Contacts of the helix formed by residues 404 - 426 (chain E) in PDB entry 4UJ3
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 SER 404 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379E CYS* 3.9 14.9 - - - -
382E THR* 4.7 2.1 + - - -
386E LYS* 4.9 18.4 - - - -
388E CYS* 3.4 15.4 - - - -
390E HIS* 5.8 0.2 - - - -
403E ILE* 1.3 80.3 - - - +
405E PRO* 1.3 76.7 - - - +
406E PHE* 3.8 6.6 + - - +
407E CYS* 3.1 28.9 + - - -
408E ARG* 3.0 18.1 + - - +
296K GLU* 4.7 2.8 + - - -
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Residues in contact with PRO 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386E LYS* 5.3 7.2 - - + -
387E SER 3.6 22.0 - - - +
388E CYS* 4.7 1.3 - - - -
389E LYS* 5.1 10.3 - - + +
390E HIS* 5.0 10.7 - - + -
403E ILE 3.9 1.3 - - - +
404E SER* 1.3 87.4 - - - +
406E PHE* 1.3 61.9 + - + +
408E ARG* 3.2 10.1 + - + +
409E TYR* 3.2 18.0 + - - +
456E PHE* 3.9 23.0 - - + -
457E LYS 4.7 2.1 - - - +
458E GLU* 4.5 26.5 - - + +
296K GLU* 5.9 1.3 - - - +
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Residues in contact with PHE 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E PHE* 5.6 0.4 - + - -
382E THR* 6.1 3.4 - - + -
404E SER* 3.2 3.6 + - - +
405E PRO* 1.3 80.1 - - - +
407E CYS* 1.3 69.1 + - - +
409E TYR* 3.4 4.0 + - - +
410E ARG* 3.1 67.8 + - + +
451E ALA 3.9 4.0 - - - -
454E GLY* 3.5 29.4 - - - -
456E PHE* 3.5 36.9 - + + -
296K GLU* 3.2 58.8 - - + +
297K ALA 4.7 5.4 - - - -
298K ASP* 4.7 4.3 - - + -
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Residues in contact with CYS 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E PHE* 4.3 19.2 - - + -
379E CYS* 3.7 21.8 - - - -
381E LEU* 4.3 11.4 - - + -
382E THR* 3.9 12.3 - - - -
403E ILE* 3.4 23.8 - - + -
404E SER* 3.1 20.3 + - - +
406E PHE* 1.3 85.5 - - - +
408E ARG* 1.3 64.3 + - - +
410E ARG* 3.3 10.0 + - - +
411E ILE* 3.1 28.3 + - + +
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Residues in contact with ARG 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D HIS 3.9 11.1 + - - -
131D LEU* 4.5 14.1 + - - +
355E ILE* 4.4 15.3 - - + +
390E HIS* 3.4 48.0 + - + -
392E ILE* 5.6 0.9 - - + -
403E ILE* 3.8 9.6 - - + +
404E SER 3.0 12.0 + - - +
405E PRO* 3.5 13.2 + - + +
406E PHE 3.2 0.2 - - - -
407E CYS* 1.3 76.7 - - - +
409E TYR* 1.3 64.8 + - - +
411E ILE* 3.2 5.1 + - - +
412E THR* 2.8 70.0 + - + +
457E LYS 5.5 4.9 + - - -
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Residues in contact with TYR 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E PRO 3.2 8.1 + - - +
406E PHE 3.8 3.4 - - - +
407E CYS 3.3 0.2 - - - -
408E ARG* 1.3 86.4 - - - +
410E ARG* 1.3 60.8 + - + +
412E THR* 3.4 7.9 + - - -
413E SER* 2.6 46.5 + - - -
447E GLU* 2.1 42.2 + - - -
450E LEU* 5.2 3.7 - - - +
451E ALA* 3.6 18.4 - - + -
455E TYR 3.6 16.4 + - - -
456E PHE* 3.4 29.6 - - + -
457E LYS* 3.4 53.6 - - + +
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Residues in contact with ARG 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E PRO 3.0 25.9 + - - -
332E CYS* 3.1 32.4 + - - +
333E LEU* 5.2 0.2 - - - -
334E THR 3.9 4.9 + - - -
335E PHE* 3.8 23.5 - - + -
382E THR* 5.8 1.8 - - - +
406E PHE* 3.1 55.6 + - + +
407E CYS* 3.3 7.3 + - - +
408E ARG 3.2 0.2 - - - -
409E TYR* 1.3 79.8 - - + +
411E ILE* 1.3 62.3 + - - +
413E SER* 3.5 3.1 + - - -
414E VAL* 3.2 25.3 + - - +
451E ALA* 3.7 33.4 + - + +
452E LYS 4.0 8.1 + - - -
298K ASP* 3.2 35.0 + - - -
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Residues in contact with ILE 411 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333E LEU* 3.8 21.5 - - + -
335E PHE* 4.5 5.2 - - + -
344E VAL* 4.0 20.0 - - + -
348E VAL* 4.6 3.4 - - + -
353E LEU* 3.5 31.6 - - + -
355E ILE* 4.3 7.6 - - + -
381E LEU* 3.8 27.8 - - + -
392E ILE* 4.6 17.9 - - + -
403E ILE* 5.6 0.4 - - + -
407E CYS* 3.1 18.7 + - + +
408E ARG* 3.8 4.0 - - - +
410E ARG* 1.3 74.0 - - - +
412E THR* 1.3 65.6 + - - +
414E VAL* 3.1 6.9 + - - +
415E CYS* 2.9 20.8 + - - -
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Residues in contact with THR 412 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D HIS* 3.9 14.1 - - + +
131D LEU* 4.3 7.2 - - + -
355E ILE* 3.7 22.7 - - + -
408E ARG* 2.8 59.0 + - + +
409E TYR* 3.4 12.0 + - - -
411E ILE* 1.3 72.1 - - - +
413E SER* 1.3 62.1 + - - +
415E CYS* 3.0 9.9 + - - +
416E ASN* 2.8 38.8 + - - -
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Residues in contact with SER 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409E TYR* 2.6 46.0 + - - -
410E ARG* 3.5 7.4 - - - -
411E ILE 3.2 0.2 - - - -
412E THR* 1.3 81.4 + - - +
414E VAL* 1.3 61.2 + - - +
416E ASN* 3.8 10.1 + - - +
417E PHE* 3.6 12.0 + - - +
444E LEU* 4.4 6.2 - - - +
447E GLU* 4.3 9.7 + - - +
448E MET* 3.6 33.9 - - - +
451E ALA* 4.7 1.1 - - - -
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Residues in contact with VAL 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E ILE* 4.0 21.8 - - + +
332E CYS* 3.9 22.0 - - + -
333E LEU* 4.6 13.9 - - + -
348E VAL* 4.0 9.4 - - + -
410E ARG 3.2 17.5 - - - +
411E ILE* 3.1 9.3 + - - +
413E SER* 1.3 76.1 - - - +
415E CYS* 1.3 66.1 + - - +
417E PHE* 3.0 15.0 + - + +
418E PHE* 3.1 37.3 + - + -
448E MET* 3.9 15.3 - - + -
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Residues in contact with CYS 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D HIS* 3.3 38.1 - - + +
348E VAL* 3.9 22.0 - - - -
353E LEU* 3.4 33.9 - - - -
411E ILE* 2.9 19.2 + - - -
412E THR* 3.5 2.9 - - - +
414E VAL* 1.3 77.1 - - - +
416E ASN* 1.3 57.1 + - - +
418E PHE* 3.3 4.4 + - - +
419E THR* 2.8 32.8 + - - +
422E ARG* 4.9 0.3 + - - -
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Residues in contact with ASN 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D HIS* 2.9 21.4 + - - -
131D LEU* 3.7 19.0 - - - +
412E THR* 2.8 23.3 + - - +
413E SER* 4.0 6.7 - - - +
415E CYS* 1.3 76.2 - - - +
417E PHE* 1.3 61.5 + - - +
419E THR* 2.5 19.8 + - - -
420E TYR* 3.1 14.7 + - - +
444E LEU* 3.7 20.3 - - + +
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Residues in contact with PHE 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320E PHE* 4.2 3.8 - + - -
321E LEU* 3.9 21.1 - - + -
324E ILE* 3.6 31.0 - - + -
329E ILE* 4.2 14.6 - - + -
413E SER 3.6 9.5 + - - +
414E VAL 3.0 9.2 + - - +
416E ASN* 1.3 78.7 - - - +
418E PHE* 1.3 77.1 + + - +
420E TYR* 3.3 2.8 + - + +
421E ILE* 2.9 60.3 + - + +
441E VAL* 4.1 18.8 - - + -
444E LEU* 3.7 26.8 - - + +
448E MET* 4.2 20.0 - - + -
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Residues in contact with PHE 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E MET* 3.8 26.9 - - + -
321E LEU* 5.9 2.7 - - + -
325E TYR* 3.2 31.9 - + - -
329E ILE* 3.7 23.1 - - + -
345E LEU* 4.9 1.3 - - + -
348E VAL* 3.3 32.8 - - + +
349E GLU* 4.1 18.6 - - + -
414E VAL* 3.1 36.8 + - + -
415E CYS* 3.8 7.2 - - - +
417E PHE* 1.3 89.3 - + - +
419E THR* 1.3 58.0 + - - +
421E ILE* 3.6 3.8 - - + +
422E ARG* 2.8 48.6 + - - +
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Residues in contact with THR 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D ASP 6.0 1.6 - - - +
128D LEU* 5.3 7.4 - - + -
130D HIS* 3.7 21.3 - - + +
351E ASN* 4.9 2.2 - - - +
415E CYS* 2.8 16.6 + - + +
416E ASN* 2.5 30.7 + - - -
418E PHE* 1.3 75.5 - - - +
420E TYR* 1.3 54.4 + - - -
422E ARG* 3.4 28.5 + - - +
423E TYR* 2.9 51.3 + - + +
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Residues in contact with TYR 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 5.8 2.5 - - + -
416E ASN 3.1 16.3 + - - +
417E PHE 4.0 2.9 - - - +
419E THR* 1.3 73.9 - - - +
421E ILE* 1.3 69.5 + - + +
423E TYR* 3.2 19.2 + + + +
424E ILE* 3.1 51.5 + - + +
429E VAL* 4.3 12.3 - - + +
432E GLN* 2.6 30.5 + - - -
437E MET* 3.6 24.1 - - - +
440E GLU* 3.2 44.4 - - + +
441E VAL* 4.3 9.9 - - + -
444E LEU* 4.6 12.1 - - + -
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Residues in contact with ILE 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E TRP* 3.7 34.9 - - + -
313E THR 5.2 0.2 - - - +
314E MET* 3.3 30.7 - - + -
320E PHE* 3.8 20.6 - - + -
321E LEU* 5.1 6.7 - - + -
417E PHE* 2.9 49.8 + - + +
418E PHE* 3.6 6.7 - - + +
420E TYR* 1.3 79.9 - - + +
422E ARG* 1.3 60.5 + - - +
424E ILE* 3.3 13.2 + - + +
425E GLN* 3.2 18.7 + - - +
441E VAL* 5.1 7.6 - - + -
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Residues in contact with ARG 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E MET* 3.9 28.9 - - + +
348E VAL 5.1 1.6 + - - -
349E GLU 5.0 8.5 + - - -
351E ASN* 3.1 49.3 + - - +
415E CYS 4.9 0.4 + - - -
418E PHE* 2.8 30.4 + - - +
419E THR* 3.4 36.3 + - - +
421E ILE* 1.3 69.8 - - - +
423E TYR* 1.3 70.7 + - - +
424E ILE 3.0 2.5 + - - -
425E GLN* 3.1 13.1 + - - +
426E GLN* 3.0 35.7 + - - +
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Residues in contact with TYR 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D LEU* 3.5 32.0 - - + +
127D ASP* 3.8 1.5 + - - -
128D LEU* 3.6 14.0 - - - +
156D LEU* 3.5 24.0 - - + +
200D GNP 3.4 25.1 + - - -
419E THR* 2.9 40.1 + - + +
420E TYR* 3.2 22.2 + + + +
422E ARG* 1.3 81.1 - - + +
424E ILE* 1.3 49.2 + - - +
426E GLN* 4.2 15.0 - - - -
427E GLY* 2.8 33.1 + - - -
428E LEU* 3.2 14.7 - - + +
429E VAL* 3.5 13.7 - - + +
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Residues in contact with ILE 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305E PHE* 4.9 6.3 - - + -
308E TRP* 4.1 29.6 - - + -
309E LYS* 4.6 13.4 + - + +
312E PRO* 4.5 9.8 - - + +
420E TYR* 3.1 39.2 + - + +
421E ILE* 3.5 11.2 - - + +
422E ARG 3.0 0.6 - - - -
423E TYR* 1.3 76.3 - - - +
425E GLN* 1.3 66.4 + - - +
426E GLN 3.3 0.2 - - - -
427E GLY* 3.0 10.3 + - - -
429E VAL* 3.9 14.1 - - + -
437E MET* 3.0 39.5 - - + -
441E VAL* 5.1 0.7 - - + -
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Residues in contact with GLN 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E TRP* 5.8 1.1 - - + -
312E PRO* 4.0 27.6 - - + +
313E THR* 5.7 1.1 - - - +
314E MET* 5.2 13.5 - - + -
421E ILE 3.2 9.5 + - - +
422E ARG* 3.1 11.8 + - + +
424E ILE* 1.3 80.4 - - - +
426E GLN* 1.3 59.0 + - + +
427E GLY 3.2 1.4 + - - -
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Residues in contact with GLN 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D LEU* 5.4 5.1 - - - +
422E ARG* 3.0 33.1 + - - +
423E TYR* 4.1 9.1 - - - +
425E GLN* 1.3 75.6 - - - +
427E GLY* 1.3 64.4 + - - +
428E LEU* 2.9 34.8 + - + +
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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