Contacts of the helix formed by residues 923 - 954 (chain A) in PDB entry 3KSS
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 SER 923 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561A PHE* 5.5 1.3 - - - -
562A LEU* 3.9 21.5 - - - +
563A PRO* 4.4 2.0 - - - -
922A LEU* 1.3 81.2 - - - +
924A VAL* 1.3 64.3 + - - +
925A ALA* 2.9 18.9 - - - +
926A THR* 2.8 42.1 + - - +
927A GLY* 2.9 6.9 + - - -
1011A ARG* 3.3 21.1 - - - +
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Residues in contact with VAL 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE* 4.3 21.8 - - + +
467A LEU* 3.9 28.7 - - + -
471A GLU* 5.0 5.4 - - + +
472A GLY* 6.2 0.7 - - - +
475A PHE* 3.5 31.6 - - + -
562A LEU* 4.3 23.3 - - + +
923A SER* 1.3 73.2 - - - +
925A ALA* 1.3 49.6 + - - +
927A GLY* 3.4 3.6 + - - +
928A THR* 2.6 39.4 + - - +
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Residues in contact with ALA 925 (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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475A PHE* 3.3 22.9 - - + -
562A LEU* 5.7 1.1 - - + -
563A PRO* 6.1 1.1 - - + -
923A SER* 2.9 16.0 - - - +
924A VAL* 1.3 77.3 - - - +
926A THR* 1.3 58.8 + - - +
928A THR* 2.8 16.6 + - - -
929A GLY 2.8 12.3 + - - -
1008A VAL* 3.9 11.9 - - + +
1011A ARG* 3.7 9.4 - - + -
1012A ILE* 3.0 28.2 - - + +
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Residues in contact with THR 926 (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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915A LEU* 4.9 12.8 - - + -
920A PHE* 5.6 1.1 - - + -
922A LEU* 3.3 26.9 - - - +
923A SER* 2.8 47.5 + - - +
925A ALA* 1.3 73.3 - - - +
927A GLY* 1.3 56.4 + - - +
929A GLY 3.3 0.9 + - - -
930A PHE* 2.9 38.7 + - - -
1011A ARG* 2.9 36.1 - - + +
1015A PRO* 3.5 8.7 - - - +
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Residues in contact with GLY 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A ILE* 5.2 4.3 - - - -
922A LEU* 6.4 0.2 - - - -
923A SER 2.9 8.1 + - - -
924A VAL* 3.4 6.5 - - - -
926A THR* 1.3 82.2 + - - +
928A THR* 1.3 58.2 + - - +
930A PHE* 3.6 10.4 - - - +
931A ILE* 2.9 35.4 + - - +
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Residues in contact with THR 928 (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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461A PHE* 3.3 28.8 - - + -
464A ILE* 4.6 6.0 - - - +
475A PHE* 3.0 29.3 - - + -
478A LEU* 4.4 6.1 - - + -
482A LYS* 5.9 0.9 - - + -
924A VAL* 2.6 21.9 + - - +
925A ALA* 2.8 15.9 + - - -
927A GLY* 1.3 76.4 - - - +
929A GLY* 1.3 62.3 + - - +
931A ILE* 3.4 8.5 + - - +
932A ALA* 3.2 20.1 + - - +
1012A ILE* 4.0 19.1 - - + -
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Residues in contact with GLY 929 (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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925A ALA 2.8 10.7 + - - -
926A THR 3.3 3.3 + - - -
928A THR* 1.3 74.7 - - - +
930A PHE* 1.3 54.1 + - - +
932A ALA* 2.9 2.6 + - - -
933A LEU* 2.7 32.4 + - - +
1012A ILE* 3.2 30.9 - - - +
1015A PRO* 4.1 4.7 - - - -
1016A MET* 2.8 15.1 - - - +
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Residues in contact with PHE 930 (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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554A LEU* 5.2 9.6 - - + -
908A LEU* 4.2 31.3 - - + +
911A GLY* 4.4 2.2 - - - -
912A ILE* 3.8 40.4 - - + -
915A LEU* 4.8 8.1 - - + -
926A THR* 2.9 23.0 + - - +
927A GLY* 3.6 10.5 - - - +
929A GLY* 1.3 73.8 - - - +
931A ILE* 1.3 59.1 + - + +
933A LEU* 3.2 10.1 + - + +
934A ALA* 2.9 33.3 + - - +
1015A PRO* 3.1 37.7 - - + -
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Residues in contact with ILE 931 (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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457A ILE* 5.4 1.4 - - - +
460A SER* 3.5 33.4 + - - +
461A PHE* 3.6 32.3 - - + -
463A PRO* 5.8 5.2 - - + -
464A ILE* 4.1 22.2 - - + -
927A GLY 2.9 28.6 + - - +
928A THR* 3.6 7.4 - - - +
929A GLY 3.2 0.2 - - - -
930A PHE* 1.3 78.1 - - + +
932A ALA* 1.3 61.1 + - - +
934A ALA* 3.8 7.1 + - + +
935A GLY* 3.4 15.2 + - - -
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Residues in contact with ALA 932 (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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398A ILE* 5.8 3.8 - - + -
402A ALA* 5.4 6.5 - - + -
457A ILE* 5.2 7.6 - - + +
461A PHE* 5.0 7.4 - - + -
482A LYS* 4.9 14.8 - - - +
486A MET* 6.4 0.4 - - + -
928A THR 3.2 9.4 + - - +
929A GLY* 2.9 9.2 + - - +
931A ILE* 1.3 79.2 - - - +
933A LEU* 1.3 65.0 + - - +
935A GLY* 2.9 11.2 + - - -
936A VAL* 3.0 14.4 + - - +
1012A ILE* 6.0 1.6 - - + -
1016A MET* 3.5 20.0 - - + -
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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
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907A ALA* 3.6 27.1 - - + +
908A LEU* 3.5 31.4 - - + +
911A GLY* 4.7 0.7 - - - -
929A GLY 2.7 16.3 + - - +
930A PHE* 3.5 11.4 - - + +
932A ALA* 1.3 71.6 - - - +
934A ALA* 1.3 67.0 + - - +
935A GLY 3.0 0.5 + - - -
936A VAL* 3.1 14.9 + - + +
937A ALA* 3.0 22.8 + - + -
1015A PRO* 3.0 33.7 - - + +
1016A MET* 3.2 15.1 - - + +
1019A GLY* 3.3 24.5 - - - +
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Residues in contact with ALA 934 (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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904A VAL* 3.4 33.6 - - + +
908A LEU* 4.1 6.3 - - + -
930A PHE 2.9 16.6 + - - +
931A ILE* 4.0 7.2 - - + +
933A LEU* 1.3 78.7 - - - +
935A GLY* 1.3 60.0 + - - +
937A ALA* 4.1 1.8 - - - -
938A ALA* 3.3 23.6 + - - +
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Residues in contact with GLY 935 (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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457A ILE* 3.5 40.3 - - - +
460A SER* 5.7 1.3 - - - -
931A ILE 3.4 9.0 + - - -
932A ALA 2.9 8.9 + - - -
934A ALA* 1.3 79.1 - - - +
936A VAL* 1.3 63.8 + - - +
938A ALA* 3.6 4.7 + - - +
939A GLU 3.2 16.6 + - - -
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Residues in contact with VAL 936 (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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402A ALA* 5.6 16.4 - - + +
405A ASP* 4.5 10.3 - - + +
457A ILE* 4.4 5.5 - - + +
932A ALA 3.0 9.2 + - - +
933A LEU* 3.1 23.8 + - + +
935A GLY* 1.3 73.4 - - - +
937A ALA* 1.3 66.9 + - + +
939A GLU* 3.1 20.9 - - - +
940A PHE* 2.9 44.0 + - + -
987A THR* 5.9 0.2 - - - +
991A ILE* 5.5 4.5 - - + -
1016A MET* 6.0 5.4 - - + -
1020A MET* 4.0 29.4 - - + -
1023A ALA* 5.2 1.6 - - + -
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Residues in contact with ALA 937 (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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903A SER* 6.2 0.7 - - - +
904A VAL* 5.1 4.3 - - + -
907A ALA* 3.8 28.9 - - + -
933A LEU* 3.0 16.5 + - + +
934A ALA* 4.4 3.8 - - - +
936A VAL* 1.3 77.5 - - - +
938A ALA* 1.3 64.5 + - - +
940A PHE* 3.0 13.7 + - - +
941A GLY* 2.9 21.0 + - - -
1023A ALA* 4.2 11.7 - - + -
1026A LEU* 4.3 8.5 - - + +
1027A SER* 4.3 1.9 + - - -
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Residues in contact with ALA 938 (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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453A SER* 4.7 0.4 - - - +
456A ILE* 5.5 14.4 - - + -
887A LEU* 5.6 1.6 - - + -
900A ILE* 4.2 29.9 - - + +
904A VAL* 5.8 3.3 - - + +
934A ALA 3.3 19.1 + - - +
935A GLY* 3.7 6.3 - - - +
936A VAL 3.3 0.4 - - - -
937A ALA* 1.3 77.3 - - - +
939A GLU* 1.3 62.4 + - - +
941A GLY* 3.3 2.6 + - - -
942A VAL* 3.1 27.5 + - - +
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Residues in contact with GLU 939 (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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405A ASP* 2.9 34.4 - - - +
409A VAL* 4.2 8.0 - - - +
450A LEU* 5.6 4.9 - - + +
453A SER* 2.7 34.5 + - - +
454A LEU* 5.9 0.2 - - + -
457A ILE* 4.6 2.0 - - + -
935A GLY 3.2 9.9 + - - +
936A VAL* 3.1 13.4 - - - +
937A ALA 3.1 0.2 - - - -
938A ALA* 1.3 79.1 - - - +
940A PHE* 1.3 97.4 + - - +
942A VAL* 3.1 5.4 + - - +
943A VAL* 2.9 35.2 + - + +
984A LYS* 3.8 3.5 + - - -
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Residues in contact with PHE 940 (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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405A ASP* 4.7 3.8 - - + -
409A VAL* 5.7 0.7 - - + -
936A VAL* 2.9 26.9 + - + -
937A ALA* 3.0 8.7 + - - +
939A GLU* 1.3 100.8 - - - +
941A GLY* 1.3 60.1 + - - +
943A VAL* 2.9 20.7 - - - +
944A MET* 3.1 11.8 + - - +
984A LYS* 3.2 31.0 - - + -
987A THR* 3.2 38.1 - - + -
988A VAL* 4.6 7.2 - - + -
1020A MET* 3.5 31.6 - - + -
1023A ALA* 4.4 11.2 - - + -
1024A PRO* 4.9 2.2 - - + -
1027A SER* 3.0 28.4 - - - +
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Residues in contact with GLY 941 (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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899A LEU* 6.3 0.2 - - - -
900A ILE* 6.0 5.6 - - - -
937A ALA 2.9 13.2 + - - -
938A ALA* 3.7 3.8 - - - -
939A GLU 3.2 0.4 - - - -
940A PHE* 1.3 76.9 - - - +
942A VAL* 1.3 55.3 + - - +
944A MET* 3.2 4.7 + - - +
945A LEU* 2.8 32.5 + - - +
1027A SER* 4.1 4.4 + - - -
1030A ILE* 4.6 21.1 - - - -
1031A ILE* 3.9 3.7 - - - +
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Residues in contact with VAL 942 (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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449A ALA* 3.3 42.2 - - + +
450A LEU* 4.9 0.4 - - - +
452A ILE* 5.4 4.0 - - + -
453A SER* 5.0 6.5 - - - -
456A ILE* 6.5 0.9 - - + -
887A LEU* 4.8 20.4 - - + +
890A ALA* 5.8 0.4 - - + -
891A PHE* 4.1 13.6 - - + -
900A ILE* 6.0 3.1 - - + +
938A ALA 3.1 16.0 + - - +
939A GLU* 3.1 11.5 + - - +
941A GLY* 1.3 75.7 - - - +
943A VAL* 1.3 66.6 + - + +
944A MET 3.1 0.2 + - - -
945A LEU* 3.1 6.8 + - - +
946A MET* 3.1 24.1 + - - +
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Residues in contact with VAL 943 (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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409A VAL* 4.1 24.7 - - + -
446A VAL* 5.8 1.1 - - + -
449A ALA* 5.6 2.0 - - - -
450A LEU* 6.1 5.8 - - + +
939A GLU* 2.9 19.1 + - + +
940A PHE 2.9 24.9 - - - +
942A VAL* 1.3 80.9 - - + +
944A MET* 1.3 59.7 + - - +
946A MET* 4.0 5.4 + - - +
947A TYR* 2.9 48.8 + - + +
984A LYS* 2.9 36.1 - - - +
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Residues in contact with MET 944 (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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525A TYR* 5.3 0.4 - - - +
940A PHE 3.1 15.2 + - - +
941A GLY 3.7 0.4 - - - +
942A VAL 3.0 0.6 - - - -
943A VAL* 1.3 83.5 - - + +
945A LEU* 1.3 64.8 + - - +
946A MET 3.3 0.2 - - - -
947A TYR* 3.4 18.8 + - + +
948A LEU* 3.5 13.9 + - + +
973A LEU 5.4 1.3 - - - +
976A GLY* 3.0 36.1 - - - +
977A ALA* 3.6 8.1 - - + +
980A ARG* 3.4 55.0 - - + +
1027A SER 4.1 2.0 - - - +
1028A LEU 6.2 0.2 - - - +
1031A ILE* 3.2 39.3 - - + +
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Residues in contact with LEU 945 (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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891A PHE* 4.9 5.8 - - + -
896A GLU* 3.1 49.1 - - + +
899A LEU* 5.5 9.6 - - + -
941A GLY 2.8 18.1 + - - +
942A VAL* 3.1 7.2 + - - +
944A MET* 1.3 74.7 - - - +
946A MET* 1.3 66.7 + - - +
948A LEU* 3.0 25.6 - - + +
949A ARG* 3.1 18.1 + - + +
1030A ILE 5.8 0.7 - - - +
1031A ILE* 3.3 21.7 - - + +
1035A TYR* 3.8 29.4 - - + -
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Residues in contact with MET 946 (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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445A GLU* 4.2 31.6 - - + +
449A ALA* 5.2 5.8 - - + -
891A PHE* 3.2 40.7 - - + -
942A VAL 3.1 10.6 + - - +
943A VAL* 4.0 7.6 - - - +
945A LEU* 1.3 77.9 - - - +
947A TYR* 1.3 73.7 + - + +
949A ARG* 3.1 7.3 + - + +
950A HIS* 2.9 39.7 + - + +
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Residues in contact with TYR 947 (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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409A VAL* 4.8 3.1 - - - +
412A GLU* 5.1 8.1 - - - +
413A ASN* 3.5 29.2 + - - +
446A VAL* 4.3 11.5 - - + +
943A VAL* 2.9 43.7 + - + +
944A MET* 3.4 19.4 + - + +
945A LEU 3.2 0.6 - - - -
946A MET* 1.3 90.7 - - + +
948A LEU* 1.3 58.4 + - - +
950A HIS* 3.4 11.2 + + + +
951A ALA* 3.0 24.8 + - - +
975A HIS* 5.0 1.7 - - - -
976A GLY* 4.7 11.1 - - - -
979A LEU* 3.3 43.0 - - + +
980A ARG* 5.1 4.3 - - + -
983A PRO* 5.9 1.9 - - + +
984A LYS* 5.8 0.7 - - - -
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Residues in contact with LEU 948 (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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944A MET* 3.5 8.8 + - + +
945A LEU* 3.0 15.5 - - + +
947A TYR* 1.3 80.4 - - - +
949A ARG* 1.3 78.6 + - + +
951A ALA* 3.2 9.7 - - - +
952A ILE* 3.1 30.8 + - + +
973A LEU* 4.7 23.8 - - + +
975A HIS* 5.7 0.4 - - - -
976A GLY* 5.8 3.6 - - - -
1031A ILE* 3.2 51.4 - - + +
1032A PRO* 5.1 1.3 - - + -
1035A TYR* 3.1 43.3 - - + -
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Residues in contact with ARG 949 (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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891A PHE* 4.9 16.2 - - + -
893A ARG* 6.0 3.4 - - - -
896A GLU* 4.2 12.3 - - - +
945A LEU* 3.6 22.0 - - + +
946A MET* 3.1 13.1 + - + +
948A LEU* 1.3 80.4 - - + +
950A HIS* 1.3 65.8 + - - +
952A ILE* 3.5 29.9 + - - +
953A GLU* 3.1 29.4 + - - +
1035A TYR* 2.9 33.5 + - - +
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Residues in contact with HIS 950 (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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417A ARG* 5.8 5.2 + - - -
445A GLU* 5.9 3.6 - - - -
946A MET* 2.9 30.4 + - + +
947A TYR* 3.5 14.2 + + + +
949A ARG* 1.3 75.6 - - - +
951A ALA* 1.3 64.1 + - - +
953A GLU* 3.1 18.1 + - - +
954A ALA* 2.8 41.6 + - + +
975A HIS* 5.4 4.3 - + - -
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Residues in contact with ALA 951 (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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947A TYR 3.0 11.6 + - - +
948A LEU* 3.2 16.4 - - + +
950A HIS* 1.3 81.5 + - - +
952A ILE* 1.3 55.4 + - + +
954A ALA* 2.5 25.5 + - - -
956A PRO* 2.9 25.5 - - + +
972A ALA* 4.8 4.7 - - + +
973A LEU* 5.4 2.2 - - + -
975A HIS* 3.1 36.1 - - + +
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Residues in contact with ILE 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A LEU* 3.1 12.5 + - + +
949A ARG* 3.8 34.3 - - - +
950A HIS 3.5 0.2 - - - -
951A ALA* 1.3 78.8 - - + +
953A GLU* 1.3 63.0 + - - +
954A ALA 3.2 3.1 + - - +
956A PRO* 3.8 11.4 - - + +
957A SER* 3.1 36.4 + - - +
958A LEU* 3.8 4.2 - - - +
969A LEU* 6.4 2.0 - - + -
973A LEU* 5.3 11.7 - - + -
1035A TYR* 4.2 20.9 - - + +
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Residues in contact with GLU 953 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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949A ARG* 3.1 21.2 + - - +
950A HIS* 3.3 22.2 - - - +
952A ILE* 1.3 78.2 - - - +
954A ALA* 1.3 59.2 + - - +
958A LEU* 3.9 9.7 - - - +
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Residues in contact with ALA 954 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950A HIS* 2.8 28.6 + - + +
951A ALA* 2.5 18.1 + - - +
952A ILE 3.7 1.2 - - - +
953A GLU* 1.3 70.8 - - - +
955A VAL* 1.3 74.5 + - + +
956A PRO* 3.5 2.6 - - + -
958A LEU* 3.0 26.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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