Contacts of the helix formed by residues 282 - 310 (chain B) in PDB entry 1BJW
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 GLN 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ARG* 3.2 49.1 + - - +
84B GLU* 5.9 0.4 - - - +
278B ALA 5.2 0.2 - - - -
279B LEU 3.8 16.8 + - - +
280B THR* 3.1 8.8 + - - +
281B ASN* 1.3 71.0 - - - +
283B GLU* 1.3 59.6 + - - +
285B SER* 4.1 5.3 - - - -
286B ARG* 2.9 55.2 + - - +
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Residues in contact with GLU 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ASN* 3.2 8.9 + - - +
282B GLN* 1.3 81.4 - - - +
284B ALA* 1.3 62.3 + - - +
286B ARG* 3.8 16.3 + - - +
287B ALA* 3.3 21.3 + - - +
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Residues in contact with ALA 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 3.6 30.9 + - + -
281B ASN* 3.1 29.8 + - - +
283B GLU* 1.3 77.7 - - - +
285B SER* 1.3 64.6 + - - +
287B ALA* 3.4 8.0 + - - +
288B PHE* 3.2 19.4 + - - +
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Residues in contact with SER 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 2.9 26.0 + - - -
236B PHE* 3.8 20.3 - - - -
278B ALA* 2.7 30.8 + - - +
281B ASN 3.2 9.3 + - - -
282B GLN* 4.1 4.5 - - - -
284B ALA* 1.3 74.4 - - - +
286B ARG* 1.3 60.5 + - - +
288B PHE* 3.1 6.2 + - - +
289B VAL* 2.9 33.8 + - - +
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Residues in contact with ARG 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B GLN* 2.9 49.9 + - - +
283B GLU* 3.8 12.8 + - - +
285B SER* 1.3 75.7 - - - +
287B ALA* 1.3 58.0 + - - +
289B VAL* 3.4 5.9 + - - +
290B GLU* 2.9 51.3 + - + +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLU 3.3 11.3 + - - +
284B ALA* 3.5 12.3 - - - +
285B SER 3.2 0.6 - - - -
286B ARG* 1.3 79.5 - - - +
288B PHE* 1.3 62.1 + - - +
290B GLU* 4.1 3.9 - - - +
291B MET* 3.1 23.7 + - - +
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Residues in contact with PHE 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 5.9 0.9 - - + -
43B PHE* 3.9 15.0 - + + -
44B ASP 3.7 15.9 - - - -
46B PRO* 3.9 31.6 - - + -
235B ALA 3.4 27.1 - - - -
236B PHE* 3.8 20.2 - + + -
237B ALA* 3.9 21.5 - - + -
284B ALA 3.2 12.1 + - - +
285B SER* 3.1 9.9 + - - +
287B ALA* 1.3 75.7 - - - +
289B VAL* 1.3 64.0 + - - +
291B MET* 3.2 31.5 + - + +
292B ALA* 2.9 31.8 + - + +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B HIS* 3.9 33.0 - - + +
209B LEU* 6.0 1.3 - - + -
235B ALA* 3.8 20.4 - - + +
236B PHE* 3.9 16.4 - - + -
285B SER 2.9 18.4 + - - +
286B ARG* 3.9 6.1 - - - +
288B PHE* 1.3 76.7 - - - +
290B GLU* 1.3 71.7 + - - +
292B ALA* 3.9 4.5 - - - +
293B ARG* 2.9 46.1 + - - +
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Residues in contact with GLU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ARG* 2.9 38.5 + - + +
287B ALA* 4.2 3.8 - - - +
289B VAL* 1.3 83.8 - - - +
291B MET* 1.3 62.8 + - - +
293B ARG* 2.4 43.5 + - - +
294B GLU* 3.0 25.8 + - - +
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Residues in contact with MET 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 4.1 27.1 - - + -
287B ALA 3.1 18.4 + - - +
288B PHE* 3.5 41.1 - - + +
290B GLU* 1.3 77.4 - - - +
292B ALA* 1.3 63.5 + - - +
294B GLU* 3.6 5.5 + - - +
295B ALA* 3.2 22.1 + - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.9 25.1 - - + -
209B LEU* 6.0 3.1 - - + -
235B ALA 5.5 1.6 - - - +
288B PHE* 2.9 29.2 + - + +
289B VAL* 3.9 5.8 - - - +
291B MET* 1.3 75.6 - - + +
293B ARG* 1.3 58.1 + - - +
295B ALA* 3.2 3.3 + - - +
296B TYR* 2.9 52.7 + - + +
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLU 5.1 1.0 + - - -
208B HIS* 3.0 39.7 + - - +
209B LEU* 5.6 1.8 - - - +
210B LEU* 3.3 30.2 + - - +
211B TYR* 3.7 13.7 - - + -
289B VAL* 2.9 24.6 + - - +
290B GLU* 2.4 46.8 + - - +
292B ALA* 1.3 75.0 - - - +
294B GLU* 1.3 63.5 + - - +
296B TYR* 4.3 7.8 - - - -
297B ARG* 3.1 36.6 + - - +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLU 3.0 17.5 + - - +
291B MET* 3.9 6.1 - - - +
292B ALA 3.3 0.2 - - - -
293B ARG* 1.3 77.6 - - - +
295B ALA* 1.3 64.6 + - - +
297B ARG* 3.5 9.6 + - - +
298B ARG* 2.8 62.2 + - + +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.7 23.6 - - + -
291B MET* 3.2 16.7 + - + +
292B ALA 3.5 4.3 - - - +
294B GLU* 1.3 81.3 - - - +
296B TYR* 1.3 61.6 + - - +
298B ARG* 3.3 13.5 + - - +
299B ARG* 3.1 37.6 + - - +
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 3.4 34.3 - - - +
42B ASP* 3.9 4.7 - - - -
43B PHE* 3.7 19.7 - + - -
209B LEU* 4.0 28.3 - - + -
211B TYR* 3.1 30.1 - + + +
234B LLP 4.9 1.1 + - - -
292B ALA* 2.9 35.2 + - + +
293B ARG* 4.3 3.8 - - - -
295B ALA* 1.3 72.7 - - - +
297B ARG* 1.3 55.7 + - - +
299B ARG* 3.3 31.0 + - - +
300B ARG* 2.8 30.8 + - - +
321B PHE* 4.1 19.8 - + + -
364B TYR* 3.2 20.3 - - + -
365B ALA* 4.4 4.3 - - - -
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LEU 4.3 4.2 + - - -
211B TYR* 3.0 56.8 + - + +
212B GLU* 3.9 7.7 + - - -
293B ARG* 3.1 28.9 + - - +
294B GLU* 3.8 9.2 - - - +
296B TYR* 1.3 77.0 - - - +
298B ARG* 1.3 64.0 + - - +
300B ARG* 3.3 23.8 + - - +
301B ASP* 3.0 38.4 + - - +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 2.8 51.0 + - + +
295B ALA* 3.3 10.7 + - - +
297B ARG* 1.3 78.0 - - + +
299B ARG* 1.3 57.4 + - - +
301B ASP* 3.3 7.1 + - - +
302B LEU* 3.0 28.1 + - - +
368B GLU* 3.8 17.9 + - - +
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Residues in contact with ARG 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP* 2.8 41.8 + - - -
43B PHE* 4.1 18.5 - - - -
295B ALA* 3.1 25.4 + - - +
296B TYR* 3.5 24.8 - - - +
297B ARG 3.2 0.2 - - - -
298B ARG* 1.3 75.1 - - - +
300B ARG* 1.3 65.9 + - - +
302B LEU* 3.4 5.4 + - - +
303B LEU* 3.0 24.6 + - - +
364B TYR* 3.2 21.3 + - + -
366B THR 2.9 25.8 + - - +
367B SER* 4.4 7.9 - - - +
368B GLU* 4.5 17.5 - - + +
371B LEU* 3.6 24.7 - - + +
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B TYR* 3.7 18.6 - - + +
212B GLU* 2.7 33.1 + - - -
296B TYR 2.8 20.9 + - - +
297B ARG* 3.6 23.3 + - - +
299B ARG* 1.3 73.0 - - - +
301B ASP* 1.3 81.6 + - - +
303B LEU* 3.3 2.7 + - - +
304B LEU* 2.9 41.3 + - + +
316B ARG* 3.2 24.7 - - - +
317B PRO* 2.9 36.5 + - + -
323B VAL* 5.1 0.7 - - + -
364B TYR* 3.5 36.3 - - + +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG* 3.0 31.6 + - - +
298B ARG* 3.7 6.7 - - - +
300B ARG* 1.3 104.1 + - - +
302B LEU* 1.3 63.1 + - - +
304B LEU* 3.4 6.8 + - - +
305B GLU* 3.0 39.1 + - - +
316B ARG* 4.8 3.5 + - - -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG 3.0 14.8 + - - +
299B ARG* 3.6 3.8 - - - +
301B ASP* 1.3 76.9 - - - +
303B LEU* 1.3 65.8 + - - +
305B GLU* 3.6 10.7 - - - +
306B GLY* 3.2 18.9 + - - -
368B GLU* 3.8 46.9 - - + +
371B LEU* 3.9 24.9 - - + -
372B ARG* 4.1 23.8 - - + +
375B LEU* 4.1 16.7 - - + +
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Residues in contact with LEU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.7 3.1 - - + -
299B ARG 3.0 17.1 + - - +
300B ARG* 3.6 4.0 - - - +
302B LEU* 1.3 82.7 - - + +
304B LEU* 1.3 63.7 + - + +
306B GLY* 3.2 2.8 + - - -
307B LEU* 3.0 44.7 + - + +
323B VAL* 4.0 27.6 - - + -
362B LEU* 4.0 27.6 - - + -
363B SER 5.6 0.2 - - - -
364B TYR* 4.3 17.5 - - + +
371B LEU* 4.4 18.8 - - + +
375B LEU* 4.2 14.1 - - + +
378B PHE* 5.4 1.6 - - + -
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ARG* 2.9 36.7 + - + +
301B ASP* 4.0 6.1 - - - +
303B LEU* 1.3 69.7 - - + +
305B GLU* 1.3 64.2 + - - +
307B LEU* 3.4 7.4 + - + +
308B THR* 2.9 32.0 + - - +
314B ALA* 4.4 13.7 - - + +
316B ARG* 3.5 39.9 - - + +
317B PRO* 3.9 22.2 - - + -
323B VAL* 4.2 22.9 - - + -
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ASP* 3.0 32.4 + - - +
302B LEU* 3.6 8.3 - - - +
304B LEU* 1.3 76.0 - - - +
306B GLY* 1.3 64.1 + - - +
308B THR* 3.4 6.5 + - - -
309B ALA* 3.0 22.7 + - - +
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Residues in contact with GLY 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B LEU 3.2 7.5 + - - -
303B LEU 3.2 3.6 + - - -
305B GLU* 1.3 77.6 - - - +
307B LEU* 1.3 64.2 + - - +
309B ALA* 3.2 9.7 + - - +
310B LEU* 3.2 24.9 + - - +
375B LEU* 3.8 26.5 - - - -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LEU* 3.0 40.5 + - + +
304B LEU* 3.8 10.3 - - + +
306B GLY* 1.3 74.2 - - - +
308B THR* 1.3 59.2 + - - +
310B LEU* 3.0 19.5 + - - +
311B GLY 3.0 9.2 + - - -
312B LEU* 3.1 33.7 + - + +
314B ALA* 3.8 28.5 - - + -
323B VAL* 4.3 11.7 - - + -
325B MET* 3.9 31.2 - - + -
362B LEU* 4.6 2.7 - - + -
375B LEU* 4.0 11.0 - - + +
378B PHE* 4.2 6.1 - - + -
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Residues in contact with THR 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 2.9 21.4 + - - +
305B GLU* 3.6 6.9 - - - -
307B LEU* 1.3 78.2 - - - +
309B ALA* 1.3 57.5 + - - +
311B GLY* 3.0 17.4 + - - -
312B LEU 4.3 7.2 + - - -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B GLU 3.0 13.8 + - - +
306B GLY* 3.4 13.0 - - - +
308B THR* 1.3 76.6 - - - +
310B LEU* 1.3 64.0 + - + +
311B GLY 3.5 0.2 + - - -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLY 3.2 13.6 + - - +
307B LEU 3.0 9.4 + - - +
309B ALA* 1.3 81.6 - - + +
311B GLY* 1.3 58.0 + - - +
312B LEU* 3.2 14.0 + - + -
375B LEU* 3.9 30.1 - - + +
378B PHE* 3.9 17.7 - - + -
379B ALA* 4.0 25.1 - - + +
382B LEU* 3.7 28.0 - - + +
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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