Contacts of the helix formed by residues 905 - 942 (chain A) in PDB entry 3RJO
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 LEU 905 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A TRP* 4.2 20.4 - - + -
866A LEU* 3.3 52.7 - - + +
867A GLY* 4.3 8.3 - - - -
868A SER 5.9 0.9 - - - +
871A ILE* 4.4 3.6 - - + -
872A ALA* 6.1 0.7 - - + +
875A VAL* 5.1 0.2 - - + -
895A PHE* 5.4 0.7 - - + -
901A ASN 4.7 4.0 - - - +
903A SER 3.5 5.6 - - - +
904A GLN* 1.3 81.4 - - - +
906A ARG* 1.3 64.3 + - - +
907A CYS* 3.7 23.8 - - - -
908A VAL* 3.3 33.5 + - + +
909A GLN* 3.7 7.8 + - - +
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Residues in contact with ARG 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A MET* 6.2 1.1 - - + -
904A GLN 3.4 4.4 + - - +
905A LEU* 1.3 73.6 - - - +
907A CYS* 1.3 59.2 + - - +
909A GLN* 3.3 14.9 + - + +
910A GLN* 2.9 30.6 + - + +
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Residues in contact with CYS 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A ILE* 5.1 0.2 - - - -
872A ALA* 3.7 33.9 - - + +
875A VAL* 4.2 17.9 - - + -
876A MET* 3.4 33.7 - - + +
905A LEU* 3.7 27.1 - - - -
906A ARG* 1.3 80.3 - - + +
908A VAL* 1.3 53.9 + - - +
910A GLN* 3.7 2.7 - - - +
911A THR* 2.4 38.7 + - - -
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Residues in contact with VAL 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A VAL* 4.5 4.5 - - + -
891A VAL* 5.4 0.8 - - + +
895A PHE* 3.5 56.5 - - + -
903A SER* 4.5 14.1 - - - +
905A LEU* 3.5 33.4 - - + +
906A ARG 3.2 0.4 - - - -
907A CYS* 1.3 77.6 - - - +
909A GLN* 1.3 65.7 + - + +
911A THR* 4.1 4.5 + - - -
912A ILE* 3.1 44.1 + - + +
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Residues in contact with GLN 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A SER 5.6 1.8 + - - -
904A GLN* 4.7 17.8 + - - -
905A LEU 3.7 5.5 + - - +
906A ARG* 3.3 14.1 + - - +
908A VAL* 1.3 80.1 - - + +
910A GLN* 1.3 57.8 + - - +
912A ILE* 3.4 10.8 + - + +
913A GLU* 3.0 40.3 + - - +
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Residues in contact with GLN 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A MET* 4.9 13.7 - - + -
906A ARG* 2.9 19.1 + - + +
907A CYS* 4.2 7.0 - - - +
908A VAL 3.3 0.2 - - - -
909A GLN* 1.3 74.6 - - - +
911A THR* 1.3 62.5 + - - +
913A GLU* 3.4 10.3 + - - +
914A THR* 3.0 32.0 + - + +
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Residues in contact with THR 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A VAL* 3.6 14.7 - - - +
876A MET* 3.8 13.8 - - + +
879A THR* 2.7 32.1 - - - +
880A ASN* 3.5 29.8 - - + +
891A VAL* 5.3 4.9 - - - -
907A CYS 2.4 26.8 + - - -
908A VAL* 4.1 3.1 + - - -
910A GLN* 1.3 72.0 - - - +
912A ILE* 1.3 60.4 + - - +
914A THR* 2.7 18.4 + - - -
915A ILE* 2.8 25.0 + - + +
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Residues in contact with ILE 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LEU* 4.5 12.3 - - + +
891A VAL* 4.3 15.7 - - + -
892A LYS* 3.7 37.9 - - + -
908A VAL* 3.1 38.5 + - + +
909A GLN* 3.7 9.6 - - + +
911A THR* 1.3 76.1 - - - +
913A GLU* 1.3 59.7 + - + +
915A ILE* 3.5 7.7 + - + +
916A GLU* 2.9 48.9 + - - +
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Residues in contact with GLU 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A GLN* 3.0 27.9 + - - +
910A GLN* 3.6 10.0 - - - +
911A THR 3.2 0.2 - - - -
912A ILE* 1.3 78.5 - - + +
914A THR* 1.3 58.6 + - + +
916A GLU* 3.1 15.5 + - - +
917A GLU* 2.9 42.4 + - + +
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Residues in contact with THR 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A ASN* 4.0 23.1 - - + +
910A GLN* 3.0 15.7 + - + +
911A THR* 2.7 25.6 + - - -
913A GLU* 1.3 74.5 - - + +
915A ILE* 1.3 57.6 + - - +
917A GLU* 3.1 15.4 + - - +
918A ASN* 2.8 37.4 + - - +
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Residues in contact with ILE 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A THR* 3.5 32.1 - - - +
880A ASN* 4.6 2.5 - - - -
882A PHE* 3.6 30.5 - - + +
884A THR 4.4 2.2 - - - +
888A LEU* 3.9 30.5 - - + -
891A VAL* 3.8 36.6 - - + -
911A THR* 2.8 28.8 + - + +
912A ILE* 3.8 7.0 - - + +
914A THR* 1.3 70.7 + - - +
916A GLU* 1.3 58.4 + - - +
918A ASN* 3.2 3.2 + - - +
919A ILE* 2.8 39.9 + - + +
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Residues in contact with GLU 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LEU* 3.8 19.5 - - + +
892A LYS* 3.6 22.3 + - - -
912A ILE* 2.9 33.1 + - - +
913A GLU* 3.1 15.5 + - - +
915A ILE* 1.3 76.0 - - - +
917A GLU* 1.3 62.3 + - + +
919A ILE* 3.4 10.3 + - + +
920A GLY* 3.2 17.8 + - - -
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Residues in contact with GLU 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EDO 4.5 7.4 - - - +
913A GLU* 2.9 26.5 + - + +
914A THR* 3.1 14.9 + - - +
916A GLU* 1.3 72.7 - - + +
918A ASN* 1.3 54.3 + - - +
920A GLY* 3.2 3.1 + - - -
921A TRP* 2.8 37.6 + - + +
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Residues in contact with ASN 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EDO 3.4 19.1 + - - -
686A LEU* 4.0 17.5 - - + +
880A ASN 2.7 31.1 + - - -
881A GLN* 4.0 4.6 - - - +
882A PHE 3.0 27.4 + - - +
883A SER* 3.7 9.6 - - - -
914A THR* 2.8 23.8 + - - +
915A ILE* 3.3 6.2 - - - +
917A GLU* 1.3 66.0 - - - +
919A ILE* 1.3 67.1 + - - +
921A TRP* 4.5 1.6 - - - +
922A MET* 2.9 30.3 + - - +
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Residues in contact with ILE 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A SER 3.6 27.6 - - - +
884A THR* 3.8 19.3 - - - +
885A ARG* 3.8 12.1 - - + +
888A LEU* 3.5 33.7 - - + -
915A ILE* 2.8 23.5 + - + +
916A GLU* 3.6 10.5 - - + +
917A GLU 3.3 0.2 - - - -
918A ASN* 1.3 72.2 - - - +
920A GLY* 1.3 63.8 + - - +
922A MET* 3.9 0.5 - - - +
923A ASP* 3.0 47.6 + - - +
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Residues in contact with GLY 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916A GLU 3.2 6.8 + - - -
917A GLU* 3.2 6.5 + - - -
919A ILE* 1.3 80.7 - - - +
921A TRP* 1.3 61.1 + - - +
923A ASP* 4.1 4.5 - - - +
924A LYS* 3.2 25.1 + - - +
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Residues in contact with TRP 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A EDO 3.5 28.6 + - - +
644A PHE 5.3 1.2 + - - -
647A VAL* 4.1 11.5 - - - +
648A SER* 3.6 33.0 + - - -
654A ILE* 4.3 10.5 - - + -
683A MET* 3.4 47.9 - - + +
686A LEU* 3.9 14.8 - - + -
687A MET* 5.9 0.9 - - + -
917A GLU 2.8 21.0 + - - +
918A ASN* 3.3 2.9 + - - +
920A GLY* 1.3 72.8 - - - +
922A MET* 1.3 80.3 + - - +
924A LYS* 3.5 1.5 + - - -
925A ASN* 2.8 60.5 + - + +
929A ILE* 3.7 22.4 - - + -
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Residues in contact with MET 922 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A MET 4.9 2.7 - - - +
686A LEU* 3.7 30.3 - - + -
687A MET* 4.3 9.9 - - + -
690A ARG* 3.7 17.7 - - - +
692A MET* 3.3 43.5 - - + -
883A SER* 3.9 13.5 - - - +
918A ASN 2.9 19.9 + - - +
919A ILE 4.0 1.8 - - - +
921A TRP* 1.3 96.2 - - - +
923A ASP* 1.3 63.3 + - - +
925A ASN 4.3 0.2 - - - +
926A PHE* 2.8 46.3 + - + +
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Residues in contact with ASP 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ARG* 5.0 7.6 + - - -
883A SER 4.8 4.5 - - - +
919A ILE* 3.0 37.0 + - - +
920A GLY* 4.1 4.2 - - - +
922A MET* 1.3 78.5 - - - +
924A LYS* 1.3 61.8 + - - +
926A PHE 4.8 0.3 + - - -
927A ASP* 5.0 9.2 + - - +
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Residues in contact with LYS 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A VAL* 5.1 6.2 + - + +
650A GLY* 4.1 25.1 + - - -
652A LEU 5.9 0.4 + - - -
920A GLY 3.2 17.6 + - - +
921A TRP* 3.9 3.1 - - - +
923A ASP* 1.3 80.2 - - - +
925A ASN* 1.3 78.7 + - - +
926A PHE 3.7 0.4 + - - -
927A ASP* 4.7 2.5 + - - +
928A LYS* 3.3 35.7 + - - +
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Residues in contact with ASN 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A VAL* 3.9 11.9 - - - +
654A ILE* 3.2 34.3 - - + +
921A TRP* 2.8 56.1 + - + +
924A LYS* 1.3 96.1 - - - +
926A PHE* 1.3 65.6 + - - +
927A ASP 3.3 2.5 - - - -
928A LYS* 3.3 10.3 + - - +
929A ILE* 2.9 36.0 + - + +
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Residues in contact with PHE 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A MET* 4.5 10.3 - - + -
692A MET* 3.5 57.2 - - + -
695A VAL* 3.6 45.8 - - + -
922A MET* 2.8 37.7 + - + +
924A LYS 3.7 0.4 - - - -
925A ASN* 1.3 72.9 - - - +
927A ASP* 1.3 73.8 + - - +
929A ILE* 3.3 6.3 + - + +
930A ARG* 2.8 36.2 + - - +
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Residues in contact with ASP 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A MET 4.7 0.2 + - - -
923A ASP 5.0 8.3 + - - +
924A LYS 4.7 3.4 + - - +
925A ASN 3.3 0.4 - - - -
926A PHE* 1.3 86.9 - - - +
928A LYS* 1.3 65.7 + - + +
930A ARG* 3.0 34.8 + - - +
931A VAL* 2.9 30.9 + - + +
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Residues in contact with LYS 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A SER* 6.0 1.6 - - - -
654A ILE* 3.6 14.6 - - + +
655A GLU* 3.5 29.7 + - - +
924A LYS* 3.3 41.3 - - - +
925A ASN* 3.3 18.8 + - - +
926A PHE 3.2 0.4 - - - -
927A ASP* 1.3 79.0 - - + +
929A ILE* 1.3 57.7 + - - +
931A VAL* 3.2 7.9 + - - +
932A TRP* 3.0 30.3 + - - +
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Residues in contact with ILE 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A ILE* 3.7 27.8 - - + -
658A LEU* 3.9 10.1 - - + -
683A MET* 4.6 7.2 - - - -
687A MET* 4.2 11.2 - - + -
695A VAL* 4.1 10.5 - - + -
699A PHE* 4.2 15.9 - - + -
921A TRP* 3.7 31.0 - - + -
925A ASN* 2.9 21.9 + - + +
926A PHE* 3.8 5.2 - - - +
928A LYS* 1.3 71.4 - - - +
930A ARG* 1.3 67.5 + - - +
932A TRP* 3.4 6.1 + - - +
933A LEU* 2.9 42.8 + - + +
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Residues in contact with ARG 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A VAL* 3.4 36.7 - - + +
698A GLN* 4.9 2.0 - - - +
926A PHE* 2.8 23.4 + - + +
927A ASP* 3.0 37.7 + - - +
929A ILE* 1.3 79.9 - - - +
931A VAL* 1.3 82.9 + - - +
933A LEU* 3.5 2.8 + - - +
934A GLN* 3.3 36.4 + - + +
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Residues in contact with VAL 931 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A GLU* 5.6 4.5 - - + +
927A ASP* 2.9 25.4 + - + +
928A LYS* 4.2 6.1 - - - +
930A ARG* 1.3 96.6 - - - +
932A TRP* 1.3 63.1 + - - +
934A GLN* 3.4 13.6 - - - +
935A SER* 2.8 37.3 + - - -
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Residues in contact with TRP 932 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A EDO 3.3 29.1 + - - -
655A GLU* 3.7 36.9 + - + -
658A LEU* 3.5 48.5 - - + -
659A ASP* 2.9 28.4 + - - -
662A LEU* 3.9 13.2 - - + -
702A PHE* 3.5 36.3 - + - -
928A LYS 3.0 16.7 + - - +
929A ILE 3.9 3.1 - - - +
931A VAL* 1.3 77.9 - - - +
933A LEU* 1.3 77.8 + - + +
935A SER* 4.6 0.7 - - - -
936A GLU* 2.9 42.3 + - + +
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Residues in contact with LEU 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A LEU* 6.3 0.2 - - + -
695A VAL* 3.8 20.9 - - + +
698A GLN* 3.6 36.3 - - + +
699A PHE* 3.8 23.3 - - + +
702A PHE* 3.7 26.0 - - + -
705A ARG* 5.4 2.2 - - - +
929A ILE* 2.9 38.8 + - + +
930A ARG* 4.0 2.5 - - - +
931A VAL 3.2 0.4 - - - -
932A TRP* 1.3 91.6 - - + +
934A GLN* 1.3 66.2 + - - +
936A GLU* 3.5 6.0 + - + +
937A LYS* 3.1 24.3 + - - +
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Residues in contact with GLN 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A GLN* 4.1 13.0 + - - +
930A ARG* 3.3 30.2 + - + +
931A VAL* 3.4 17.1 - - - +
933A LEU* 1.3 80.1 - - - +
935A SER* 1.3 67.4 + - - +
937A LYS* 3.4 11.2 + - - +
938A LEU* 3.0 48.1 + - + +
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Residues in contact with SER 935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A EDO 3.2 18.9 + - - -
931A VAL* 2.8 23.6 + - - -
932A TRP* 4.1 1.6 - - - -
934A GLN* 1.3 82.2 - - - +
936A GLU* 1.3 60.9 + - - +
938A LEU* 3.4 9.4 + - - +
939A GLU* 3.1 32.6 + - - +
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Residues in contact with GLU 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A EDO 3.5 29.6 - - - +
662A LEU* 4.0 19.1 - - + +
702A PHE* 4.9 1.7 - - - -
705A ARG* 2.6 31.1 + - - -
932A TRP* 2.9 43.3 + - + +
933A LEU* 4.1 6.6 - - + +
934A GLN 3.4 0.2 - - - -
935A SER* 1.3 71.8 + - - +
937A LYS* 1.3 67.0 + - - +
939A GLU* 3.5 5.7 + - + +
940A ARG* 2.7 57.8 + - - +
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Residues in contact with LYS 937 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A GLN* 3.9 28.8 - - + +
705A ARG* 5.5 4.5 - - - +
933A LEU 3.1 17.8 + - - +
934A GLN* 3.8 11.0 - - - +
936A GLU* 1.3 80.0 + - - +
938A LEU* 1.3 70.8 + - + +
940A ARG* 3.6 19.3 + - - +
941A MET* 3.4 30.7 + - + +
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Residues in contact with LEU 938 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934A GLN* 3.0 42.5 + - - +
935A SER* 3.8 7.6 - - - +
937A LYS* 1.3 86.0 - - + +
939A GLU* 1.3 57.7 + - + +
941A MET* 3.0 27.0 + - + +
942A HIS* 3.0 27.6 + - - +
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Residues in contact with GLU 939 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A EDO 3.5 31.3 + - - -
935A SER* 3.1 23.7 + - - +
936A GLU* 3.9 5.3 - - - +
937A LYS 3.4 0.2 - - - -
938A LEU* 1.3 74.1 - - + +
940A ARG* 1.3 65.0 + - - +
942A HIS 3.4 18.5 - - - +
943A HIS* 3.4 42.7 + - + +
946A HIS* 4.1 3.5 + - - -
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Residues in contact with ARG 940 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A LEU* 6.3 0.4 - - - -
705A ARG* 3.3 38.4 - - - +
936A GLU* 2.7 62.2 + - - +
937A LYS* 3.6 13.2 + - - +
939A GLU* 1.3 74.0 - - + +
941A MET* 1.3 64.6 + - - +
946A HIS* 3.5 13.9 - - - -
----------------------------------------------------------
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Residues in contact with MET 941 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A LYS* 3.4 24.8 + - + +
938A LEU* 3.0 26.3 + - + +
940A ARG* 1.3 80.2 - - - +
942A HIS* 1.3 63.6 + - + +
946A HIS* 3.9 7.5 + - - -
----------------------------------------------------------
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Residues in contact with HIS 942 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A LEU 3.0 15.7 + - - +
939A GLU* 3.4 10.1 - - - +
940A ARG 3.4 0.4 - - - -
941A MET* 1.3 80.8 - - + +
943A HIS* 1.3 80.6 + - - +
944A HIS* 4.9 0.2 - - - -
946A HIS* 3.7 18.0 + - + +
947A HIS* 4.1 28.7 - + - -
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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