Contacts of the helix formed by residues 794 - 819 (chain A) in PDB entry 6PUO
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 ALA 794 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A TRP* 3.4 26.0 - - + +
745A GLY* 4.4 5.6 - - - -
746A GLN* 4.4 3.6 - - - +
747A LEU* 4.6 9.9 - - + -
790A ALA 3.8 8.3 + - - +
791A PHE 3.6 11.2 + - - +
792A PHE 3.3 1.6 - - - -
793A THR* 1.3 78.8 - - - +
795A PRO* 1.3 70.6 - - + +
796A VAL* 3.3 5.2 - - + +
797A VAL* 3.1 18.5 + - + +
798A VAL* 3.3 11.6 + - - +
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Residues in contact with PRO 795 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A VAL* 3.9 15.0 - - + +
743A TRP* 3.2 46.5 - - + +
745A GLY* 4.3 4.7 - - - -
793A THR 3.6 4.7 - - - +
794A ALA* 1.3 80.7 - - + +
796A VAL* 1.3 57.8 + - - -
798A VAL* 3.7 11.6 - - + +
799A PHE* 2.9 28.9 + - - +
1071A ILE* 5.6 1.3 - - + +
1074A TYR* 3.8 28.3 - - + +
1075A HIS* 4.4 14.4 - - + +
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Residues in contact with VAL 796 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A TRP* 3.3 54.1 - - + +
744A TRP* 3.8 41.1 - - + -
756A VAL* 5.3 4.9 - - + -
794A ALA* 3.3 3.5 - - + -
795A PRO* 1.3 76.4 - - - +
797A VAL* 1.3 61.8 + - + +
799A PHE* 3.2 4.3 + - + +
800A HIS* 2.9 48.9 + - + +
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Residues in contact with VAL 797 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A LEU* 5.5 1.3 - - + -
756A VAL* 6.0 4.9 - - + +
760A MET* 6.0 4.9 - - + -
791A PHE* 3.4 44.6 - - + +
792A PHE* 3.7 37.5 - - + +
794A ALA* 3.1 15.1 + - + +
796A VAL* 1.3 80.6 - - + +
798A VAL* 1.3 57.5 + - + +
800A HIS* 3.2 7.8 + - + +
801A LEU* 2.9 41.3 + - + +
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Residues in contact with VAL 798 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A PHE 3.8 16.8 - - - +
793A THR 4.6 3.8 - - - +
794A ALA 3.3 17.0 + - - +
795A PRO* 3.9 11.4 - - + +
796A VAL 3.3 0.2 - - - -
797A VAL* 1.3 75.8 - - + +
799A PHE* 1.3 57.7 + - - +
801A LEU* 3.9 7.3 - - + +
802A ASN* 2.9 30.8 + - + +
1074A TYR* 5.1 10.3 - - + +
1077A ARG* 4.7 17.3 - - + +
1078A PRO 4.1 8.3 - - - +
1079A ALA* 4.1 32.5 - - + +
1080A ALA 5.3 4.0 - - - +
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Residues in contact with PHE 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743A TRP* 3.9 20.9 - + + -
795A PRO 2.9 19.6 + - - +
796A VAL* 3.5 6.3 - - + +
798A VAL* 1.3 76.6 - - - +
800A HIS* 1.3 73.5 + + - +
802A ASN* 3.4 4.1 + - + +
803A ILE* 2.9 40.1 + - + +
912A HIS* 5.9 5.8 - + - -
913A ILE* 4.8 24.5 - - + -
916A ILE* 4.0 31.4 - - + -
1070A LEU* 5.7 4.5 - - + -
1074A TYR* 3.5 41.2 - + + -
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Residues in contact with HIS 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A LEU* 5.4 9.9 + - + +
756A VAL* 5.2 10.4 - - + +
757A THR* 4.9 14.7 - - + +
760A MET* 3.7 27.3 - - + +
796A VAL* 2.9 41.0 + - + +
797A VAL* 3.2 6.0 + - - +
799A PHE* 1.3 88.5 - + - +
801A LEU* 1.3 62.0 + - - +
803A ILE* 3.2 15.9 - - + +
804A LEU* 3.0 34.0 + - + +
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Residues in contact with LEU 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A MET* 3.7 32.1 - - + -
792A PHE* 5.0 12.6 - - + -
797A VAL* 2.9 32.5 + - + +
798A VAL* 4.0 6.3 - - + +
800A HIS* 1.3 75.7 - - - +
802A ASN* 1.3 57.8 + - - +
804A LEU* 3.8 6.3 - - + +
805A SER* 3.0 29.5 + - - -
1079A ALA 5.4 4.3 - - - +
1081A PRO* 4.7 28.2 - - + +
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Residues in contact with ASN 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798A VAL* 2.9 20.5 + - + +
799A PHE* 3.7 6.3 - - - +
801A LEU* 1.3 76.9 - - - +
803A ILE* 1.3 58.8 + - - +
805A SER* 3.4 5.6 + - - -
806A TYR* 2.9 30.0 + - - +
1074A TYR* 4.2 10.9 + - + +
1077A ARG* 3.1 32.1 + - - +
1080A ALA 5.0 4.8 + - - -
1081A PRO* 5.4 1.7 - - + +
1082A PRO* 3.5 31.3 - - - +
1085A ILE* 6.2 1.2 - - - +
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Residues in contact with ILE 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799A PHE* 2.9 31.2 + - + +
800A HIS* 3.2 27.6 - - + +
802A ASN* 1.3 78.2 - - - +
804A LEU* 1.3 68.7 + - + +
806A TYR* 3.7 9.7 - - + +
807A PHE* 2.9 27.9 + - + +
910A LEU* 3.9 15.9 - - + -
913A ILE* 3.8 39.5 - - + -
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Residues in contact with LEU 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760A MET* 4.7 20.2 - - + -
800A HIS* 3.0 30.3 + - + +
801A LEU* 3.8 8.7 - - + +
803A ILE* 1.3 85.7 - - + +
805A SER* 1.3 59.7 + - - +
807A PHE* 3.3 14.1 + - + +
808A ALA* 3.0 28.4 + - - +
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Residues in contact with SER 805 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801A LEU 3.0 17.4 + - - -
802A ASN 3.8 1.1 - - - -
803A ILE 3.4 0.2 - - - -
804A LEU* 1.3 75.5 - - - +
806A TYR* 1.3 58.6 + - - +
808A ALA* 3.4 4.6 + - - +
809A PHE 2.9 23.0 + - - -
835A TRP* 3.2 28.3 + - - -
1081A PRO* 4.3 8.7 - - - -
1082A PRO* 3.3 32.1 - - - +
1083A PRO* 3.4 4.5 - - - +
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Residues in contact with TYR 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A ASN* 2.9 22.4 + - - +
803A ILE* 3.7 12.8 - - + +
804A LEU 3.3 0.2 - - - -
805A SER* 1.3 78.5 + - - +
807A PHE* 1.3 56.0 + - - +
809A PHE* 3.3 23.1 + + - +
810A LEU* 3.0 39.7 + - + +
835A TRP* 5.4 2.0 - - - +
839A LEU* 4.4 22.4 - - + -
906A PHE* 2.7 37.5 + + - +
909A ARG* 3.3 25.3 - - + +
910A LEU* 3.6 39.3 - - + -
1082A PRO* 6.2 1.3 - - + -
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Residues in contact with PHE 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803A ILE* 2.9 17.9 + - + +
804A LEU* 3.3 16.6 + - + +
806A TYR* 1.3 79.6 - - - +
808A ALA* 1.3 58.4 + - - +
810A LEU* 3.2 9.5 + - + +
811A CYS* 3.0 33.8 + - + +
910A LEU* 4.4 24.7 - - + -
939D PHE* 5.7 9.2 - + - -
943D VAL* 5.5 8.3 - - + -
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Residues in contact with ALA 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A LEU 3.0 16.3 + - - +
805A SER* 3.8 6.5 - - - +
806A TYR 3.4 0.2 - - - -
807A PHE* 1.3 75.7 - - - +
809A PHE* 1.3 60.2 + - - +
811A CYS* 3.4 6.5 + - - +
812A LEU* 3.0 32.1 + - - +
835A TRP* 4.7 9.4 - - + -
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Residues in contact with PHE 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A SER 2.9 18.1 + - - +
806A TYR* 3.4 27.8 - + - +
808A ALA* 1.3 76.3 - - - +
810A LEU* 1.3 68.9 - - + +
812A LEU* 3.5 3.2 + - + +
813A PHE* 2.9 41.9 + + + +
832A ILE* 4.1 26.0 - - + -
835A TRP* 3.4 60.0 - + + +
836A LEU* 4.7 22.0 - - + -
839A LEU* 5.3 4.0 - - + -
906A PHE* 4.9 17.5 - + - -
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Residues in contact with LEU 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A TYR* 3.0 32.3 + - + +
807A PHE* 3.2 11.6 + - + +
809A PHE* 1.3 87.9 - - + +
811A CYS* 1.3 56.3 + - - +
813A PHE* 3.3 5.8 + - + +
814A ALA* 3.0 29.1 + - - +
903A PHE* 3.8 26.8 - - + -
906A PHE* 4.1 26.7 - - + +
907A CYS* 4.0 20.4 - - + +
910A LEU* 3.9 28.0 - - + -
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Residues in contact with CYS 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
807A PHE* 3.0 26.2 + - + +
808A ALA* 3.4 6.7 + - - +
810A LEU* 1.3 75.3 - - - +
812A LEU* 1.3 58.5 + - - +
814A ALA* 3.3 7.4 + - - +
815A TYR* 3.0 28.1 + - - +
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Residues in contact with LEU 812 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A ALA 3.0 17.5 + - - +
809A PHE* 4.0 4.7 - - + +
811A CYS* 1.3 77.5 - - - +
813A PHE* 1.3 58.9 + - - +
815A TYR* 3.3 10.8 + - + +
816A VAL* 3.0 46.2 + - + +
828A CYS* 4.7 12.6 - - + +
831A ALA* 5.2 7.4 - - + -
832A ILE* 3.7 24.2 - - + -
835A TRP* 5.3 14.4 - - + -
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Residues in contact with PHE 813 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A PHE* 2.9 33.1 + + + +
810A LEU* 3.7 10.3 - - + +
811A CYS 3.3 0.2 - - - -
812A LEU* 1.3 77.9 - - - +
814A ALA* 1.3 55.4 + - - +
816A VAL* 3.4 2.3 + - - +
817A LEU* 2.9 50.3 + - + +
832A ILE* 3.6 41.0 - - + +
879A PHE* 4.3 19.3 - + - -
899A LEU* 4.0 22.7 - - + -
902A ASP* 4.9 7.2 - - - -
903A PHE* 3.4 47.8 - + + -
906A PHE* 5.5 6.5 - + - -
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Residues in contact with ALA 814 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810A LEU 3.0 17.1 + - - +
811A CYS* 3.7 7.9 - - - +
812A LEU 3.3 0.2 - - - -
813A PHE* 1.3 77.2 - - - +
815A TYR* 1.3 57.1 + - - +
817A LEU* 3.4 6.5 + - - +
818A MET* 2.9 35.1 + - - +
903A PHE* 3.8 25.8 - - + -
950D VAL* 5.0 13.0 - - + +
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Residues in contact with TYR 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A CYS* 3.0 18.9 + - - +
812A LEU* 3.7 11.2 - - + +
813A PHE 3.3 0.2 - - - -
814A ALA* 1.3 77.1 - - - +
816A VAL* 1.3 73.7 + - + +
818A MET* 3.4 12.5 + - + +
819A VAL* 3.4 39.7 + - + +
820A ASP* 3.8 9.4 + - + +
828A CYS* 5.5 8.3 - - - -
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Residues in contact with VAL 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A LEU* 3.0 31.3 + - + +
813A PHE* 3.9 4.0 - - + +
815A TYR* 1.3 84.7 - - + +
817A LEU* 1.3 63.1 + - - +
820A ASP* 3.1 37.4 + - + +
821A PHE* 3.1 14.1 + - + -
828A CYS* 3.7 28.5 - - + +
829A GLU* 4.8 13.0 - - + +
832A ILE* 4.1 22.4 - - + -
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Residues in contact with LEU 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A PHE* 2.9 37.0 + - + +
814A ALA* 3.9 6.1 - - - +
816A VAL* 1.3 78.5 - - - +
818A MET* 1.3 60.7 + - + +
821A PHE* 4.3 9.0 - - + +
896A ARG* 2.8 33.0 + - + +
899A LEU* 3.3 46.4 - - + +
900A SER* 3.8 11.9 - - - +
903A PHE* 4.2 10.1 - - + -
950D VAL* 6.1 2.5 - - + -
954D ALA* 3.7 28.3 - - + -
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Residues in contact with MET 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814A ALA* 2.9 21.3 + - - +
815A TYR* 3.9 6.5 - - + +
816A VAL 3.2 0.4 - - - -
817A LEU* 1.3 80.1 - - + +
819A VAL* 1.3 76.8 + - + +
821A PHE 5.0 0.2 - - - -
896A ARG* 2.6 24.0 + - - +
950D VAL* 4.1 27.8 - - + -
953D GLN* 3.4 32.1 - - - +
954D ALA* 5.4 6.1 - - + +
959D ASN* 4.0 8.3 - - - +
960D GLU 5.5 4.3 - - - +
967D PHE* 6.5 1.3 - - + -
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Residues in contact with VAL 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A TYR* 3.4 39.2 + - + +
818A MET* 1.3 95.5 - - + +
820A ASP* 1.3 63.5 + - + +
821A PHE 3.2 14.5 + - - +
959D ASN* 4.1 16.0 - - + +
960D GLU 4.5 19.5 - - - +
961D ARG* 5.4 6.3 - - + -
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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