* 1.3 72.9 + - + +
308B PRO* 3.8 4.8 - - - +
306D GLN* 3.7 22.9 - - - +
307D PHE* 3.6 31.4 - - + -
----------------------------------------------------------
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Residues in contact with PHE 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU 2.9 12.9 + - - +
304B LEU* 3.3 5.7 - - - +
306B GLN* 1.3 95.7 - - + +
308B PRO* 1.3 60.9 - - - +
309B GLN 3.1 5.4 - - - -
310B SER* 2.9 24.6 + - - +
299D ASP 5.2 1.8 - - - -
302D TYR* 4.3 16.4 - + + -
303D GLU* 3.8 51.8 - - + +
306D GLN* 3.6 28.5 - - + -
307D PHE* 3.8 28.5 - + - -
----------------------------------------------------------
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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