Contacts of the helix formed by residues 860 - 899 (chain A) in PDB entry 4KSC
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 ILE 860 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A LEU* 3.1 21.3 - - + +
857A LEU* 3.1 8.9 + - + +
859A ALA* 1.3 86.7 - - + +
861A VAL* 1.3 63.0 + - + +
862A PRO 3.4 1.6 - - - -
863A ILE* 2.9 6.3 + - - +
864A ILE* 2.8 48.4 + - + +
944A MET* 5.3 0.7 - - + -
947A PHE* 3.5 42.0 - - + +
948A SER* 3.3 35.2 - - - +
951A ALA* 4.6 11.2 - - + -
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Residues in contact with VAL 861 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 3.1 33.5 + - + +
858A LEU* 4.9 0.2 - - - -
860A ILE* 1.3 83.2 - - + +
862A PRO* 1.3 71.3 - - + +
864A ILE* 3.2 16.6 - - + +
865A ALA* 2.9 27.3 + - + +
976A ALA 5.9 1.6 - - - +
977A ILE* 5.3 15.3 - - + -
980A GLY* 5.3 13.7 - - - -
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Residues in contact with PRO 862 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A LEU* 3.1 41.3 - - + +
861A VAL* 1.3 95.0 - - + +
863A ILE* 1.3 62.2 + - + +
865A ALA* 3.2 5.8 + - + +
866A ILE* 2.8 44.2 + - + +
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Residues in contact with ILE 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A LEU 4.3 5.2 - - - +
859A ALA* 3.3 33.0 - - - +
860A ILE 2.9 6.8 + - - +
862A PRO* 1.3 84.5 - - + +
864A ILE* 1.3 54.2 + - - +
866A ILE* 3.4 8.5 + - + +
867A ALA* 2.8 37.7 + - + +
940A PHE* 6.0 2.2 - - + -
944A MET* 3.8 27.4 - - + -
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Residues in contact with ILE 864 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A ILE* 2.8 40.0 + - + +
861A VAL* 3.2 24.5 - - + +
863A ILE* 1.3 69.3 - - - +
865A ALA* 1.3 63.7 + - - +
867A ALA* 3.7 8.9 - - - +
868A GLY* 2.8 23.2 + - - -
941A THR* 6.1 0.9 - - - +
944A MET* 3.6 36.8 - - + -
948A SER* 4.2 7.4 - - - +
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Residues in contact with ALA 865 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A VAL* 2.9 22.4 + - + +
862A PRO* 3.4 8.3 - - + +
863A ILE 3.2 0.2 - - - -
864A ILE* 1.3 76.9 - - + +
866A ILE* 1.3 55.2 + - + +
868A GLY* 2.9 4.0 + - - -
869A VAL* 2.6 41.8 + - + +
984A VAL* 5.5 10.8 - - + -
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Residues in contact with ILE 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A PRO* 2.8 32.5 + - + +
863A ILE* 3.9 7.2 - - + +
865A ALA* 1.3 73.0 - - + +
867A ALA* 1.3 54.6 + - - +
869A VAL* 3.8 13.7 - - + -
870A VAL* 2.6 40.5 + - + +
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Residues in contact with ALA 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A ILE* 2.8 24.8 + - + +
864A ILE* 3.7 10.3 - - - +
866A ILE* 1.3 73.4 - - - +
868A GLY* 1.3 60.0 + - - +
870A VAL* 3.4 21.7 - - - +
871A GLU* 3.5 13.2 + - - +
940A PHE* 3.9 32.1 - - + -
941A THR* 4.9 7.1 + - - -
944A MET* 4.8 4.7 - - + -
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Residues in contact with GLY 868 (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 ILE 2.8 16.4 + - - -
865A ALA* 3.2 5.2 - - - -
867A ALA* 1.3 77.9 - - - +
869A VAL* 1.3 60.7 + - - +
871A GLU* 3.8 11.9 - - - +
872A MET* 3.5 17.7 + - - +
941A THR* 5.5 6.5 - - - -
----------------------------------------------------------
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Residues in contact with VAL 869 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A ALA* 2.6 25.0 + - + +
866A ILE* 2.9 16.6 + - + +
868A GLY* 1.3 71.3 - - - +
870A VAL* 1.3 63.1 + - - +
871A GLU 3.1 1.6 - - - -
872A MET* 3.0 24.1 + - + +
873A LYS* 3.2 13.3 + - + +
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Residues in contact with VAL 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A ILE* 2.6 28.8 + - + +
867A ALA* 3.4 16.6 - - - +
869A VAL* 1.3 76.1 - - + +
871A GLU* 1.3 64.4 + - - +
873A LYS* 3.5 8.6 + - + +
874A MET* 3.1 31.2 + - + +
940A PHE* 6.5 0.4 - - + -
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Residues in contact with GLU 871 (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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867A ALA 3.5 14.2 + - - +
868A GLY* 3.8 9.0 - - - +
869A VAL 3.1 0.2 - - - -
870A VAL* 1.3 81.6 - - + +
872A MET* 1.3 56.1 + - - +
874A MET* 3.3 5.9 + - - +
875A LEU* 2.8 47.1 + - + +
937A THR* 4.2 30.3 + - + +
938A PHE* 5.0 9.4 + - - +
941A THR* 2.6 32.7 + - - +
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Residues in contact with MET 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A GLY 3.5 9.4 + - - +
869A VAL* 3.0 14.4 + - - +
871A GLU* 1.3 79.0 - - - +
873A LYS* 1.3 69.5 + - - +
875A LEU* 3.5 12.9 + - + +
876A SER* 3.3 33.4 + - - +
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Residues in contact with LYS 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A VAL* 3.2 12.3 + - + +
870A VAL* 3.8 12.6 - - + +
871A GLU 3.2 0.2 - - - -
872A MET* 1.3 83.0 - - - +
874A MET* 1.3 61.7 + - + +
876A SER* 3.5 4.4 + - - -
877A GLY* 2.9 36.0 + - - +
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Residues in contact with MET 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A VAL* 3.1 22.7 + - + +
871A GLU* 3.7 5.8 - - - +
873A LYS* 1.3 80.9 - - + +
875A LEU* 1.3 56.9 + - - +
877A GLY* 3.6 3.2 - - - -
878A GLN* 2.9 53.6 + - + +
933A VAL* 4.1 23.6 - - + -
937A THR* 5.1 9.2 - - + -
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Residues in contact with LEU 875 (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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871A GLU* 2.8 30.2 + - + +
872A MET* 3.6 12.1 - - + +
873A LYS 3.2 0.2 - - - -
874A MET* 1.3 76.2 - - - +
876A SER* 1.3 72.2 + - - +
878A GLN* 3.2 7.9 + - - +
879A ALA* 2.9 28.8 + - + +
934A PHE* 4.5 27.8 - - + -
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Residues in contact with SER 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A MET* 3.3 27.4 + - - +
873A LYS* 4.2 4.7 - - - -
875A LEU* 1.3 85.0 - - - +
877A GLY* 1.3 57.0 + - - +
879A ALA* 3.4 10.5 - - - +
880A LEU* 2.7 36.9 + - - +
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Residues in contact with GLY 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A LYS* 2.9 30.2 + - - +
874A MET* 3.6 5.8 - - - -
875A LEU 3.2 0.2 - - - -
876A SER* 1.3 77.4 - - - +
878A GLN* 1.3 60.4 + - - +
880A LEU* 4.0 5.6 - - - +
881A LYS* 3.2 24.9 + - - +
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Residues in contact with GLN 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A MET* 2.9 39.5 + - + +
875A LEU* 3.5 5.2 - - - +
877A GLY* 1.3 77.4 - - - +
879A ALA* 1.3 64.3 + - - +
881A LYS* 4.0 9.3 - - - +
882A ASP* 3.1 26.5 + - - +
926A ASN* 4.2 19.4 + - - +
929A LYS* 5.5 9.8 - - - +
930A LYS* 4.4 15.2 - - + +
933A VAL* 4.2 28.9 - - + +
934A PHE* 4.4 20.4 - - + -
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Residues in contact with ALA 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A LEU* 2.9 18.3 + - + +
876A SER* 3.1 14.3 + - - +
878A GLN* 1.3 78.1 - - - +
880A LEU* 1.3 61.1 + - - +
882A ASP* 3.7 4.9 - - - +
883A LYS* 3.2 38.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A SER 2.7 19.3 + - - +
877A GLY* 4.0 7.2 - - - +
879A ALA* 1.3 72.1 - - - +
881A LYS* 1.3 66.0 + - - +
883A LYS* 3.2 18.6 + - + +
884A LYS* 3.2 31.2 + - + +
----------------------------------------------------------
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Residues in contact with LYS 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A GLY 3.2 16.7 + - - +
878A GLN* 4.2 11.2 - - - +
880A LEU* 1.3 79.2 - - - +
882A ASP* 1.3 59.4 + - - +
884A LYS* 3.5 10.1 + - + +
885A GLU* 3.1 48.9 + - + +
926A ASN* 4.7 12.1 - - - +
929A LYS* 6.3 3.8 - - - +
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Residues in contact with ASP 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878A GLN 3.1 20.0 + - - +
879A ALA* 3.7 5.8 - - - +
881A LYS* 1.3 76.4 - - - +
883A LYS* 1.3 70.5 + - + +
885A GLU* 3.2 24.9 + - - +
886A LEU* 3.2 27.9 + - - +
923A PRO* 4.3 12.0 - - - +
926A ASN* 4.2 15.7 + - - +
930A LYS* 5.7 5.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS 883 (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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176A SER* 6.1 3.8 - - - -
879A ALA* 3.2 23.1 + - + +
880A LEU* 3.2 14.9 + - + +
882A ASP* 1.3 83.8 + - - +
884A LYS* 1.3 59.1 + - + +
886A LEU* 3.3 27.4 - - + +
887A GLU* 3.1 29.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 884 (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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880A LEU* 3.2 30.2 + - + +
881A LYS* 3.7 10.8 - - + +
882A ASP 3.1 0.4 - - - -
883A LYS* 1.3 79.6 - - + +
885A GLU* 1.3 63.7 + - + +
887A GLU* 3.2 34.9 + - - +
888A GLY* 3.5 4.9 + - - -
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Residues in contact with GLU 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A LYS* 3.1 36.0 + - + +
882A ASP* 3.2 8.0 + - - +
884A LYS* 1.3 79.6 - - + +
886A LEU* 1.3 61.7 + - - +
887A GLU 3.3 0.2 + - - -
888A GLY* 3.5 1.9 + - - -
889A SER* 3.4 20.2 + - - -
922A ILE* 4.4 18.1 - - + +
923A PRO* 3.6 24.3 - - + +
926A ASN* 3.6 40.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 5.2 22.0 - - - +
882A ASP* 3.2 37.4 + - - +
883A LYS* 3.3 41.5 - - + +
885A GLU* 1.3 76.8 - - - +
887A GLU* 1.3 57.7 + - + +
888A GLY 3.4 0.2 - - - -
889A SER* 3.5 8.5 - - - -
890A GLY* 2.4 36.1 + - - -
920A LEU* 6.3 1.8 - - + -
923A PRO* 4.6 9.8 - - + +
----------------------------------------------------------
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Residues in contact with GLU 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A LYS 3.1 18.8 + - - +
884A LYS* 3.2 38.5 + - - +
886A LEU* 1.3 79.2 - - + +
888A GLY* 1.3 57.5 + - - +
890A GLY* 3.0 2.2 + - - -
891A LYS* 2.6 77.8 + - + +
----------------------------------------------------------
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Residues in contact with GLY 888 (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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884A LYS 3.5 8.2 + - - -
885A GLU 3.5 3.5 + - - -
886A LEU 3.4 0.2 - - - -
887A GLU* 1.3 79.0 - - - +
889A SER* 1.3 61.3 + - - +
891A LYS* 3.9 7.8 - - - +
892A ILE* 3.1 32.9 + - - +
----------------------------------------------------------
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Residues in contact with SER 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 4.7 3.0 - - - -
885A GLU 3.4 13.4 + - - -
886A LEU* 3.3 11.5 + - - -
887A GLU 3.2 0.4 - - - -
888A GLY* 1.3 75.5 - - - +
890A GLY* 1.3 57.5 + - - +
892A ILE* 3.2 14.5 - - - +
893A ALA* 3.0 27.4 + - - +
916A TYR* 4.3 3.2 - - - -
919A SER* 3.2 37.6 + - - -
920A LEU* 4.1 18.2 - - - -
923A PRO* 5.2 1.1 - - - +
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Residues in contact with GLY 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 5.5 3.6 - - - -
886A LEU 2.4 25.6 + - - -
887A GLU* 3.4 2.5 - - - -
889A SER* 1.3 69.4 - - - +
891A LYS* 1.3 51.8 + - - +
893A ALA* 3.2 7.5 - - - +
894A THR* 2.3 43.1 + - - -
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Residues in contact with LYS 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A GLU* 2.6 58.9 + - + +
888A GLY* 3.9 8.1 - - - +
890A GLY* 1.3 69.0 - - - +
892A ILE* 1.3 57.2 + - + +
893A ALA 3.0 1.1 - - - -
894A THR* 3.0 9.3 + - - -
895A GLU* 2.5 35.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A GLY 3.1 20.3 + - - +
889A SER* 3.2 14.6 - - - +
891A LYS* 1.3 77.1 - - + +
893A ALA* 1.3 53.9 + - - +
895A GLU* 3.5 22.9 - - - +
896A ALA* 3.4 9.9 + - - +
912A PHE* 6.1 0.3 - - - -
915A MET* 5.0 16.6 - - + +
916A TYR* 2.3 40.3 + - + -
919A SER* 3.3 25.8 - - - +
----------------------------------------------------------
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Residues in contact with ALA 893 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A PHE* 3.7 31.9 - - + -
889A SER 3.0 20.6 + - - +
890A GLY* 3.2 10.1 - - - +
892A ILE* 1.3 75.8 - - - +
894A THR* 1.3 63.7 + - - +
896A ALA* 3.2 13.3 + - - +
897A ILE* 3.4 18.4 + - - +
916A TYR* 3.1 14.0 - - + -
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Residues in contact with THR 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY* 6.3 1.3 - - - -
890A GLY 2.3 35.5 + - - -
891A LYS* 3.4 8.9 - - - -
893A ALA* 1.3 72.4 - - - +
895A GLU* 1.3 62.3 + - - +
897A ILE* 3.6 17.0 - - + +
898A GLU* 3.4 32.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A PHE* 3.7 17.0 - - + +
477A ALA* 3.2 37.7 + - - +
478A THR* 5.7 0.3 - - - +
891A LYS 2.5 19.0 + - - +
892A ILE* 3.5 27.2 - - - +
893A ALA 3.1 0.2 - - - -
894A THR* 1.3 74.6 - - - +
896A ALA* 1.3 62.0 + - - +
898A GLU* 3.7 5.4 + - - +
899A ASN* 2.7 39.6 + - - +
912A PHE* 5.3 7.8 - - + -
----------------------------------------------------------
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Residues in contact with ALA 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A MET* 4.7 12.1 - - + -
892A ILE 3.4 1.4 + - - +
893A ALA 3.2 4.2 + - - +
895A GLU* 1.3 77.4 - - - +
897A ILE* 1.3 60.3 + - + +
899A ASN* 2.6 35.9 + - - +
902A THR* 4.3 2.8 - - - +
912A PHE* 3.5 33.9 - - + -
916A TYR* 3.1 27.1 - - + +
----------------------------------------------------------
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Residues in contact with ILE 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 3.6 32.1 - - + -
152A MET* 4.5 12.3 - - - -
158A TRP* 4.8 19.9 + - + -
164A VAL* 4.5 9.2 - - - +
165A GLY* 4.5 13.0 - - - -
168A ASN* 3.3 37.8 - - + +
893A ALA 3.5 16.6 - - - +
894A THR* 3.6 23.1 - - + +
896A ALA* 1.3 78.3 - - + +
898A GLU* 1.3 78.4 + - + +
899A ASN 3.4 4.0 + - - +
900A PHE* 4.5 1.9 + - - +
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Residues in contact with GLU 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL 5.0 8.7 - - - +
523A ARG* 4.2 24.8 + - - +
894A THR* 3.4 24.7 + - + +
895A GLU* 3.9 5.7 - - - +
896A ALA 3.1 0.2 - - - -
897A ILE* 1.3 87.9 - - + +
899A ASN* 1.3 65.1 + - - +
900A PHE* 3.7 13.6 + - - -
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Residues in contact with ASN 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TRP* 5.0 0.7 - - - -
474A VAL* 3.9 27.1 - - + +
476A PHE* 4.2 25.3 - - + -
523A ARG* 4.0 23.7 + - - +
895A GLU* 2.7 28.0 + - - +
896A ALA* 2.6 22.8 + - - +
897A ILE 4.2 1.3 - - - +
898A GLU* 1.3 83.0 + - - +
900A PHE* 1.3 56.4 + - - +
901A ARG* 3.2 13.3 - - + +
902A THR* 3.2 18.1 - - - +
----------------------------------------------------------
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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