Contacts of the helix formed by residues 384 - 407 (chain E) in PDB entry 2GPV
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 384 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292E LEU* 5.4 1.3 - - + -
293E SER* 5.5 3.6 - - - +
296E ASP* 3.0 14.5 + - - +
382E ILE* 3.8 2.7 - - - -
383E GLU* 1.3 76.9 - - + +
385E VAL* 1.3 64.5 + - - +
386E GLU* 3.6 16.6 + - - +
387E ALA* 3.2 31.2 + - + +
388E VAL* 3.1 25.6 + - - +
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Residues in contact with VAL 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LYS* 4.6 23.3 - - - +
382E ILE* 4.0 30.5 - - + +
383E GLU 3.8 3.0 + - - +
384E ASP* 1.3 71.8 + - - +
386E GLU* 1.3 66.8 + - + +
388E VAL* 4.1 1.8 - - - +
389E GLN* 2.9 33.0 + - + +
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Residues in contact with GLU 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E ASP* 3.2 12.4 + - - +
385E VAL* 1.3 84.1 + - + +
387E ALA* 1.3 59.5 + - - +
389E GLN* 3.4 9.8 - - - +
390E LYS* 2.9 27.9 + - - +
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Residues in contact with ALA 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E LEU* 3.5 24.7 - - + +
384E ASP* 3.2 29.9 + - + +
386E GLU* 1.3 80.1 - - - +
388E VAL* 1.3 58.8 + - - +
390E LYS* 3.4 8.9 + - - +
391E LEU* 3.0 24.8 + - - +
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Residues in contact with VAL 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E LEU* 4.2 17.9 - - + -
296E ASP* 3.7 14.1 - - + +
300E LEU* 4.2 23.3 - - + -
375E ALA* 4.0 18.3 - - - +
382E ILE* 3.7 24.0 - - + -
384E ASP 3.1 17.2 + - - +
385E VAL* 4.1 3.8 - - - +
387E ALA* 1.3 72.8 - - - +
389E GLN* 1.3 64.6 + - - +
390E LYS 3.2 0.2 - - - -
391E LEU* 3.3 8.7 + - + +
392E GLN* 3.1 28.6 + - - +
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Residues in contact with GLN 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B SER* 6.1 0.9 - - - -
359B MET* 6.2 0.3 - - - +
416B LYS* 4.5 14.6 - - - +
385E VAL* 2.9 25.1 + - + +
386E GLU* 3.4 10.5 - - - +
388E VAL* 1.3 77.3 - - - +
390E LYS* 1.3 60.2 + - - +
392E GLN* 3.2 21.3 + - - +
393E ASP* 3.0 39.4 + - - +
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Residues in contact with LYS 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E GLU 2.9 17.5 + - - +
387E ALA* 3.5 9.6 - - - +
388E VAL 3.2 0.2 - - - -
389E GLN* 1.3 76.1 - - + +
391E LEU* 1.3 61.5 + - - +
393E ASP* 3.0 17.5 + - + +
394E VAL* 2.9 52.9 + - + +
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Residues in contact with LEU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ILE* 4.1 13.2 - - + -
287E PRO 3.0 31.9 - - - +
288E GLY* 4.1 4.0 - - - -
289E PHE* 4.1 33.9 - - + +
292E LEU* 4.3 16.8 - - + -
300E LEU* 4.7 5.6 - - + -
374E LEU* 6.2 0.7 - - + -
375E ALA* 4.1 20.4 - - + -
387E ALA 3.0 14.0 + - - +
388E VAL* 3.6 10.8 - - - +
389E GLN 3.3 0.2 - - - -
390E LYS* 1.3 76.2 - - - +
392E GLN* 1.3 61.0 + - - +
394E VAL* 4.7 5.4 - - + +
395E LEU* 3.3 31.0 + - + +
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Residues in contact with GLN 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B LYS* 5.3 2.5 + - - +
419B MET* 3.4 19.8 - - + +
372E ILE* 5.5 2.6 - - - +
375E ALA* 3.2 38.7 + - + +
376E ASN* 3.1 24.6 + - - +
378E ASP* 5.8 1.4 + - - -
388E VAL* 3.1 25.2 + - - +
389E GLN* 3.3 22.6 + - - +
390E LYS 3.1 0.2 - - - -
391E LEU* 1.3 75.3 - - - +
393E ASP* 1.3 58.4 + - - +
395E LEU* 3.4 2.8 + - - +
396E HIS* 2.9 31.6 + - - +
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Residues in contact with ASP 393 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 3.0 35.5 + - - +
416B LYS* 3.0 37.9 + - - +
389E GLN* 3.0 20.3 + - - +
390E LYS* 3.0 24.5 + - + +
392E GLN* 1.3 78.2 - - - +
394E VAL* 1.3 57.1 + - - +
396E HIS* 3.4 6.5 + - - +
397E GLU* 3.0 30.1 + - - +
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Residues in contact with VAL 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ILE* 3.2 30.3 - - + +
287E PRO* 5.1 10.8 - - + +
390E LYS* 2.9 41.7 + - + +
391E LEU* 4.1 7.6 - - + +
393E ASP* 1.3 77.0 - - + +
395E LEU* 1.3 63.6 + - + +
397E GLU* 3.5 14.0 + - - +
398E ALA* 3.2 20.1 + - - +
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Residues in contact with LEU 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ILE* 4.0 22.7 - - + -
241E LEU* 4.5 6.1 - - + -
286E ILE* 4.4 16.6 - - + -
287E PRO* 5.0 3.1 - - + +
368E THR* 3.7 12.1 - - + +
371E ALA* 3.8 46.2 - - + +
372E ILE* 4.0 12.7 - - + +
375E ALA* 3.9 14.4 - - + -
391E LEU* 3.3 32.3 + - + +
392E GLN* 4.0 2.7 - - - +
394E VAL* 1.3 78.3 - - + +
396E HIS* 1.3 65.3 + - - +
398E ALA* 3.5 7.2 - - - +
399E LEU* 3.3 15.6 + - - +
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Residues in contact with HIS 396 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ARG* 3.4 42.9 - - + +
415B GLY* 3.5 24.0 - - - -
416B LYS* 3.6 11.5 + - - +
419B MET* 4.2 17.4 - - - -
372E ILE* 4.4 8.9 - - + +
392E GLN 2.9 19.9 + - - +
393E ASP* 3.5 9.1 + - - +
395E LEU* 1.3 74.0 - - - +
397E GLU* 1.3 53.8 + - - +
399E LEU* 2.7 28.3 + - + +
400E GLN* 2.7 37.2 + - + -
414E ALA* 5.9 0.8 - - + +
418E LEU* 3.7 20.1 - - + +
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Residues in contact with GLU 397 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B ARG* 3.0 44.3 + - - +
237E ILE* 6.1 0.5 - - - +
393E ASP 3.0 18.1 + - - +
394E VAL* 3.6 14.0 - - - +
395E LEU 3.4 0.2 - - - -
396E HIS* 1.3 75.5 - - - +
398E ALA* 1.3 56.6 + - - +
400E GLN* 3.2 7.6 - - + +
401E ASP* 2.8 53.5 + - - +
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Residues in contact with ALA 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ASN* 3.5 23.6 + - - +
237E ILE* 4.0 28.0 - - + -
238E VAL* 4.1 12.3 - - + +
368E THR* 4.6 4.0 - - + -
394E VAL 3.2 11.0 + - - +
395E LEU 3.5 10.3 - - - +
396E HIS 3.1 0.6 - - - -
397E GLU* 1.3 75.5 - - - +
399E LEU* 1.3 60.6 + - - +
401E ASP 3.6 0.2 + - - -
402E TYR* 3.0 29.1 + - - +
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Residues in contact with LEU 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E GLU* 4.9 12.8 - - + +
368E THR* 4.0 27.1 - - + +
369E LEU* 4.7 5.2 - - + -
372E ILE* 4.0 9.6 - - + -
395E LEU 3.3 4.9 + - - +
396E HIS* 2.7 17.3 + - + +
398E ALA* 1.3 72.6 - - - +
400E GLN* 1.3 66.6 + - - +
402E TYR* 3.2 6.2 + - + +
403E GLU* 3.0 50.5 + - + +
414E ALA* 3.9 26.0 - - + +
417E MET* 4.3 13.5 - - + -
418E LEU* 3.8 31.0 - - + -
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Residues in contact with GLN 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B GLN* 5.0 10.4 + - - +
411B PRO* 3.2 26.1 + - - +
412B ARG* 4.0 19.9 - - + +
415B GLY 5.9 1.2 - - - +
396E HIS* 2.7 28.6 + - + +
397E GLU* 3.2 15.3 - - + +
399E LEU* 1.3 75.0 - - - +
401E ASP* 1.3 64.3 + - - +
403E GLU* 3.1 2.8 + - - +
404E ALA* 2.8 30.6 + - + +
414E ALA* 3.6 21.7 - - - +
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Residues in contact with ASP 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E TYR* 6.1 0.2 - - - +
235E ASN* 3.8 21.1 + - + +
397E GLU* 2.8 38.0 + - - +
400E GLN* 1.3 77.1 - - - +
402E TYR* 1.3 65.0 + - - +
404E ALA* 3.7 8.5 - - - +
405E GLY* 3.2 18.5 + - - -
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Residues in contact with TYR 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E TYR* 3.4 45.3 - + + -
235E ASN* 4.8 3.1 - - + +
238E VAL* 4.4 14.6 - - + -
362E GLU* 2.6 29.0 + - - -
364E GLU* 3.5 34.5 + - + -
365E GLU* 3.7 20.4 - - + -
368E THR* 5.9 0.2 - - - +
398E ALA 3.0 19.5 + - - +
399E LEU* 3.6 7.2 - - + +
401E ASP* 1.3 76.8 - - - +
403E GLU* 1.3 74.5 + - - +
406E GLN* 2.9 53.1 + - + +
407E HIS* 4.2 8.3 - + - -
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Residues in contact with GLU 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E GLU* 2.5 36.0 - - - +
399E LEU* 3.0 32.3 + - + +
400E GLN 3.8 2.9 - - - +
402E TYR* 1.3 82.6 - - - +
404E ALA* 1.3 56.4 + - - +
405E GLY 3.3 0.2 - - - -
407E HIS* 2.8 44.2 + - - +
408E MET* 4.2 0.3 - - - -
410E ASP 4.9 1.2 - - - +
413E ARG* 3.1 33.2 - - + +
414E ALA* 3.7 33.0 - - + +
417E MET* 4.2 3.6 - - - +
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Residues in contact with ALA 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400E GLN* 2.8 18.5 + - + +
401E ASP* 3.7 11.2 - - - +
402E TYR 3.2 0.2 - - - -
403E GLU* 1.3 78.5 - - - +
405E GLY* 1.3 58.6 + - - +
407E HIS 4.5 0.2 - - - -
408E MET* 3.8 30.2 - - - +
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Residues in contact with GLY 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E ASP 3.2 12.4 + - - -
402E TYR 4.0 0.9 - - - -
404E ALA* 1.3 80.0 - - - +
406E GLN* 1.3 62.4 + - - +
407E HIS 3.4 1.2 + - - -
408E MET* 4.7 11.5 + - - +
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Residues in contact with GLN 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E TYR* 5.3 8.3 - - + -
362E GLU* 4.5 2.8 + - - +
402E TYR* 2.9 50.3 + - + +
405E GLY* 1.3 76.7 - - - +
407E HIS* 1.3 78.3 + - + +
408E MET 3.9 0.7 - - - -
409E GLU* 4.5 4.0 - - - +
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Residues in contact with HIS 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E GLU* 2.6 38.6 + - - -
365E GLU* 4.2 0.2 - - - -
402E TYR* 4.2 4.0 - + - -
403E GLU* 2.8 45.1 + - + +
406E GLN* 1.3 104.6 + - + +
408E MET* 1.3 63.8 + - - +
409E GLU* 3.0 28.9 + - - +
410E ASP 3.3 18.5 + - - +
411E PRO* 5.0 0.2 - - - +
413E ARG* 3.6 28.6 + - + -
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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
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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