Contacts of the helix formed by residues 362 - 395 (chain B) in PDB entry 5OY0
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 ASP 362 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ARG* 3.0 31.0 + - - +
86B PRO* 4.4 5.9 - - - +
117B TYR* 5.0 1.7 - - - -
122B HIS* 3.4 31.7 + - - +
358B PHE 4.0 1.3 + - - +
359B ILE 3.0 11.8 + - - +
361B GLN* 1.3 74.9 - - - +
363B HIS* 1.3 62.8 + - - +
364B THR* 3.7 6.6 + - - -
365B THR* 2.8 56.2 + - - +
366B GLN* 3.0 12.7 + - - +
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Residues in contact with HIS 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ALA 3.8 17.6 + - - -
361B GLN* 3.4 18.7 + - - -
362B ASP* 1.3 70.4 + - - +
364B THR* 1.3 61.6 + - - +
366B GLN* 3.7 5.7 - - + +
367B ALA* 2.9 32.6 + - - +
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Residues in contact with THR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 3.5 42.3 - - + +
362B ASP* 3.4 4.7 + - - -
363B HIS* 1.3 79.7 - - - +
365B THR* 1.3 56.7 + - - +
367B ALA* 3.8 4.8 - - + +
368B ALA* 2.9 31.3 + - + +
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Residues in contact with THR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 5.5 0.7 - - + -
116B ALA 4.0 7.2 - - - +
117B TYR* 3.5 41.5 - - + +
119B GLY* 4.2 17.0 - - - +
122B HIS* 5.0 2.2 - - + -
359B ILE* 4.1 11.1 - - - +
362B ASP* 2.8 49.2 + - - +
364B THR* 1.3 75.8 - - - +
366B GLN* 1.3 57.4 + - - +
368B ALA* 3.7 1.1 - - - +
369B LEU* 2.8 36.8 + - - +
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Residues in contact with GLN 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B MET* 3.5 23.5 + - - -
351B TYR* 4.0 23.7 + - + +
354B PRO* 3.9 17.0 - - - +
359B ILE* 3.3 40.8 + - - +
360B ALA* 4.1 10.6 - - - +
362B ASP 3.0 11.7 + - - +
363B HIS* 3.7 7.2 - - + +
364B THR 3.3 0.2 - - - -
365B THR* 1.3 80.6 + - - +
367B ALA* 1.3 63.4 + - - +
369B LEU* 3.8 8.1 - - - +
370B TYR* 3.0 25.5 + - - +
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Residues in contact with ALA 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B HIS 2.9 16.6 + - - +
364B THR* 3.8 5.2 - - + +
366B GLN* 1.3 77.0 - - - +
368B ALA* 1.3 61.9 + - - +
370B TYR* 3.3 5.2 + - - +
371B THR* 2.9 31.9 + - - +
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Residues in contact with ALA 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 4.0 22.7 - - + +
364B THR* 2.9 21.4 + - + +
365B THR 3.8 3.8 - - - +
367B ALA* 1.3 75.4 - - - +
369B LEU* 1.3 57.2 + - - +
371B THR* 3.9 4.3 - - - -
372B HIS* 2.9 32.5 + - - +
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR 4.8 3.1 - - - +
118B SER* 3.7 28.7 - - - +
119B GLY* 4.8 1.8 - - - -
350B MET* 5.1 17.3 - - + -
356B TYR* 6.1 0.7 - - + -
359B ILE* 4.0 27.6 - - + -
365B THR 2.8 28.1 + - - +
366B GLN* 3.8 11.0 - - - +
368B ALA* 1.3 70.3 - - - +
370B TYR* 1.3 66.8 + - - +
372B HIS* 3.4 7.9 + - + +
373B HIS* 3.0 51.2 + - + +
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Residues in contact with TYR 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ALA* 3.3 42.1 - - + +
348B GLN* 3.0 28.6 + - - -
351B TYR* 3.5 34.2 - + + -
366B GLN 3.0 17.4 + - - +
367B ALA* 3.8 5.6 - - - +
369B LEU* 1.3 76.6 - - - +
371B THR* 1.3 69.2 + - - +
373B HIS* 3.9 0.3 - - - -
374B GLN* 3.0 51.1 + - + +
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Residues in contact with THR 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA* 2.9 19.8 + - - +
368B ALA* 3.9 4.5 - - - -
370B TYR* 1.3 83.5 - - - +
372B HIS* 1.3 64.9 + - - +
374B GLN* 3.3 3.3 + - - -
375B TYR* 2.9 55.8 + - + -
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Residues in contact with HIS 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B ALA 2.9 20.8 + - - +
369B LEU* 3.6 7.6 - - + +
371B THR* 1.3 77.8 - - - +
373B HIS* 1.3 104.7 + + - +
375B TYR* 3.2 4.7 + - - +
376B ILE* 3.0 51.7 + - + +
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Residues in contact with HIS 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 3.2 28.9 - - + +
346B VAL* 4.3 24.1 - - + +
347B ALA* 3.8 20.8 - - + -
350B MET* 4.9 9.1 - - - +
369B LEU* 3.0 45.4 + - + +
372B HIS* 1.3 101.4 + + - +
374B GLN* 1.3 59.9 + - - +
376B ILE* 3.3 3.6 + - + -
377B ALA* 2.9 25.1 + - - +
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Residues in contact with GLN 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B SER* 2.9 34.3 + - - -
347B ALA* 3.8 11.9 - - + -
348B GLN* 3.5 18.4 - - - +
370B TYR* 3.0 57.1 + - + +
371B THR* 3.9 4.5 - - - +
373B HIS* 1.3 76.5 - - - +
375B TYR* 1.3 59.9 + - + +
377B ALA* 3.3 2.8 + - - +
378B GLY* 2.9 24.4 + - - -
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Residues in contact with TYR 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B THR* 2.9 49.7 + - + +
372B HIS* 3.6 6.1 - - - +
374B GLN* 1.3 76.8 - - + +
376B ILE* 1.3 66.4 + - + +
378B GLY* 3.2 2.4 + - - -
379B PHE* 3.0 47.0 + + + -
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Residues in contact with ILE 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B THR* 4.4 9.9 - - + +
372B HIS* 3.0 49.4 + - + +
373B HIS* 3.7 6.3 - - + +
375B TYR* 1.3 75.8 - - + +
377B ALA* 1.3 57.7 + - - +
379B PHE* 3.3 13.2 + - + +
380B LEU* 2.9 49.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B GLY* 3.4 22.8 - - - +
343B THR* 3.7 6.2 - - - +
344B SER* 3.2 33.9 - - - +
373B HIS 2.9 16.8 + - - +
374B GLN* 3.6 4.9 - - - +
376B ILE* 1.3 77.7 - - - +
378B GLY* 1.3 56.8 + - - +
380B LEU* 3.2 2.6 + - - +
381B MET* 2.9 35.3 + - + +
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Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B GLN 2.9 14.8 + - - -
375B TYR* 3.2 3.8 + - - -
377B ALA* 1.3 77.5 - - - +
379B PHE* 1.3 61.4 + - - +
381B MET* 3.3 7.0 + - - +
382B VAL* 3.0 30.0 + - - +
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Residues in contact with PHE 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B TYR* 3.0 44.0 + + + -
376B ILE* 3.5 15.5 - - + +
378B GLY* 1.3 74.7 - - - +
380B LEU* 1.3 66.3 + - + +
382B VAL* 3.4 7.8 + - + +
383B GLY* 2.9 20.3 + - - -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 3.5 46.7 - - + +
339B LEU* 3.6 21.5 - - + -
340B GLY* 3.6 17.9 - - - +
343B THR* 3.6 24.5 - - - +
376B ILE* 2.9 34.1 + - + +
377B ALA* 3.2 6.7 + - - +
379B PHE* 1.3 79.0 - - + +
381B MET* 1.3 56.5 + - - +
383B GLY* 3.2 1.7 + - - -
384B ALA* 2.9 24.8 + - - +
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Residues in contact with MET 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ALA* 3.7 37.5 - - + +
340B GLY* 4.5 5.8 - - - -
341B VAL* 4.4 13.9 - - + -
344B SER* 6.0 0.7 - - - +
377B ALA* 2.9 22.1 + - + +
378B GLY* 3.7 6.7 - - - +
380B LEU* 1.3 72.8 - - - +
382B VAL* 1.3 66.9 + - + +
384B ALA* 3.1 5.3 + - + +
385B PHE* 3.1 55.7 + - + -
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Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLY 3.0 20.3 + - - +
379B PHE* 3.8 7.9 - - + +
381B MET* 1.3 75.3 - - + +
383B GLY* 1.3 58.7 + - - +
385B PHE* 3.3 7.2 + - - +
386B ALA* 2.9 30.1 + - + +
527B THR* 6.0 5.8 - - - -
----------------------------------------------------------
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B LEU* 3.5 15.0 - - - -
379B PHE 2.9 15.7 + - - -
380B LEU 3.6 2.7 - - - -
381B MET 3.2 0.4 - - - -
382B VAL* 1.3 76.7 - - - +
384B ALA* 1.3 64.0 + - - +
386B ALA* 3.3 7.2 + - - +
387B HIS* 2.9 32.3 + - - -
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B GLY* 3.3 33.9 - - - +
336B LEU* 3.6 9.7 - - + +
337B ALA* 3.3 28.5 - - + +
380B LEU 2.9 8.6 + - - +
381B MET* 3.5 10.8 - - + +
383B GLY* 1.3 76.2 - - - +
385B PHE* 1.3 58.4 + - + +
387B HIS 3.3 1.6 + - - -
388B GLY* 3.0 23.9 + - - -
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Residues in contact with PHE 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B MET* 3.1 44.3 + - + -
382B VAL* 3.9 7.9 - - - +
384B ALA* 1.3 75.2 - - + +
386B ALA* 1.3 67.4 + - - +
388B GLY* 3.3 2.7 + - - +
389B ALA* 3.0 22.9 + - - +
527B THR 5.9 5.2 - - - -
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Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 2.9 20.7 + - + +
383B GLY* 3.5 10.1 - - - +
385B PHE* 1.3 77.0 - - - +
387B HIS* 1.3 60.0 + - + +
389B ALA* 3.2 8.9 + - - +
390B ILE* 2.9 38.2 + - + +
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Residues in contact with HIS 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B HIS* 3.1 52.5 + + - +
332B LEU* 3.3 34.4 - - + +
333B GLY* 4.2 7.2 - - - +
336B LEU* 4.1 7.6 - - + +
383B GLY* 2.9 27.1 + - - +
384B ALA 4.0 2.9 - - - +
386B ALA* 1.3 77.2 - - + +
388B GLY* 1.3 60.9 + - - +
390B ILE* 3.6 18.0 - - + +
391B PHE* 2.8 27.9 + - - +
----------------------------------------------------------
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Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B HIS 4.7 1.5 + - - -
330B PHE* 6.0 1.8 - - - -
333B GLY* 4.9 2.2 - - - -
384B ALA 3.0 15.2 + - - -
385B PHE* 3.3 4.9 + - - -
387B HIS* 1.3 76.6 - - - +
389B ALA* 1.3 60.5 + - - +
391B PHE* 3.2 10.6 + - - +
392B PHE* 3.0 31.2 + - - -
----------------------------------------------------------
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B PHE 3.0 12.2 + - - +
386B ALA* 3.2 12.1 + - - +
388B GLY* 1.3 76.2 - - - +
390B ILE* 1.3 58.1 + - + +
392B PHE* 3.2 10.7 + - - +
393B VAL* 2.9 34.6 + - + +
----------------------------------------------------------
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B HIS* 3.4 32.5 - - + +
386B ALA* 2.9 28.1 + - + +
387B HIS* 3.6 30.3 - - + +
388B GLY 3.3 0.2 - - - -
389B ALA* 1.3 76.1 - - + +
391B PHE* 1.3 57.7 + - - +
393B VAL* 3.2 8.6 + - + +
394B ARG* 2.9 46.9 + - + +
----------------------------------------------------------
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Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B THR* 4.0 12.3 - - + -
327B SER* 3.1 26.7 - - - +
329B HIS* 3.8 14.7 - - + +
330B PHE* 3.8 30.7 - + - +
387B HIS 2.8 14.0 + - - +
388B GLY* 3.4 13.9 - - - +
389B ALA 3.2 0.2 - - - -
390B ILE* 1.3 76.1 - - - +
392B PHE* 1.3 94.8 + + - +
395B ASP* 2.7 44.7 + - + +
396B TYR* 3.2 24.5 + + + -
406B LEU* 3.6 33.2 - - + -
----------------------------------------------------------
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Residues in contact with PHE 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B GLY 3.0 18.4 + - - -
389B ALA* 3.6 10.5 - - - +
391B PHE* 1.3 96.0 - + - +
393B VAL* 1.3 63.0 + - + +
396B TYR* 3.7 38.5 + + + +
406B LEU* 3.5 25.1 - - + -
409B MET* 6.0 1.8 - - + -
410B LEU* 3.5 44.9 - - + -
----------------------------------------------------------
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ALA* 2.9 23.6 + - + +
390B ILE* 3.6 11.0 - - + +
391B PHE 3.1 0.4 - - - -
392B PHE* 1.3 81.1 - - + +
394B ARG* 1.3 70.5 + - + +
----------------------------------------------------------
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Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 2.9 41.8 + - - -
32B GLU* 3.0 29.6 + - - +
33B THR* 3.6 14.6 - - - +
329B HIS* 3.9 11.1 + - + -
390B ILE* 2.9 32.2 + - + +
393B VAL* 1.3 91.2 - - + +
395B ASP* 1.3 72.5 + - - +
396B TYR 3.8 0.7 - - - -
----------------------------------------------------------
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Residues in contact with ASP 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLU* 4.5 7.9 - - - +
326B ASN 4.7 5.2 - - - +
327B SER* 2.6 43.4 + - - +
328B LEU 4.2 0.7 + - - -
329B HIS* 3.5 20.5 - - - +
391B PHE* 2.7 23.6 + - + +
394B ARG* 1.3 87.4 - - - +
396B TYR* 1.3 64.2 + - - +
397B ASP* 3.3 6.1 + - - +
----------------------------------------------------------
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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