Contacts of the helix formed by residues 279 - 307 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 3.5 23.0 - - - +
277D SER* 3.2 19.4 + - - +
278D PRO* 1.3 80.2 - - + +
280D ASP* 1.3 80.6 + - - +
281D LYS* 2.8 20.3 + - - +
282D VAL* 3.5 14.1 + - + +
283D ALA* 3.2 17.5 + - - +
335D ARG* 4.0 0.7 - - - -
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Residues in contact with ASP 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D PRO 3.4 5.2 + - - +
279D ASN* 1.3 74.6 + - - +
281D LYS* 1.3 59.2 + - - +
283D ALA* 3.5 1.2 + - - -
284D SER* 2.9 33.6 + - - -
335D ARG* 3.1 34.5 + - - +
346D ASN* 5.5 4.2 - - + +
347D VAL* 3.8 28.8 + - + +
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Residues in contact with LYS 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ASN* 4.3 28.4 + - - +
238D ILE* 3.9 20.9 - - + -
279D ASN* 2.8 17.8 + - - +
280D ASP* 1.3 71.8 - - - +
282D VAL* 1.3 59.2 + - - +
284D SER* 3.4 5.8 + - - -
285D MET* 3.0 39.1 + - + +
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Residues in contact with VAL 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D ILE* 3.3 16.8 - - + -
241D GLN* 3.3 29.8 - - - +
245D PHE* 5.7 1.1 - - + -
274D THR* 3.6 26.2 - - + +
277D SER* 3.5 29.8 - - - +
279D ASN* 3.5 16.2 + - + +
281D LYS* 1.3 73.5 - - - +
283D ALA* 1.3 66.3 + - - +
285D MET* 3.2 21.1 - - - +
286D THR* 2.9 17.0 - - - +
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274D THR 3.6 11.4 - - - +
275D MET* 3.7 21.2 - - - +
277D SER 4.2 6.3 - - - +
279D ASN 3.2 14.2 + - - +
280D ASP 3.9 3.8 - - - +
282D VAL* 1.3 79.1 - - - +
284D SER* 1.3 57.4 + - - +
286D THR* 3.4 4.6 + - - +
287D VAL* 3.0 33.5 + - - +
332D LEU* 4.2 8.5 - - + -
335D ARG* 4.3 2.7 - - - +
347D VAL* 3.9 14.8 - - + -
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ASN* 4.8 16.9 + - - -
280D ASP 2.9 20.6 + - - -
281D LYS* 3.6 8.7 - - - -
282D VAL 3.2 0.2 - - - -
283D ALA* 1.3 72.7 - - - +
285D MET* 1.3 67.8 + - - +
287D VAL* 3.0 7.5 + - - +
288D GLU* 2.9 26.2 + - - +
345D TRP* 6.1 0.2 - - - -
346D ASN 4.5 0.9 - - - -
347D VAL* 3.4 29.3 + - - +
350D SER* 4.2 10.1 + - - -
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Residues in contact with MET 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ASN* 6.0 2.1 - - - +
238D ILE* 3.5 45.3 - - + +
241D GLN* 3.5 14.8 - - + +
242D ALA* 3.3 39.9 - - + +
245D PHE* 3.6 32.1 - - + +
249D CYS* 5.4 0.3 - - - -
281D LYS* 3.0 27.1 + - + +
282D VAL* 3.2 12.8 - - - +
284D SER* 1.3 78.9 - - - +
286D THR* 1.3 61.3 + - - +
288D GLU* 3.3 8.1 + - - +
289D PHE* 3.2 15.8 + - - +
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Residues in contact with THR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D PHE* 3.6 22.4 - - + -
271D THR* 3.4 21.4 + - - -
274D THR* 3.2 42.8 - - - +
275D MET* 3.7 13.3 - - - +
282D VAL 2.9 19.1 - - - +
283D ALA 3.6 7.0 - - - +
285D MET* 1.3 72.2 - - - +
287D VAL* 1.3 64.8 + - - +
289D PHE* 3.3 4.9 + - - +
290D TRP* 3.2 22.7 + - - -
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Residues in contact with VAL 287 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D MET* 4.6 8.1 - - + -
283D ALA 3.0 25.1 + - - +
284D SER* 3.0 10.6 + - - +
286D THR* 1.3 75.7 - - - +
288D GLU* 1.3 59.7 + - - +
290D TRP* 3.0 8.9 + - - +
291D SER* 2.9 27.6 + - - +
329D LEU* 4.1 7.9 - - + -
332D LEU* 3.4 29.2 - - + -
347D VAL* 4.6 3.6 - - + -
350D SER* 3.5 36.8 - - - +
351D ALA* 4.0 2.2 - - - +
354D CYS* 3.5 17.5 - - + -
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Residues in contact with GLU 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 2.7 70.1 + - - +
141C LYS* 3.9 19.8 + - + +
143C ASN* 5.6 1.0 - - - +
249D CYS* 4.3 6.7 - - - -
284D SER* 2.9 11.5 + - - +
285D MET* 3.4 12.6 - - - +
287D VAL* 1.3 79.8 - - - +
289D PHE* 1.3 56.4 + - - +
291D SER* 3.3 5.6 + - - -
292D THR* 2.9 33.7 + - - +
350D SER* 3.8 21.0 + - - +
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Residues in contact with PHE 289 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D PHE* 3.9 21.3 - + + -
248D LEU* 3.8 51.1 - - + -
249D CYS* 3.7 14.7 - - - -
252D MET* 3.8 31.9 - - + -
263D MET* 4.0 15.3 - - + -
267D LEU* 4.4 6.7 - - + -
271D THR* 3.8 29.6 - - + -
285D MET 3.2 5.9 + - - -
286D THR 3.3 8.5 - - - +
288D GLU* 1.3 75.1 - - - +
290D TRP* 1.3 64.4 + + - +
292D THR* 3.2 5.5 + - - -
293D ILE* 3.0 40.7 + - + +
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Residues in contact with TRP 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D MET* 3.8 27.4 - - + -
268D TYR* 5.0 6.5 - + - -
271D THR* 3.3 28.3 + - - -
275D MET* 3.5 24.3 - - + +
286D THR* 3.2 20.3 + - - +
287D VAL 3.0 9.6 + - - +
289D PHE* 1.3 86.5 - + - +
291D SER* 1.3 58.0 + - - +
293D ILE* 3.5 23.9 + - + +
294D CYS* 3.2 31.4 + - - -
317D PHE 3.7 17.5 - - - -
318D ALA* 3.9 11.9 - - + -
321D SER* 3.2 27.4 - - - -
325D VAL* 3.8 17.8 - - + +
354D CYS* 4.0 14.1 - - - -
358D PHE* 3.9 18.4 - + + -
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Residues in contact with SER 291 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 3.6 25.8 + - - -
287D VAL* 2.9 10.8 + - - +
288D GLU* 3.6 11.0 + - - -
289D PHE 3.2 0.2 - - - -
290D TRP* 1.3 74.4 - - - +
292D THR* 1.3 66.4 + - - +
294D CYS* 3.2 4.2 + - - +
295D GLU* 2.8 29.8 + - - +
350D SER 4.7 0.9 + - - -
353D ALA* 5.3 0.2 - - - +
354D CYS* 3.2 35.0 + - - +
357D LEU* 3.6 12.0 - - - +
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Residues in contact with THR 292 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 4.9 0.6 - - - +
141C LYS* 4.7 6.6 + - - +
249D CYS* 3.4 31.4 - - + +
252D MET* 4.3 12.3 - - + -
253D SER* 3.4 25.1 - - - +
288D GLU* 2.9 16.8 + - - +
289D PHE* 3.4 7.9 - - - -
291D SER* 1.3 74.5 - - - +
293D ILE* 1.3 62.9 + - - +
295D GLU* 3.2 18.4 + - - +
296D GLU* 3.0 27.6 + - + +
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Residues in contact with ILE 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D MET* 3.7 29.6 - - + -
256D TYR* 4.7 1.5 - - + -
263D MET* 3.7 22.7 - - + -
289D PHE* 3.0 42.5 + - + +
290D TRP* 3.5 31.6 - - + +
291D SER 3.2 0.2 - - - -
292D THR* 1.3 76.6 - - - +
294D CYS* 1.3 62.8 + - - +
296D GLU* 3.5 2.2 + - - +
297D GLU* 3.0 32.9 + - - +
317D PHE* 3.8 26.0 - - + -
318D ALA* 4.3 4.3 - - + +
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Residues in contact with CYS 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D TRP 3.2 16.5 + - - -
291D SER 3.6 7.0 - - - +
293D ILE* 1.3 75.5 - - - +
295D GLU* 1.3 57.1 + - - +
297D GLU* 3.1 1.7 + - - +
298D ILE* 2.7 41.4 + - - +
318D ALA* 4.0 8.7 - - - -
354D CYS 4.7 0.4 - - - -
357D LEU* 3.7 23.6 - - + +
358D PHE* 3.7 40.8 - - - -
361D ASN* 3.7 21.1 - - - +
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Residues in contact with GLU 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C VAL* 4.6 7.2 - - - +
140C ARG* 2.9 21.8 + - - -
141C LYS* 2.8 36.2 + - - -
291D SER 2.8 20.5 + - - +
292D THR* 3.2 17.4 + - - +
294D CYS* 1.3 73.8 - - - +
296D GLU* 1.3 62.6 + - + +
298D ILE* 3.2 8.1 + - - +
299D ASP* 3.0 37.4 + - - +
357D LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 296 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLN* 4.6 13.7 - - - +
311B PRO* 4.0 22.3 - - - +
252D MET* 4.5 9.3 - - + +
253D SER* 3.5 44.5 - - - +
256D TYR* 4.7 10.3 - - + -
292D THR* 3.0 19.0 + - + +
293D ILE* 4.4 2.5 - - - +
295D GLU* 1.3 80.3 - - + +
297D GLU* 1.3 57.4 + - - +
299D ASP* 3.7 20.8 + - - +
300D ILE* 3.2 33.7 + - - +
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Residues in contact with GLU 297 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D TYR* 2.7 33.3 + - + +
293D ILE* 3.0 22.1 + - - +
294D CYS 3.6 0.2 - - - +
296D GLU* 1.3 76.1 - - - +
298D ILE* 1.3 62.8 + - - +
300D ILE* 3.3 8.4 + - - +
301D ALA* 3.2 19.9 + - - +
314D SER* 3.6 16.5 + - - +
316D ASN* 4.0 4.0 - - - -
317D PHE* 2.7 34.8 + - - +
318D ALA* 3.6 13.4 + - - +
319D LEU* 4.7 0.5 + - - +
361D ASN* 2.8 35.8 + - - +
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Residues in contact with ILE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D CYS 2.7 23.2 + - - +
295D GLU* 3.5 5.8 - - - +
297D GLU* 1.3 71.5 - - - +
299D ASP* 1.3 70.3 + - - +
301D ALA* 3.1 18.5 + - + +
302D TYR* 3.2 28.5 + - + -
357D LEU* 3.8 32.5 - - + +
360D GLN* 3.7 31.9 - - + +
361D ASN* 3.7 20.9 - - + +
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Residues in contact with ASP 299 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 5.2 2.6 - - + -
295D GLU* 3.0 20.2 + - - +
296D GLU* 3.9 23.5 - - - +
298D ILE* 1.3 81.8 - - - +
300D ILE* 1.3 65.0 + - - +
302D TYR* 3.4 11.3 + - - +
303D GLU* 3.0 27.2 + - - +
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Residues in contact with ILE 300 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PRO* 4.6 10.3 - - + -
256D TYR* 3.7 39.9 - - + -
296D GLU 3.2 18.7 + - - +
297D GLU* 3.5 9.6 - - - +
298D ILE 3.2 0.4 - - - -
299D ASP* 1.3 77.2 - - + +
301D ALA* 1.3 58.4 + - - +
303D GLU* 3.0 7.9 + - - +
304D LEU* 2.9 43.1 + - + +
312D LEU* 3.8 31.4 - - + -
313D GLN 4.3 6.1 - - - +
314D SER* 3.9 26.2 - - - +
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D GLU 3.2 11.0 + - - +
298D ILE* 3.1 13.8 + - + +
300D ILE* 1.3 77.7 - - - +
302D TYR* 1.3 62.5 + - + +
304D LEU* 3.5 9.7 + - - +
305D ALA* 3.1 24.4 + - - +
361D ASN* 6.0 0.7 - - - +
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Residues in contact with TYR 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B PHE* 4.3 13.5 - + + -
298D ILE* 3.2 27.6 + - + -
299D ASP* 3.6 12.8 - - - +
300D ILE 3.3 0.4 - - - -
301D ALA* 1.3 79.8 - - + +
303D GLU* 1.3 61.8 + - - +
305D ALA* 3.4 8.7 + - + +
306D GLN* 3.3 27.0 + - - +
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Residues in contact with GLU 303 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU* 3.0 31.1 - - + +
307B PHE* 3.8 41.1 - - + +
310B SER* 2.7 41.4 + - - -
311B PRO* 4.7 1.7 - - - +
299D ASP* 3.0 16.0 + - - +
300D ILE* 3.0 11.8 + - - +
302D TYR* 1.3 77.8 - - - +
304D LEU* 1.3 57.0 + - + +
306D GLN* 3.3 2.6 + - - -
307D PHE* 2.8 33.4 + - - +
310D SER* 5.6 0.2 - - - -
312D LEU* 3.5 14.5 - - + +
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Residues in contact with LEU 304 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ILE* 2.9 32.2 + - + +
301D ALA* 3.9 7.6 - - - +
303D GLU* 1.3 74.5 - - + +
305D ALA* 1.3 62.3 + - - +
307D PHE 3.9 4.7 - - - +
308D PRO* 3.0 38.4 - - + +
310D SER* 4.0 22.4 - - - +
312D LEU* 3.3 31.4 - - + +
313D GLN* 5.0 6.7 - - + -
314D SER* 5.2 2.2 - - - +
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Residues in contact with ALA 305 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D ALA 3.1 18.9 + - - +
302D TYR* 3.6 10.1 - - + +
303D GLU 3.3 0.2 - - - -
304D LEU* 1.3 76.9 - - - +
306D GLN* 1.3 58.7 + - - +
308D PRO* 4.5 5.5 - - - +
----------------------------------------------------------
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Residues in contact with GLN 306 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLN* 3.7 23.4 - - - +
307B PHE* 3.6 26.7 - - + -
302D TYR* 3.3 18.5 + - - +
303D GLU 4.0 2.2 - - - +
304D LEU 3.1 0.4 - - - -
305D ALA* 1.3 78.3 - - - +
307D PHE* 1.3 69.4 + - + +
308D PRO* 3.7 5.5 - - - +
309D GLN* 4.8 0.3 + - - -
----------------------------------------------------------
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Residues in contact with PHE 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP* 5.0 2.5 - - + -
302B TYR* 3.9 39.3 - + + -
303B GLU* 3.7 35.4 - - + +
306B GLN* 3.6 29.8 - - + -
307B PHE* 3.8 24.9 - + - -
303D GLU 2.8 13.9 + - - +
304D LEU* 3.3 6.1 - - - +
306D GLN* 1.3 92.4 - - + +
308D PRO* 1.3 59.7 - - - +
309D GLN* 3.0 27.1 - - - +
310D SER* 2.8 24.7 + - - -
----------------------------------------------------------
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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