Contacts of the helix formed by residues 866 - 896 (chain A) in PDB entry 6J8H
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 866 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 6.4 0.4 - - + -
405A TYR* 5.4 4.5 - - - +
861A ASN* 2.9 22.2 + - + +
862A SER* 3.3 6.5 - - - +
865A ALA* 1.3 84.7 - - + +
867A GLY* 1.3 63.5 + - - +
868A ASN 3.2 2.9 - - - -
869A LEU* 3.1 18.0 + - + +
870A THR* 2.9 22.7 + - - +
962A LEU* 4.1 9.9 - - + -
965A ALA* 3.9 18.2 - - + +
966A LEU* 3.7 44.2 - - + +
969A SER* 5.2 9.0 - - - +
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Residues in contact with GLY 867 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A SER 3.1 6.5 + - - -
863A VAL* 4.0 9.6 - - - -
864A GLY 3.1 16.7 + - - -
865A ALA 3.2 0.6 - - - -
866A LEU* 1.3 78.4 - - - +
868A ASN* 1.3 62.2 + - - +
870A THR* 2.7 27.3 - - - +
871A LEU* 2.9 13.0 + - - +
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Residues in contact with ASN 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 5.2 3.1 - - - +
229A PRO 3.5 22.2 + - - +
230A GLY* 3.6 20.6 + - - -
231A LEU* 3.8 12.3 - - + +
234A ILE* 3.7 20.5 - - + +
864A GLY 4.9 0.2 + - - -
865A ALA 4.4 5.3 + - - +
866A LEU 3.2 1.2 - - - -
867A GLY* 1.3 77.3 - - - +
869A LEU* 1.3 61.7 + - - +
871A LEU* 3.2 12.3 + - - +
872A VAL* 3.2 24.1 + - - +
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Residues in contact with LEU 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 4.0 33.2 - - + +
238A LEU* 4.4 16.6 - - + -
405A TYR* 5.9 1.1 - - + -
866A LEU* 3.1 22.8 + - + +
868A ASN* 1.3 77.8 - - - +
870A THR* 1.3 64.7 + - - +
872A VAL* 3.3 13.8 + - + +
873A LEU* 3.5 5.2 + - - +
958A VAL* 4.4 15.0 - - + +
961A ASN* 4.4 10.8 - - + +
962A LEU* 4.2 24.6 - - + +
965A ALA* 4.2 24.7 - - + -
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Residues in contact with THR 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A SER* 2.5 38.4 + - - +
863A VAL* 4.5 5.7 - - + +
866A LEU 2.9 6.8 + - - +
867A GLY* 2.7 27.8 - - - +
869A LEU* 1.3 73.9 - - - +
871A LEU* 1.3 61.0 + - - +
873A LEU* 3.1 15.2 + - - +
874A ALA* 3.2 11.1 + - - +
962A LEU* 4.3 26.0 - - - +
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Residues in contact with LEU 871 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 4.1 29.6 - - + -
231A LEU* 4.4 13.9 - - + -
867A GLY 2.9 18.4 + - - +
868A ASN* 3.4 11.2 - - - +
869A LEU 3.2 0.2 - - - -
870A THR* 1.3 78.4 - - - +
872A VAL* 1.3 56.1 + - - +
874A ALA* 3.1 13.7 + - + -
875A ILE* 2.9 36.7 + - + +
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Residues in contact with VAL 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 5.0 11.2 - - + -
231A LEU* 4.2 21.5 - - + +
234A ILE* 3.9 21.8 - - + -
235A VAL* 5.2 11.9 - - + +
238A LEU* 5.5 7.6 - - + -
868A ASN 3.2 14.0 + - - +
869A LEU* 3.5 11.0 - - + +
870A THR 3.2 0.4 - - - -
871A LEU* 1.3 77.1 - - - +
873A LEU* 1.3 62.9 + - - +
875A ILE* 3.1 8.9 + - - +
876A ILE* 2.9 37.6 + - + +
958A VAL* 4.4 15.3 - - + -
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Residues in contact with LEU 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A LEU 3.5 4.6 + - - +
870A THR* 3.1 14.8 + - - +
872A VAL* 1.3 79.4 - - - +
874A ALA* 1.3 63.0 + - - +
876A ILE* 3.5 6.2 + - + -
877A VAL* 3.1 36.9 + - + +
924A LEU* 4.4 7.2 - - + -
955A GLY* 5.0 2.7 - - - +
958A VAL* 4.0 26.9 - - + +
959A VAL* 3.9 32.3 - - + -
962A LEU* 4.1 21.3 - - + -
1446A PHE* 6.2 1.6 - - + -
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Residues in contact with ALA 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A THR 3.2 6.7 + - - +
871A LEU* 3.1 20.1 + - + +
873A LEU* 1.3 81.4 - - - +
875A ILE* 1.3 61.7 + - + +
877A VAL* 3.5 5.3 + - - +
878A PHE* 3.1 23.4 + - - +
----------------------------------------------------------
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Residues in contact with ILE 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ALA* 4.7 3.4 - - + +
224A THR* 3.4 25.1 - - - +
225A ILE* 4.1 19.5 - - + -
228A ILE* 4.4 8.3 - - + -
231A LEU* 3.8 28.3 - - + -
871A LEU* 2.9 27.7 + - + +
872A VAL* 3.1 8.7 + - - +
874A ALA* 1.3 77.2 - - - +
876A ILE* 1.3 59.0 + - + +
878A PHE* 3.3 8.9 + - + +
879A ILE* 3.0 43.8 + - + +
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Residues in contact with ILE 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ILE* 6.2 1.8 - - + -
238A LEU* 5.6 3.4 - - + -
872A VAL* 2.9 30.1 + - + +
873A LEU* 4.0 7.0 - - + +
875A ILE* 1.3 77.8 - - + +
877A VAL* 1.3 67.6 + - + +
879A ILE* 3.3 9.7 + - + +
880A PHE* 3.2 50.1 + - + -
954A ILE* 4.1 16.8 - - + -
955A GLY* 4.8 10.5 - - - -
958A VAL* 4.0 24.0 - - + -
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Residues in contact with VAL 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A LEU* 3.1 36.3 + - + +
874A ALA* 3.9 5.8 - - - +
876A ILE* 1.3 77.3 - - + +
878A PHE* 1.3 62.6 + - - +
880A PHE* 3.5 2.8 + - - +
881A ALA* 3.1 21.5 + - - +
917A PHE* 3.6 35.2 - - + -
920A VAL* 4.2 20.6 - - + +
921A PHE* 5.3 5.2 - - + +
924A LEU* 4.2 16.8 - - + -
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Residues in contact with PHE 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A CYS* 3.6 51.6 - - + -
141A ILE* 6.0 2.2 - - + -
143A MET* 4.7 8.7 - - + -
144A THR* 4.1 8.7 - - - -
221A ALA* 4.5 9.4 - - + -
874A ALA 3.1 14.2 + - - +
875A ILE* 3.5 12.6 - - + +
876A ILE 3.2 0.2 - - - -
877A VAL* 1.3 77.2 - - - +
879A ILE* 1.3 71.6 - - + +
881A ALA* 3.4 4.6 + - - +
882A VAL* 3.2 29.7 + - + +
913A PHE* 3.7 33.4 - + - -
917A PHE* 6.3 0.4 - - - -
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Residues in contact with ILE 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 3.4 18.8 - - + +
221A ALA* 4.0 24.2 - - + -
222A LEU* 3.7 38.8 - - + +
875A ILE* 3.0 32.8 + - + +
876A ILE* 3.3 11.2 + - + +
878A PHE* 1.3 77.9 - - + +
880A PHE* 1.3 62.1 + - + +
882A VAL* 2.9 8.0 - - - +
883A VAL* 2.7 44.6 + - + +
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Residues in contact with PHE 880 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A ILE* 3.2 43.7 + - + +
877A VAL* 4.0 4.9 - - - +
879A ILE* 1.3 84.7 - - + +
881A ALA* 1.3 60.8 + - - +
883A VAL* 3.8 10.2 - - + +
884A GLY* 2.8 28.4 + - - -
910A MET* 5.3 0.3 - - - +
920A VAL* 4.0 20.0 - - + +
947A VAL* 5.2 6.2 - - + +
950A MET* 4.2 22.4 - - + -
951A VAL* 3.9 48.7 - - + -
954A ILE* 4.4 15.9 - - + -
955A GLY* 4.7 3.8 - - - -
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Residues in contact with ALA 881 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A VAL 3.1 18.1 + - - +
878A PHE 3.8 1.3 - - - +
879A ILE 3.3 0.2 - - - -
880A PHE* 1.3 75.9 - - - +
882A VAL* 1.3 58.8 + - - +
884A GLY* 5.3 0.2 - - - -
885A MET* 3.1 16.6 + - - +
913A PHE* 3.8 20.4 - - + -
916A SER* 2.1 33.0 + - - +
917A PHE* 3.7 25.6 - - + -
920A VAL* 3.8 10.0 - - + +
----------------------------------------------------------
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Residues in contact with VAL 882 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 3.7 34.3 - - + +
144A THR 4.9 0.4 - - - +
218A VAL* 3.5 26.7 - - + -
878A PHE* 3.2 22.6 + - + +
879A ILE* 2.9 21.1 - - - +
881A ALA* 1.3 77.8 - - - +
883A VAL* 1.3 63.6 + - - +
885A MET* 3.2 22.7 + - + +
886A GLN* 3.0 38.6 + - - +
913A PHE* 4.4 6.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 883 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 3.8 23.7 - - + +
218A VAL* 3.6 26.2 - - + -
879A ILE* 2.7 40.3 + - + +
880A PHE* 3.8 12.3 - - + +
882A VAL* 1.3 69.9 - - - +
884A GLY* 1.3 67.7 + - - +
886A GLN* 3.4 3.6 + - - +
887A LEU* 3.1 34.7 + - + +
947A VAL* 5.4 9.0 - - + -
----------------------------------------------------------
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Residues in contact with GLY 884 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A PHE 2.8 16.7 + - - -
881A ALA 4.0 0.7 - - - -
883A VAL* 1.3 77.9 - - - +
885A MET* 1.3 61.8 + - - +
887A LEU* 4.8 0.2 - - - -
888A PHE* 3.0 42.7 + - - +
889A GLY 4.0 0.2 + - - -
910A MET* 4.1 24.9 - - - +
947A VAL* 5.1 4.9 - - - +
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Residues in contact with MET 885 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET 4.3 10.5 - - - +
144A THR* 4.4 2.2 - - - +
146A ASN* 3.7 31.4 - - + -
881A ALA 3.1 12.9 + - - +
882A VAL* 3.5 22.7 - - + +
883A VAL 3.2 0.2 - - - -
884A GLY* 1.3 77.6 - - - +
886A GLN* 1.3 63.5 + - - +
889A GLY* 2.9 28.6 + - - -
910A MET 3.8 18.8 - - - +
911A ASN 4.1 10.8 - - - +
912A ASP 4.5 3.4 - - - -
913A PHE* 3.7 45.1 - - + -
916A SER* 3.9 6.7 + - - +
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Residues in contact with GLN 886 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 4.2 17.9 + - - +
146A ASN* 6.0 1.6 - - - -
211A SER* 3.8 23.8 + - - +
214A ARG* 5.5 4.9 - - + +
215A THR* 4.5 19.5 - - + +
217A ARG* 4.5 19.4 - - - +
218A VAL* 4.6 11.5 - - + +
882A VAL* 3.0 33.5 + - + +
883A VAL* 3.8 5.8 - - - +
884A GLY 3.3 0.2 - - - -
885A MET* 1.3 82.9 - - + +
887A LEU* 1.3 63.3 + - - +
889A GLY* 4.3 1.6 + - - -
890A LYS* 5.2 4.5 + - - +
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Residues in contact with LEU 887 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER* 4.1 11.0 - - - +
212A ALA* 4.3 10.5 - - + -
215A THR* 3.1 31.9 - - + +
883A VAL* 3.1 30.7 + - + +
884A GLY 4.0 1.6 - - - +
886A GLN* 1.3 82.1 - - - +
888A PHE* 1.3 77.6 + - + +
890A LYS* 5.2 2.1 + - - +
891A SER* 4.6 6.1 + - - -
943A MET* 4.7 22.2 - - + +
947A VAL* 4.1 21.5 - - + -
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Residues in contact with PHE 888 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A GLY* 3.0 27.1 + - - +
887A LEU* 1.3 87.8 - - + +
889A GLY* 1.3 65.5 + - - +
890A LYS 3.4 2.5 - - - -
891A SER* 3.5 7.6 + - - -
892A TYR* 3.3 40.6 + - + -
910A MET* 3.8 20.9 - - + -
935A CYS* 3.9 17.9 - - - -
939A ALA* 3.4 28.3 - - + -
943A MET* 3.8 33.0 - - + -
944A CYS* 4.1 1.1 - - - -
947A VAL* 3.6 43.1 - - + -
948A TYR* 4.9 2.5 - + - -
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Residues in contact with GLY 889 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A GLY 4.0 0.2 + - - -
885A MET 2.9 23.6 + - - -
886A GLN 4.3 0.8 + - - -
887A LEU 3.6 1.4 - - - -
888A PHE* 1.3 78.4 - - - +
890A LYS* 1.3 62.2 + - - +
892A TYR* 3.7 7.1 + - - +
893A LYS* 3.8 7.6 + - - +
910A MET 3.8 15.3 - - - -
911A ASN* 3.8 25.6 + - - -
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Residues in contact with LYS 890 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER* 4.9 14.4 + - - +
886A GLN 5.2 4.3 + - - +
887A LEU 5.2 1.5 + - - +
888A PHE 3.4 0.4 - - - -
889A GLY* 1.3 73.2 - - - +
891A SER* 1.3 65.9 + - - +
893A LYS* 3.4 6.5 + - - +
894A GLU* 3.2 48.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 891 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU 4.6 9.2 + - - -
888A PHE* 3.5 11.1 + - - -
889A GLY 3.3 0.2 - - - -
890A LYS* 1.3 77.0 - - - +
892A TYR* 1.3 66.3 + - - +
894A GLU* 4.2 8.8 + - - -
895A CYS* 2.9 32.1 + - - +
938A VAL* 4.0 29.1 + - - -
939A ALA* 4.6 8.7 - - - +
943A MET* 5.7 1.7 - - - +
----------------------------------------------------------
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Residues in contact with TYR 892 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A PHE* 3.3 33.1 + - + +
889A GLY 4.0 5.4 - - - +
890A LYS 3.3 0.6 - - - -
891A SER* 1.3 78.6 - - - +
893A LYS* 1.3 58.1 + - - +
896A VAL* 3.0 33.3 + - - +
899A ILE* 3.9 24.0 - - + -
905A LEU* 3.7 9.2 - - + +
906A PRO* 4.6 2.5 - - + -
908A TRP 4.4 5.2 + - - -
909A HIS* 3.7 24.9 - - + -
910A MET* 3.6 33.5 - - + +
911A ASN* 4.8 9.2 - - + +
919A ILE* 4.4 12.5 - - - +
931A THR* 4.3 3.5 + - - +
934A ASP* 4.1 9.9 - - + +
935A CYS* 3.7 29.7 + - + +
938A VAL* 4.3 17.9 - - + -
948A TYR* 4.4 1.7 + - - -
----------------------------------------------------------
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Residues in contact with LYS 893 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A GLY 3.8 4.3 + - - +
890A LYS* 3.4 9.3 + - - +
891A SER 3.2 0.6 - - - -
892A TYR* 1.3 81.1 - - - +
894A GLU* 1.3 66.4 + - + +
896A VAL* 3.1 23.7 - - + +
905A LEU* 4.4 22.9 - - + +
911A ASN* 3.9 16.4 + - - +
136C HIS* 5.7 9.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU 894 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A LYS* 3.2 44.5 + - - +
891A SER* 4.2 9.2 + - - +
893A LYS* 1.3 80.9 - - + +
895A CYS* 1.3 59.2 + - - +
896A VAL* 3.4 3.3 - - - +
29C SER 5.1 21.5 - - - +
55C CYS* 4.8 8.8 - - + +
56C TYR* 2.8 26.4 + - - -
134C ASP* 4.1 8.7 - - - +
136C HIS* 5.9 4.0 - - - -
----------------------------------------------------------
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Residues in contact with CYS 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A SER* 2.9 23.4 + - - +
894A GLU* 1.3 74.8 - - - +
896A VAL* 1.3 48.0 - - - +
897A CYS* 2.1 27.9 + - - -
898A LYS* 3.0 11.8 + - + -
938A VAL* 3.0 45.3 - - + -
55C CYS* 2.5 41.7 - - - -
56C TYR* 3.0 15.3 + - - -
----------------------------------------------------------
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Residues in contact with VAL 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A TYR 3.0 16.4 + - - +
893A LYS* 3.1 23.8 - - + +
894A GLU 3.4 7.4 - - - +
895A CYS* 1.3 72.8 - - - +
897A CYS* 1.3 61.7 + - - +
898A LYS 3.4 0.7 - - - -
899A ILE* 2.7 17.1 - - + +
900A ASN* 2.6 36.6 + - - +
903A CYS* 4.3 17.0 - - - +
904A THR* 4.2 2.5 - - - +
905A LEU* 3.1 46.0 - - + +
938A VAL* 4.4 1.4 - - - +
56C TYR* 4.1 3.4 - - - +
----------------------------------------------------------
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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