Contacts of the helix formed by residues 389 - 411 (chain C) in PDB entry 3MY0
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 CYS 389 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 3.3 31.6 + - + +
387C THR 3.4 1.2 - - - -
388C ASP* 1.3 80.1 - - - +
390C PHE* 1.3 68.4 + - - +
391C GLU* 3.8 22.0 - - - -
392C SER* 3.4 28.3 - - - +
393C TYR* 3.5 11.5 - - - -
395C TRP* 5.4 2.7 - - - -
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Residues in contact with PHE 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C HIS 5.0 0.2 - - - -
325C ALA* 3.4 45.5 - - + -
326C ILE 3.8 4.0 - - - -
327C ALA* 3.9 19.7 - - + -
353C VAL* 3.5 33.4 - - + -
354C MET 4.3 2.0 - - - -
355C HIS* 3.4 42.8 - - + +
362C LEU* 5.7 5.2 - - + -
388C ASP 4.3 0.2 - - - -
389C CYS* 1.3 71.8 - - - +
391C GLU* 1.3 68.2 + - - +
393C TYR* 3.0 20.9 + + - +
394C LYS* 3.4 35.9 + - + -
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Residues in contact with GLU 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C CYS* 3.4 11.7 - - - -
390C PHE* 1.3 79.1 - - - +
392C SER* 1.3 62.7 + - - +
394C LYS* 3.0 32.8 + - - +
395C TRP* 3.1 44.9 + - + -
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Residues in contact with SER 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C GLU* 5.0 1.3 - - - +
385C ILE* 3.9 18.3 - - - +
386C ARG* 3.6 31.5 + - - +
389C CYS* 3.4 23.6 + - - +
391C GLU* 1.3 78.2 - - - +
393C TYR* 1.3 62.1 + - - +
395C TRP* 3.1 30.5 + - - +
396C THR* 3.2 18.0 + - - +
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Residues in contact with TYR 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ALA* 3.9 18.5 - - + +
329C ARG* 3.5 41.2 + - + +
353C VAL* 3.9 23.3 - - + -
364C ILE* 5.5 7.7 - - + +
385C ILE* 4.2 17.9 - - + -
386C ARG 4.9 0.4 - - - -
387C THR* 2.8 49.8 + - + +
388C ASP 5.7 0.2 - - - -
389C CYS 3.5 23.8 - - - -
390C PHE* 3.0 14.2 + + - +
392C SER* 1.3 76.3 - - - +
394C LYS* 1.3 61.1 + - - +
396C THR* 2.8 25.5 + - + -
397C ASP* 3.2 11.6 + - - +
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Residues in contact with LYS 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C HIS* 3.5 55.2 + - + +
327C ALA* 4.1 2.7 - - + +
390C PHE* 3.4 37.0 + - + +
391C GLU* 3.0 24.4 + - - +
393C TYR* 1.3 77.9 - - - +
395C TRP* 1.3 67.3 + - + +
397C ASP* 3.1 6.4 + - - +
398C ILE* 3.1 26.7 + - + +
481C THR* 6.4 0.6 - - - +
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Residues in contact with TRP 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C GLU* 4.6 0.4 - - - +
386C ARG* 5.8 3.1 - - - -
389C CYS* 5.4 2.5 - - - -
391C GLU* 3.1 44.4 + - + -
392C SER* 3.1 22.4 + - - +
394C LYS* 1.3 81.5 - - + +
396C THR* 1.3 57.3 + - - +
398C ILE* 3.5 12.2 + - + +
399C TRP 3.2 15.2 + - - -
476C PRO* 3.4 45.3 + - + +
477C SER* 3.8 32.4 + - - +
479C ARG* 2.8 37.0 + - + +
480C LEU 5.1 1.8 - - - -
481C THR* 5.6 7.8 - - + +
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Residues in contact with THR 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C ARG* 4.7 10.2 - - - +
375C TYR 4.9 1.4 - - - +
377C ALA* 4.3 8.6 + - + +
379C GLU* 3.8 14.4 - - - +
380C VAL* 3.8 28.3 - - + -
385C ILE* 4.1 12.6 - - + -
392C SER 3.2 13.4 + - - +
393C TYR* 2.8 18.7 + - + -
395C TRP* 1.3 74.3 - - - +
397C ASP* 1.3 68.6 + - - +
398C ILE 3.2 0.4 - - - -
399C TRP* 3.6 8.9 + - - +
400C ALA* 3.2 22.3 + - - +
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Residues in contact with ASP 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU* 3.9 12.3 - - + +
314C HIS* 2.8 28.3 + - + +
327C ALA* 3.5 2.1 - - - -
328C HIS* 2.7 32.4 + - - +
329C ARG* 2.8 30.0 + - - -
330C ASP 4.6 0.2 + - - -
331C PHE* 4.4 8.3 + - + +
393C TYR 3.2 9.2 + - - +
394C LYS 3.1 10.4 + - - +
396C THR* 1.3 81.5 + - - +
398C ILE* 1.3 58.4 + - - +
400C ALA* 3.3 8.3 + - - +
401C PHE* 2.8 28.0 + - - +
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Residues in contact with ILE 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C LEU* 4.3 6.1 - - + -
314C HIS* 4.3 9.2 - - + +
394C LYS* 3.1 16.8 + - + +
395C TRP* 3.6 13.9 - - + +
396C THR 3.2 0.4 - - - -
397C ASP* 1.3 72.3 - - - +
399C TRP* 1.3 67.6 + - - +
401C PHE* 2.9 14.7 + - + +
402C GLY 3.0 11.4 + - - -
471C CYS* 3.7 30.9 - - + +
479C ARG* 4.2 7.6 - - + -
480C LEU 3.4 22.7 - - - +
481C THR* 3.9 2.5 - - - -
482C ALA* 3.6 39.5 - - + +
485C ILE* 4.3 7.6 - - + -
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Residues in contact with TRP 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C TYR 3.3 21.5 - - - -
376C MET 3.4 11.7 + - - -
377C ALA* 3.7 15.3 - - + -
378C PRO* 3.5 35.9 - - + -
395C TRP 3.2 4.4 + - - +
396C THR 3.6 8.1 - - - +
398C ILE* 1.3 80.7 - - - +
400C ALA* 1.3 60.3 + - - +
402C GLY* 3.0 11.1 + - - -
403C LEU* 3.2 28.5 + - + +
425C PHE* 4.5 17.8 - + - -
442C VAL* 4.0 15.9 - - + -
447C GLN 4.7 1.1 - - - -
448C THR* 4.0 20.0 - - + -
471C CYS 3.5 26.2 + - - -
472C TRP* 3.5 39.2 + + + -
474C PRO 5.5 0.2 - - - -
479C ARG* 3.8 21.5 - - - +
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Residues in contact with ALA 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C PHE* 3.1 35.4 - - + +
375C TYR* 4.0 16.3 - - + +
396C THR 3.2 11.2 + - - +
397C ASP 3.5 8.1 - - - +
399C TRP* 1.3 85.5 - - - +
401C PHE* 1.3 60.8 + - - +
403C LEU* 3.3 11.2 + - - +
404C VAL* 3.1 25.5 + - - +
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Residues in contact with PHE 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA* 4.0 7.9 - - - -
306C ALA* 4.0 14.8 - - + -
307C ALA* 3.8 42.6 - - + -
310C LEU* 3.8 18.4 - - + -
331C PHE* 3.7 25.8 - + + -
397C ASP 2.8 13.8 + - - +
398C ILE* 2.9 14.1 + - + +
400C ALA* 1.3 74.5 - - - +
402C GLY* 1.3 67.2 + - - +
404C VAL* 2.9 7.5 + - + +
405C LEU* 2.9 51.5 + - + +
471C CYS* 4.6 0.7 - - - -
485C ILE* 3.8 33.0 - - + -
489C LEU* 5.4 0.4 - - + -
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Residues in contact with GLY 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C ILE 3.0 10.7 + - - -
399C TRP 3.0 5.6 + - - -
401C PHE* 1.3 76.9 - - - +
403C LEU* 1.3 59.7 + - - +
405C LEU* 3.3 10.4 + - - +
406C TRP 3.2 18.0 + - - -
468C MET* 3.8 4.0 - - - +
471C CYS* 3.7 19.9 - - - -
472C TRP* 3.3 24.0 - - - -
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Residues in contact with LEU 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C ARG 4.0 7.4 - - - +
375C TYR* 3.4 43.3 - - + -
399C TRP* 3.2 36.0 + - + +
400C ALA* 3.4 7.0 - - - +
401C PHE 3.1 0.2 - - - -
402C GLY* 1.3 76.3 - - - +
404C VAL* 1.3 61.4 - - - +
406C TRP* 3.3 7.0 - - - +
407C GLU* 3.2 25.1 + - - +
424C PRO* 4.0 9.6 - - + +
425C PHE* 3.9 13.9 - - + -
449C PRO* 3.7 27.6 - - + -
472C TRP* 3.7 17.7 - - + +
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Residues in contact with VAL 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU* 3.5 30.3 - - + -
331C PHE* 3.6 25.8 - - + -
332C LYS* 3.9 6.7 - - - -
333C SER* 3.6 28.5 - - - +
336C VAL* 5.4 0.7 - - + -
375C TYR* 4.2 1.3 - - + -
400C ALA 3.1 16.0 + - - +
401C PHE* 2.9 11.8 + - + +
403C LEU* 1.3 73.5 - - - +
405C LEU* 1.3 65.4 + - + +
407C GLU* 3.2 14.4 + - - +
408C ILE* 3.1 25.3 + - + +
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Residues in contact with LEU 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA* 3.8 29.8 - - + -
401C PHE* 2.9 42.0 + - + +
402C GLY* 3.5 10.5 - - - +
404C VAL* 1.3 73.4 - - + +
406C TRP* 1.3 55.6 + - - +
408C ILE* 2.9 12.7 + - + +
409C ALA* 2.7 35.2 + - - +
464C LEU* 4.6 12.1 - - + +
467C MET* 3.6 37.2 - - + -
468C MET* 4.0 25.0 - - + +
471C CYS* 5.1 2.0 - - - -
489C LEU* 5.7 0.7 - - + -
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Residues in contact with TRP 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C GLY 3.2 9.7 + - - +
403C LEU* 3.3 11.4 - - - +
405C LEU* 1.3 77.8 - - - +
407C GLU* 1.3 74.4 + - + +
409C ALA* 3.1 2.7 + - - +
410C ARG* 2.8 58.6 + - + +
422C ARG 3.3 22.0 - - - -
423C PRO 3.6 12.3 - - - -
424C PRO* 3.7 13.7 - - + -
425C PHE 5.1 0.7 - - - -
426C TYR* 3.4 37.7 - + - -
449C PRO* 3.5 27.5 - - + +
450C THR 3.2 26.0 + - - -
451C ILE* 4.8 0.2 - - - -
452C PRO* 4.1 19.0 - - + +
468C MET* 4.0 12.6 - - - +
472C TRP* 4.1 16.4 - + + -
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Residues in contact with GLU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 3.4 21.5 - - + +
333C SER* 2.5 30.7 + - - -
375C TYR* 2.3 37.0 + - - -
403C LEU 3.2 8.3 + - - +
404C VAL* 3.2 14.8 + - + +
406C TRP* 1.3 87.0 - - + +
408C ILE* 1.3 61.4 + - - +
410C ARG* 3.8 4.9 + - - +
411C ARG* 3.6 14.4 + - - +
421C TYR* 2.7 34.1 + - + +
422C ARG 4.6 1.3 - - - +
424C PRO* 3.7 17.5 - - + +
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Residues in contact with ILE 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU* 4.1 29.2 - - + -
289C LEU* 4.1 11.7 - - + -
294C LEU* 3.9 8.4 - - + +
299C ALA* 3.8 35.9 - - + +
302C LEU* 4.3 9.0 - - + +
303C ALA* 4.2 30.5 - - + +
404C VAL* 3.1 18.0 + - + +
405C LEU* 2.9 14.6 + - + +
407C GLU* 1.3 72.4 - - - +
409C ALA* 1.3 61.9 + - - +
411C ARG* 3.1 12.1 + - - +
412C THR* 2.8 22.5 + - - -
464C LEU* 6.3 2.5 - - + -
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Residues in contact with ALA 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ALA* 5.9 0.2 - - - -
405C LEU 2.7 19.3 + - - +
406C TRP* 3.5 4.7 - - - +
408C ILE* 1.3 74.4 - - - +
410C ARG* 1.3 63.1 + - - +
412C THR* 3.0 28.1 + - - +
452C PRO* 5.1 12.9 - - + +
454C ARG* 4.6 4.2 + - - -
464C LEU* 5.7 7.2 - - + -
468C MET* 3.6 24.9 - - + -
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Residues in contact with ARG 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C TRP* 2.8 47.5 + - + +
407C GLU* 3.9 7.4 - - - +
408C ILE 3.3 0.2 - - - -
409C ALA* 1.3 73.6 - - - +
411C ARG* 1.3 58.2 - - - +
412C THR 3.3 0.2 - - - -
418C VAL* 3.6 3.5 - - - +
419C GLU* 2.8 66.9 + - + +
420C ASP* 2.9 24.8 + - - +
421C TYR* 4.9 2.5 - - + +
422C ARG* 3.6 17.9 - - - +
426C TYR* 2.7 45.5 + - - -
452C PRO* 5.1 8.9 - - + +
454C ARG* 3.9 9.5 + - - +
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Residues in contact with ARG 411 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 2.6 37.7 + - + +
290C GLN 3.1 22.4 + - - -
291C ARG 4.2 5.5 + - - -
292C GLN 3.5 19.5 + - - +
293C THR* 3.5 26.3 - - - +
294C LEU* 2.9 25.7 + - + +
407C GLU 3.6 13.9 + - - +
408C ILE 3.1 5.8 + - - +
409C ALA 3.1 0.8 - - - -
410C ARG* 1.3 78.4 - - - +
412C THR* 1.3 56.1 + - - +
418C VAL* 3.4 21.0 - - - +
419C GLU 3.0 26.0 + - - -
420C ASP* 4.1 3.2 - - - +
421C TYR* 3.7 28.7 - - - +
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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