Contacts of the helix formed by residues 904 - 943 (chain S) in PDB entry 1I84
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 904 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901S LYS 3.4 7.5 + - - -
902S LEU 2.5 12.8 + - - +
903S GLN 1.7 49.3 + - - -
905S GLU* 1.3 64.4 + - - +
907S GLU* 3.1 1.6 + - - -
908S LEU* 2.9 21.5 + - - -
----------------------------------------------------------
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Residues in contact with GLU 905 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901S LYS 4.6 0.8 + - - -
904S ALA* 1.3 76.2 - - - +
906S THR* 1.3 50.1 + - - +
908S LEU* 3.1 2.5 + - - +
909S TYR 2.8 7.3 + - - -
902V LEU 5.5 0.2 - - - -
904V ALA 4.0 5.8 - - - +
905V GLU* 2.7 32.9 + - - -
906V THR* 2.8 8.0 + - - +
----------------------------------------------------------
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Residues in contact with THR 906 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901S LYS 4.4 0.2 + - - -
902S LEU* 2.3 38.1 + - - +
905S GLU* 1.3 68.8 - - - +
907S GLU* 1.3 56.7 + - - +
910S ALA* 2.9 8.5 + - - -
898V LEU 5.7 0.2 - - - -
901V LYS* 4.8 1.2 - - - -
902V LEU* 4.0 7.5 + - - +
904V ALA 4.0 7.1 - - - +
905V GLU* 2.6 30.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 907 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902S LEU 2.6 19.3 + - - -
903S GLN* 4.3 7.9 - - - +
904S ALA 3.6 3.1 - - - -
906S THR* 1.3 71.7 - - - +
908S LEU* 1.3 61.5 + - - +
910S ALA* 3.1 3.1 + - - +
911S GLU* 2.9 21.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 908 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904S ALA 2.9 14.2 + - - -
905S GLU* 3.6 3.4 - - - +
907S GLU* 1.3 75.6 - - - +
909S TYR* 1.3 57.5 + - - +
911S GLU* 3.1 3.0 + - - +
912S ALA* 2.8 26.2 + - - -
905V GLU 2.8 3.1 - - - +
906V THR* 3.4 5.3 - - - +
909V TYR* 4.4 0.9 - - - -
----------------------------------------------------------
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Residues in contact with TYR 909 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908S LEU* 1.3 66.8 - - - +
910S ALA* 1.3 55.0 + - - +
913S GLU* 2.8 26.5 + - - -
901V LYS* 5.2 1.3 - - - -
904V ALA 3.2 3.6 - - - -
905V GLU* 1.2 115.6 - - - +
906V THR 2.5 0.2 - - - +
908V LEU* 3.4 4.4 - - - -
909V TYR 3.1 3.5 + - - -
----------------------------------------------------------
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Residues in contact with ALA 910 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906S THR 2.9 9.2 + - - -
907S GLU* 3.1 3.8 + - - +
909S TYR* 1.3 73.3 - - - +
911S GLU* 1.3 62.1 + - - +
913S GLU* 3.1 2.5 + - - +
914S GLU* 2.9 20.6 + - - -
901V LYS* 5.3 2.8 - - - +
905V GLU* 2.8 7.1 - - - +
----------------------------------------------------------
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Residues in contact with GLU 911 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907S GLU 2.9 13.2 + - - -
908S LEU* 3.6 3.6 - - - +
910S ALA* 1.3 76.0 - - - +
912S ALA* 1.3 63.8 + - - +
914S GLU* 3.1 2.8 + - - +
915S MET* 2.9 20.8 + - - -
----------------------------------------------------------
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Residues in contact with ALA 912 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908S LEU 2.8 11.4 + - - -
911S GLU* 1.3 74.9 - - - +
913S GLU* 1.3 56.4 + - - +
915S MET* 3.1 2.9 + - - +
916S ARG* 2.8 27.4 + - - -
908V LEU 3.5 0.4 - - - -
909V TYR* 2.5 35.3 - - - +
912V ALA* 3.7 3.1 - - - -
913V GLU 4.7 0.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 913 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909S TYR 2.8 13.4 + - - -
910S ALA* 3.1 3.8 + - - +
912S ALA* 1.3 75.6 - - - +
914S GLU* 1.3 61.9 + - - +
916S ARG* 3.1 2.1 + - - +
917S VAL* 2.9 21.1 + - - -
908V LEU* 3.3 16.0 - - - +
912V ALA* 4.7 2.4 - - - +
----------------------------------------------------------
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Residues in contact with GLU 914 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910S ALA 2.9 14.2 + - - -
911S GLU 3.6 3.1 - - - -
913S GLU* 1.3 75.9 - - - +
915S MET* 1.3 62.8 + - - +
917S VAL* 3.1 3.2 + - - +
918S ARG* 2.9 20.3 + - - -
----------------------------------------------------------
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Residues in contact with MET 915 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911S GLU 2.9 13.4 + - - -
912S ALA* 3.6 3.8 - - - +
914S GLU* 1.3 76.6 - - - +
916S ARG* 1.3 57.3 + - - +
918S ARG* 3.1 3.0 + - - +
919S LEU* 2.8 27.0 + - - -
----------------------------------------------------------
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Residues in contact with ARG 916 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912S ALA 2.8 10.7 + - - -
913S GLU 3.1 0.9 + - - -
915S MET* 1.3 74.9 - - - +
917S VAL* 1.3 57.1 + - - +
919S LEU* 3.1 2.4 + - - +
920S ALA* 2.8 27.0 + - - -
912V ALA* 2.9 43.2 - - - +
913V GLU 4.7 0.2 - - - +
915V MET* 5.2 1.5 - - - -
916V ARG* 4.7 2.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 917 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
913S GLU 2.9 14.2 + - - -
914S GLU* 3.1 3.8 + - - +
916S ARG* 1.3 75.9 - - - +
918S ARG* 1.3 62.7 + - - +
920S ALA* 3.1 2.9 + - - +
921S ALA* 2.9 21.0 + - - -
----------------------------------------------------------
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Residues in contact with ARG 918 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914S GLU 2.9 14.2 + - - -
915S MET* 3.6 3.1 - - - +
917S VAL* 1.3 76.2 - - - +
919S LEU* 1.3 62.7 + - - +
921S ALA* 3.1 3.1 + - - +
922S LYS* 2.9 21.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 919 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915S MET 2.8 14.6 + - - -
916S ARG 3.6 3.4 - - - -
918S ARG* 1.3 75.1 - - - +
920S ALA* 1.3 57.1 + - - +
922S LYS* 3.1 2.6 + - - +
923S LYS* 2.8 27.9 + - - -
916V ARG* 4.5 19.0 - - - +
919V LEU* 5.4 0.7 - - - -
----------------------------------------------------------
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Residues in contact with ALA 920 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
916S ARG 2.8 13.6 + - - -
917S VAL* 3.1 4.0 + - - +
919S LEU* 1.3 75.9 - - - +
921S ALA* 1.3 61.4 + - - +
923S LYS* 3.1 3.0 + - - +
924S GLN* 2.9 21.0 + - - -
915V MET 5.2 9.2 - - - -
916V ARG* 4.7 1.8 - - - +
919V LEU* 5.7 3.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 921 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917S VAL 2.9 13.2 + - - -
918S ARG* 3.1 4.2 + - - +
920S ALA* 1.3 76.3 - - - +
922S LYS* 1.3 61.5 + - - +
924S GLN* 3.1 2.7 + - - +
925S GLU* 2.9 21.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 922 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918S ARG 2.9 13.6 + - - -
919S LEU* 3.6 3.8 - - - +
921S ALA* 1.3 76.2 - - - +
923S LYS* 1.3 56.3 - - - +
925S GLU* 3.1 3.1 + - - +
926S LEU* 2.8 26.9 + - - -
----------------------------------------------------------
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Residues in contact with LYS 923 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919S LEU 2.8 14.1 + - - -
920S ALA 3.6 3.6 - - - -
922S LYS* 1.3 75.1 - - - +
924S GLN* 1.3 57.2 + - - +
926S LEU* 3.1 3.1 + - - +
927S GLU* 2.8 27.4 + - - -
919V LEU* 4.3 29.3 - - - +
920V ALA* 5.7 0.9 - - - +
923V LYS* 5.0 3.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 924 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920S ALA 2.9 13.8 + - - -
921S ALA* 3.1 3.8 + - - +
923S LYS* 1.3 75.9 - - - +
925S GLU* 1.3 62.7 + - - +
927S GLU* 3.1 3.1 + - - +
928S GLU* 2.9 20.1 + - - -
----------------------------------------------------------
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Residues in contact with GLU 925 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921S ALA 2.9 14.2 + - - -
922S LYS* 3.6 3.6 - - - +
924S GLN* 1.3 75.6 - - - +
926S LEU* 1.3 62.9 + - - +
928S GLU* 3.1 3.3 + - - +
929S ILE* 2.9 21.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 926 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922S LYS 2.8 13.6 + - - -
923S LYS* 3.6 4.0 - - - +
925S GLU* 1.3 75.1 - - - +
927S GLU* 1.3 57.3 + - - +
929S ILE* 3.1 2.8 + - - +
930S LEU* 2.8 27.2 + - - -
923V LYS* 5.1 9.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU 927 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923S LYS 2.8 14.7 + - - -
924S GLN* 3.1 4.0 + - - +
926S LEU* 1.3 75.7 - - - +
928S GLU* 1.3 62.2 + - - +
930S LEU* 3.1 2.8 + - - +
931S HIS* 2.9 20.6 + - - -
922V LYS 5.7 1.6 - - - -
923V LYS* 4.8 11.2 - - - +
926V LEU* 5.7 6.3 - - - +
----------------------------------------------------------
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Residues in contact with GLU 928 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924S GLN 2.9 14.2 + - - -
925S GLU* 3.6 3.4 - - - +
927S GLU* 1.3 76.4 - - - +
929S ILE* 1.3 62.0 + - - +
931S HIS* 3.1 2.4 + - - +
932S GLU* 2.9 20.8 + - - -
----------------------------------------------------------
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Residues in contact with ILE 929 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925S GLU 2.9 14.1 + - - -
926S LEU* 3.6 3.6 - - - +
928S GLU* 1.3 75.2 - - - +
930S LEU* 1.3 56.1 + - - +
932S GLU* 3.1 2.9 + - - +
933S MET* 2.8 27.0 + - - -
----------------------------------------------------------
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Residues in contact with LEU 930 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926S LEU 2.8 13.7 + - - -
927S GLU* 3.6 3.8 - - - +
929S ILE* 1.3 75.3 - - - +
931S HIS* 1.3 57.7 + - - +
933S MET* 3.1 2.2 + - - +
934S GLU* 2.8 27.2 + - - -
926V LEU* 4.6 21.8 - - - -
927V GLU* 4.9 5.4 - - - +
930V LEU* 4.2 7.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 931 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927S GLU 2.9 14.0 + - - -
928S GLU* 3.6 3.6 - - - +
930S LEU* 1.3 75.7 - - - +
932S GLU* 1.3 63.3 + - - +
934S GLU* 3.1 2.9 + - - +
935S ALA* 2.9 20.3 + - - -
926V LEU* 5.8 0.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU 932 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928S GLU 2.9 13.4 + - - -
929S ILE* 3.6 4.0 - - - +
931S HIS* 1.3 74.8 - - - +
933S MET* 1.3 63.5 + - - +
935S ALA* 3.1 2.9 + - - +
936S ARG* 2.9 21.0 + - - -
----------------------------------------------------------
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Residues in contact with MET 933 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929S ILE 2.8 13.9 + - - -
930S LEU* 3.6 3.8 - - - +
932S GLU* 1.3 74.2 - - - +
934S GLU* 1.3 58.1 + - - +
936S ARG* 3.1 3.0 + - - +
937S ILE* 2.8 27.2 + - - -
930V LEU* 4.7 4.7 - - - +
----------------------------------------------------------
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Residues in contact with GLU 934 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930S LEU 2.8 12.0 + - - -
931S HIS* 3.6 4.0 - - - +
933S MET* 1.3 74.8 - - - +
935S ALA* 1.3 62.1 + - - +
937S ILE* 3.1 2.1 + - - -
938S GLU* 2.9 20.6 + - - -
929V ILE 5.1 0.2 - - - -
930V LEU* 3.5 29.6 - - - +
933V MET* 4.5 7.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 935 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931S HIS 2.9 14.0 + - - -
932S GLU* 3.6 3.6 - - - +
934S GLU* 1.3 76.5 - - - +
936S ARG* 1.3 63.7 + - - +
938S GLU* 3.1 2.9 + - - +
939S GLU* 2.9 20.6 + - - -
----------------------------------------------------------
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Residues in contact with ARG 936 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932S GLU 2.9 14.1 + - - -
933S MET* 3.6 3.4 - - - +
935S ALA* 1.3 76.0 - - - +
937S ILE* 1.3 57.3 + - - +
939S GLU* 3.1 2.7 + - - +
940S GLU* 2.8 27.0 + - - -
----------------------------------------------------------
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Residues in contact with ILE 937 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933S MET 2.8 13.6 + - - -
934S GLU 3.6 2.0 - - - -
936S ARG* 1.3 75.7 - - - +
938S GLU* 1.3 57.2 + - - +
940S GLU* 3.1 2.8 + - - +
941S GLU 2.8 26.2 + - - -
934V GLU* 3.2 33.1 - - - +
937V ILE* 3.1 5.2 - - - -
938V GLU 4.1 0.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 938 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934S GLU 2.9 14.2 + - - -
935S ALA* 3.6 3.4 - - - +
937S ILE* 1.3 76.1 - - - +
939S GLU* 1.3 62.3 + - - +
941S GLU 3.1 1.7 + - - -
942S GLU* 2.9 20.4 + - - -
933V MET* 3.7 12.8 + - - +
937V ILE* 3.4 5.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 939 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935S ALA 2.9 13.8 + - - -
936S ARG* 3.6 4.0 - - - +
938S GLU* 1.3 75.8 - - - +
940S GLU* 1.3 62.1 + - - +
942S GLU* 3.1 3.0 + - - +
943S ARG* 2.9 20.6 + - - -
----------------------------------------------------------
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Residues in contact with GLU 940 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936S ARG 2.8 14.3 + - - -
937S ILE* 3.6 2.9 - - - +
939S GLU* 1.3 75.5 - - - +
941S GLU* 1.3 64.3 + - - +
943S ARG* 3.1 18.3 + - - +
937V ILE 3.5 0.7 - - - -
938V GLU* 4.0 5.0 + - - -
941V GLU* 3.9 1.9 - - - -
----------------------------------------------------------
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Residues in contact with GLU 941 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937S ILE 2.8 2.4 + - - -
938S GLU 3.1 0.2 + - - -
940S GLU* 1.3 75.2 - - - +
942S GLU* 1.3 47.8 + - - +
937V ILE* 1.1 81.8 - - - +
938V GLU 2.5 0.4 - - - +
940V GLU* 2.4 4.3 - - - -
941V GLU* 1.5 43.9 + - - -
----------------------------------------------------------
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Residues in contact with GLU 942 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938S GLU 2.9 14.0 + - - -
939S GLU* 3.1 3.3 + - - +
941S GLU* 1.3 78.2 - - - +
943S ARG* 1.3 63.5 + - - +
937V ILE* 3.6 0.6 - - - +
940V GLU* 3.9 8.3 - - - +
941V GLU* 3.4 4.6 + - - +
----------------------------------------------------------
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Residues in contact with ARG 943 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939S GLU 2.9 13.8 + - - -
940S GLU* 3.1 10.2 + - - +
942S GLU* 1.3 82.5 - - - +
941V GLU* 3.0 29.6 - - - +
----------------------------------------------------------
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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