Contacts of the helix formed by residues 282 - 310 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 5.6 2.4 + - - -
83A ARG* 3.7 38.9 - - - +
279A LEU 4.2 14.1 + - - +
280A THR* 2.9 19.9 + - - +
281A ASN* 1.3 70.0 - - - +
283A GLU* 1.3 56.8 + - - +
285A SER* 4.2 4.9 - - - -
286A ARG* 3.0 32.7 + - - +
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 3.0 7.4 + - - +
282A GLN* 1.3 80.5 - - - +
284A ALA* 1.3 64.6 + - + +
286A ARG* 4.2 7.2 + - - +
287A ALA* 3.2 22.2 + - - +
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Residues in contact with ALA 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 3.6 34.6 + - + +
281A ASN* 3.1 22.1 + - - +
283A GLU* 1.3 75.4 - - + +
285A SER* 1.3 64.8 + - - +
287A ALA* 3.4 7.8 + - - +
288A PHE* 3.1 22.7 + - - +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A HIS* 2.9 25.0 - - - -
236A PHE* 3.9 17.0 - - - -
278A ALA* 2.6 31.8 + - - +
281A ASN 3.0 11.9 + - - -
282A GLN* 4.2 4.7 - - - -
284A ALA* 1.3 76.7 - - - +
286A ARG* 1.3 58.5 + - - +
288A PHE* 3.3 5.1 + - - +
289A VAL* 3.0 32.9 + - - +
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Residues in contact with ARG 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN 3.0 19.8 + - - +
283A GLU* 4.2 6.4 + - - +
285A SER* 1.3 73.4 - - - +
287A ALA* 1.3 69.5 + - - +
288A PHE 3.2 0.2 + - - -
289A VAL* 3.2 6.0 + - + -
290A GLU* 2.9 60.9 + - - +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU 3.2 16.3 + - - +
284A ALA* 3.6 8.3 - - - +
285A SER 3.3 0.2 - - - -
286A ARG* 1.3 82.2 - - - +
288A PHE* 1.3 61.4 + - - +
290A GLU* 4.1 5.0 - - - +
291A MET* 3.1 24.4 + - - +
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Residues in contact with PHE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 6.1 0.2 - - + -
43A PHE* 4.1 16.4 - + + -
44A ASP 4.0 7.2 - - - -
46A PRO* 3.8 44.9 - - + -
235A ALA 3.4 25.8 - - - -
236A PHE* 3.7 19.7 - + + -
237A ALA* 4.0 15.9 - - + -
284A ALA 3.1 13.4 + - - +
285A SER* 3.6 8.5 - - - +
286A ARG 3.1 0.2 - - - -
287A ALA* 1.3 75.2 - - - +
289A VAL* 1.3 58.8 - - - +
291A MET* 3.3 29.3 + - + +
292A ALA* 2.9 37.2 + - + +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A HIS* 3.8 40.3 - - + +
209A LEU* 5.7 3.5 - - + +
235A ALA 3.9 18.8 - - - +
236A PHE* 4.1 16.8 - - + -
285A SER 3.0 19.8 + - - +
286A ARG* 3.8 7.2 - - + +
288A PHE* 1.3 77.1 - - + +
290A GLU* 1.3 67.9 + - - +
292A ALA* 3.3 4.6 + - - +
293A ARG* 2.9 39.9 + - - +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ARG* 2.9 64.4 + - + +
287A ALA* 4.1 4.7 - - - +
289A VAL* 1.3 76.9 - - - +
291A MET* 1.3 65.7 + - - +
293A ARG* 2.5 40.1 + - - +
294A GLU* 3.1 24.3 + - - +
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Residues in contact with MET 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE* 3.6 37.2 - - + -
287A ALA 3.1 19.6 + - - +
288A PHE* 3.4 26.9 - - + +
290A GLU* 1.3 79.3 - - - +
292A ALA* 1.3 63.4 + - - +
294A GLU* 3.4 6.1 + - - +
295A ALA* 3.1 20.5 + - - +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.4 16.4 - - + -
209A LEU* 5.1 4.3 - - + -
235A ALA 5.6 1.8 - - - +
288A PHE* 2.9 28.7 + - + +
289A VAL* 3.7 6.7 - - - +
291A MET* 1.3 84.9 - - - +
293A ARG* 1.3 57.0 + - - +
295A ALA* 3.2 3.5 + - - +
296A TYR* 2.8 55.0 + - + +
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU 4.9 1.6 + - - -
208A HIS* 2.9 43.1 + - - +
209A LEU* 5.4 2.2 - - + +
210A LEU* 3.5 26.2 + - - +
211A TYR* 3.5 16.3 - - + -
289A VAL* 2.9 24.7 + - - +
290A GLU* 2.5 38.9 + - - +
291A MET 3.4 0.2 - - - -
292A ALA* 1.3 76.4 - - - +
294A GLU* 1.3 55.7 + - - +
296A TYR* 4.1 8.7 - - - -
297A ARG* 2.9 43.3 + - - +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLU 3.1 17.9 + - - +
291A MET* 3.7 6.2 - - - +
293A ARG* 1.3 72.3 - - - +
295A ALA* 1.3 69.2 + - - +
297A ARG* 3.3 12.1 + - - +
298A ARG* 3.0 62.7 + - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.6 28.3 - - + -
291A MET* 3.1 10.8 + - - +
292A ALA 3.6 7.2 - - - +
294A GLU* 1.3 83.5 - - - +
296A TYR* 1.3 62.2 + - - +
298A ARG* 3.3 9.7 + - - +
299A ARG* 3.0 38.8 + - - +
368A GLU* 6.1 0.2 - - - -
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Residues in contact with TYR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO* 3.3 32.2 - - - +
42A ASP* 3.9 4.0 - - - -
43A PHE* 3.4 18.8 - + - -
209A LEU* 3.7 31.2 - - + -
211A TYR* 3.0 31.2 - - + +
234A LLP 4.9 0.6 + - - -
292A ALA* 2.8 39.2 + - + +
293A ARG* 4.1 2.5 - - - -
295A ALA* 1.3 71.0 - - - +
297A ARG* 1.3 58.7 + - - +
299A ARG* 3.3 26.1 + - - -
300A ARG* 2.9 26.0 + - - +
321A PHE* 4.1 22.9 - + + -
364A TYR* 3.3 21.8 - + + -
365A ALA* 4.3 5.8 - - - -
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU 4.7 0.4 + - - -
211A TYR* 3.0 48.3 + - + +
212A GLU* 4.3 4.8 + - - -
293A ARG* 2.9 43.4 + - - +
294A GLU* 3.6 11.3 - - - +
295A ALA 3.3 0.2 - - - -
296A TYR* 1.3 72.0 - - - +
298A ARG* 1.3 67.4 + - + +
300A ARG* 3.3 19.1 + - - +
301A ASP* 3.1 36.9 + - - +
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A GLU* 3.0 57.3 + - + +
295A ALA* 3.6 9.9 - - - +
297A ARG* 1.3 77.0 - - + +
299A ARG* 1.3 64.4 + - - +
301A ASP* 3.4 6.4 + - - +
302A LEU* 3.1 23.8 + - - +
368A GLU* 4.0 22.7 - - - +
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Residues in contact with ARG 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASP* 2.7 42.2 + - - -
43A PHE* 3.7 18.7 - - - -
295A ALA* 3.0 24.4 + - - +
296A TYR* 3.7 17.4 - - - +
298A ARG* 1.3 74.8 - - - +
300A ARG* 1.3 63.7 + - - +
302A LEU* 3.5 3.7 + - - +
303A LEU* 3.1 24.6 + - - +
364A TYR* 3.3 23.1 + - + -
366A THR 3.2 27.6 + - - +
367A SER* 4.5 7.9 - - - +
368A GLU* 3.9 24.3 + - + +
371A LEU* 3.6 20.2 - - + +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TYR* 3.5 19.8 - - + +
212A GLU* 2.6 41.8 + - - -
296A TYR 2.9 13.3 + - - +
297A ARG* 3.3 19.7 + - - +
299A ARG* 1.3 77.3 - - - +
301A ASP* 1.3 84.0 + - - +
303A LEU* 3.2 4.0 + - - +
304A LEU* 2.8 50.1 + - + +
316A ARG* 3.8 13.7 - - - +
317A PRO* 2.9 31.7 + - + -
323A VAL* 5.0 0.4 - - + -
364A TYR* 3.5 40.8 - - + +
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG* 3.1 25.1 + - - +
298A ARG* 3.7 6.0 - - - +
300A ARG* 1.3 107.5 + - - +
302A LEU* 1.3 56.5 + - - +
304A LEU* 3.9 7.1 - - - +
305A GLU* 3.0 47.0 + - - +
316A ARG* 5.3 2.3 + - - -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ARG 3.1 14.9 + - - +
299A ARG* 3.8 1.3 - - - +
300A ARG 3.3 0.2 - - - -
301A ASP* 1.3 75.7 - - - +
303A LEU* 1.3 62.9 + - - +
305A GLU* 3.4 15.3 + - - +
306A GLY* 3.1 25.5 + - - -
368A GLU* 3.6 33.0 - - + +
371A LEU* 3.4 36.8 - - + -
372A ARG* 3.4 39.3 - - + +
375A LEU* 4.0 15.0 - - + +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 5.2 4.5 - - + -
299A ARG 3.1 17.5 + - - +
300A ARG 3.6 3.6 - - - +
302A LEU* 1.3 81.4 - - + +
304A LEU* 1.3 64.7 + - - +
306A GLY* 3.5 0.9 + - - -
307A LEU* 3.1 32.2 + - + +
323A VAL* 3.8 34.1 - - + -
362A LEU* 4.4 23.3 - - + -
363A SER 5.5 0.9 - - - +
364A TYR* 4.2 17.0 - - + +
371A LEU* 3.9 20.9 - - + +
375A LEU* 4.0 23.6 - - + -
378A PHE* 5.1 3.1 - - + -
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Residues in contact with LEU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ARG* 2.8 40.9 + - + +
301A ASP* 3.9 5.8 - - - +
303A LEU* 1.3 78.4 - - + +
305A GLU* 1.3 61.9 + - - +
307A LEU* 3.4 7.8 + - + +
308A THR* 3.0 28.6 + - - +
314A ALA* 4.8 11.7 - - + +
316A ARG* 3.7 40.4 - - + +
317A PRO* 4.1 7.4 - - + -
323A VAL* 4.2 30.5 - - + -
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ASP* 3.0 37.1 + - + +
302A LEU* 3.5 13.6 - - - +
304A LEU* 1.3 77.7 - - + +
306A GLY* 1.3 62.5 + - - +
308A THR* 3.4 6.8 + - - -
309A ALA* 3.1 24.1 + - - +
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Residues in contact with GLY 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU 3.1 12.7 + - - -
304A LEU 3.4 0.2 - - - -
305A GLU* 1.3 80.9 - - - +
307A LEU* 1.3 61.4 + - - +
309A ALA* 3.5 7.5 + - - +
310A LEU* 3.2 27.4 + - - +
375A LEU* 3.9 22.4 - - - -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LEU* 3.1 29.9 + - + +
304A LEU* 3.8 9.6 - - + +
306A GLY* 1.3 73.6 - - - +
308A THR* 1.3 66.6 + - - +
310A LEU* 3.0 11.7 + - + +
312A LEU* 3.0 40.9 + - + +
314A ALA* 4.0 27.4 - - + -
323A VAL* 4.3 14.4 - - + -
325A MET* 3.8 30.7 - - + -
362A LEU* 4.5 4.5 - - + -
375A LEU* 4.1 1.5 - - + +
378A PHE* 3.9 26.2 - - + -
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A LEU* 3.0 16.9 + - - +
305A GLU* 3.7 6.5 - - - -
306A GLY 3.4 0.2 - - - -
307A LEU* 1.3 77.4 - - - +
309A ALA* 1.3 58.9 + - - +
311A GLY* 2.9 19.8 + - - -
312A LEU 4.1 8.1 + - - -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLU 3.1 16.7 + - - +
306A GLY* 3.6 9.2 - - - +
307A LEU 3.2 0.2 - - - -
308A THR* 1.3 76.7 - - - +
310A LEU* 1.3 63.3 + - + +
311A GLY 3.5 0.5 + - - -
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLY 3.2 19.2 + - - +
307A LEU* 3.0 9.6 + - - +
309A ALA* 1.3 77.9 - - + +
311A GLY* 1.3 61.7 + - - +
312A LEU* 4.1 18.2 - - + +
375A LEU* 3.9 15.5 - - + +
378A PHE* 3.7 35.0 - - + -
379A ALA* 4.6 16.4 - - + -
382A LEU* 4.1 34.4 - - + +
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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