Contacts of the helix formed by residues 326 - 347 (chain A) in PDB entry 1U67
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 GLU 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A TYR* 4.7 11.8 + - - -
245A ARG* 2.6 34.1 + - - +
247A PHE* 6.3 0.4 - - - -
325A ASP* 1.3 79.3 - - + +
327A GLN* 1.3 51.6 + - - +
329A PHE* 2.9 4.4 + - - +
330A GLN* 2.7 54.4 + - + +
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Residues in contact with GLN 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A TRP* 3.1 69.1 + - + +
324A GLY* 4.2 9.4 + - - +
325A ASP 3.3 0.6 - - - -
326A GLU* 1.3 73.4 - - - +
328A LEU* 1.3 54.7 + - - +
329A PHE 2.6 16.9 + - - -
330A GLN* 4.4 5.4 - - - +
331A THR* 3.0 31.8 + - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ASP* 4.4 19.1 - - - +
250A GLY* 3.4 24.1 - - - +
313A CYS* 3.7 17.3 - - + +
316A LEU* 3.4 12.1 - - + -
317A LYS* 3.4 44.6 - - + +
320A HIS 4.6 0.9 - - - +
321A PRO 5.1 1.6 - - - +
323A TRP* 3.4 45.3 - - + +
324A GLY 3.3 21.1 + - - +
325A ASP 3.1 6.3 + - - +
327A GLN* 1.3 76.5 - - - +
329A PHE* 1.3 56.3 + - - +
332A ALA* 3.7 6.6 - - - +
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Residues in contact with PHE 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A TYR* 3.6 22.2 - + - -
241A GLN* 3.2 28.9 - - - -
245A ARG* 3.4 40.2 - - + +
250A GLY* 3.6 9.9 - - - +
252A LEU* 3.4 27.1 - - + -
309A HIS* 3.5 22.9 - + - -
325A ASP 3.1 9.6 + - - +
326A GLU 3.2 8.5 - - - +
327A GLN 2.6 6.7 + - - -
328A LEU* 1.3 76.2 - - - +
330A GLN* 1.3 84.8 + - - +
331A THR 3.3 0.9 - - - -
332A ALA* 3.0 3.5 + - - +
333A ARG* 2.8 35.9 + - - +
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLN* 4.7 3.6 + - - +
245A ARG* 4.8 0.2 - - - +
326A GLU* 2.7 38.7 + - + +
327A GLN* 4.2 4.3 - - - +
329A PHE* 1.3 111.2 - - - +
331A THR* 1.3 64.3 + - - +
333A ARG* 3.0 20.6 + - - +
334A LEU* 3.0 35.5 + - + +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 3.6 24.0 - - + -
323A TRP* 3.7 15.1 - - + -
327A GLN* 3.0 25.7 + - - +
330A GLN* 1.3 78.2 - - - +
332A ALA* 1.3 65.3 + - - +
334A LEU* 3.5 11.4 + - - +
335A ILE* 3.2 22.1 + - + +
549A THR 4.4 2.4 + - - +
550A PHE* 3.5 38.6 - - - +
551A GLY 3.9 2.2 + - - +
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Residues in contact with ALA 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A HIS* 3.6 23.8 - - + +
312A VAL* 3.6 28.0 - - + +
313A CYS* 3.8 4.3 - - - -
316A LEU* 3.7 5.5 - - + +
327A GLN 4.2 0.4 + - - -
328A LEU 3.7 15.9 - - - +
329A PHE 3.0 9.9 + - - +
331A THR* 1.3 80.7 - - - +
333A ARG* 1.3 67.4 + - - +
335A ILE* 3.2 9.7 + - - +
336A LEU* 3.4 14.0 + - - +
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP* 3.0 32.4 + - - +
231A GLY* 4.4 6.1 - - - +
234A TYR* 3.0 58.2 - - + +
235A GLY 4.4 8.1 + - - -
241A GLN* 3.4 26.1 - - - +
309A HIS* 4.2 0.2 - - - -
329A PHE* 2.8 22.5 + - + +
330A GLN* 3.0 23.3 + - - +
332A ALA* 1.3 70.9 - - - +
334A LEU* 1.3 55.5 + - + +
336A LEU* 2.4 33.8 + - - +
337A ILE* 2.9 23.7 - - + +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLN* 3.0 26.2 + - + +
331A THR* 3.7 5.8 - - - +
333A ARG* 1.3 79.6 - - + +
335A ILE* 1.3 56.5 + - - +
337A ILE* 2.8 15.7 + - + +
338A GLY* 2.8 27.0 + - - -
539A ILE* 3.8 27.5 - - + +
544A TYR* 5.7 4.3 - - + -
549A THR* 3.8 34.1 - - + +
550A PHE* 3.8 13.7 - - + -
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A VAL* 4.2 20.0 - - + -
316A LEU* 4.3 16.6 - - + -
331A THR* 3.2 16.6 + - + +
332A ALA 3.4 7.9 - - - +
333A ARG 2.9 2.6 + - - -
334A LEU* 1.3 72.9 - - - +
336A LEU* 1.3 65.8 + - + +
338A GLY 3.7 0.2 - - - -
339A GLU* 3.0 32.1 + - - +
550A PHE* 3.7 18.8 - - + -
555A GLY* 3.6 26.0 - - - -
558A LEU* 3.9 34.1 - - + -
559A VAL* 3.8 10.5 - - + +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 3.1 20.0 - - + -
233A ILE* 4.7 1.3 - - + -
234A TYR* 3.3 22.9 - - + +
305A TRP* 3.3 47.0 - - + +
308A GLU* 3.9 3.1 - - + -
309A HIS* 4.2 5.6 - - + +
312A VAL* 3.8 25.8 - - + -
332A ALA 3.7 9.9 - - - +
333A ARG 2.4 27.8 + - - +
335A ILE* 1.3 69.7 - - + +
337A ILE* 1.3 54.7 + - - -
338A GLY 3.1 1.8 - - - -
339A GLU* 3.9 15.3 - - - +
340A THR* 2.7 38.1 + - - -
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Residues in contact with ILE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A VAL* 3.4 27.1 - - + +
229A ASP* 4.5 7.4 - - - +
230A LEU* 4.0 18.8 - - + -
333A ARG* 2.9 45.5 - - + +
334A LEU* 2.8 18.0 + - + +
336A LEU* 1.3 77.4 - - - +
338A GLY* 1.3 65.7 + - - +
340A THR* 3.9 0.4 - - - -
341A ILE* 3.0 25.3 + - + +
537A ASN* 3.4 18.6 - - - +
539A ILE* 3.4 20.0 - - + -
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Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A LEU 2.8 11.0 + - - -
337A ILE* 1.3 73.4 - - - +
339A GLU* 1.3 67.9 + - - +
340A THR 2.6 3.0 + - - -
341A ILE* 2.9 4.6 + - - +
342A LYS* 2.8 21.4 + - - +
361A PHE* 4.7 1.0 - - - -
539A ILE* 3.9 11.8 - - - +
559A VAL* 3.2 34.3 - - - -
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305A TRP* 4.2 11.9 - - + -
308A GLU* 3.1 40.1 - - - +
311A ARG* 5.0 0.2 + - - -
335A ILE* 3.0 23.2 + - + +
336A LEU* 3.9 12.3 - - - +
338A GLY* 1.3 72.4 - - - +
340A THR* 1.3 56.4 + - - +
342A LYS* 3.3 2.0 - - - +
343A ILE* 2.8 37.1 + - + +
558A LEU* 3.5 28.2 - - - +
559A VAL* 3.9 3.8 - - - +
562A ALA* 3.3 27.9 - - + +
566A LYS* 6.1 1.0 - - - +
567A LEU* 4.5 5.5 - - + +
570A LEU* 6.1 1.2 - - - +
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Residues in contact with THR 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE* 5.0 2.2 - - + -
205A PHE* 3.8 20.9 - - + -
208A GLN* 4.7 1.3 - - - +
228A VAL* 3.8 22.4 - - + -
230A LEU* 3.8 15.1 - - + +
232A HIS* 5.9 2.0 - - + +
305A TRP* 2.9 31.7 - - + -
336A LEU 2.7 27.8 + - - -
337A ILE 3.9 3.1 - - - -
338A GLY 2.6 4.4 + - - -
339A GLU* 1.3 68.1 - - - +
341A ILE* 1.3 63.7 + - - +
342A LYS 2.9 4.9 + - - -
343A ILE* 3.1 4.2 + - - +
344A VAL* 2.9 29.0 + - + +
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A VAL* 3.8 22.7 - - + -
337A ILE* 3.0 36.9 + - + +
338A GLY 2.9 5.8 + - - +
340A THR* 1.3 74.7 - - - +
342A LYS* 1.3 62.0 + - - +
344A VAL* 4.0 0.9 - - - +
345A ILE* 3.4 24.4 + - + +
361A PHE* 3.3 35.7 - - + -
534A LEU* 3.6 35.2 - - + +
537A ASN* 3.7 21.1 - - + +
539A ILE* 3.9 9.2 - - + -
540A CYS* 4.4 2.2 - - - -
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Residues in contact with LYS 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A GLY 2.8 15.7 + - - +
339A GLU* 3.3 8.1 - - - +
340A THR 2.9 0.4 + - - -
341A ILE* 1.3 79.3 - - - +
343A ILE* 1.3 68.4 + - - +
345A ILE* 3.1 8.1 + - - +
346A GLU* 3.2 53.4 + - + +
361A PHE* 3.7 25.5 + - + -
559A VAL 3.0 21.4 + - - +
560A LYS* 3.1 30.4 + - - +
561A THR 4.9 0.9 - - - -
562A ALA* 3.8 22.7 - - + +
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Residues in contact with ILE 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE* 4.4 16.6 - - + -
305A TRP* 5.2 7.2 - - + -
339A GLU* 2.8 25.8 + - + +
340A THR* 3.9 3.8 - - - +
342A LYS* 1.3 73.6 - - - +
344A VAL* 1.3 63.7 + - - +
346A GLU* 5.6 0.4 - - - -
347A GLU* 3.0 29.6 + - + +
348A TYR 2.8 20.1 + - - -
562A ALA* 3.1 27.4 - - + +
563A THR* 3.0 35.4 - - - +
564A LEU* 3.7 15.7 - - + +
567A LEU* 5.8 3.6 - - + -
580A PHE* 4.2 10.8 - - + -
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A PHE* 4.2 13.4 - - + -
205A PHE* 3.6 42.0 - - + -
340A THR* 2.9 25.0 + - + +
341A ILE* 4.0 6.3 - - - +
343A ILE* 1.3 75.6 - - - +
345A ILE* 1.3 53.2 + - - +
348A TYR* 3.0 27.6 - - + +
349A ALA* 2.5 38.2 + - + +
534A LEU* 3.6 26.5 - - + -
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Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A MET* 4.7 7.0 - - + -
117A LEU* 5.5 0.9 - - + -
341A ILE* 3.4 12.3 + - + +
342A LYS 3.1 3.5 + - - +
344A VAL* 1.3 77.1 - - - +
346A GLU* 1.3 60.9 + - - +
347A GLU 3.0 10.1 + - - -
349A ALA* 3.3 19.6 - - + +
350A GLN 3.3 5.9 + - - -
359A LEU* 3.6 19.1 - - + +
360A LYS 4.2 23.1 - - - +
361A PHE* 3.8 22.4 - - + -
531A LEU* 4.6 11.0 - - + -
534A LEU* 3.5 28.5 - - + -
535A LEU* 3.6 31.2 - - + -
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Residues in contact with GLU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ARG* 4.6 5.9 + - - -
342A LYS* 3.2 44.0 + - + +
343A ILE* 5.6 0.4 - - - -
345A ILE* 1.3 72.4 - - - +
347A GLU* 1.3 65.9 + - + +
350A GLN* 3.6 17.1 - - - +
359A LEU* 3.8 13.4 - - - +
360A LYS* 3.7 18.2 - - - +
361A PHE* 2.9 41.9 + - + +
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 3.0 20.3 + - + +
345A ILE 3.0 0.6 + - - -
346A GLU* 1.3 86.3 - - + +
348A TYR* 1.3 70.8 + - - +
349A ALA 3.5 0.2 - - - -
350A GLN* 3.5 4.8 - - - +
351A GLN* 3.2 23.2 + - - +
562A ALA 4.3 1.4 - - - +
563A THR* 3.3 21.1 - - - +
564A LEU* 2.8 41.8 + - - +
565A LYS 4.9 0.2 + - - -
579A SER* 6.0 1.2 - - - -
580A PHE* 3.8 12.3 - - + -
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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
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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