Contacts of the helix formed by residues 404 - 426 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E GLU* 5.0 5.0 + - - -
379K CYS* 4.0 18.1 - - - +
382K THR* 4.1 4.4 + - - -
384K GLN* 5.7 4.5 - - - -
386K LYS* 5.4 7.2 - - - -
388K CYS* 3.5 10.0 - - - -
403K ILE* 1.3 78.0 - - - +
405K PRO* 1.3 71.1 - - - +
406K PHE* 3.8 7.2 + - - +
407K CYS* 2.9 35.2 + - - -
408K ARG* 2.9 26.8 + - - +
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Residues in contact with PRO 405 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E GLU* 5.5 0.7 - - - +
386K LYS* 4.9 16.8 - - + -
387K SER 4.0 20.9 - - - +
388K CYS* 5.0 0.7 - - - -
389K LYS 5.7 0.9 - - - +
390K HIS* 5.3 8.9 - - + -
403K ILE 3.9 0.6 - - - +
404K SER* 1.3 88.4 - - - +
406K PHE* 1.3 62.5 + - + +
408K ARG* 3.3 9.2 + - + +
409K TYR* 3.2 23.0 + - - +
456K PHE* 4.0 15.3 - - + -
457K LYS 4.8 1.7 - - - +
458K GLU* 3.2 32.7 - - + +
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Residues in contact with PHE 406 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296E GLU* 3.6 51.6 - - + +
297E ALA 4.7 5.8 - - - -
298E ASP* 4.7 5.8 - - + -
382K THR* 5.4 8.1 - - + -
404K SER* 3.2 4.2 - - - +
405K PRO* 1.3 82.1 - - - +
407K CYS* 1.3 71.1 + - - +
409K TYR* 3.4 3.1 + - - +
410K ARG* 3.2 67.6 + - + +
451K ALA 3.9 3.6 - - - -
454K GLY* 3.4 29.8 - - - -
456K PHE* 3.5 36.3 - + + -
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Residues in contact with CYS 407 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335K PHE* 3.3 38.1 - - + -
379K CYS* 3.7 20.4 - - - -
381K LEU* 4.1 6.3 - - + -
382K THR* 3.8 10.1 - - - -
403K ILE* 3.3 19.3 - - + -
404K SER* 2.9 27.1 + - - +
406K PHE* 1.3 81.5 - - - +
408K ARG* 1.3 63.9 + - - +
410K ARG* 3.3 3.4 + - - +
411K ILE* 2.9 28.4 + - - +
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Residues in contact with ARG 408 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J HIS 4.2 10.3 + - - -
131J LEU* 4.9 12.9 + - - +
132J ARG 5.5 2.6 + - - -
355K ILE* 4.4 13.2 - - + +
390K HIS* 3.3 54.5 + - + -
403K ILE* 3.8 9.8 - - + +
404K SER 2.9 12.0 + - - +
405K PRO* 3.6 11.6 + - + +
406K PHE 3.2 0.2 - - - -
407K CYS* 1.3 77.0 - - - +
409K TYR* 1.3 61.1 + - - +
411K ILE* 3.2 4.3 + - - +
412K THR* 2.8 63.4 + - + +
457K LYS 5.7 4.4 + - - -
458K GLU* 6.2 2.4 - - - +
459K GLU 6.0 5.3 - - - +
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Residues in contact with TYR 409 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405K PRO 3.2 8.7 + - - +
406K PHE 3.8 3.6 - - - +
408K ARG* 1.3 84.3 - - - +
410K ARG* 1.3 58.4 + - - +
412K THR* 3.3 7.0 + - - -
413K SER* 2.7 48.0 + - - -
447K GLU* 2.2 42.7 + - - -
450K LEU* 5.2 4.6 - - + +
451K ALA* 3.8 20.6 - - + -
455K TYR 4.1 8.2 + - - -
456K PHE* 3.5 26.2 - - + -
457K LYS* 3.0 62.5 - - + +
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Residues in contact with ARG 410 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298E ASP* 3.2 26.2 + - - +
331K PRO 2.7 30.3 + - - -
332K CYS* 3.0 31.1 + - - +
333K LEU* 5.2 0.7 - - - -
334K THR 3.7 15.6 + - - -
335K PHE* 4.2 14.8 - - + -
382K THR* 5.7 2.0 - - - +
406K PHE* 3.2 54.9 + - + +
407K CYS 3.7 6.1 - - - +
409K TYR* 1.3 80.4 - - + +
411K ILE* 1.3 62.1 + - - +
413K SER* 3.7 2.6 - - - -
414K VAL* 3.2 27.9 + - - +
451K ALA* 3.6 33.8 + - + +
452K LYS 4.0 8.6 + - - -
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Residues in contact with ILE 411 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333K LEU* 4.5 14.4 - - + -
335K PHE* 4.4 11.2 - - + -
344K VAL* 4.5 8.3 - - + -
348K VAL* 4.7 6.7 - - + -
353K LEU* 3.3 31.6 - - + -
355K ILE* 4.2 8.3 - - + -
381K LEU* 3.7 27.1 - - + -
392K ILE* 4.4 25.4 - - + -
403K ILE* 5.1 1.6 - - + -
407K CYS* 2.9 22.8 + - + +
408K ARG* 3.8 4.5 - - - +
410K ARG* 1.3 75.2 - - - +
412K THR* 1.3 67.1 + - - +
414K VAL* 3.1 5.9 + - - +
415K CYS* 3.1 22.3 + - - -
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Residues in contact with THR 412 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J HIS* 4.0 20.0 - - + +
131J LEU* 4.2 15.3 - - + -
355K ILE* 4.0 15.7 - - + -
408K ARG* 2.8 56.5 + - + +
409K TYR* 3.3 12.0 + - - -
411K ILE* 1.3 73.0 - - - +
413K SER* 1.3 61.8 + - - +
415K CYS* 3.2 3.8 + - - +
416K ASN* 2.9 38.8 + - - +
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Residues in contact with SER 413 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409K TYR* 2.7 42.8 + - - -
410K ARG* 3.7 6.5 - - - -
411K ILE 3.2 0.2 - - - -
412K THR* 1.3 81.9 + - - +
414K VAL* 1.3 61.1 + - - +
416K ASN* 3.6 12.8 + - - +
417K PHE* 3.4 14.2 + - - +
444K LEU* 4.7 4.5 - - - +
447K GLU* 4.3 9.3 + - - +
448K MET* 3.7 33.8 - - - +
451K ALA* 4.8 1.1 - - - -
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Residues in contact with VAL 414 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329K ILE* 3.7 20.6 - - + +
332K CYS* 3.8 24.2 - - + -
333K LEU* 4.1 18.2 - - + -
348K VAL* 4.4 8.1 - - + -
410K ARG 3.2 17.0 - - - +
411K ILE 3.1 5.7 + - - +
413K SER* 1.3 73.9 - - - +
415K CYS* 1.3 66.6 + - - +
417K PHE* 3.0 12.6 + - - +
418K PHE* 3.2 41.2 + - + -
448K MET* 3.7 20.2 - - + -
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Residues in contact with CYS 415 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J HIS* 3.5 35.4 - - + +
348K VAL* 3.6 29.8 - - - -
353K LEU* 3.7 28.7 - - - -
411K ILE* 3.1 16.9 + - - +
412K THR 3.6 3.1 - - - +
414K VAL* 1.3 77.1 - - - +
416K ASN* 1.3 50.3 + - - +
418K PHE* 3.3 3.9 + - - +
419K THR* 2.7 41.6 + - - -
422K ARG* 4.9 0.9 + - - -
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Residues in contact with ASN 416 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J HIS* 3.1 20.3 + - - -
131J LEU* 3.8 15.9 - - - +
412K THR* 2.9 28.5 + - - +
413K SER* 3.7 9.0 + - - +
414K VAL 3.2 0.2 - - - -
415K CYS* 1.3 73.2 - - - +
417K PHE* 1.3 64.9 + - - +
419K THR* 3.4 7.8 + - - +
420K TYR* 3.0 23.7 + - - +
444K LEU* 3.5 23.6 - - + +
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Residues in contact with PHE 417 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320K PHE* 4.3 0.2 - + - -
321K LEU* 3.8 19.1 - - + -
324K ILE* 3.8 38.6 - - + -
325K TYR* 5.9 0.4 - + - -
329K ILE* 4.3 16.6 - - + -
413K SER 3.4 4.7 + - - +
414K VAL 3.0 9.4 + - - +
416K ASN* 1.3 79.8 - - - +
418K PHE* 1.3 78.1 + + - +
420K TYR* 3.2 4.7 + + - +
421K ILE* 2.9 58.5 + - + +
441K VAL* 4.2 13.5 - - + -
444K LEU* 3.8 24.1 - - + +
445K ARG* 4.9 1.8 - - + -
448K MET* 4.1 25.6 - - + -
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Residues in contact with PHE 418 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314K MET* 4.2 24.7 - - + -
321K LEU* 6.1 3.4 - - + -
325K TYR* 3.3 36.8 - + - -
329K ILE* 4.0 15.5 - - + -
333K LEU* 6.2 0.2 - - + -
345K LEU* 5.2 1.3 - - + -
348K VAL* 3.6 23.6 - - + +
349K GLU* 3.9 24.7 - - + -
414K VAL* 3.2 41.6 + - + -
415K CYS* 3.6 7.9 - - - +
417K PHE* 1.3 90.4 - + - +
419K THR* 1.3 57.2 + - - +
421K ILE* 3.2 5.0 + - + +
422K ARG* 2.8 50.6 + - - +
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Residues in contact with THR 419 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J LEU* 4.8 8.7 - - + +
130J HIS* 3.4 21.5 - - + +
415K CYS 2.7 26.1 + - - -
416K ASN* 3.4 11.0 - - - +
417K PHE 3.2 0.2 - - - -
418K PHE* 1.3 74.3 - - - +
420K TYR* 1.3 57.2 + - - +
422K ARG* 4.0 18.3 + - - +
423K TYR* 3.1 66.1 + - + +
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Residues in contact with TYR 420 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J LEU* 6.1 2.0 - - + -
416K ASN 3.0 15.3 + - - +
417K PHE* 3.8 4.0 - + + +
419K THR* 1.3 75.6 - - + +
421K ILE* 1.3 68.8 + - + +
423K TYR* 3.2 16.4 + + + +
424K ILE* 3.0 52.8 + - + +
429K VAL* 4.4 8.5 - - + +
432K GLN* 2.9 25.6 + - - -
437K MET* 3.4 33.1 - - - +
440K GLU* 3.1 47.2 - - + +
441K VAL* 4.0 11.2 - - + -
444K LEU* 4.4 13.2 - - + -
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Residues in contact with ILE 421 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308K TRP* 3.3 40.0 - - + -
314K MET* 3.7 24.5 - - + -
320K PHE* 3.8 21.1 - - + -
321K LEU* 4.8 7.0 - - + -
417K PHE* 2.9 47.9 + - + +
418K PHE* 3.6 7.0 - - + +
420K TYR* 1.3 81.0 - - + +
422K ARG* 1.3 58.4 + - - +
424K ILE* 2.9 26.8 + - + +
425K GLN* 3.0 11.6 + - - +
441K VAL* 5.0 4.0 - - + -
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Residues in contact with ARG 422 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J HIS* 5.9 0.2 - - - -
314K MET* 3.6 28.2 - - + +
348K VAL 4.9 2.6 + - - -
349K GLU 4.5 11.9 + - - -
351K ASN* 3.4 45.6 + - - +
415K CYS 4.9 0.6 + - - -
418K PHE* 2.8 31.1 + - - +
419K THR* 4.0 26.6 + - - +
421K ILE* 1.3 68.4 - - - +
423K TYR* 1.3 75.7 + - - +
424K ILE 3.0 1.7 + - - -
425K GLN* 3.1 10.6 + - - +
426K GLN* 2.9 46.7 + - - +
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Residues in contact with TYR 423 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J LEU* 3.9 37.9 - - + -
127J ASP* 3.3 22.3 + - - -
128J LEU* 3.4 16.7 - - + +
156J LEU* 4.0 21.3 - - + -
200J GNP 3.5 5.9 + - - -
419K THR* 3.1 43.5 + - + +
420K TYR* 3.2 18.4 + + + +
422K ARG* 1.3 85.2 - - + +
424K ILE* 1.3 57.6 + - - +
426K GLN* 4.3 15.7 - - - -
427K GLY* 2.7 25.8 + - - -
428K LEU* 3.2 14.7 - - + +
429K VAL* 3.5 9.5 - - + +
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Residues in contact with ILE 424 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305K PHE* 4.7 7.9 - - + -
308K TRP* 3.6 30.3 - - + -
309K LYS* 5.0 7.2 - - + +
312K PRO* 4.6 11.3 - - + +
420K TYR* 3.1 45.8 - - + +
421K ILE* 2.9 14.8 + - + +
423K TYR* 1.3 78.4 - - - +
425K GLN* 1.3 61.5 + - - +
427K GLY* 3.0 14.9 + - - -
429K VAL* 4.0 12.5 - - + +
437K MET* 3.3 31.6 - - + -
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Residues in contact with GLN 425 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308K TRP* 5.0 1.8 - - + -
312K PRO* 3.9 38.0 + - + +
313K THR* 5.3 0.9 - - - +
314K MET* 4.2 26.6 - - + +
421K ILE 3.0 11.6 + - - +
422K ARG* 3.1 12.3 + - - +
424K ILE* 1.3 76.5 - - - +
426K GLN* 1.3 68.1 + - - +
427K GLY 3.1 1.8 + - - -
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Residues in contact with GLN 426 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J LEU* 5.7 3.8 - - - +
422K ARG* 2.9 43.9 + - - +
423K TYR* 4.5 8.9 - - - -
425K GLN* 1.3 83.7 - - - +
427K GLY* 1.3 64.1 + - - +
428K LEU* 3.1 33.6 + - + +
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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