Contacts of the helix formed by residues 395 - 416 (chain C) in PDB entry 4BGG
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 395 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A GLN* 5.1 0.2 - - - -
394A ASP 4.0 11.9 + - - +
395A CYS* 2.1 49.4 - - + -
392C GLN* 3.0 15.3 + - + +
393C VAL 3.4 0.6 - - - -
394C ASP* 1.3 78.3 - - - +
396C PHE* 1.3 66.2 + - - +
397C ASP* 3.6 15.9 - - - -
398C SER* 3.2 35.1 + - - +
399C TYR* 3.6 8.8 - - - -
401C ARG* 5.1 4.3 - - - -
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Residues in contact with PHE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLN* 3.9 19.3 + - - +
331C ALA* 3.6 40.2 - - + -
332C ILE 3.9 1.8 - - - -
333C ALA* 3.9 12.3 - - + -
359C VAL* 3.6 37.0 - - + -
360C MET 4.4 1.8 - - - -
361C HIS* 3.5 40.6 - + + +
394C ASP 4.0 2.4 + - - -
395C CYS* 1.3 73.3 - - - +
397C ASP* 1.3 63.3 + - + +
399C TYR* 3.0 18.2 + + - +
400C LYS* 3.5 40.0 + - + -
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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
----------------------------------------------------------
392A GLN* 4.8 6.4 + - - +
395A CYS* 4.6 3.7 - - - -
401A ARG* 5.7 5.2 - - - +
395C CYS* 3.3 10.8 - - - -
396C PHE* 1.3 79.2 - - - +
398C SER* 1.3 62.2 + - - +
400C LYS* 3.2 23.6 + - - +
401C ARG* 3.1 54.0 + - - +
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Residues in contact with SER 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C GLU* 4.7 1.6 - - - +
391C ILE* 3.9 19.9 - - - +
392C GLN* 2.9 39.4 + - - +
395C CYS* 3.2 17.8 + - - +
396C PHE 3.1 0.2 - - - -
397C ASP* 1.3 78.8 - - - +
399C TYR* 1.3 62.3 + - - +
401C ARG* 3.4 13.6 + - - +
402C VAL* 3.2 27.5 + - - +
482C PRO* 6.0 1.3 - - - -
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Residues in contact with TYR 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333C ALA* 3.7 19.7 - - + +
335C ARG* 4.0 37.2 + - + +
359C VAL* 4.0 17.9 - - + -
370C VAL* 5.1 15.3 - - + +
391C ILE* 4.3 19.5 - - + -
392C GLN 4.8 0.7 - - - -
393C VAL* 2.7 44.4 + - + +
394C ASP 5.4 0.2 - - - -
395C CYS 3.6 17.7 - - - -
396C PHE* 3.0 16.3 + + + +
398C SER* 1.3 74.8 - - - +
400C LYS* 1.3 65.3 + - - +
402C VAL* 3.4 10.0 + - + +
403C ASP* 3.3 23.0 + - - +
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Residues in contact with LYS 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A SER* 5.8 1.8 + - - -
320C HIS* 3.6 57.1 + - + +
331C ALA* 5.5 0.6 - - - +
333C ALA* 4.4 2.0 - - + -
396C PHE* 3.5 41.5 + - + +
397C ASP* 3.2 21.2 + - - +
399C TYR* 1.3 78.2 - - - +
401C ARG* 1.3 59.8 + - + +
403C ASP* 3.0 17.0 + - - +
404C ILE* 3.1 19.0 + - + +
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Residues in contact with ARG 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ASP* 2.9 31.3 + - - +
401A ARG* 3.6 18.8 - - - +
385C GLU* 4.6 0.4 - - - +
392C GLN* 5.2 7.3 - - - +
395C CYS* 5.1 5.1 - - - -
397C ASP* 3.1 39.9 + - - +
398C SER* 3.8 9.6 + - - +
399C TYR 3.2 0.2 - - - -
400C LYS* 1.3 76.0 - - + +
402C VAL* 1.3 65.5 + - - +
404C ILE* 3.3 10.6 + - + +
405C TRP 3.1 14.7 + - - -
482C PRO* 3.4 36.8 + - + +
483C SER* 4.0 17.0 + - - +
485C ARG* 3.1 30.1 + - + +
486C LEU 6.0 1.1 - - - +
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Residues in contact with VAL 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ARG* 5.1 15.9 - - + +
381C TYR 5.2 1.9 - - - +
382C MET* 6.1 1.1 - - - -
383C ALA* 4.3 12.8 - - + +
385C GLU* 3.7 16.2 - - - +
386C VAL* 3.8 19.5 - - + -
391C ILE* 3.8 21.5 - - + -
398C SER 3.2 15.3 + - - +
399C TYR* 3.5 13.2 - - + +
401C ARG* 1.3 76.5 - - - +
403C ASP* 1.3 66.6 + - - +
405C TRP* 3.5 5.4 + - - +
406C ALA* 3.3 19.6 + - + +
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Residues in contact with ASP 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU* 3.9 11.4 - - + +
320C HIS* 2.9 27.1 + - + +
333C ALA* 3.6 2.3 - - - +
334C HIS* 2.8 34.2 + - - +
335C ARG* 2.8 30.4 + - - -
336C ASP 4.5 0.5 + - - -
337C LEU* 3.7 10.1 + - + +
399C TYR 3.3 10.8 + - - +
400C LYS 3.0 10.5 + - - +
402C VAL* 1.3 79.5 - - - +
404C ILE* 1.3 59.1 + - - +
406C ALA* 3.4 6.4 + - - +
407C PHE* 2.9 28.8 + - - +
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Residues in contact with ILE 404 (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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316C LEU* 4.3 11.4 - - + -
320C HIS* 4.4 4.5 - - + +
400C LYS* 3.1 17.9 + - + +
401C ARG* 3.6 12.1 - - + +
402C VAL 3.2 0.4 - - - -
403C ASP* 1.3 73.9 - - - +
405C TRP* 1.3 67.8 + - - +
407C PHE* 3.2 5.1 + - + +
408C GLY 3.1 18.4 + - - -
477C CYS* 3.5 32.8 - - + +
485C ARG* 4.2 9.0 - - + -
486C LEU 3.4 23.8 - - - +
487C THR* 3.9 2.2 - - - -
488C ALA* 3.6 37.5 - - + +
491C ILE* 4.1 8.7 - - + -
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Residues in contact with TRP 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C TYR 3.2 23.3 + - - -
382C MET 3.3 13.4 + - - -
383C ALA* 3.7 18.6 - - + -
384C PRO* 3.5 29.8 - - + -
401C ARG 3.1 12.4 + - - +
402C VAL 3.6 8.3 - - - +
404C ILE* 1.3 75.3 - - - +
406C ALA* 1.3 62.6 + - - +
408C GLY* 3.1 12.0 + - - -
409C LEU* 3.3 28.1 + - + +
431C PHE* 4.5 17.2 - + - -
448C VAL* 4.1 12.3 - - + -
453C GLN 5.0 0.7 - - - -
454C ARG* 3.5 32.8 - - - -
455C PRO* 6.1 0.2 - - + -
477C CYS 3.6 13.4 + - - +
478C TRP* 3.4 48.8 + + + -
485C ARG* 4.0 10.3 - - - +
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Residues in contact with ALA 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337C LEU* 3.6 33.4 - - + +
381C TYR* 4.1 20.9 - - + +
402C VAL* 3.3 10.4 + - + +
403C ASP* 3.7 8.1 - - - +
404C ILE 3.3 0.2 - - - -
405C TRP* 1.3 82.3 - - - +
407C PHE* 1.3 66.3 + - - +
409C LEU* 3.2 6.0 + - - +
410C VAL* 3.1 25.8 + - - +
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Residues in contact with PHE 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C VAL* 4.2 7.6 - - + -
312C ILE* 3.5 40.8 - - + -
313C ALA* 4.1 15.3 - - + -
316C LEU* 4.2 15.0 - - + -
337C LEU* 4.0 12.1 - - + +
403C ASP 2.9 18.0 + - - +
404C ILE* 3.2 8.9 + - - +
406C ALA* 1.3 76.7 - - - +
408C GLY* 1.3 57.5 + - - +
410C VAL* 3.1 9.9 + - + +
411C LEU* 2.9 55.7 + - + +
477C CYS* 4.2 2.5 - - - -
491C ILE* 3.5 47.3 - - + -
495C LEU* 4.6 3.4 - - + -
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Residues in contact with GLY 408 (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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404C ILE 3.1 10.3 + - - -
405C TRP 3.1 5.1 + - - -
407C PHE* 1.3 76.8 - - - +
409C LEU* 1.3 61.3 + - - +
411C LEU* 3.3 10.9 - - - +
412C TRP 3.1 16.5 + - - -
474C MET* 3.8 3.8 - - - +
477C CYS* 3.9 19.5 - - - -
478C TRP* 3.5 26.0 - - - -
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Residues in contact with LEU 409 (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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380C ARG 3.9 7.9 - - - +
381C TYR* 3.8 40.4 - - + -
405C TRP* 3.3 37.1 + - + +
406C ALA* 3.2 6.6 + - - +
408C GLY* 1.3 77.1 - - - +
410C VAL* 1.3 57.0 + - - +
412C TRP* 3.2 9.6 + - - +
413C GLU* 3.0 30.6 + - - +
430C PRO* 4.0 17.2 - - + +
431C PHE* 4.1 11.7 - - + -
455C PRO* 3.7 30.3 - - + -
478C TRP* 3.9 11.4 - - + +
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Residues in contact with VAL 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 4.1 18.4 - - + -
309C VAL* 6.3 0.4 - - + -
312C ILE* 4.2 12.1 - - + -
337C LEU* 5.0 2.7 - - + -
338C LYS* 4.0 27.1 - - - +
339C SER* 4.0 5.2 - - - +
342C ILE* 4.1 22.0 - - + -
381C TYR* 4.0 2.5 - - + -
406C ALA 3.1 15.9 + - - +
407C PHE* 3.5 12.6 - - + +
409C LEU* 1.3 72.1 - - - +
411C LEU* 1.3 66.8 + - - +
413C GLU* 3.1 21.0 + - + +
414C VAL* 3.0 22.1 + - + +
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Residues in contact with LEU 411 (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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309C VAL* 3.5 32.5 - - + -
407C PHE* 2.9 45.2 + - + +
408C GLY* 3.3 13.5 - - - +
410C VAL* 1.3 78.2 - - - +
412C TRP* 1.3 55.5 + - - +
414C VAL* 3.3 5.6 + - - +
415C ALA* 2.9 32.0 + - - +
470C LEU* 4.2 25.4 - - + +
473C LEU* 4.2 27.4 - - + -
474C MET* 3.9 16.4 - - + +
477C CYS* 5.0 0.9 - - - -
495C LEU* 5.4 0.9 - - + -
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Residues in contact with TRP 412 (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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408C GLY 3.1 7.3 + - - +
409C LEU* 3.3 10.3 - - - +
410C VAL 3.2 0.2 - - - -
411C LEU* 1.3 76.0 - - - +
413C GLU* 1.3 86.9 + - + +
415C ALA* 4.0 1.5 - - - +
416C ARG* 3.1 57.5 + - + +
428C LYS* 3.6 26.2 - - + -
429C PRO 3.8 1.1 - - - -
430C PRO* 3.7 25.6 - - + -
431C PHE 5.0 1.1 - - - -
432C TYR* 3.9 29.4 - + - -
455C PRO* 3.5 25.9 - - + +
456C ASN* 3.0 31.0 + - + -
461C TRP* 4.0 12.8 - + - -
474C MET* 3.3 38.1 - - + -
478C TRP* 4.2 4.5 - - + -
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Residues in contact with GLU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 4.2 13.5 - - + +
339C SER* 2.7 23.1 + - - -
381C TYR* 2.4 36.8 + - - -
409C LEU 3.0 13.2 + - - +
410C VAL* 3.1 18.4 + - + +
412C TRP* 1.3 83.5 - - + +
414C VAL* 1.3 62.7 + - + +
416C ARG* 3.2 19.3 - - - +
427C TYR* 2.5 39.1 + - + -
428C LYS 4.0 10.8 - - - +
430C PRO* 3.7 17.1 - - + +
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Residues in contact with VAL 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 3.9 28.9 - - + -
295C LEU* 4.0 25.3 - - + +
300C LEU* 5.4 7.8 - - + +
305C CYS* 4.0 21.0 - - + +
308C ILE* 4.1 21.1 - - + -
309C VAL* 3.9 24.2 - - + -
312C ILE* 5.2 0.2 - - + -
410C VAL* 3.0 21.5 + - + +
411C LEU 3.8 3.8 - - - +
413C GLU* 1.3 78.0 - - - +
415C ALA* 1.3 63.5 + - - +
416C ARG 3.5 8.0 + - - +
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Residues in contact with ALA 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C CYS* 4.6 11.4 - - - -
309C VAL* 5.9 0.2 - - - +
411C LEU 2.9 18.4 + - - +
412C TRP* 4.0 0.7 - - - +
414C VAL* 1.3 72.4 - - - +
416C ARG* 1.3 70.8 + - - +
461C TRP* 3.8 35.3 + - + -
467C LEU* 5.6 6.7 - - + +
470C LEU* 4.3 23.3 - - + -
474C MET* 5.1 0.9 - - - -
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Residues in contact with ARG 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412C TRP* 3.1 58.1 + - + +
413C GLU* 3.2 17.0 - - - +
414C VAL 3.5 10.7 - - - +
415C ALA* 1.3 82.7 - - - +
425C GLU* 3.5 57.0 + - - +
426C ASP 3.0 30.6 + - - +
427C TYR* 5.8 2.2 - - - -
428C LYS* 3.1 35.7 - - - +
432C TYR* 4.0 16.2 + - - -
456C ASN 5.8 0.6 + - - -
458C PRO* 5.4 5.4 - - - +
461C TRP* 3.6 10.8 - - + -
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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