Contacts of the helix formed by residues 889 - 911 (chain A) in PDB entry 4D86
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 889 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886A SER* 3.0 25.1 + - - +
888A TYR* 1.3 87.7 - - + +
890A ALA* 1.3 62.7 + - - +
891A PRO* 3.4 4.5 - - - -
892A ARG* 3.2 18.4 + - + +
893A CYS* 3.0 26.2 + - - -
1158A LYS* 2.7 40.7 + - - -
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Residues in contact with ALA 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A TRP* 3.7 27.5 - - + -
886A SER 3.3 6.4 + - - -
887A GLY* 3.7 11.9 + - - +
888A TYR 3.7 2.0 - - - -
889A GLU* 1.3 76.1 - - - +
891A PRO* 1.3 69.6 - - + +
893A CYS* 3.1 3.3 + - - +
894A VAL* 2.9 34.7 + - + +
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Residues in contact with PRO 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A TYR 5.5 1.1 - - - +
889A GLU* 3.7 3.6 - - - -
890A ALA* 1.3 95.3 - - + +
892A ARG* 1.3 54.9 + - - +
894A VAL* 3.4 9.4 + - + +
895A TYR* 3.0 26.7 + - - +
1189A ARG* 4.3 24.3 + - - +
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Residues in contact with ARG 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A GLU* 3.2 22.4 + - + +
890A ALA 3.1 1.0 - - - -
891A PRO* 1.3 76.5 - - - +
893A CYS* 1.3 61.8 + - - +
895A TYR* 3.3 20.3 + - - +
896A LEU* 2.8 58.9 + - + +
899A ARG* 5.3 0.4 - - - +
1109A GLU* 3.4 29.5 + - - -
1147A LEU 5.0 0.8 + - - -
1150A SER* 2.8 48.0 + - - -
1151A GLU* 4.2 7.4 + - - +
1154A LYS* 3.8 46.3 - - + +
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Residues in contact with CYS 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A PRO* 3.5 20.5 - - + +
884A ARG 3.8 14.4 - - - -
885A TRP* 3.8 19.5 - - + -
886A SER* 3.6 30.1 - - - -
889A GLU* 3.0 23.1 + - - -
890A ALA 3.5 7.4 - - - +
892A ARG* 1.3 74.3 - - - +
894A VAL* 1.3 65.8 + - - +
896A LEU* 3.2 3.0 + - - -
897A LEU* 2.9 23.6 + - - +
928A PHE* 4.0 7.6 - - + -
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Residues in contact with VAL 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A TRP* 5.0 3.1 - - + -
890A ALA* 2.9 21.6 + - + +
891A PRO* 3.6 10.5 - - + +
893A CYS* 1.3 76.8 - - - +
895A TYR* 1.3 64.6 + - - +
897A LEU 3.3 0.2 + - - -
898A ARG* 3.0 27.9 + - + +
928A PHE* 4.1 20.0 - - + -
932A ARG* 3.5 31.9 - - - +
936A THR* 3.6 21.9 - - + +
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Residues in contact with TYR 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A PRO 3.0 15.6 + - - +
892A ARG* 3.3 26.2 + - - +
894A VAL* 1.3 77.8 - - - +
896A LEU* 1.3 73.3 + - + +
898A ARG* 3.6 15.7 - - - +
899A ARG* 2.9 76.8 + - + +
902A GLN* 6.0 0.7 - - - -
1109A GLU* 4.4 0.2 - - - -
1143A ILE 4.8 1.2 + - - -
1146A GLU* 3.4 34.3 - - + -
1147A LEU* 3.2 25.7 - - + +
1150A SER* 3.5 27.1 - - - +
1185A GLU* 5.8 0.7 - - - -
1189A ARG* 4.4 8.7 - - - +
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Residues in contact with LEU 896 (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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861A PRO* 3.7 37.5 - - + +
862A GLY* 3.3 15.5 - - - +
883A PRO* 4.0 21.5 - - + -
892A ARG* 2.8 50.5 + - + +
893A CYS* 3.2 5.1 + - - +
895A TYR* 1.3 88.6 - - + +
897A LEU* 1.3 60.1 + - - +
899A ARG* 3.4 18.2 + - - +
900A ALA* 3.0 25.1 + - - +
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Residues in contact with LEU 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A GLY* 4.9 0.7 - - - -
883A PRO* 3.7 12.9 - - + +
893A CYS 2.9 16.1 + - - +
894A VAL 3.8 2.9 - - - +
896A LEU* 1.3 72.2 - - - +
898A ARG* 1.3 66.5 + - - +
900A ALA* 3.3 4.4 + - + +
901A VAL* 3.1 28.1 + - + +
921A ILE* 3.6 39.0 - - + +
922A SER* 4.4 4.3 - - - +
928A PHE* 3.5 30.1 - - + -
933A CYS* 3.7 34.5 - - - +
936A THR* 3.8 10.3 - - + -
937A ILE* 4.3 11.7 - - + -
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Residues in contact with ARG 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A VAL* 3.0 22.2 + - + +
895A TYR* 3.6 16.9 + - - +
897A LEU* 1.3 78.4 - - - +
899A ARG* 1.3 57.0 + - - +
901A VAL* 3.2 5.4 + - - +
902A GLN* 2.8 50.3 + - - +
936A THR* 3.7 17.6 - - + +
939A SER* 5.1 5.0 + - - -
940A ALA* 3.7 28.1 - - + +
943A GLU* 3.0 28.3 + - - +
1146A GLU* 3.8 20.6 + - - +
1185A GLU* 3.5 12.7 + - - -
1188A ARG* 3.5 29.9 - - - +
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Residues in contact with ARG 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A LEU* 5.6 1.8 - - - +
861A PRO 3.2 25.1 + - - -
862A GLY* 2.8 19.2 + - - +
863A ASN* 3.9 7.1 - - - +
892A ARG* 5.3 0.2 - - - +
895A TYR* 2.9 49.6 + - + +
896A LEU* 3.6 17.0 - - - +
897A LEU 3.3 0.2 - - - -
898A ARG* 1.3 74.0 - - - +
900A ALA* 1.3 59.9 + - - +
902A GLN* 3.2 16.3 + - + +
903A LEU* 2.8 46.2 + - + +
1105A LEU* 3.9 29.0 - - - +
1109A GLU* 2.7 32.7 + - - -
1143A ILE* 5.2 8.5 - - + -
1147A LEU* 4.4 3.0 - - - +
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Residues in contact with ALA 900 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A GLY* 4.1 5.9 - - - -
863A ASN 3.8 16.4 - - - +
864A ALA* 4.1 1.7 - - - +
880A ALA* 4.2 9.4 - - + -
881A VAL 3.7 26.0 - - - +
882A GLY* 4.5 4.7 - - - +
896A LEU 3.0 17.0 + - - +
897A LEU* 3.3 7.6 + - + +
899A ARG* 1.3 75.2 - - - +
901A VAL* 1.3 57.8 + - + +
903A LEU* 3.5 2.0 + - - +
904A SER* 2.8 33.9 + - - -
921A ILE* 5.4 0.9 - - + -
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Residues in contact with VAL 901 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A LEU* 3.1 15.7 + - + +
898A ARG* 3.5 7.2 - - - +
900A ALA* 1.3 73.1 - - - +
902A GLN* 1.3 65.2 + - - +
904A SER* 3.2 6.6 + - - -
905A LEU* 3.0 37.9 + - + +
918A ILE* 4.8 8.7 - - + -
921A ILE* 3.9 24.9 - - + -
937A ILE* 3.9 36.1 - - + +
940A ALA* 3.6 21.1 - - + -
941A ILE* 4.4 7.0 - - + -
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Residues in contact with GLN 902 (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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895A TYR* 6.0 0.9 - - - -
898A ARG* 2.8 39.0 + - - +
899A ARG* 3.2 22.4 + - - +
901A VAL* 1.3 73.0 - - - +
903A LEU* 1.3 58.9 + - + +
905A LEU* 3.4 10.7 + - + +
906A CYS* 3.0 33.7 + - - -
940A ALA* 4.4 12.8 - - + +
943A GLU* 3.4 19.8 + - - +
944A ASN* 5.1 3.7 - - + +
1142A ASN* 4.1 8.4 - - - +
1143A ILE* 3.9 24.6 - - + +
1146A GLU* 2.9 27.9 + - - +
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Residues in contact with LEU 903 (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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862A GLY 3.4 26.0 - - - +
863A ASN* 3.8 13.0 - - - -
864A ALA* 3.8 17.5 - - + +
899A ARG* 2.8 24.6 + - + +
900A ALA 3.9 0.7 - - - +
902A GLN* 1.3 78.2 - - + +
904A SER* 1.3 56.4 + - - +
906A CYS* 3.3 6.8 + - + +
907A LEU* 3.0 32.2 + - + +
1097A TRP* 3.7 35.9 - - + -
1099A ASN 4.9 3.3 - - - +
1100A GLY* 4.1 13.7 - - - +
1105A LEU* 3.6 18.6 - - + -
1143A ILE* 4.5 8.3 - - + -
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Residues in contact with SER 904 (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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820A VAL* 3.7 16.9 - - - +
864A ALA* 3.6 7.5 - - - +
878A ILE* 3.6 32.2 - - - +
880A ALA* 3.5 21.3 - - - +
900A ALA 2.8 22.1 + - - -
901A VAL* 3.2 7.7 + - - -
903A LEU* 1.3 74.7 - - - +
905A LEU* 1.3 65.3 + - - +
907A LEU* 3.3 1.6 + - - -
908A ALA* 3.0 19.6 + - - +
916A ILE* 4.8 2.2 - - - -
918A ILE* 5.9 1.8 - - - -
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Residues in contact with LEU 905 (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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901A VAL* 3.0 33.3 + - + +
902A GLN* 3.6 8.7 - - - +
904A SER* 1.3 76.3 - - - +
906A CYS* 1.3 56.0 + - - +
908A ALA* 3.1 5.4 + - - +
909A GLU* 2.9 35.9 + - - +
916A ILE* 4.5 8.3 - - + -
918A ILE* 4.1 22.9 - - + -
940A ALA 4.4 2.2 - - - +
941A ILE* 4.2 16.8 - - + -
944A ASN* 3.6 44.4 - - + +
954A LEU* 3.8 23.1 - - + -
957A ILE* 5.1 6.1 - - + -
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Residues in contact with CYS 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A GLN* 3.0 21.2 + - - +
903A LEU* 3.5 13.7 - - + +
904A SER 3.3 0.2 - - - -
905A LEU* 1.3 75.9 - - - +
907A LEU* 1.3 57.6 + - + +
909A GLU* 3.2 7.0 + - - +
910A LYS* 2.9 28.9 + - - +
944A ASN* 5.3 6.1 - - - -
1097A TRP* 5.2 7.9 - - + +
1099A ASN 6.1 2.2 - - - +
1140A PRO* 5.2 8.5 - - - -
1143A ILE* 4.3 19.7 - - - -
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Residues in contact with LEU 907 (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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864A ALA* 3.8 12.8 - - + +
865A THR* 3.7 43.1 - - - +
866A ILE* 4.2 16.6 - - + +
878A ILE* 4.1 14.4 - - + -
903A LEU* 3.0 18.6 + - + +
904A SER 3.7 6.7 - - - +
905A LEU 3.3 0.2 - - - -
906A CYS* 1.3 76.3 - - + +
908A ALA* 1.3 62.7 + - - +
910A LYS* 3.2 4.6 + - + +
911A TYR* 3.1 36.7 + - + -
1099A ASN* 4.1 37.0 - - + +
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Residues in contact with ALA 908 (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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818A VAL* 4.5 7.2 - - + -
878A ILE* 3.8 9.7 - - + +
904A SER 3.0 14.6 + - - +
905A LEU 3.5 7.9 - - - +
907A LEU* 1.3 76.0 - - - +
909A GLU* 1.3 62.3 + - - +
911A TYR* 3.3 3.1 + - - -
912A LYS 3.2 3.3 + - - -
913A TYR* 3.0 35.5 + - + +
916A ILE* 3.8 23.3 - - + -
954A LEU* 4.2 17.5 - - + -
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Residues in contact with GLU 909 (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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905A LEU* 2.9 18.3 + - - +
906A CYS* 3.2 5.6 + - - +
908A ALA* 1.3 75.8 - - - +
910A LYS* 1.3 59.5 + - - +
912A LYS* 2.9 28.3 + - - +
913A TYR 4.9 1.1 - - - +
944A ASN* 3.1 22.0 + - - +
945A PHE* 4.6 0.2 - - - -
951A GLY 5.3 4.3 - - - +
952A HIS* 2.9 32.5 + - - +
953A CYS* 3.0 37.1 + - - +
954A LEU* 3.2 26.7 + - + +
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Residues in contact with LYS 910 (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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906A CYS 2.9 13.4 + - - +
907A LEU* 3.2 13.2 + - + +
909A GLU* 1.3 77.6 - - - +
911A TYR* 1.3 74.9 + - + +
912A LYS* 3.3 17.2 + - - +
1099A ASN* 2.6 44.6 + - - +
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Residues in contact with TYR 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A ILE* 3.7 42.1 - - + +
876A HIS* 4.1 31.4 + + - -
907A LEU* 3.1 26.6 + - + +
909A GLU 3.3 0.2 - - - -
910A LYS* 1.3 93.5 + - + +
912A LYS* 1.3 70.4 + - - +
913A TYR* 3.2 35.3 + + + -
1099A ASN* 5.7 0.4 - - - -
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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