Contacts of the helix formed by residues 328 - 352 (chain C) in PDB entry 3JCK
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 328 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C GLN* 3.6 12.0 + - - -
263C LYS* 3.8 18.1 - - + +
264C TYR* 2.8 30.9 + - - -
324C GLU* 2.8 17.4 + - + +
325C LEU 2.8 20.5 - - - +
327C GLY* 1.3 70.7 - - - +
329C GLU* 1.3 66.1 + - - +
330C LEU* 3.6 5.9 + - - +
331C THR* 2.4 33.2 + - + +
332C ARG* 3.5 9.5 + - - +
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Residues in contact with GLU 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C LYS* 5.5 3.5 - - - +
187C LYS* 2.2 36.5 + - - -
189C ARG* 4.6 10.6 + - - +
326C MET 5.4 2.7 - - - +
327C GLY 3.4 11.2 + - - +
328C ASP* 1.3 73.4 + - - +
330C LEU* 1.3 63.3 + - - +
332C ARG* 3.4 21.1 + - - +
333C SER* 2.9 29.7 + - - -
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C ILE* 4.7 19.7 - - + -
227C CYS* 4.3 21.1 - - + -
228C GLU* 3.6 19.3 - - - +
239C PHE* 6.0 0.2 - - + -
264C TYR* 4.3 28.5 - - + +
267C LEU* 4.5 4.7 - - + -
328C ASP* 3.6 3.6 + - - +
329C GLU* 1.3 74.7 - - - +
331C THR* 1.3 68.1 + - - +
333C SER* 2.1 30.6 + - - +
334C HIS* 2.9 37.8 + - + +
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Residues in contact with THR 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LYS* 4.6 3.4 - - + +
264C TYR* 3.4 11.4 - - - -
267C LEU* 3.7 21.0 - - + +
299C MET* 4.9 7.0 - - + -
324C GLU* 6.5 0.2 - - - -
325C LEU* 3.6 14.1 - - + -
328C ASP* 2.4 37.3 + - + -
330C LEU* 1.3 80.1 - - - +
332C ARG* 1.3 65.8 + - - +
334C HIS* 3.0 2.9 + - - +
335C PHE* 2.9 53.7 + - + -
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Residues in contact with ARG 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C LEU* 6.2 3.4 - - + -
325C LEU* 3.1 37.3 + - + +
326C MET* 4.1 14.5 + - - +
328C ASP 3.5 6.7 + - - +
329C GLU* 3.4 22.5 + - - +
330C LEU 3.4 0.2 - - - -
331C THR* 1.3 80.5 - - - +
333C SER* 1.3 65.8 + - - +
335C PHE* 3.2 11.2 + - + +
336C ASN* 2.8 47.9 + - - +
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Residues in contact with SER 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329C GLU 2.9 14.4 + - - -
330C LEU* 2.1 34.4 + - - +
332C ARG* 1.3 78.7 - - - +
334C HIS* 1.3 67.9 + - - -
336C ASN* 2.5 33.8 + - - +
337C ALA* 2.9 11.4 + - - +
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Residues in contact with HIS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C CYS* 2.9 33.1 + - + +
228C GLU* 4.8 2.2 - - - -
230C LYS* 4.4 10.5 - - - -
232C TYR* 3.1 29.9 + + - -
267C LEU* 4.3 14.1 - - + +
271C MET* 3.5 22.2 - - + +
330C LEU* 2.9 36.4 + - + +
331C THR 3.8 4.7 - - - +
333C SER* 1.3 96.0 + - - +
335C PHE* 1.3 61.0 + - + +
337C ALA* 3.9 10.0 - - + +
338C LEU* 2.9 29.4 + - - +
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Residues in contact with PHE 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C LEU* 4.6 7.0 - - + -
270C ILE* 4.1 32.8 - - + -
271C MET* 4.1 17.5 - - + -
298C ALA* 6.5 0.2 - - + -
299C MET* 4.2 15.0 - - + -
302C VAL* 4.2 26.7 - - + -
314C PHE* 3.7 10.1 - - + -
318C LEU* 4.6 11.4 - - + -
325C LEU* 3.6 28.7 - - + -
331C THR* 2.9 38.2 + - + -
332C ARG* 3.6 8.5 - - - +
333C SER 2.8 0.2 + - - -
334C HIS* 1.3 82.2 - - - +
336C ASN* 1.3 61.3 + - - +
338C LEU* 4.4 5.2 - - + -
339C TYR* 2.8 30.5 + - - +
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Residues in contact with ASN 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C LEU* 4.8 16.8 - - - +
332C ARG* 2.8 46.8 + - - +
333C SER* 2.5 15.4 + - - +
335C PHE* 1.3 71.7 + - - +
337C ALA* 1.3 67.8 + - - +
339C TYR* 3.4 9.5 + - - +
340C ASP* 2.9 20.6 + - - +
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C MET* 6.0 1.3 - - - -
333C SER 2.9 9.5 + - - +
334C HIS* 3.9 14.6 - - + +
336C ASN* 1.3 74.2 - - - +
338C LEU* 1.3 66.1 + - - +
340C ASP* 2.7 20.8 + - - +
341C THR* 2.9 18.4 + - + +
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Residues in contact with LEU 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 3.8 26.0 - - + +
271C MET* 3.6 34.0 - - + +
306C TYR* 3.4 46.4 - - + +
314C PHE* 4.5 11.4 - - + -
334C HIS 2.9 19.6 + - - +
335C PHE* 4.2 4.7 - - + +
337C ALA* 1.3 76.2 - - - +
339C TYR* 1.3 64.1 + - - +
341C THR* 3.1 14.4 + - - +
342C LEU* 2.8 22.5 + - - +
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Residues in contact with TYR 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LEU* 3.6 23.6 - - + +
314C PHE* 3.4 34.3 - + + -
315C ASN* 3.1 30.0 + - - -
318C LEU* 4.3 9.2 - - + -
335C PHE 2.8 21.6 + - - +
336C ASN* 3.6 9.9 - - - +
338C LEU* 1.3 76.5 - - - +
340C ASP* 1.3 70.9 + - + +
342C LEU* 3.2 7.0 + - - +
343C LEU* 3.0 42.0 + - + +
368C LEU* 4.3 11.1 - - - +
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Residues in contact with ASP 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ASN 2.9 12.2 + - - +
337C ALA* 2.7 16.7 + - - +
339C TYR* 1.3 76.3 - - + +
341C THR* 1.3 70.6 + - - +
342C LEU 2.7 1.6 + - - -
343C LEU* 2.6 29.0 + - - +
344C GLU* 2.9 14.8 + - - +
376C LYS* 2.5 35.9 + - - +
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Residues in contact with THR 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C TYR* 5.3 3.7 + - - -
337C ALA* 2.9 12.3 + - + +
338C LEU* 3.1 27.9 + - - +
340C ASP* 1.3 87.3 - - - +
342C LEU* 1.3 57.9 + - - +
344C GLU* 3.0 27.3 - - + +
345C SER* 3.7 6.4 + - - -
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Residues in contact with LEU 342 (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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305C ALA 5.1 0.2 - - - +
306C TYR* 4.0 34.1 - - + +
309C ARG* 3.6 42.8 - - + +
310C SER 5.2 0.2 - - - +
311C LEU* 3.5 26.9 - - + -
314C PHE* 4.6 16.4 - - + -
338C LEU 2.8 17.6 + - - +
339C TYR* 3.4 6.1 - - - +
340C ASP 2.7 4.2 + - - -
341C THR* 1.3 74.0 - - - +
343C LEU* 1.3 65.7 + - - +
345C SER* 2.4 32.2 + - - +
346C ASN* 3.0 13.9 + - - +
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Residues in contact with LEU 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LEU* 3.9 27.3 - - + +
339C TYR* 3.0 39.8 + - + +
340C ASP* 2.6 14.2 + - - +
342C LEU* 1.3 68.8 - - - +
344C GLU* 1.3 67.3 + - - +
346C ASN* 3.4 1.6 + - - +
347C LEU* 3.0 40.1 + - + +
366C ILE* 5.2 3.1 - - + -
368C LEU* 3.6 25.6 - - + -
372C GLN 5.7 2.0 - - - +
373C VAL* 6.0 2.5 - - + -
376C LYS* 3.4 34.8 - - + -
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Residues in contact with GLU 344 (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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340C ASP* 2.9 17.2 + - - +
341C THR* 3.0 21.7 - - + +
343C LEU* 1.3 77.3 - - - +
345C SER* 1.3 91.4 + - - -
347C LEU* 2.9 8.6 + - - +
348C CYS* 2.9 41.5 + - - +
376C LYS* 4.2 18.7 - - + +
380C MET* 4.4 11.6 - - + +
385C ILE* 5.3 7.8 - - + +
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Residues in contact with SER 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C ARG* 5.3 3.3 + - - -
341C THR 3.8 4.7 - - - -
342C LEU* 2.4 39.9 + - - +
344C GLU* 1.3 94.2 + - - +
346C ASN* 1.3 69.8 + - - +
348C CYS* 2.9 16.2 + - - +
349C LYS* 2.9 23.9 + - - +
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Residues in contact with ASN 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C ARG* 3.8 33.5 + - - +
311C LEU* 3.5 28.5 - - + +
342C LEU* 3.0 18.2 + - - +
343C LEU 3.9 5.4 - - - +
345C SER* 1.3 83.5 + - - +
347C LEU* 1.3 63.3 + - - +
349C LYS* 3.2 13.0 + - - +
350C ILE* 2.9 31.5 + - + +
366C ILE* 3.5 22.5 - - + +
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Residues in contact with LEU 347 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343C LEU* 3.0 38.6 + - + +
344C GLU 2.9 8.8 + - - +
346C ASN* 1.3 75.9 - - - +
348C CYS* 1.3 56.4 + - - +
350C ILE* 2.7 26.4 + - + -
351C ILE* 3.1 19.5 + - + +
362C ILE* 3.7 30.7 - - + -
366C ILE* 5.0 13.5 - - + -
373C VAL* 4.7 11.0 - - + +
376C LYS* 4.0 18.2 - - + -
377C LEU* 4.2 18.8 - - + -
380C MET* 4.0 16.8 - - + -
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Residues in contact with CYS 348 (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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344C GLU* 2.9 28.1 + - - +
345C SER* 2.9 13.7 + - - +
347C LEU* 1.3 71.5 - - - +
349C LYS* 1.3 59.1 + - + +
351C ILE* 3.8 16.6 - - - +
352C GLU* 2.7 20.4 - - - +
380C MET* 3.5 25.8 - - - -
385C ILE* 4.1 15.3 - - - -
386C PHE* 5.4 2.2 - - - -
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Residues in contact with LYS 349 (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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381B SER* 6.0 1.0 - - - -
385B ASN* 3.9 19.0 + - - +
309C ARG* 5.0 16.4 - - - +
345C SER* 2.9 21.6 + - - +
346C ASN* 3.7 14.8 - - - +
347C LEU 3.0 0.2 - - - -
348C CYS* 1.3 76.8 - - + +
350C ILE* 1.3 60.7 + - + +
352C GLU* 2.6 32.6 - - - +
353C PRO* 3.8 4.2 - - - +
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Residues in contact with ILE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C ASN* 3.1 18.4 - - + +
347C LEU* 2.7 16.9 + - + +
349C LYS* 1.3 76.2 - - + +
351C ILE* 1.3 59.1 + - + +
353C PRO* 3.7 3.0 - - - +
354C PHE* 3.0 28.6 - - + -
362C ILE* 4.8 19.3 - - + +
365C ILE* 3.8 44.0 - - + -
366C ILE* 3.9 33.4 - - + +
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Residues in contact with ILE 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU* 3.4 21.3 - - + +
348C CYS* 3.8 15.9 - - - +
350C ILE* 1.3 82.6 - - + +
352C GLU* 1.3 57.0 + - + +
353C PRO 3.3 0.2 - - - -
354C PHE* 2.6 45.0 + - + +
357C VAL* 5.3 2.2 - - + -
362C ILE* 4.6 15.7 - - + -
377C LEU* 4.9 7.6 - - + -
380C MET* 5.0 1.3 - - + -
386C PHE* 3.7 48.2 - - + -
397C LEU* 4.1 22.0 - - + -
399C VAL* 4.5 12.1 - - + -
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Residues in contact with GLU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 4.5 14.5 - - + +
385B ASN* 2.7 31.2 + - - +
392B LYS* 3.7 25.6 - - - +
348C CYS 2.7 19.4 - - - +
349C LYS* 2.6 20.5 - - - +
351C ILE* 1.3 77.5 - - + +
353C PRO* 1.3 72.4 - - + +
354C PHE 3.0 3.3 + - - +
399C VAL* 5.6 3.6 - - - -
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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