Contacts of the helix formed by residues 277 - 301 (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 TYR 277 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 3.8 24.0 - + - -
136D PRO* 3.3 27.9 - - + +
137D PHE* 3.3 38.0 - + - -
138D ASP* 4.7 1.1 + - - -
210D ILE* 4.1 0.6 - - + +
273D LEU* 4.5 11.9 - - + -
274D ILE* 2.9 49.1 + - + +
275D GLY 2.4 6.5 + - - -
276D LYS* 1.3 70.8 - - + +
278D MET* 1.3 53.4 + - - +
279D LEU 2.9 4.7 - - - -
280D PHE* 2.7 66.9 + + - +
281D THR* 4.3 0.5 + - - -
431D ILE* 4.8 10.3 - - + +
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Residues in contact with MET 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ASN* 4.9 4.9 - - - +
261D VAL* 5.0 9.6 - - + -
264D ILE* 3.6 39.5 - - + -
268D SER* 6.2 1.1 - - - +
273D LEU* 5.5 9.2 - - + +
275D GLY* 2.9 14.0 + - - +
277D TYR* 1.3 74.7 - - - +
279D LEU* 1.3 50.3 + - + +
281D THR* 2.6 49.7 + - - -
282D MET* 2.8 63.6 + - + +
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Residues in contact with LEU 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D GLY 3.7 8.1 - - - +
276D LYS* 3.2 36.8 - - + +
277D TYR 2.8 0.4 + - - -
278D MET* 1.3 77.8 - - + +
280D PHE* 1.3 69.7 + - + +
282D MET* 3.2 24.6 - - + +
283D ILE* 3.5 14.1 + - - +
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Residues in contact with PHE 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D LYS* 2.6 28.9 - - + -
277D TYR* 2.7 50.5 + + + +
279D LEU* 1.3 76.3 - - + +
281D THR* 1.3 59.0 + - + +
283D ILE* 5.7 0.2 - - - -
284D PHE* 2.6 63.9 + + + -
424D SER 5.8 1.3 - - - -
427D ALA* 5.6 8.3 - - + -
428D GLY* 5.4 12.6 - - - -
431D ILE* 4.0 25.4 - - + -
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Residues in contact with THR 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D VAL* 4.0 27.1 - - + -
222D CYS* 6.2 3.8 - - - -
260D ILE* 6.5 0.4 - - + -
261D VAL* 6.3 0.7 - - - -
264D ILE* 5.5 7.0 - - + -
277D TYR 4.3 0.3 + - - -
278D MET* 2.6 45.5 + - - -
280D PHE* 1.3 75.3 - - + +
282D MET* 1.3 67.8 + - - +
284D PHE* 3.9 9.8 - - + -
285D VAL* 2.7 31.2 + - + +
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Residues in contact with MET 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C ASN* 3.9 26.7 - - - +
234C THR* 5.3 11.0 - - + -
261D VAL* 5.5 6.7 - - + -
278D MET* 2.8 36.3 + - + +
279D LEU* 3.2 23.1 - - + +
280D PHE 3.2 0.2 - - - -
281D THR* 1.3 79.4 - - - +
283D ILE* 1.3 55.7 + - + +
285D VAL* 3.6 6.4 - - + +
286D ILE* 2.7 67.3 + - + +
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Residues in contact with ILE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279D LEU 3.6 14.4 - - - +
280D PHE* 3.9 3.4 - - - +
282D MET* 1.3 79.3 - - + +
284D PHE* 1.3 69.0 + - + +
286D ILE* 3.1 18.1 - - + +
287D SER* 2.5 37.4 + - - -
290D ILE* 4.8 1.0 - - - +
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Residues in contact with PHE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D PHE* 5.9 1.1 - - + -
280D PHE* 2.6 60.0 + + + +
281D THR* 3.8 8.7 - - + +
283D ILE* 1.3 87.8 - - + +
285D VAL* 1.3 60.0 + - + +
287D SER* 2.6 28.6 + - - -
288D SER* 3.3 4.5 + - - -
420D ILE* 4.6 12.3 - - + +
423D VAL* 5.3 5.8 - - + -
424D SER* 2.9 52.9 - - - +
427D ALA* 6.6 0.2 - - + -
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Residues in contact with VAL 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D CYS* 5.3 0.2 - - - -
225D PHE* 3.1 43.3 - - + -
257D LEU* 4.2 29.1 - - + +
261D VAL* 5.6 8.7 - - + -
281D THR* 2.7 27.2 + - + +
282D MET* 4.0 8.3 - - + +
284D PHE* 1.3 72.4 - - + +
286D ILE* 1.3 70.3 + - + +
287D SER 2.6 4.7 - - - -
288D SER* 2.8 18.3 + - - +
289D ILE* 3.0 13.2 + - + +
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C THR* 5.7 6.7 - - + -
238C LEU* 4.0 29.8 - - + -
282D MET* 2.7 77.4 + - + +
283D ILE* 3.1 18.2 - - + +
285D VAL* 1.3 76.1 - - + +
287D SER* 1.3 51.6 + - - +
289D ILE* 3.0 6.9 + - + -
290D ILE* 2.4 56.2 + - + +
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Residues in contact with SER 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D ILE 2.5 13.1 + - - -
284D PHE* 2.6 19.7 - - - -
285D VAL 2.6 0.8 - - - -
286D ILE* 1.3 76.2 - - - +
288D SER* 1.3 55.6 + - - -
290D ILE* 2.9 23.6 - - - +
291D VAL* 2.7 47.8 + - - +
417D ILE* 5.7 0.5 - - - +
420D ILE* 3.1 28.7 - - - +
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Residues in contact with SER 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D PHE* 5.2 9.5 - - - -
229D THR* 3.1 32.1 - - - +
253D LEU* 4.8 7.7 - - - +
257D LEU* 5.4 7.1 - - - +
284D PHE 3.3 3.9 + - - -
285D VAL* 2.8 22.4 + - - -
287D SER* 1.3 74.5 - - - +
289D ILE* 1.3 59.2 + - - +
291D VAL* 3.9 4.6 - - - +
292D THR* 2.7 31.2 + - - -
417D ILE* 6.0 6.1 - - - -
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Residues in contact with ILE 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C LEU* 3.6 35.9 - - + -
241C PHE* 4.6 3.6 - - + -
253D LEU* 5.7 4.5 - - + -
254D THR* 4.7 9.0 - - - +
257D LEU* 4.8 17.5 - - + -
258D LEU* 4.6 20.0 - - + -
285D VAL* 3.0 12.1 + - + +
286D ILE* 3.4 14.6 - - + +
287D SER 3.0 0.4 - - - -
288D SER* 1.3 73.8 - - - +
290D ILE* 1.3 57.9 + - + +
291D VAL 3.0 0.2 + - - -
292D THR* 3.0 11.4 + - + +
293D VAL* 2.5 51.2 + - + +
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Residues in contact with ILE 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D ILE 4.8 1.1 - - - +
286D ILE* 2.4 50.9 + - + +
287D SER* 2.7 51.4 - - - +
289D ILE* 1.3 67.2 - - + +
291D VAL* 1.3 66.9 + - + +
293D VAL* 2.8 30.3 - - - +
294D VAL* 3.0 13.9 + - - +
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Residues in contact with VAL 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D PHE* 3.7 9.0 - - + -
287D SER* 2.7 41.6 + - - +
288D SER* 3.9 5.4 - - - +
290D ILE* 1.3 79.0 - - + +
292D THR* 1.3 56.4 + - - +
293D VAL 2.9 1.2 + - - -
294D VAL* 3.0 3.4 + - - -
295D VAL* 2.4 68.1 + - + +
413D VAL* 3.4 35.0 - - + -
417D ILE* 5.4 3.6 - - + -
420D ILE* 5.9 0.2 - - + -
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Residues in contact with THR 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C PHE* 6.1 0.7 - - + -
229D THR* 6.5 0.7 - - - -
232D VAL* 4.9 3.2 - - - +
250D LEU* 2.5 39.7 - - + +
253D LEU* 5.2 3.1 - - + -
288D SER* 2.7 20.2 + - - +
289D ILE* 3.2 20.9 - - + +
291D VAL* 1.3 73.7 - - - +
293D VAL* 1.3 69.8 - - + +
295D VAL* 3.0 13.0 - - - +
296D ILE* 2.7 50.4 + - + +
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Residues in contact with VAL 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C PHE* 2.9 45.1 - - + -
245C LEU* 4.8 2.9 - - + -
289D ILE* 2.5 39.2 + - + +
290D ILE* 2.8 15.0 - - - +
292D THR* 1.3 77.3 - - + +
294D VAL* 1.3 61.8 + - + +
297D ASN* 2.4 54.9 + - - +
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Residues in contact with VAL 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ILE 3.0 11.0 + - - +
291D VAL* 3.8 4.9 - - - +
293D VAL* 1.3 86.9 - - + +
295D VAL* 1.3 59.5 + - + +
297D ASN* 4.1 3.1 - - - -
298D THR* 2.3 60.7 + - + +
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Residues in contact with VAL 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D VAL* 4.0 24.0 - - + -
233D PHE* 3.9 11.4 - - + -
291D VAL* 2.4 67.4 + - + +
292D THR* 3.0 16.6 - - - +
294D VAL* 1.3 72.1 - - + +
296D ILE* 1.3 62.5 - - - +
298D THR* 3.1 7.5 - - - +
299D HIS* 2.2 35.5 + - - +
409D ILE* 4.4 21.2 - - + +
413D VAL* 4.2 8.7 - - + -
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D VAL* 4.4 8.5 - - + -
246D SER* 3.5 17.5 - - - +
247D ILE* 4.4 16.6 - - + +
250D LEU* 3.0 29.6 - - + -
292D THR* 2.7 49.7 + - + +
293D VAL 4.7 0.2 - - - +
295D VAL* 1.3 77.9 - - - +
297D ASN* 1.3 63.1 + - - +
299D HIS* 2.9 29.5 - - + +
300D HIS* 2.4 50.3 + - + +
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Residues in contact with ASN 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C PHE* 5.1 0.6 - - - -
245C LEU* 3.0 46.3 - - - +
249C LEU* 4.3 15.2 - - - +
252C GLU* 5.1 1.9 - - - +
292D THR 4.3 1.4 + - - -
293D VAL* 2.4 42.1 + - - +
294D VAL* 3.4 4.3 - - - +
296D ILE* 1.3 78.0 - - - +
298D THR* 1.3 53.3 + - - +
300D HIS* 3.1 6.3 + - - +
301D ARG* 2.7 31.6 + - - +
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Residues in contact with THR 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D VAL* 2.3 58.9 + - + +
295D VAL* 3.4 7.6 - - - -
297D ASN* 1.3 65.7 - - - +
299D HIS* 1.3 60.6 + - - -
301D ARG* 2.6 74.2 + - + +
405D VAL* 5.7 1.8 - - + -
409D ILE* 5.0 13.2 - - + -
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Residues in contact with HIS 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D VAL* 3.6 9.3 + - - +
235D LEU* 5.4 0.4 - - + -
236D PRO* 2.8 55.1 - - + +
240D GLY* 5.0 0.6 - - - -
243D MET* 4.4 19.1 - - + +
246D SER* 3.9 18.9 + - - -
295D VAL 2.2 30.4 + - - +
296D ILE* 2.7 34.9 + - + +
298D THR* 1.3 72.6 - - - +
300D HIS* 1.3 53.8 + + - +
301D ARG* 3.4 9.9 + - - +
302D SER* 5.6 0.2 + - - -
306D HIS 2.3 22.2 - - - +
406D ILE* 4.5 7.2 - - + -
409D ILE* 6.5 1.1 - - + -
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Residues in contact with HIS 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LEU* 6.0 7.9 - - + -
252C GLU* 3.1 17.9 - - + +
253C SER* 4.8 3.4 - - - -
256C LYS* 3.9 31.8 - - + +
243D MET* 3.6 40.2 + - + +
244D THR* 4.6 1.3 - - - -
247D ILE* 3.9 22.3 - - + +
296D ILE* 2.4 50.8 + - + +
297D ASN* 3.5 5.2 - - - +
299D HIS* 1.3 68.9 - + + -
301D ARG* 1.3 49.1 + - - +
302D SER 2.6 18.6 + - - +
306D HIS* 2.6 43.1 + - + +
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Residues in contact with ARG 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C GLU* 2.9 25.9 - - - +
297D ASN 2.7 7.7 + - - +
298D THR* 2.6 65.7 + - + +
299D HIS* 4.2 6.2 + - - +
300D HIS* 1.3 69.7 - - - +
302D SER* 1.3 67.9 + - - +
303D PRO* 4.0 3.3 - - - +
400D LYS 5.5 4.0 + - - -
401D TYR* 6.4 0.4 - - - +
402D VAL* 5.9 4.2 - - - +
405D VAL* 3.2 45.1 - - - +
406D ILE* 3.9 23.0 - - - +
409D ILE* 5.3 1.6 - - - +
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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