Contacts of the strand formed by residues 423 - 445 (chain B) in PDB entry 1US1
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 LYS 423 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 3.9 1.9 + - - +
87B ALA* 5.7 3.0 - - - +
414B HIS* 3.5 3.5 - - - +
415B PHE* 2.9 61.1 + - + +
417B LEU 5.6 0.4 - - - +
418B GLU 5.1 0.6 + - - -
419B SER* 3.3 33.5 - - - +
421B ALA* 3.6 9.4 + - + +
422B PRO* 1.3 78.2 - - - +
424B THR* 1.3 67.1 + - - +
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Residues in contact with THR 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ARG* 3.1 25.2 + - - +
412B ASP* 3.8 24.9 - - + +
413B TRP 3.4 7.4 - - - +
414B HIS* 2.4 36.8 + - + +
415B PHE* 4.3 0.6 - - - -
423B LYS* 1.3 75.1 + - - +
425B ILE* 1.3 67.2 + - - +
426B ARG* 3.9 15.2 + - + +
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LYS 3.9 13.0 - - - +
395B THR* 3.4 31.2 - - + +
396B THR 4.3 0.9 - - - -
397B PRO* 4.2 23.6 - - + -
413B TRP* 2.8 45.4 + - + +
415B PHE* 3.7 28.3 - - + -
424B THR* 1.3 73.4 - - - +
426B ARG* 1.3 64.5 + - - +
428B ALA* 3.4 21.5 - - + +
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Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PRO* 3.3 23.1 - - - +
400B ARG* 6.2 0.2 - - - +
412B ASP* 3.2 26.2 - - - +
424B THR* 3.9 15.6 + - + +
425B ILE* 1.3 70.4 - - - +
427B ASP* 1.3 79.0 + - - +
756B SER* 5.3 5.9 + - - -
757B HIS 3.7 21.8 + - - +
758B GLY* 3.8 26.0 + - - +
759B GLY* 5.1 1.6 - - - -
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Residues in contact with ASP 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B PRO* 4.6 1.3 - - + -
398B LEU* 2.8 43.6 + - - +
400B ARG* 2.8 39.9 + - - -
410B TYR* 3.7 20.1 - - + +
411B VAL 3.5 7.8 + - - -
412B ASP* 3.4 15.9 + - - +
425B ILE 3.6 0.4 + - - -
426B ARG* 1.3 81.4 + - - +
428B ALA* 1.3 62.5 + - - +
429B PHE 3.4 4.9 + - - -
756B SER* 4.2 3.3 + - - -
757B HIS* 4.4 1.0 - - - -
758B GLY* 3.8 18.0 + - - -
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 5.0 0.9 - - + -
395B THR* 4.0 17.2 - - + +
396B THR 4.3 9.4 - - - +
398B LEU* 3.6 11.7 - - - +
411B VAL 2.9 6.3 + - - +
413B TRP* 3.7 23.8 - - + -
425B ILE* 3.4 27.1 - - + +
426B ARG 3.3 1.3 - - - -
427B ASP* 1.3 77.8 - - - +
429B PHE* 1.3 62.9 + - + +
464B SER* 3.6 18.0 - - - -
465B MET 4.4 0.3 + - - -
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Residues in contact with PHE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 4.3 2.0 - - - -
339B PHE* 3.6 35.9 - + + -
340B GLY* 4.0 18.8 - - - -
341B LEU* 3.4 40.4 - - + -
398B LEU* 3.5 3.3 - - - +
410B TYR* 3.4 8.7 - - - +
411B VAL* 3.0 39.4 + - + +
412B ASP 3.7 20.6 - - - -
413B TRP* 3.7 27.6 - + + -
427B ASP 4.0 1.0 - - - -
428B ALA* 1.3 79.7 - - + +
430B CYS* 1.3 64.0 + - - +
431B VAL* 5.3 0.4 - - + -
462B VAL* 4.8 7.6 - - + -
463B ARG 3.3 7.6 - - - +
464B SER* 4.4 13.0 - - - -
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Residues in contact with CYS 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B LEU* 3.5 1.5 - - + +
404B CYS* 2.1 48.2 - - + -
408B ALA* 4.5 2.0 - - + -
409B THR 3.3 6.7 - - - +
410B TYR* 3.5 22.4 - - + -
411B VAL 5.0 0.2 - - - +
429B PHE* 1.3 74.8 - - - +
431B VAL* 1.3 65.3 + - - +
432B PHE* 3.7 11.7 - - - -
461B VAL 3.7 0.3 - - - +
462B VAL* 3.4 5.7 - - - +
463B ARG* 3.1 38.4 + - - -
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Residues in contact with VAL 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B PHE* 3.5 19.2 - - + -
325B VAL* 4.1 15.5 - - + -
330B VAL* 4.3 26.5 - - + -
339B PHE* 4.9 5.8 - - + -
408B ALA* 3.7 0.2 - - - +
409B THR* 2.9 41.6 + - - +
411B VAL* 4.8 9.9 - - + -
429B PHE* 5.3 0.4 - - + -
430B CYS* 1.3 81.4 - - - +
432B PHE* 1.3 64.9 + - - +
460B LEU* 4.3 8.1 - - + -
461B VAL 3.2 10.8 - - - +
462B VAL* 4.1 21.1 - - + -
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Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLY* 4.9 2.9 - - - -
317B TYR* 3.8 8.7 - - - +
323B PHE* 3.9 8.5 - - - -
405B PRO* 3.5 29.2 - - + -
408B ALA* 3.6 17.7 - - + -
430B CYS* 3.7 22.7 - - - -
431B VAL* 1.3 81.3 - - - +
433B GLU* 1.3 68.3 + - - +
434B GLN* 3.9 16.6 - - + -
460B LEU* 3.6 7.2 - - - +
461B VAL* 2.8 70.8 + - + +
463B ARG* 3.5 34.1 - - + -
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Residues in contact with GLU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PRO* 4.1 9.0 - - + +
315B GLN* 4.1 4.3 - - - +
317B TYR* 3.5 40.5 + - + -
322B ARG* 2.8 67.9 + - - +
323B PHE* 3.8 9.1 - - + -
405B PRO* 5.5 1.2 - - - +
432B PHE* 1.3 79.8 - - - +
434B GLN* 1.3 59.5 + - - +
458B THR* 3.8 13.6 - - + +
459B VAL 3.2 8.5 - - - +
460B LEU* 4.4 14.6 - - + -
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Residues in contact with GLN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLN* 3.9 3.4 - - - +
435A ASN* 3.1 27.8 + - - +
436A GLN* 3.1 23.3 + - - +
437A GLY* 3.9 3.8 - - - +
315B GLN* 3.5 19.1 + - - +
405B PRO* 4.2 11.6 - - - +
432B PHE* 3.9 23.1 - - + -
433B GLU* 1.3 75.3 - - - +
435B ASN* 1.3 69.7 + - - +
436B GLN* 3.1 27.6 + - - +
458B THR* 4.3 3.6 - - - -
459B VAL* 2.9 39.2 + - + +
461B VAL* 4.7 0.9 - - + -
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Residues in contact with ASN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PRO* 4.9 2.9 - - - +
313A PRO* 3.1 33.9 - - + +
314A LEU* 5.5 0.9 - - - -
315A GLN* 5.9 2.2 - - + +
405A PRO* 5.6 4.4 - - - +
434A GLN* 3.1 11.8 + - - +
315B GLN* 3.0 34.8 + - - +
434B GLN* 1.3 74.9 - - - +
436B GLN* 1.3 58.6 + - - +
437B GLY* 2.7 25.7 - - - +
438B LEU 5.1 0.8 + - - -
456B ALA* 4.8 13.5 - - - +
457B GLU 4.0 9.3 + - - -
458B THR* 4.1 10.8 + - - +
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Residues in contact with GLN 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A GLN* 3.0 19.3 + - - +
436A GLN* 5.3 3.8 + - - -
463A ARG* 5.5 0.5 + - - -
434B GLN* 3.1 40.7 - - - +
435B ASN* 1.3 75.1 - - - +
437B GLY* 1.3 54.7 + - - +
438B LEU* 3.2 16.9 + - + +
457B GLU* 3.0 43.0 + - + +
459B VAL* 3.9 24.0 - - + +
478B VAL* 5.6 1.0 - - - +
480B HIS* 4.7 5.0 - - - -
486B GLU* 5.7 0.2 - - - +
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Residues in contact with GLY 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL 4.4 1.0 - - - +
403A ASP 3.5 6.8 - - - +
404A CYS* 3.7 9.2 - - - -
405A PRO* 4.1 14.8 - - - -
432A PHE* 4.8 2.5 - - - -
434A GLN* 3.8 13.0 - - - +
463A ARG* 2.9 23.6 + - - -
435B ASN* 2.7 21.9 - - - +
436B GLN* 1.3 70.8 - - - +
438B LEU* 1.3 62.5 + - - +
456B ALA* 6.1 0.7 - - - -
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL 4.1 1.5 - - - +
463A ARG* 3.5 26.6 - - - +
474A VAL* 4.4 4.7 - - + -
476A ASP* 3.9 9.9 - - - +
490A TYR* 3.4 47.8 - - + +
696A THR* 4.0 19.7 - - + +
436B GLN* 3.2 16.7 + - + +
437B GLY* 1.3 81.6 + - - +
439B PRO* 1.3 78.1 - - + +
456B ALA* 3.9 4.3 - - - +
457B GLU* 3.1 28.7 + - - +
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Residues in contact with PRO 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A VAL* 3.4 17.9 - - + +
403A ASP* 3.8 23.8 - - - +
463A ARG* 4.6 0.2 - - - +
465A MET* 3.8 22.7 - - + -
474A VAL* 4.8 5.4 - - + -
492A THR* 5.9 0.9 - - - +
696A THR* 2.9 30.5 + - + +
438B LEU* 1.3 101.1 - - + +
440B LEU* 1.3 58.7 + - - +
441B ARG 3.9 19.3 - - - +
442B ARG* 4.7 4.7 - - + -
455B LEU 3.6 6.7 - - - +
457B GLU* 3.9 2.0 - - - +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A VAL* 3.4 30.8 - - + -
696A THR* 3.0 31.1 + - - +
697A VAL* 3.5 19.3 - - + -
439B PRO* 1.3 73.5 - - - +
441B ARG* 1.3 60.9 + - + +
455B LEU* 2.7 29.2 + - + +
457B GLU* 3.4 28.3 - - + +
481B PRO* 3.7 20.9 - - + -
482B SER* 4.3 9.0 - - - +
716B SER* 3.6 33.4 - - - +
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 4.0 29.1 + - - +
492A THR* 4.2 8.7 - - - -
692A PRO* 5.0 4.4 - - - +
693A ASN* 4.0 21.8 - - + +
694A THR 4.0 13.9 - - - +
695A VAL* 4.4 5.4 - - + -
439B PRO* 3.2 6.1 - - - +
440B LEU* 1.3 84.5 - - - +
442B ARG* 1.3 67.6 + - - +
453B GLY 4.1 2.0 + - - -
454B GLY* 3.3 15.4 + - - +
455B LEU* 3.2 45.1 + - + +
714B ASP* 3.6 16.7 + - - -
716B SER* 2.9 36.9 + - - -
717B PHE* 4.1 8.4 + - - +
722B SER* 3.2 25.3 + - - -
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Residues in contact with ARG 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A THR* 2.7 32.1 + - - -
397A PRO 3.6 13.1 + - - -
398A LEU* 4.6 0.2 - - - +
402A VAL* 5.0 0.2 - - + -
403A ASP* 2.7 43.8 + - - +
465A MET* 3.2 35.4 - - - +
467A THR* 3.6 3.4 + - - -
472A ASP* 2.9 27.2 + - - +
474A VAL* 5.3 1.8 - - - -
492A THR* 3.3 12.9 + - - +
493A GLY* 3.2 24.8 + - - -
693A ASN* 3.4 5.2 - - - +
439B PRO* 4.5 6.1 - - + -
441B ARG* 1.3 81.4 - - - +
443B HIS* 1.3 62.4 + - - +
444B HIS* 3.4 19.2 - - - +
452B PHE* 3.7 17.3 - - + -
453B GLY 3.5 9.4 - - - +
454B GLY* 4.2 2.5 - - - -
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Residues in contact with HIS 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 4.0 11.6 - + - -
302A LEU* 4.9 2.9 - - + -
467A THR* 3.7 10.1 - - + -
469A LEU 3.4 24.8 + - - -
470A ASN* 3.7 11.3 + - - -
472A ASP* 2.6 26.6 + - - -
493A GLY* 4.3 0.9 - - - -
494A TYR* 3.6 17.7 - + + -
693A ASN* 3.7 17.3 - - - +
442B ARG* 1.3 75.3 - - - +
444B HIS* 1.3 64.2 + - - +
445B SER* 3.9 11.8 - - - -
451B TYR* 3.5 33.2 + + - +
452B PHE* 3.5 9.4 - - - -
453B GLY 3.2 30.6 + - - +
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Residues in contact with HIS 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A THR* 3.7 10.8 - - - +
397A PRO* 3.7 23.8 - - + +
467A THR* 3.4 23.5 - - - +
472A ASP* 3.2 7.1 + - - -
757A HIS* 3.6 18.1 - - - -
759A GLY 3.5 17.3 + - - -
760A PHE* 3.4 20.2 - + - -
442B ARG* 3.4 21.8 - - - +
443B HIS* 1.3 75.6 - - - +
445B SER* 1.3 60.3 + - - +
446B ASP* 3.1 38.3 + - - -
451B TYR 4.0 1.6 - - - -
452B PHE* 4.0 18.2 - + + -
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Residues in contact with SER 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A PHE* 3.4 6.4 - - - -
443B HIS* 3.9 9.7 + - - -
444B HIS* 1.3 73.3 + - - +
446B ASP* 1.3 58.3 + - - +
447B LEU* 3.2 17.3 + - - +
449B SER 2.6 22.2 + - - +
450B HIS* 3.4 4.7 - - - -
451B TYR* 3.1 65.3 + - - -
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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
------------------------------------------------------------
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