Contacts of the helix formed by residues 831 - 857 (chain A) in PDB entry 3W5D
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 831 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A SER* 1.3 67.9 - - - +
832A TRP* 1.3 65.8 + - - -
834A PHE* 3.1 20.2 + - - +
835A PHE* 3.2 10.7 + - - +
1005A PTY 2.9 48.8 - - - +
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Residues in contact with TRP 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A SER 3.5 3.2 + - - +
831A GLY* 1.3 71.8 - - - -
833A LEU* 1.3 67.2 + - + +
835A PHE* 3.0 34.2 + + - +
836A ARG* 2.9 55.0 + - + +
919A ASN* 5.5 0.4 - - - -
984A LEU* 3.3 32.0 + - + -
987A ILE* 3.3 37.7 - - + -
988A ALA* 3.7 22.0 - - + +
992A LEU* 3.7 26.5 - - + -
1005A PTY 3.5 33.3 + - + +
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Residues in contact with LEU 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762A ARG* 3.2 35.0 - - - +
828A LEU 4.3 6.1 - - - +
829A ILE* 4.3 4.3 - - + -
830A SER* 3.8 22.1 + - - +
831A GLY 3.1 0.4 - - - -
832A TRP* 1.3 95.1 - - + +
834A PHE* 1.3 64.8 + - - +
836A ARG* 4.2 21.1 - - - +
837A TYR* 3.1 48.6 + - + +
918A GLU* 3.8 21.5 - - - +
919A ASN* 5.3 1.3 - - - +
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Residues in contact with PHE 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A ILE* 4.0 20.9 - - + +
830A SER* 5.0 0.9 - - - -
831A GLY 3.1 20.9 + - - +
833A LEU* 1.3 78.8 - - - +
835A PHE* 1.3 54.7 + - - +
837A TYR* 4.0 1.5 - - - +
838A MET* 2.8 69.8 + - + +
1005A PTY 4.9 17.0 - - + -
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Residues in contact with PHE 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A GLY 3.2 7.8 + - - +
832A TRP* 3.0 38.3 + + - +
834A PHE* 1.3 80.7 - - - +
836A ARG* 1.3 59.8 + - - +
838A MET* 3.1 8.2 + - + +
839A ALA* 2.7 44.2 + - + +
984A LEU* 4.1 21.8 - - + -
1005A PTY 4.4 27.6 - - + +
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Residues in contact with ARG 836 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A TRP* 2.9 52.0 + - + +
833A LEU* 3.6 18.1 - - - +
835A PHE* 1.3 73.6 - - - +
837A TYR* 1.3 80.6 + - + +
839A ALA* 3.2 2.6 + - - +
840A ILE* 2.8 40.2 + - - +
914A ASN 4.6 3.2 + - - -
917A SER 5.2 0.2 + - - -
918A GLU* 2.8 39.2 + - - +
919A ASN* 3.7 11.0 - - - +
981A ASP* 2.9 40.3 + - - +
984A LEU* 3.9 26.2 - - + +
985A LYS* 4.0 11.3 - - - +
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Residues in contact with TYR 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759A GLN* 5.0 5.9 + - - -
762A ARG* 3.6 45.7 + - + +
763A TYR* 5.7 1.1 - - - -
766A SER* 3.7 36.1 + - - -
769A VAL* 4.0 11.0 - - + +
829A ILE* 4.5 16.8 - - + -
833A LEU* 3.1 38.1 + - + +
834A PHE* 4.3 2.2 - - - +
836A ARG* 1.3 106.2 + - + +
838A MET* 1.3 58.1 - - - +
840A ILE* 3.9 11.8 - - + +
841A GLY* 2.7 29.8 + - - -
911A ASN* 5.2 7.4 - - - -
915A SER* 5.6 4.0 + - - -
918A GLU* 5.5 2.8 - - - +
981A ASP* 5.5 1.6 - - - -
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Residues in contact with MET 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769A VAL* 3.7 32.5 - - + -
773A VAL* 5.4 6.3 - - + -
834A PHE* 2.8 56.4 + - + +
835A PHE* 3.3 11.0 - - + +
837A TYR* 1.3 76.8 - - - +
839A ALA* 1.3 56.8 + - - +
841A GLY* 3.3 1.0 + - - -
842A GLY* 2.9 25.6 + - - -
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Residues in contact with ALA 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A PHE* 2.7 34.0 + - + +
836A ARG 3.6 4.0 - - - +
838A MET* 1.3 68.9 - - - +
840A ILE* 1.3 67.2 + - - +
842A GLY* 3.3 2.8 + - - +
843A TYR* 3.0 23.4 + - - +
980A LEU* 4.2 10.7 - - + +
984A LEU* 4.4 15.0 - - + -
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Residues in contact with ILE 840 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A SER* 3.9 17.3 - - - +
836A ARG 2.8 32.4 + - - +
837A TYR* 3.9 14.4 - - + +
839A ALA* 1.3 71.2 - - - +
841A GLY* 1.3 64.2 + - - +
843A TYR* 3.3 2.6 + - - +
844A VAL* 3.0 34.8 + - + +
911A ASN* 3.9 22.4 - - - +
977A VAL* 4.6 7.4 - - + -
980A LEU* 3.7 30.1 - - + -
981A ASP* 3.6 35.2 - - + +
984A LEU* 4.2 4.0 - - + -
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Residues in contact with GLY 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A SER 4.7 2.7 - - - -
769A VAL* 3.7 17.9 - - - -
770A GLY* 3.6 15.8 - - - -
773A VAL* 4.2 5.7 - - - +
837A TYR 2.7 23.2 + - - -
838A MET 3.6 1.1 - - - -
840A ILE* 1.3 70.8 - - - +
842A GLY* 1.3 66.5 + - - +
844A VAL* 2.9 4.5 + - - -
845A GLY* 2.9 21.3 + - - -
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Residues in contact with GLY 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773A VAL* 3.9 16.4 - - - +
838A MET* 2.9 17.6 + - - +
839A ALA* 3.3 4.7 + - - -
841A GLY* 1.3 71.0 - - - +
843A TYR* 1.3 61.6 + - - +
845A GLY* 3.2 1.2 + - - -
846A ALA* 2.9 24.8 + - - +
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Residues in contact with TYR 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839A ALA 3.0 15.7 + - - +
840A ILE 3.8 3.6 - - - +
842A GLY* 1.3 74.6 - - - +
844A VAL* 1.3 58.3 + - - +
846A ALA* 3.8 6.2 - - + +
847A ALA* 2.9 35.9 + - + +
907A ILE* 3.8 16.8 - - + -
973A ILE* 2.5 36.3 + - + +
976A PRO* 2.8 25.7 - - + +
977A VAL* 3.9 32.3 - - + -
980A LEU* 3.9 18.6 - - + -
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Residues in contact with VAL 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766A SER 5.9 1.8 - - - +
770A GLY* 4.1 16.2 - - - -
840A ILE* 3.0 32.2 + - + +
841A GLY* 2.9 5.1 + - - +
843A TYR* 1.3 76.7 - - - +
845A GLY* 1.3 63.2 + - - +
847A ALA* 3.4 1.7 + - - +
848A THR* 3.1 27.2 + - + +
904A LEU* 4.1 20.6 - - + -
907A ILE* 3.5 38.4 - - + -
908A GLU* 4.0 19.1 - - - +
911A ASN* 6.0 0.7 - - - -
977A VAL* 4.7 4.3 - - + -
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Residues in contact with GLY 845 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A GLY 3.3 21.9 + - - -
773A VAL* 3.4 21.3 - - - -
774A CYS* 3.7 3.6 - - - -
777A LEU* 4.0 1.3 - - - -
841A GLY 2.9 9.7 + - - -
844A VAL* 1.3 78.8 - - - +
846A ALA* 1.3 58.4 + - - +
848A THR* 3.0 15.8 + - - -
849A VAL* 3.3 19.1 - - - +
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Residues in contact with ALA 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777A LEU* 3.7 18.9 - - + +
842A GLY 2.9 17.6 + - - +
843A TYR* 3.8 9.6 - - + +
845A GLY* 1.3 73.8 - - - +
847A ALA* 1.3 59.5 + - - +
848A THR 3.2 0.2 + - - -
849A VAL* 3.4 2.4 + - - +
850A GLY* 2.8 29.3 + - - -
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Residues in contact with ALA 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A TYR* 2.9 25.0 + - + +
844A VAL 3.7 4.9 - - - +
846A ALA* 1.3 77.4 - - - +
848A THR* 1.3 57.4 + - - +
851A ALA* 2.9 28.1 + - - +
903A VAL* 3.8 6.9 - - + +
907A ILE* 3.8 22.4 - - + -
973A ILE* 3.6 33.5 - - + +
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Residues in contact with THR 848 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A GLY 4.9 0.2 + - - -
774A CYS* 3.2 26.1 - - - +
786A ALA* 4.9 0.2 - - - -
787A LEU* 4.6 4.0 - - + -
844A VAL* 3.1 14.3 + - + +
845A GLY* 3.0 15.9 + - - -
847A ALA* 1.3 74.6 - - - +
849A VAL* 1.3 65.6 + - - +
851A ALA* 3.2 9.0 + - - +
852A ALA* 3.3 8.7 + - - +
900A ALA* 3.3 41.3 - - - +
903A VAL* 3.9 7.0 - - + -
904A LEU* 3.7 31.0 - - + +
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Residues in contact with VAL 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A CYS* 3.6 28.4 - - - +
777A LEU* 3.9 18.2 - - + -
778A THR* 4.4 7.6 - - - +
781A LEU* 4.8 9.4 - - + -
783A LEU* 3.5 32.1 - - + -
786A ALA* 4.5 9.6 - - + -
845A GLY 3.3 15.3 - - - +
846A ALA 3.4 4.9 + - - +
848A THR* 1.3 75.8 + - - +
850A GLY* 1.3 58.3 + - - +
852A ALA* 2.9 10.1 + - + +
853A ALA* 2.8 28.2 + - + +
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Residues in contact with GLY 850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A ALA 2.8 21.1 + - - -
847A ALA 3.8 1.8 - - - -
849A VAL* 1.3 73.8 - - - +
851A ALA* 1.3 55.7 + - - +
853A ALA* 3.9 8.4 - - - +
854A TRP* 3.1 29.5 + - - +
973A ILE* 4.7 9.6 - - - +
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Residues in contact with ALA 851 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847A ALA 2.9 19.5 + - - +
848A THR 3.4 6.7 - - - +
849A VAL 3.1 0.4 - - - -
850A GLY* 1.3 74.4 - - - +
852A ALA* 1.3 66.7 + - - +
854A TRP* 3.7 5.5 + - - +
855A TRP 3.6 10.9 + - - -
899A MET* 3.4 37.9 - - + +
900A ALA* 4.0 0.7 - - - +
903A VAL* 3.4 27.1 - - + -
969A MET* 6.3 2.5 - - - -
973A ILE* 4.5 5.8 - - + +
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Residues in contact with ALA 852 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784A PRO 5.8 2.2 - - - +
786A ALA* 4.6 12.8 - - + -
848A THR 3.3 7.4 + - - +
849A VAL* 2.9 9.3 + - + +
851A ALA* 1.3 76.3 - - - +
853A ALA* 1.3 65.3 + - - +
855A TRP* 3.0 15.8 + - - +
856A PHE* 3.0 23.1 + - + -
896A PRO* 3.8 35.2 + - + +
899A MET* 4.3 0.4 - - - +
900A ALA* 4.5 4.7 - - + -
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Residues in contact with ALA 853 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A LEU* 5.1 15.7 - - + -
849A VAL* 2.8 23.3 + - + +
850A GLY* 3.9 9.6 - - - +
852A ALA* 1.3 72.4 - - - +
854A TRP* 1.3 56.3 + - - +
856A PHE* 3.0 14.5 + - - +
857A MET* 2.9 50.9 + - + +
870A LEU* 5.8 0.2 - - - -
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Residues in contact with TRP 854 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850A GLY 3.1 19.5 + - - +
851A ALA* 3.8 4.3 - - - +
852A ALA 3.2 0.4 + - - -
853A ALA* 1.3 76.5 - - - +
855A TRP* 1.3 79.6 + + + +
857A MET* 4.4 1.5 - - - +
858A TYR* 3.0 56.5 + + + +
859A ALA* 3.1 29.4 + - + -
860A GLU* 5.7 0.9 - - - -
899A MET* 3.7 36.8 - - + -
965A THR* 4.3 17.7 - - + -
966A GLN* 4.1 20.6 - - + -
969A MET* 3.8 46.1 - - + -
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Residues in contact with TRP 855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A ALA 3.6 5.1 + - - +
852A ALA 3.0 9.2 + - - +
854A TRP* 1.3 90.0 - + + +
856A PHE* 1.3 89.8 + + - +
857A MET 3.1 0.7 + - - -
859A ALA* 3.7 29.2 - - + +
861A ASP* 3.3 32.8 + - + +
862A GLY* 3.5 35.3 - - - -
863A PRO* 4.4 2.7 - - + -
890A ILE* 4.5 8.1 - - + -
893A ALA* 3.7 20.9 - - + -
895A GLU* 3.3 37.4 - - + +
896A PRO* 3.6 23.1 - - + -
899A MET* 4.2 8.7 - - + -
966A GLN* 3.6 19.0 + - - -
----------------------------------------------------------
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Residues in contact with PHE 856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A LEU* 5.4 1.3 - - + -
784A PRO* 3.9 24.2 - - + -
852A ALA* 3.0 27.5 + - + -
853A ALA* 3.0 13.4 + - - +
855A TRP* 1.3 93.8 - + - +
857A MET* 1.3 54.6 + - + +
863A PRO* 2.6 31.1 - - + +
865A VAL* 3.4 17.0 - - - +
870A LEU* 3.6 32.8 - - + -
890A ILE* 3.7 22.4 - - + -
891A PHE* 3.8 25.1 - + - -
896A PRO* 3.5 30.3 - - + -
----------------------------------------------------------
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Residues in contact with MET 857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A ALA* 2.9 38.5 + - + +
854A TRP* 4.5 0.9 - - - +
855A TRP 3.1 0.4 - - - -
856A PHE* 1.3 81.9 - - + +
858A TYR* 1.3 87.5 + - + +
859A ALA 2.8 19.8 + - - +
863A PRO 3.3 9.1 - - - +
864A GLY* 3.4 12.6 - - - -
865A VAL* 3.5 19.7 - - + +
866A THR* 4.2 8.6 - - - +
867A TYR* 3.7 28.7 - - + -
868A HIS 5.2 0.4 - - - -
869A GLN* 5.7 3.6 - - - +
870A LEU* 6.1 2.7 - - + -
----------------------------------------------------------
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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