Contacts of the helix formed by residues 635 - 658 (chain B) in PDB entry 4MVY
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 THR 635 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A PRO* 3.7 34.5 - - + +
425A GLY* 3.8 21.8 - - - +
634B TYR* 1.3 73.7 - - - +
636B GLU* 1.3 59.9 + - - +
637B GLU* 3.4 8.8 + - - +
638B ASP* 2.9 33.9 + - - +
639B GLU* 2.9 31.7 + - - +
694B ARG* 3.7 14.1 + - - +
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Residues in contact with GLU 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A LYS* 4.4 18.1 - - - +
654A HIS* 3.0 42.0 + - - +
657A LEU* 3.7 40.0 - - + +
658A ILE* 4.1 20.4 - - + +
635B THR* 1.3 74.4 - - - +
637B GLU* 1.3 57.9 + - - +
639B GLU* 3.1 7.8 + - - +
640B SER* 2.9 27.7 + - - -
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Residues in contact with GLU 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A VAL* 5.8 2.1 - - - +
429A PRO* 6.0 0.7 - - - +
430A GLU* 5.1 5.9 + - - +
658A ILE* 3.9 36.8 - - + +
663A LYS* 6.1 2.0 - - - -
635B THR* 3.3 9.2 + - - +
636B GLU* 1.3 78.3 - - - +
638B ASP* 1.3 63.1 + - - +
640B SER* 2.9 20.1 + - - +
641B LEU* 3.2 8.0 + - - +
678B TYR* 4.1 23.9 - - + -
681B ASP* 2.6 35.8 - - - +
682B MET* 4.6 7.9 - - - +
694B ARG* 5.8 0.9 - - - +
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Residues in contact with ASP 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B TYR* 3.5 13.0 - - + -
635B THR* 2.9 34.2 + - - +
637B GLU* 1.3 74.4 - - - +
639B GLU* 1.3 62.3 + - - +
641B LEU* 3.2 5.2 + - - +
642B ILE* 3.0 26.9 + - - +
678B TYR* 2.5 33.5 + - - -
694B ARG* 2.6 37.8 + - - -
697B THR* 3.7 2.4 - - - +
701B ILE* 3.6 19.8 - - + +
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Residues in contact with GLU 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A HIS* 3.8 23.7 + - + +
634B TYR* 3.9 32.6 - - + +
635B THR 2.9 23.2 + - - +
636B GLU* 3.1 13.9 + - - +
638B ASP* 1.3 76.8 - - - +
640B SER* 1.3 57.4 + - - +
642B ILE* 3.4 14.0 + - - +
643B GLN* 2.9 29.3 + - - +
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Residues in contact with SER 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A THR* 5.4 1.5 - - - +
654A HIS* 3.5 30.4 - - - -
655A TYR* 3.7 28.7 + - - -
658A ILE* 4.1 6.2 - - - +
636B GLU 2.9 11.1 + - - -
637B GLU* 2.9 19.9 + - - +
639B GLU* 1.3 76.8 - - - +
641B LEU* 1.3 61.3 + - - +
643B GLN* 3.3 5.2 + - - +
644B LEU* 3.3 25.5 + - - +
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Residues in contact with LEU 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLU 3.2 6.2 + - - +
638B ASP* 3.2 8.7 + - - +
640B SER* 1.3 79.8 + - - +
642B ILE* 1.3 65.6 + - - +
644B LEU* 3.1 19.3 + - + +
645B ILE* 3.1 22.7 + - + +
671B VAL* 4.9 0.9 - - + +
674B ALA* 4.1 15.0 - - + +
675B ILE* 3.9 40.8 - - + +
678B TYR* 3.4 46.2 - - + -
701B ILE* 3.7 15.7 - - + -
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Residues in contact with ILE 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B TYR* 3.8 35.2 - - + -
638B ASP 3.0 18.2 + - - +
639B GLU* 3.7 13.7 - - - +
641B LEU* 1.3 76.0 - - - +
643B GLN* 1.3 57.3 + - - +
645B ILE* 3.2 9.8 + - - +
646B LYS* 2.9 53.4 + - + +
701B ILE* 3.7 28.9 - - + -
743B PHE* 3.8 28.7 - - + -
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Residues in contact with GLN 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A GLY* 4.7 10.7 - - - -
651A THR* 4.6 11.0 - - - +
654A HIS* 3.8 26.6 + - + -
639B GLU 2.9 18.0 + - - +
640B SER 3.6 6.1 - - - +
641B LEU 3.2 0.2 - - - -
642B ILE* 1.3 76.4 - - - +
644B LEU* 1.3 58.7 + - + +
646B LYS* 3.3 19.8 + - - +
647B ASP* 2.8 70.0 + - - +
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Residues in contact with LEU 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A THR* 4.1 31.4 - - + +
655A TYR* 3.6 19.5 - - - +
640B SER 3.3 12.3 + - - +
641B LEU* 3.1 17.1 + - + +
643B GLN* 1.3 77.5 - - + +
645B ILE* 1.3 62.1 + - - +
647B ASP* 3.4 7.5 + - + +
648B LEU* 3.1 23.0 + - - +
670B ASP 6.2 0.4 - - - -
671B VAL* 4.0 19.7 - - + +
674B ALA* 3.7 29.8 - - + -
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Residues in contact with ILE 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 3.1 32.4 + - + +
642B ILE* 3.6 5.6 - - - +
644B LEU* 1.3 74.5 - - - +
646B LYS* 1.3 64.6 + - - +
648B LEU* 3.4 7.2 + - - +
649B PRO* 3.2 19.8 - - - +
671B VAL* 4.1 18.8 - - + -
675B ILE* 4.7 2.0 - - + -
701B ILE* 4.1 10.8 - - + +
705B GLY* 3.6 30.5 - - - +
708B VAL* 3.9 34.3 - - + +
709B THR* 6.1 0.2 - - + -
741B PHE 5.1 0.5 - - - +
743B PHE* 4.0 26.9 + - + -
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Residues in contact with LYS 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-4B GLY 4.7 7.3 + - - +
642B ILE* 2.9 38.4 + - + +
643B GLN* 3.6 23.6 + - - +
645B ILE* 1.3 78.6 - - - +
647B ASP* 1.3 61.6 + - - +
649B PRO* 3.4 12.1 - - - +
741B PHE 6.0 0.2 - - - -
743B PHE* 3.8 32.8 - - + +
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Residues in contact with ASP 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLN* 5.8 0.2 + - - -
647A ASP* 3.6 37.3 - - + +
651A THR* 3.9 9.4 + - - -
-4B GLY 3.6 18.7 + - - +
643B GLN* 2.8 53.4 + - - +
644B LEU* 3.8 7.1 - - + +
645B ILE 3.2 0.4 - - - -
646B LYS* 1.3 78.4 - - - +
648B LEU* 1.3 65.6 + - - +
649B PRO* 3.4 0.4 - - - -
650B GLY* 3.4 5.1 + - - -
651B THR* 3.2 22.4 + - - +
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Residues in contact with LEU 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B LEU 3.1 15.7 + - - +
645B ILE* 3.6 5.8 - - - +
647B ASP* 1.3 76.9 - - - +
649B PRO* 1.3 64.9 - - + +
651B THR* 3.1 6.0 + - - -
652B ALA* 2.8 30.7 + - + +
667B ALA* 3.8 36.6 - - + +
668B VAL* 3.9 14.4 - - + +
671B VAL* 4.0 16.8 - - + -
708B VAL* 4.6 4.7 - - + -
709B THR* 3.7 33.4 - - + -
712B LEU* 3.6 19.5 - - + -
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Residues in contact with PRO 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B GLY* 5.3 0.7 - - - -
272B TYR* 4.7 1.4 + - - -
645B ILE 3.2 14.6 - - - +
646B LYS* 3.4 12.8 - - - +
647B ASP 3.5 0.2 - - - -
648B LEU* 1.3 92.5 - - + +
650B GLY* 1.3 55.4 + - - +
652B ALA* 3.9 0.7 - - - +
653B ASP* 2.8 31.7 + - - +
708B VAL* 4.2 9.6 - - + -
712B LEU* 3.7 15.7 - - + +
741B PHE* 3.4 54.0 - - + +
742B GLU* 5.7 0.2 - - - -
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Residues in contact with GLY 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLN* 4.1 5.8 - - - -
-4B GLY 3.6 23.1 + - - -
-2B GLY* 3.8 18.6 - - - +
646B LYS 5.0 0.2 + - - -
647B ASP 3.4 4.7 + - - -
648B LEU 3.3 0.6 - - - -
649B PRO* 1.3 79.8 - - - +
651B THR* 1.3 59.6 + - - +
653B ASP* 3.5 1.9 + - - +
654B HIS* 3.0 35.0 + - - -
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Residues in contact with THR 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A SER* 5.4 1.7 - - - +
643A GLN* 4.5 6.0 - - + +
644A LEU* 4.0 22.7 - - + +
647A ASP* 3.8 13.2 + - - -
647B ASP* 3.2 15.2 + - - +
648B LEU* 3.1 13.3 + - + -
650B GLY* 1.3 73.7 - - - +
652B ALA* 1.3 66.0 + - - +
654B HIS* 3.3 9.2 + - - +
655B TYR* 3.2 50.0 + - + -
667B ALA* 4.1 12.6 - - + -
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Residues in contact with ALA 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 2.8 25.8 + - + +
649B PRO 3.9 2.7 - - - +
651B THR* 1.3 73.6 - - - +
653B ASP* 1.3 57.9 + - - +
655B TYR* 3.3 10.8 + - - +
656B TYR* 2.9 46.1 + - + -
664B ALA* 4.8 6.5 - - + +
667B ALA* 5.2 0.9 - - - -
668B VAL* 4.7 6.5 - - + -
712B LEU* 4.1 27.1 - - + -
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Residues in contact with ASP 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2B GLY* 3.7 7.7 - - - -
-1B SER* 2.8 37.8 + - - -
272B TYR* 2.6 35.7 + - - +
276B LYS* 2.8 26.1 + - - -
649B PRO 2.8 19.5 + - - +
650B GLY 3.7 4.9 - - - +
652B ALA* 1.3 77.4 - - - +
654B HIS* 1.3 65.8 + - - +
656B TYR* 3.2 1.2 + - - +
657B LEU* 3.0 28.6 + - - +
741B PHE* 5.6 2.0 - - + -
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Residues in contact with HIS 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLU* 3.1 29.9 + - - +
639A GLU* 4.0 27.0 + - + +
640A SER* 3.6 23.6 - - - -
643A GLN* 3.5 41.0 + - + +
-3B PRO 4.2 5.4 + - - -
-2B GLY* 4.7 0.9 - - - -
-1B SER* 4.7 16.6 - - - -
650B GLY 3.0 21.6 + - - -
651B THR* 3.3 6.5 + - - +
653B ASP* 1.3 78.6 + - - +
655B TYR* 1.3 61.8 + - - +
657B LEU* 3.2 2.2 + - - -
658B ILE* 3.2 23.6 + - - +
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Residues in contact with TYR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A SER* 3.8 21.5 - - - -
644A LEU* 3.5 28.4 - - + +
674A ALA* 5.5 0.7 - - - +
651B THR* 3.2 41.0 + - + -
652B ALA 3.7 4.7 - - - +
653B ASP 3.3 0.2 - - - -
654B HIS* 1.3 77.6 - - - +
656B TYR* 1.3 57.8 + - - +
657B LEU 3.2 0.5 + - - -
658B ILE* 3.2 21.1 + - + +
660B ASP* 2.6 45.3 + - + +
663B LYS* 3.6 52.7 - - + +
664B ALA* 3.7 9.6 - - - +
667B ALA* 4.2 5.8 - - + -
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Residues in contact with TYR 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B VAL* 4.2 20.6 - - + -
269B ILE* 5.0 10.8 - - + +
272B TYR* 3.5 63.3 - + + -
273B HIS* 5.0 3.8 + - - -
652B ALA* 2.9 34.6 + - + +
653B ASP 3.2 3.6 + - - +
655B TYR* 1.3 75.7 - - - +
657B LEU* 1.3 58.9 + - - +
659B PRO* 3.3 20.9 - - - +
660B ASP 4.7 2.7 - - - +
661B ILE* 4.6 13.0 - - + -
664B ALA* 4.0 23.0 - - + +
665B ILE* 5.7 0.3 - - - +
712B LEU* 2.7 28.0 + - + -
713B LEU* 5.5 0.5 - - - +
715B PRO* 3.7 6.3 - - + +
716B ILE* 3.7 21.3 - - + +
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Residues in contact with LEU 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLU* 3.6 30.7 - - + +
-1B SER* 3.0 29.8 - - - +
242B PHE* 5.9 1.8 - - + -
272B TYR* 4.1 4.5 - - + -
273B HIS* 3.4 35.0 - - + +
276B LYS* 4.5 1.8 - - - +
512B VAL* 5.6 2.3 - - - +
541B LYS* 3.3 24.7 + - - +
653B ASP* 3.0 33.3 + - - +
654B HIS* 3.7 0.4 - - - +
655B TYR 3.1 0.4 - - - -
656B TYR* 1.3 80.6 - - - +
658B ILE* 1.3 62.8 + - - +
659B PRO* 3.5 1.8 - - - +
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Residues in contact with ILE 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A GLU* 3.9 9.6 - - + +
637A GLU* 3.8 40.8 - - + +
640A SER* 3.8 22.7 - - - +
428B VAL* 3.4 28.1 - - + +
541B LYS* 3.3 18.0 - - - +
654B HIS 3.2 15.6 + - - +
655B TYR* 3.2 19.9 + - + +
657B LEU* 1.3 73.9 - - - +
659B PRO* 1.3 76.3 - - + +
660B ASP* 4.2 11.0 - - + +
663B LYS* 5.8 0.9 - - + -
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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