Contacts of the helix formed by residues 330 - 354 (chain S) in PDB entry 5JPQ
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 PRO 330 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328S THR 3.8 1.4 - - - -
329S SER* 1.3 77.2 - - - +
331S ARG* 1.3 65.1 + - - +
332S TRP* 3.3 5.2 - - + +
333S GLN* 3.2 19.7 + - + +
334S ARG* 3.4 8.3 + - - +
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Residues in contact with ARG 331 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903 C 5.1 4.9 + - - -
329S SER 3.8 0.9 + - - -
330S PRO* 1.3 72.5 - - - +
332S TRP* 1.3 60.4 + - - +
333S GLN 3.5 0.3 + - - -
334S ARG* 3.5 19.3 + - - +
335S GLY 4.4 2.3 + - - -
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Residues in contact with TRP 332 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330S PRO* 3.3 3.8 - - + +
331S ARG* 1.3 77.0 - - - +
333S GLN* 1.3 60.3 + - - +
335S GLY* 4.7 3.6 + - - -
336S LYS* 5.0 4.0 + - - +
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Residues in contact with GLN 333 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329S SER* 4.3 14.1 - - - -
330S PRO* 3.2 16.2 + - + +
332S TRP* 1.3 77.6 - - - +
334S ARG* 1.3 65.0 + - - +
335S GLY 3.4 1.1 - - - -
336S LYS* 3.2 9.3 + - - +
337S ILE* 3.2 22.5 + - + +
374S ILE* 5.4 17.8 - - + +
375S LYS* 6.1 2.0 - - - -
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Residues in contact with ARG 334 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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903 C 5.0 9.9 - - + +
316S LYS* 5.0 2.9 - - + -
326S ILE* 4.6 23.7 - - + +
329S SER* 5.1 2.9 - - - +
330S PRO 3.4 10.1 + - - +
331S ARG* 3.6 15.3 - - - +
332S TRP 3.4 0.8 - - - -
333S GLN* 1.3 77.4 - - - +
335S GLY* 1.3 63.2 + - - +
337S ILE* 3.2 7.5 + - - +
338S ALA* 2.9 26.5 + - - +
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Residues in contact with GLY 335 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883 A 4.3 9.4 + - - -
893 A 5.0 5.4 - - - -
903 C 4.3 1.8 + - - -
316S LYS* 4.1 22.6 - - - +
331S ARG 4.4 4.0 + - - -
332S TRP 4.7 2.7 + - - -
333S GLN 3.4 0.6 - - - -
334S ARG* 1.3 79.0 - - - +
336S LYS* 1.3 57.1 + - - +
338S ALA* 3.5 3.4 + - - +
339S ARG* 3.0 28.3 + - - +
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Residues in contact with LYS 336 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873 G 6.1 0.4 - - - +
883 A 4.3 20.4 + - + +
332S TRP 5.0 3.6 + - - +
333S GLN* 3.2 12.2 + - - +
335S GLY* 1.3 71.7 - - - +
337S ILE* 1.3 64.9 + - - +
339S ARG* 3.5 2.1 + - - +
340S ALA* 3.1 24.6 + - - +
374S ILE* 5.0 13.2 - - + -
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Residues in contact with ILE 337 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325S ALA* 5.0 19.1 - - + +
326S ILE* 5.2 7.9 - - + -
329S SER* 6.0 2.0 - - - -
333S GLN* 3.2 14.2 + - + +
334S ARG* 3.8 8.7 - - - +
336S LYS* 1.3 73.2 - - - +
338S ALA* 1.3 60.3 + - - +
340S ALA* 3.5 5.1 + - - +
341S LEU* 2.9 30.1 + - - +
371S ILE* 5.8 9.2 - - + +
374S ILE* 5.7 6.2 - - + +
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Residues in contact with ALA 338 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296S GLN* 4.7 5.1 - - + +
316S LYS 3.5 24.5 - - - +
317S HIS* 4.2 15.5 - - + -
320S ILE* 5.6 7.1 - - + +
326S ILE* 5.7 5.8 - - + +
334S ARG 2.9 17.1 + - - +
335S GLY 3.5 4.0 - - - +
337S ILE* 1.3 74.4 - - - +
339S ARG* 1.3 60.4 + - - +
341S LEU* 3.1 6.5 + - - +
342S ALA* 2.8 33.5 + - - +
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Residues in contact with ARG 339 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883 A 3.0 35.4 - - + +
2623 C 4.1 11.7 - - - +
292S ALA* 5.1 1.6 - - - +
296S GLN* 5.3 3.8 - - - -
335S GLY 3.0 9.8 + - - +
336S LYS 3.7 3.4 - - - +
338S ALA* 1.3 78.5 - - - +
340S ALA* 1.3 58.2 + - - +
342S ALA* 4.0 5.0 - - - +
343S ALA* 3.1 27.7 + - - +
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Residues in contact with ALA 340 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336S LYS 3.1 17.8 + - - +
337S ILE* 3.8 6.1 - - - +
339S ARG* 1.3 74.0 - - - +
341S LEU* 1.3 66.9 + - - +
343S ALA* 3.4 7.6 - - - +
344S LYS* 3.1 22.2 + - - +
367S LEU* 5.8 5.5 - - + +
370S ARG* 4.6 21.1 - - + -
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Residues in contact with LEU 341 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320S ILE* 5.8 7.9 - - + -
323S TYR* 6.0 6.1 - - + -
337S ILE 2.9 18.8 + - - +
338S ALA* 3.6 5.8 - - - +
340S ALA* 1.3 73.3 - - - +
342S ALA* 1.3 55.6 + - - +
344S LYS* 2.9 8.3 + - - +
345S LEU* 2.7 36.7 + - - +
367S LEU* 6.0 4.7 - - - -
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Residues in contact with ALA 342 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292S ALA* 3.4 35.7 - - + +
295S ILE* 4.4 4.4 - - + +
296S GLN* 3.4 24.7 - - + +
320S ILE* 6.2 0.4 - - - +
338S ALA 2.8 19.4 + - - +
339S ARG* 4.0 3.6 - - - +
341S LEU* 1.3 71.6 - - - +
343S ALA* 1.3 64.2 + - - +
345S LEU* 3.2 9.3 + - - +
346S ALA* 3.0 20.1 + - - +
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Residues in contact with ALA 343 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843 G 6.3 4.9 - - + -
292S ALA* 3.6 13.4 - - + +
339S ARG 3.1 18.0 + - - +
340S ALA* 3.4 9.4 - - - +
342S ALA* 1.3 81.0 - - - +
344S LYS* 1.3 61.7 + - - +
346S ALA* 3.4 10.0 + - - +
347S ILE* 3.4 11.8 + - - +
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Residues in contact with LYS 344 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340S ALA 3.1 11.7 + - - +
341S LEU* 2.9 9.6 + - - +
343S ALA* 1.3 73.7 - - - +
345S LEU* 1.3 55.7 + - - +
347S ILE* 3.2 10.2 + - - +
348S ALA* 2.8 35.3 + - - +
363S LEU* 5.0 22.9 - - + +
366S GLN* 6.5 0.2 - - + -
367S LEU* 5.1 9.4 - - + -
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Residues in contact with LEU 345 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265S VAL* 5.7 1.8 - - + +
295S ILE* 5.1 8.1 - - + -
341S LEU 2.7 19.9 + - - +
342S ALA* 3.5 11.2 - - - +
344S LYS* 1.3 70.4 - - - +
346S ALA* 1.3 55.4 + - - +
348S ALA* 3.4 8.6 - - - +
349S ALA* 2.7 37.4 + - - +
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Residues in contact with ALA 346 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287S LEU 5.6 2.5 - - - -
288S ALA 4.7 3.7 - - - +
290S MET 4.2 18.8 - - - +
291S PRO* 4.8 0.4 - - + -
292S ALA* 4.3 15.7 - - + +
295S ILE* 5.5 4.7 - - + +
342S ALA 3.0 11.9 + - - +
343S ALA 3.6 9.6 - - - +
344S LYS 3.2 0.2 - - - -
345S LEU* 1.3 74.7 - - - +
347S ILE* 1.3 61.9 + - - +
349S ALA* 3.3 7.1 + - - +
350S ARG* 3.0 24.3 + - - +
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Residues in contact with ILE 347 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343S ALA 3.4 7.8 + - - +
344S LYS* 3.2 12.0 + - - +
346S ALA* 1.3 75.5 - - - +
348S ALA* 1.3 64.3 + - - +
350S ARG* 3.2 6.8 + - - +
351S VAL* 3.1 24.4 + - - +
64U GLU* 5.6 0.5 - - - +
65U ILE* 5.6 12.7 + - + +
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Residues in contact with ALA 348 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264S ASN* 3.7 20.8 - - + +
265S VAL* 3.9 26.2 - - - +
268S LEU* 5.2 5.2 - - + -
344S LYS 2.8 17.8 + - - +
345S LEU* 3.4 12.6 - - - +
347S ILE* 1.3 72.9 - - - +
349S ALA* 1.3 64.2 + - - +
351S VAL* 3.4 1.9 + - - -
352S ASP* 3.0 25.4 + - - +
363S LEU* 5.9 7.0 - - + -
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Residues in contact with ALA 349 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265S VAL* 5.2 6.9 - - + +
284S LEU* 5.0 1.8 - - - +
287S LEU* 4.2 13.5 - - + +
288S ALA* 3.8 25.1 - - - +
345S LEU 2.7 20.0 + - - +
346S ALA* 3.6 7.4 - - - +
347S ILE 3.3 0.2 - - - -
348S ALA* 1.3 72.2 - - - +
350S ARG* 1.3 53.2 + - - +
352S ASP* 3.3 7.7 + - - +
353S ALA* 2.7 36.7 + - - +
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Residues in contact with ARG 350 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288S ALA* 4.0 18.8 - - + +
346S ALA 3.0 15.8 + - - +
347S ILE* 3.2 7.1 + - - +
349S ALA* 1.3 75.8 - - - +
351S VAL* 1.3 60.1 + - - +
354S PHE* 3.0 34.2 + - + +
64U GLU* 3.3 27.5 - - - +
65U ILE* 4.7 5.2 - - - +
67U ALA* 6.0 0.2 - - + -
68U HIS* 5.8 5.8 - - + -
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Residues in contact with VAL 351 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264S ASN* 5.2 6.7 - - + -
347S ILE 3.1 15.5 + - - +
348S ALA* 4.2 4.3 - - - +
350S ARG* 1.3 75.5 - - - +
352S ASP* 1.3 60.4 + - - +
355S SER 3.5 1.7 + - - -
356S GLY* 2.9 44.9 + - - +
357S ARG 5.8 2.0 - - - +
359S ILE* 5.9 8.1 - - + +
62U PRO* 5.8 6.5 - - + -
64U GLU* 3.7 17.1 - - + +
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Residues in contact with ASP 352 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261S VAL 4.6 8.8 - - - +
262S ALA* 4.3 29.6 - - + -
263S PRO 5.0 0.4 - - - -
264S ASN* 4.7 10.8 - - + +
265S VAL* 5.1 2.0 - - + +
284S LEU* 6.2 3.4 - - + -
348S ALA 3.0 17.7 + - - +
349S ALA* 3.4 7.9 - - - +
351S VAL* 1.3 80.1 - - - +
353S ALA* 1.3 61.1 + - - +
355S SER* 3.8 7.4 + - - -
356S GLY 4.7 3.8 - - - -
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Residues in contact with ALA 353 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284S LEU* 4.3 16.6 - - + +
285S ASP* 4.5 9.6 - - + -
288S ALA* 3.5 23.3 - - + -
349S ALA 2.7 20.5 + - - +
350S ARG* 4.1 1.6 - - - +
352S ASP* 1.3 72.8 - - - +
354S PHE* 1.3 59.2 + - + +
355S SER* 3.1 10.0 + - - -
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Residues in contact with PHE 354 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350S ARG 3.0 17.2 + - - +
351S VAL* 4.1 1.1 - - - -
353S ALA* 1.3 75.5 - - + +
355S SER* 1.3 63.3 + - - +
356S GLY 3.4 8.0 + - - -
64U GLU* 4.6 5.7 - - + +
67U ALA* 4.2 24.7 - - + -
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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