Contacts of the helix formed by residues 399 - 423 (chain B) in PDB entry 4JGV
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 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398B GLU* 1.3 76.2 - - - +
400B ALA* 1.3 64.5 + - - +
401B GLY* 2.9 27.0 + - - -
402B ASP* 3.1 34.9 + - - +
403B VAL* 3.2 13.2 + - - +
477B ARG* 4.4 13.0 + - - -
581B LEU* 3.6 8.1 - - - -
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASP* 1.3 76.4 - - - +
401B GLY* 1.3 56.3 + - - +
403B VAL* 3.4 1.5 + - - +
404B GLN* 2.9 30.0 + - - +
581B LEU* 3.7 18.9 - - + +
582B VAL* 3.7 26.9 - - + +
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Residues in contact with GLY 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ASP* 2.9 10.4 + - - -
400B ALA* 1.3 75.0 - - - +
402B ASP* 1.3 66.4 + - - +
404B GLN* 3.9 7.0 - - - +
405B GLN* 3.1 24.4 + - - +
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Residues in contact with ASP 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 3.5 11.7 - - + +
399B ASP* 3.1 39.2 + - - +
401B GLY* 1.3 78.0 - - - +
403B VAL* 1.3 63.1 + - - +
405B GLN* 3.3 13.5 + - - +
406B PHE* 3.1 21.8 + - - +
474B GLN 5.4 3.8 - - - +
477B ARG* 3.4 38.8 + - - +
478B GLY* 4.0 17.4 - - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 3.9 16.8 - - + -
399B ASP 3.2 13.8 + - - +
400B ALA* 3.8 7.9 - - - +
401B GLY 3.3 0.2 - - - -
402B ASP* 1.3 75.8 - - - +
404B GLN* 1.3 63.3 + - - +
406B PHE* 3.3 7.5 + - - +
407B TYR* 3.1 47.5 + - + -
478B GLY* 5.1 2.2 - - - -
576B LEU* 4.1 22.0 - - + +
579B GLU* 3.8 21.5 - - - +
581B LEU* 4.1 6.1 - - + -
582B VAL* 3.5 18.6 - - + +
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Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ALA 2.9 17.8 + - - +
401B GLY* 3.9 7.6 - - - +
403B VAL* 1.3 79.1 - - - +
405B GLN* 1.3 51.8 + - - +
407B TYR* 3.2 8.9 + - - +
408B ASP* 2.7 71.5 + - - +
582B VAL* 3.6 26.3 - - + +
583B PRO 5.5 0.2 - - - +
585B PRO* 5.9 2.8 - - - +
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Residues in contact with GLN 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B GLY 3.1 19.3 + - - +
402B ASP* 3.6 14.4 + - - +
404B GLN* 1.3 76.2 - - - +
406B PHE* 1.3 61.6 + - - +
408B ASP* 3.3 9.2 + - - +
409B LEU* 2.9 47.9 + - + +
468B LEU* 6.2 0.9 - - + -
470B LEU* 3.8 21.1 - - + +
474B GLN* 3.7 15.4 + - - +
475B CYS* 3.6 27.3 + - - +
478B GLY* 5.5 2.6 - - - +
479B PHE* 5.0 1.2 - - - -
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Residues in contact with PHE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ASP 3.1 13.2 + - - +
403B VAL* 3.3 10.5 - - - +
405B GLN* 1.3 78.9 - - - +
407B TYR* 1.3 78.0 + + - +
409B LEU* 3.3 3.5 + - - +
410B LEU* 3.1 45.9 + - + +
478B GLY* 3.8 14.4 - - - +
479B PHE* 3.6 47.1 - + + -
482B TRP* 3.6 33.0 - + - -
572B ARG* 4.1 11.7 - - + -
573B ILE* 4.2 11.0 - - + -
576B LEU* 3.5 27.1 - - + -
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Residues in contact with TYR 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B VAL* 3.1 38.0 + - + -
404B GLN* 3.7 11.4 - - - +
406B PHE* 1.3 94.5 - + - +
408B ASP* 1.3 61.3 + - - +
410B LEU* 3.3 6.1 + - + +
411B SER* 2.8 33.9 + - - -
573B ILE* 4.4 9.6 + - + +
576B LEU* 3.6 24.8 - - + +
577B LYS* 4.2 7.3 + - - +
582B VAL* 3.7 26.6 + - + -
583B PRO 4.1 5.2 - - - -
584B PRO* 3.7 33.9 - - + +
585B PRO* 3.6 25.4 - - + +
588B ILE* 4.5 13.7 - - + -
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B GLN* 2.7 60.0 + - - +
405B GLN* 3.6 8.4 - - + +
407B TYR* 1.3 73.1 - - - +
409B LEU* 1.3 58.4 + - + +
411B SER* 3.2 8.2 + - - -
412B GLY* 2.8 27.9 + - - -
585B PRO* 6.0 0.7 - - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B GLN* 2.9 42.8 + - + +
406B PHE 3.6 4.0 - - - +
408B ASP* 1.3 78.1 - - + +
410B LEU* 1.3 63.0 + - - +
412B GLY* 3.4 3.3 + - - -
413B SER* 3.4 17.8 + - - -
447B PHE* 4.0 7.1 - - + -
464B PHE* 3.9 51.8 - - + +
466B SER* 5.8 0.9 - - - +
468B LEU* 4.0 17.7 - - + -
470B LEU* 4.8 2.7 - - + -
475B CYS* 5.1 0.2 - - + -
479B PHE* 3.9 28.3 - - + -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B PHE* 3.1 44.7 + - + +
407B TYR* 3.5 10.1 - - + +
409B LEU* 1.3 76.6 - - - +
411B SER* 1.3 63.5 + - - +
413B SER* 3.0 11.3 + - - -
414B LEU* 3.4 1.2 + - - +
443B PHE* 3.3 31.5 - - + -
444B LEU* 4.5 9.4 - - + -
447B PHE* 3.6 41.1 - - + -
479B PHE* 5.5 0.4 - - + -
482B TRP* 4.7 6.1 - - + -
573B ILE* 4.3 10.5 - - + -
588B ILE* 4.0 32.5 - - + -
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B TYR 2.8 25.8 + - - -
408B ASP* 3.4 8.6 + - - -
410B LEU* 1.3 71.6 - - - +
412B GLY* 1.3 55.5 + - - +
414B LEU* 3.0 29.4 + - - +
415B GLU* 2.4 25.7 - - - +
585B PRO* 3.4 26.0 - - - +
587B ILE* 5.3 1.5 - - - +
588B ILE* 4.0 5.2 - - - +
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Residues in contact with GLY 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ASP 2.8 16.0 + - - -
409B LEU* 3.4 4.2 + - - -
410B LEU 3.2 0.4 - - - -
411B SER* 1.3 75.9 - - - +
413B SER* 1.3 60.1 + - - +
414B LEU 3.5 0.2 + - - -
415B GLU* 3.5 12.8 - - - +
416B VAL* 3.7 17.3 - - - +
465B CYS* 4.0 6.4 - - - -
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LEU 3.4 6.6 + - - -
410B LEU 3.0 11.8 + - - -
412B GLY* 1.3 76.1 - - - +
414B LEU* 1.3 65.1 + - - +
415B GLU 3.5 0.4 - - - -
416B VAL* 3.4 3.2 + - - +
417B ILE* 3.1 36.4 + - - +
443B PHE* 4.0 7.6 - - - -
447B PHE* 3.4 34.3 - - - +
450B ARG* 4.5 4.5 + - - -
454B ARG* 5.4 1.7 + - - -
465B CYS* 3.8 21.3 - - - -
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410B LEU 3.4 3.2 + - - +
411B SER* 3.0 29.6 + - - +
413B SER* 1.3 78.1 - - - +
415B GLU* 1.3 72.6 + - - +
417B ILE* 3.2 5.5 + - - +
418B ARG* 3.2 34.3 + - - +
443B PHE* 4.0 21.5 - - + -
587B ILE* 4.0 33.4 - - + -
588B ILE* 3.8 18.6 - - + -
591B ILE* 3.9 27.4 - - + -
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B SER* 2.4 30.5 - - - +
412B GLY* 3.5 11.3 - - - +
414B LEU* 1.3 84.7 - - - +
416B VAL* 1.3 69.4 + - + +
418B ARG* 3.3 18.8 + - + +
419B LYS* 3.2 40.8 + - + +
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B SER* 3.3 36.4 - - - +
412B GLY 3.7 16.6 - - - +
413B SER 3.4 8.5 + - - +
414B LEU 3.2 0.2 - - - -
415B GLU* 1.3 80.6 - - + +
417B ILE* 1.3 57.3 + - - +
419B LYS* 3.4 13.4 + - - +
420B TRP* 2.9 26.9 + - - +
450B ARG* 3.9 14.4 - - - +
465B CYS* 3.9 19.5 - - + +
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B SER* 3.1 28.6 + - - +
414B LEU* 3.2 4.4 + - - +
416B VAL* 1.3 73.9 - - - +
418B ARG* 1.3 55.9 + - - +
420B TRP* 3.1 23.4 + - + +
421B ALA* 2.7 33.3 + - - +
439B LEU* 4.0 13.9 - - + +
443B PHE* 3.8 28.0 - - + -
446B LEU* 3.9 33.4 - - + -
447B PHE* 4.2 6.7 - - - +
450B ARG* 4.0 24.0 - - - +
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Residues in contact with ARG 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LEU* 3.2 32.3 + - - +
415B GLU* 3.3 23.5 + - - +
417B ILE* 1.3 75.7 - - - +
419B LYS* 1.3 69.6 + - + +
421B ALA* 3.3 1.9 + - - +
422B GLU* 3.1 31.6 + - + +
436B ASP* 5.2 7.5 + - - +
439B LEU* 4.3 34.5 - - + +
587B ILE* 5.8 6.3 - - - +
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415B GLU* 3.2 33.6 + - + +
416B VAL* 3.8 10.8 - - - +
418B ARG* 1.3 82.8 - - + +
420B TRP* 1.3 63.2 + - - +
422B GLU* 3.4 11.3 + - - +
423B LYS* 3.4 27.9 + - - +
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Residues in contact with TRP 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B LEU* 4.9 2.2 + - + -
371B ALA* 3.7 28.9 - - + +
372B HIS* 3.8 13.6 + - - +
375B SER* 3.9 21.3 - - - -
416B VAL 2.9 18.7 + - - +
417B ILE* 3.4 19.7 - - + +
419B LYS* 1.3 72.6 - - - +
421B ALA* 1.3 76.7 + - - +
423B LYS* 3.1 24.8 + - - +
424B ILE* 3.6 31.7 + - + +
446B LEU* 3.7 29.4 - - + -
450B ARG* 4.7 11.4 - - - +
504B ALA 5.1 1.8 + - - -
507B SER* 3.5 46.0 + - - -
508B ALA* 3.8 6.7 - - + -
511B LEU* 3.8 16.4 - - + -
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Residues in contact with ALA 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ILE 2.7 20.4 + - - +
418B ARG* 3.6 4.9 - - - +
420B TRP* 1.3 80.0 - - + +
422B GLU* 1.3 58.6 + - - +
424B ILE* 2.9 32.3 + - - +
427B PHE* 3.4 22.3 - - + +
439B LEU* 3.8 16.4 - - + -
511B LEU* 3.6 23.8 - - + -
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Residues in contact with GLU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B ARG* 3.1 20.5 + - + +
419B LYS* 3.8 7.6 - - - +
420B TRP 3.2 0.4 - - - -
421B ALA* 1.3 75.2 - - - +
423B LYS* 1.3 61.4 + - + +
424B ILE 3.2 6.6 + - - +
427B PHE* 3.2 17.3 - - - -
428B ALA* 3.4 35.3 - - - +
435B GLN* 2.9 25.3 - - - +
439B LEU* 5.0 4.9 - - - +
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Residues in contact with LYS 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B SER* 4.4 5.4 - - - +
370B ARG* 6.2 2.0 - - + -
371B ALA* 3.7 32.7 + - + +
374B ASP* 3.5 37.8 + - - +
375B SER* 5.0 1.2 - - - +
419B LYS* 3.4 22.2 + - - +
420B TRP* 3.1 12.9 + - - +
422B GLU* 1.3 76.4 - - + +
424B ILE* 1.3 62.0 + - - +
425B PRO* 3.4 9.7 - - - +
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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) + - + + + + + -
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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