Contacts of the helix formed by residues 791 - 812 (chain D) in PDB entry 3BBT
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 GLY 791 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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789D ASN 4.2 1.6 + - - -
790D ILE* 1.3 78.8 - - - +
792D SER* 1.3 64.3 + - - -
793D GLN* 3.3 4.2 + - - -
794D LEU* 3.7 8.3 + - - +
795D LEU* 3.4 24.6 + - - +
962D ILE* 4.3 8.7 - - - -
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Residues in contact with SER 792 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791D GLY* 1.3 71.1 - - - -
793D GLN* 1.3 66.4 + - - +
795D LEU* 3.8 0.3 - - - +
796D LEU* 3.0 29.1 + - - +
956D PRO* 3.4 29.3 - - - +
957D GLN* 3.6 15.2 + - - +
960D LEU* 3.6 39.7 + - - -
962D ILE* 3.9 7.7 - - - +
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Residues in contact with GLN 793 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811B GLU* 5.4 5.8 - - - +
791D GLY* 3.3 1.3 - - - -
792D SER* 1.3 81.8 + - - +
794D LEU* 1.3 60.2 + - + +
796D LEU* 3.9 0.6 - - - -
797D ASN* 2.8 70.4 + - - +
953D ALA* 3.4 32.3 + - - +
956D PRO* 3.4 20.6 - - + +
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Residues in contact with LEU 794 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782D TYR* 5.7 2.2 - - + +
789D ASN 4.6 12.6 - - - +
790D ILE* 4.3 17.7 - - + -
791D GLY 3.7 9.4 + - - +
792D SER 3.5 0.2 - - - -
793D GLN* 1.3 79.9 - - + +
795D LEU* 1.3 57.2 + - - +
797D ASN* 3.2 6.1 + - - +
798D TRP* 2.9 56.3 + - + +
829D PRO* 3.4 39.7 - - + +
830D ASN* 3.9 20.6 - - + +
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Residues in contact with LEU 795 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783D VAL* 5.3 1.1 - - + -
790D ILE* 3.8 19.5 - - + +
791D GLY 3.4 22.1 + - - +
792D SER 3.5 0.6 + - - +
793D GLN 3.3 0.4 - - - -
794D LEU* 1.3 80.8 - - - +
796D LEU* 1.3 61.9 + - - +
798D TRP* 3.3 17.3 + - + +
799D CYS* 3.3 25.3 + - - -
888D LEU* 3.5 43.8 - - + +
889D MET* 4.2 8.5 - - - +
891D PHE* 4.3 12.8 - - + -
919D ILE* 4.2 14.8 - - + -
960D LEU* 3.6 26.0 - - + -
962D ILE* 4.3 5.4 - - + -
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Residues in contact with LEU 796 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792D SER 3.0 17.7 + - - +
793D GLN* 4.0 1.8 - - - +
795D LEU* 1.3 73.9 - - - +
797D ASN* 1.3 65.7 + - - +
799D CYS* 3.2 15.2 + - - +
800D VAL* 3.3 18.4 + - - +
889D MET* 4.4 10.3 - - + -
924D VAL* 4.7 5.6 - - + -
949D PHE* 4.1 25.6 - - + +
952D MET* 3.4 37.9 - - + +
953D ALA* 4.5 13.0 - - + +
956D PRO* 3.6 26.7 - - + +
959D TYR* 4.4 4.3 - - + -
960D LEU* 3.8 22.7 - - + -
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Residues in contact with ASN 797 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793D GLN* 2.8 56.6 + - - +
794D LEU* 3.2 8.2 + - - +
796D LEU* 1.3 76.8 - - - +
798D TRP* 1.3 63.4 + - + +
800D VAL* 3.1 10.4 + - - +
801D GLN* 3.1 33.3 + - - +
830D ASN* 3.0 32.7 + - - +
953D ALA* 3.9 9.2 - - - +
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Residues in contact with TRP 798 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779D LEU* 3.7 31.6 - - + -
782D TYR* 4.0 17.0 - + - -
783D VAL* 3.4 25.4 - - + -
790D ILE* 4.0 36.6 - - + -
794D LEU* 2.9 32.2 + - + +
795D LEU* 3.6 19.5 - - + +
796D LEU 3.3 0.2 - - - -
797D ASN* 1.3 79.5 - - + +
799D CYS* 1.3 61.4 + - - +
801D GLN* 3.9 6.2 - - - +
802D ILE* 3.2 32.6 + - - +
826D VAL* 5.7 0.9 - - + -
829D PRO* 2.7 31.1 + - + -
830D ASN* 4.4 3.0 - - - +
832D VAL* 3.5 29.6 - - + +
888D LEU* 4.3 14.1 - - + -
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Residues in contact with CYS 799 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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795D LEU 3.3 15.3 - - - -
796D LEU* 3.2 11.8 + - - +
797D ASN 3.2 0.6 - - - -
798D TRP* 1.3 75.3 - - - +
800D VAL* 1.3 58.3 + - - +
802D ILE* 4.9 0.7 - - - -
803D ALA* 3.0 19.9 + - - +
881D TYR* 2.7 33.2 + - - +
885D ILE* 3.7 25.1 - - - -
888D LEU* 4.7 4.7 - - - -
889D MET* 3.7 25.4 - - - -
949D PHE* 3.8 21.5 - - + -
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Residues in contact with VAL 800 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804B LYS* 6.2 0.7 - - - -
796D LEU 3.4 15.7 - - - +
797D ASN* 3.1 10.0 + - - +
799D CYS* 1.3 76.2 - - - +
801D GLN* 1.3 54.6 + - + +
803D ALA* 3.2 7.2 + - - +
804D LYS* 2.7 60.2 + - + +
946D ALA* 4.2 12.8 - - - +
949D PHE* 3.6 11.0 - - + +
950D SER* 3.6 38.4 - - - +
953D ALA* 4.8 4.0 - - + -
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Residues in contact with GLN 801 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753B PRO* 4.2 8.9 - - + +
754D HIS* 3.2 51.1 - - + +
797D ASN* 3.1 25.5 + - - +
798D TRP* 4.1 1.9 - - - +
799D CYS 3.4 0.2 - - - -
800D VAL* 1.3 76.4 - - + +
802D ILE* 1.3 59.9 + - - +
804D LYS* 3.8 3.3 - - + +
805D GLY* 3.0 23.2 + - - -
830D ASN* 2.9 32.0 + - - +
831D HIS* 3.5 2.1 + - - -
832D VAL* 2.9 44.1 + - + +
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Residues in contact with ILE 802 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779D LEU* 4.4 5.2 - - + -
798D TRP 3.2 22.5 + - - +
799D CYS* 5.1 1.3 - - - -
801D GLN* 1.3 73.7 - - - +
803D ALA* 1.3 59.0 + - - +
805D GLY 3.4 0.2 + - - -
806D MET* 2.9 30.1 + - + +
819D LEU* 4.2 16.2 - - + -
824D VAL* 3.8 37.0 - - + -
832D VAL* 4.3 4.9 - - + -
834D ILE* 3.3 20.8 - - + +
881D TYR* 3.6 28.5 - - + -
884D THR* 4.4 11.0 - - + -
885D ILE* 5.4 1.3 - - + -
888D LEU* 4.3 18.8 - - + -
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Residues in contact with ALA 803 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799D CYS 3.0 20.1 + - - +
800D VAL 3.4 4.3 - - - +
802D ILE* 1.3 77.3 - - - +
804D LYS* 1.3 55.5 + - - +
806D MET* 3.4 2.9 + - - +
807D MET* 2.9 33.3 + - - +
881D TYR* 3.6 18.4 - - + +
942D PHE* 3.9 12.9 - - + +
945D LEU* 4.4 2.9 - - + -
946D ALA* 3.8 30.3 - - + +
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Residues in contact with LYS 804 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B VAL* 5.5 1.0 - - - +
804B LYS* 2.9 36.8 - - - +
950B SER* 5.2 4.2 + - - -
752D HIS* 3.4 24.5 + - + +
754D HIS* 4.4 9.9 - - + +
800D VAL* 2.7 42.2 + - + +
801D GLN* 3.8 9.2 - - + +
803D ALA* 1.3 72.0 - - - +
805D GLY* 1.3 64.5 + - - +
807D MET* 3.3 18.6 + - - +
808D TYR 3.2 16.6 + - - -
946D ALA* 4.4 12.1 - - + -
950D SER* 5.7 1.8 - - - -
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Residues in contact with GLY 805 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752D HIS* 3.6 20.7 + - - -
754D HIS* 4.2 2.2 - - - -
755D LEU* 3.8 18.2 - - - +
801D GLN 3.0 16.7 + - - -
802D ILE 3.4 2.0 + - - -
804D LYS* 1.3 74.8 - - - +
806D MET* 1.3 61.3 + - - +
808D TYR* 3.2 14.0 + - - +
809D LEU* 3.3 15.6 + - - +
834D ILE* 4.1 4.0 - - - -
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Residues in contact with MET 806 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802D ILE* 2.9 21.4 + - + +
803D ALA 3.6 0.4 - - - +
805D GLY* 1.3 72.3 - - - +
807D MET* 1.3 59.8 + - - +
809D LEU* 3.1 29.0 + - + +
810D GLU* 2.9 28.1 + - - +
814D LEU 5.5 0.4 - - - +
816D HIS* 4.1 9.0 - - + +
819D LEU* 3.8 24.7 - - + -
834D ILE* 3.8 16.8 - - + +
874D HIS* 6.2 1.3 - - - +
877D ASP* 3.7 39.3 - - + +
942D PHE* 3.6 42.4 - - + -
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Residues in contact with MET 807 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954B ARG* 6.2 2.0 - - - +
803D ALA 2.9 16.1 + - - +
804D LYS* 3.3 22.4 - - - +
806D MET* 1.3 76.7 - - - +
808D TYR* 1.3 55.6 + - - +
810D GLU* 3.3 7.3 + - - +
811D GLU* 2.9 36.6 + - + +
942D PHE* 3.8 21.1 - - + +
943D LYS* 3.7 32.1 - - + +
946D ALA* 3.8 19.1 - - - -
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Residues in contact with TYR 808 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797B ASN* 6.2 0.2 - - - -
830B ASN* 3.7 10.4 - - - +
749D SER 3.5 8.3 + - - -
750D MET* 4.0 10.8 - - - -
751D ASP* 3.2 48.1 + - - +
752D HIS* 3.6 31.9 - + + +
755D LEU* 3.7 17.5 - - + -
804D LYS 3.2 2.7 + - - +
805D GLY 3.2 11.3 + - - +
807D MET* 1.3 78.1 - - - +
809D LEU* 1.3 57.1 + - - +
811D GLU* 3.4 9.7 + - + +
812D ARG* 3.1 54.6 + - + +
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Residues in contact with LEU 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750D MET* 4.0 5.6 - - - -
755D LEU* 3.7 31.9 - - + -
805D GLY 3.3 7.4 + - - +
806D MET* 3.1 39.1 + - + +
808D TYR* 1.3 76.2 - - - +
810D GLU* 1.3 56.4 + - - +
812D ARG* 3.4 3.6 + - - +
813D ARG 3.0 6.6 + - - -
814D LEU* 2.8 72.6 + - + +
816D HIS* 4.5 5.4 - - + -
834D ILE* 5.0 0.4 - - + -
837D PHE* 3.8 30.1 - - + -
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Residues in contact with GLU 810 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D MET 2.9 12.1 + - - +
807D MET* 3.6 8.7 - - - +
809D LEU* 1.3 75.6 - - - +
811D GLU* 1.3 59.2 + - - +
813D ARG* 2.9 24.3 + - - +
874D HIS* 3.7 43.8 + - + +
875D GLN* 4.4 6.1 + - - -
941D LYS* 4.4 19.1 - - - +
942D PHE* 3.8 31.4 + - + +
943D LYS* 5.4 6.6 + - - -
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Residues in contact with GLU 811 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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954B ARG 5.7 1.2 - - - +
807D MET* 2.9 22.9 + - + +
808D TYR* 3.5 11.4 - - + +
810D GLU* 1.3 77.2 - - - +
812D ARG* 1.3 62.4 + - + +
813D ARG* 3.3 7.5 + - - +
943D LYS* 5.9 1.4 + - - -
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Residues in contact with ARG 812 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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746D ILE* 4.4 9.3 + - - +
749D SER* 2.7 52.8 + - - -
750D MET* 3.6 28.6 - - + +
808D TYR* 3.1 48.0 + - + +
809D LEU 3.4 2.4 + - - +
810D GLU 3.1 0.2 - - - -
811D GLU* 1.3 79.3 - - + +
813D ARG* 1.3 69.3 + - - +
814D LEU* 3.3 5.3 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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