Contacts of the helix formed by residues 1012 - 1044 (chain C) in PDB entry 3H2U
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 SER1012 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996A LYS* 4.3 3.9 + - - -
1010C ASN 4.3 0.6 - - - -
1011C ILE* 1.3 94.9 - - - +
1013C ASP* 1.3 66.0 + - - +
1014C GLU* 4.1 16.7 + - - +
1015C GLU* 3.1 41.7 + - - +
1016C SER* 3.4 5.5 + - - -
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Residues in contact with ASP1013 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011C ILE 4.3 3.5 - - - +
1012C SER* 1.3 74.8 - - - +
1014C GLU* 1.3 61.2 + - + +
1016C SER* 3.0 7.6 + - - -
1017C GLU* 2.9 33.1 + - + +
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Residues in contact with GLU1014 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
989A PRO* 6.0 2.3 - - - +
993A THR* 3.6 16.8 + - + +
996A LYS* 5.6 6.0 + - - +
1012C SER* 4.2 13.2 - - - -
1013C ASP* 1.3 81.3 - - + +
1015C GLU* 1.3 58.7 + - - +
1017C GLU* 3.9 7.1 - - - +
1018C GLN* 2.8 33.8 + - - +
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Residues in contact with GLU1015 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A LYS* 5.9 2.3 - - - +
993A THR* 3.5 13.0 - - + -
996A LYS* 2.8 47.1 + - + +
997A ILE* 3.3 18.8 + - + +
1005C MET* 4.2 7.8 - - + +
1011C ILE* 3.3 25.7 - - + +
1012C SER* 3.1 22.4 + - - +
1013C ASP 3.3 0.6 - - - -
1014C GLU* 1.3 79.8 - - - +
1016C SER* 1.3 51.0 + - - +
1018C GLN 3.3 0.2 + - - -
1019C ALA* 2.8 31.2 + - - +
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Residues in contact with SER1016 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002C LYS* 3.7 11.7 + - - -
1005C MET* 3.5 20.0 - - - -
1011C ILE* 3.3 22.3 - - - +
1012C SER 3.4 4.7 + - - -
1013C ASP* 3.0 14.4 + - - -
1015C GLU* 1.3 75.4 - - - +
1017C GLU* 1.3 70.2 + - - +
1019C ALA* 3.1 2.4 + - - +
1020C THR* 2.8 33.1 + - - -
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Residues in contact with GLU1017 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002C LYS* 5.5 0.2 - - - +
1013C ASP 2.9 16.2 + - - +
1014C GLU* 3.9 7.6 - - - +
1016C SER* 1.3 80.9 + - - +
1018C GLN* 1.3 64.4 + - - +
1020C THR* 3.2 12.0 + - - +
1021C GLU* 2.9 48.0 + - + +
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Residues in contact with GLN1018 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990A THR* 3.5 24.0 + - - +
993A THR* 3.6 21.2 + - + -
994A GLN* 2.6 46.0 + - + -
997A ILE* 3.9 2.7 - - + -
1014C GLU 2.8 19.5 + - - +
1015C GLU 3.5 3.4 - - - +
1017C GLU* 1.3 79.9 - - - +
1019C ALA* 1.3 65.8 + - - +
1021C GLU* 3.1 19.8 + - - +
1022C MET* 2.9 28.4 + - - +
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Residues in contact with ALA1019 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
997A ILE* 3.7 2.6 - - + +
998C LEU* 5.1 4.0 - - - +
1001C VAL* 3.8 20.3 - - + +
1002C LYS* 4.4 9.3 - - + +
1005C MET* 3.7 22.7 - - + -
1015C GLU 2.8 15.1 + - - +
1016C SER 3.1 8.9 + - - +
1018C GLN* 1.3 76.3 - - - +
1020C THR* 1.3 60.5 + - - +
1022C MET* 3.5 16.4 + - - +
1023C LEU* 3.2 22.9 + - - +
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Residues in contact with THR1020 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C ASN* 4.2 9.6 - - - +
937C VAL* 5.3 8.5 + - + +
1002C LYS* 2.4 41.5 + - - +
1016C SER 2.8 7.5 + - - -
1017C GLU* 3.2 17.2 - - - +
1019C ALA* 1.3 74.1 - - - +
1021C GLU* 1.3 65.8 + - + +
1023C LEU* 3.1 6.6 + - - +
1024C VAL* 2.8 47.4 + - + +
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Residues in contact with GLU1021 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017C GLU* 2.9 36.8 + - - +
1018C GLN* 3.1 24.1 + - - +
1020C THR* 1.3 81.2 - - + +
1022C MET* 1.3 58.0 + - - +
1024C VAL* 3.7 12.2 - - - +
1025C HIS* 2.9 30.5 + - - +
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Residues in contact with MET1022 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994A GLN* 3.6 42.0 - - + +
997A ILE* 3.0 55.9 - - + -
998A LEU* 5.0 7.2 - - - -
998C LEU* 3.5 29.5 - - + +
1001C VAL* 5.5 0.2 - - + -
1018C GLN* 2.9 19.3 + - - +
1019C ALA* 3.6 13.2 - - - +
1021C GLU* 1.3 76.5 - - - +
1023C LEU* 1.3 58.6 + - - +
1025C HIS* 3.9 8.6 - - - +
1026C ASN* 3.1 26.3 + - - +
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Residues in contact with LEU1023 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C MET* 3.9 14.4 - - + -
933C MET* 4.5 3.8 - - - -
937C VAL* 3.8 26.2 - - + -
947C LEU* 5.0 2.7 - - + -
995C LEU* 3.4 33.0 - - + -
998C LEU* 4.1 18.4 - - + +
999C SER* 4.0 19.1 - - - +
1002C LYS* 3.9 23.1 - - + -
1019C ALA 3.2 9.3 + - - +
1020C THR* 3.3 9.6 - - - +
1022C MET* 1.3 78.5 - - - +
1024C VAL* 1.3 56.8 + - + +
1026C ASN* 3.0 7.1 + - + +
1027C ALA* 2.8 34.6 + - - +
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Residues in contact with VAL1024 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895C ASN* 3.5 32.3 - - - +
897C PRO* 3.7 20.6 - - + -
898C MET* 4.1 15.4 - - + +
937C VAL* 6.1 1.3 - - + -
1020C THR* 2.8 32.8 + - + +
1021C GLU* 3.7 14.1 - - - +
1023C LEU* 1.3 77.8 - - + +
1025C HIS* 1.3 57.0 + - - +
1027C ALA* 3.5 2.8 + - - +
1028C GLN* 3.0 52.8 + - + +
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Residues in contact with HIS1025 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021C GLU 2.9 18.4 + - - +
1022C MET* 3.9 8.1 - - - +
1024C VAL* 1.3 73.1 - - - +
1026C ASN* 1.3 72.4 + - + +
1028C GLN* 3.0 26.2 + - - +
1029C ASN* 3.0 41.4 + - - -
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Residues in contact with ASN1026 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991C ILE* 2.6 45.4 + - - +
994C GLN* 3.5 31.1 + - - +
995C LEU* 3.3 20.5 + - + +
998C LEU* 3.8 17.6 - - + +
1022C MET 3.1 14.3 + - - +
1023C LEU* 3.0 10.2 + - - +
1025C HIS* 1.3 82.0 - - - +
1027C ALA* 1.3 57.1 + - - +
1029C ASN* 3.2 8.1 + - - +
1030C LEU* 2.9 24.5 + - - +
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Residues in contact with ALA1027 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C MET* 3.7 19.1 - - + -
901C ALA* 4.6 1.6 - - + -
930C MET* 3.4 37.0 - - + -
995C LEU* 4.7 4.9 - - + +
1023C LEU 2.8 18.1 + - - +
1024C VAL 3.6 5.8 - - - +
1026C ASN* 1.3 72.3 - - - +
1028C GLN* 1.3 59.0 + - - +
1030C LEU* 3.8 3.6 - - - -
1031C MET* 3.0 36.7 + - - +
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Residues in contact with GLN1028 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897C PRO* 3.6 19.7 + - - +
898C MET* 6.0 0.4 - - - -
901C ALA* 4.3 19.2 - - + +
1024C VAL* 3.0 33.6 + - - +
1025C HIS* 3.0 23.8 + - - +
1027C ALA* 1.3 76.1 - - - +
1029C ASN* 1.3 70.8 + - - +
1031C MET* 4.2 1.4 - - - +
1032C GLN* 3.1 25.5 + - - +
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Residues in contact with ASN1029 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991C ILE* 3.9 19.7 - - + +
1025C HIS* 3.0 48.1 + - - +
1026C ASN* 3.7 8.3 + - - +
1028C GLN* 1.3 79.0 - - - +
1030C LEU* 1.3 57.3 + - - +
1032C GLN* 4.5 3.6 - - - -
1033C SER* 2.6 38.9 + - - +
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Residues in contact with LEU1030 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926C MET* 4.3 5.4 - - + -
930C MET* 4.4 3.4 - - + -
954C ILE* 3.6 31.9 - - + -
958C SER* 4.6 4.0 - - - -
988C ILE* 4.1 16.8 - - + +
991C ILE* 3.7 27.9 - - + +
992C SER* 3.7 22.0 - - - +
995C LEU* 3.7 18.2 - - + -
1026C ASN* 2.9 18.1 + - - +
1027C ALA* 3.9 5.6 - - - +
1029C ASN* 1.3 77.6 - - - +
1031C MET* 1.3 77.7 + - + +
1033C SER* 3.5 0.7 - - - -
1034C VAL* 2.9 31.3 + - + +
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Residues in contact with MET1031 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901C ALA* 3.3 39.9 - - + +
902C ALA* 3.9 3.8 - - - +
904C GLN* 5.6 1.6 - - + -
905C LEU* 3.7 33.7 + - + +
926C MET* 3.6 39.0 - - + +
927C ALA* 4.5 0.7 - - - -
930C MET* 3.8 41.3 - - + -
954C ILE* 5.3 0.7 - - + -
1027C ALA 3.0 23.4 + - - +
1028C GLN 4.2 0.9 - - - +
1030C LEU* 1.3 81.9 - - + +
1032C GLN* 1.3 57.4 + - - +
1034C VAL 3.5 0.3 + - - -
1035C LYS* 3.1 25.9 + - - +
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Residues in contact with GLN1032 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904C GLN* 5.2 7.2 - - - +
1028C GLN 3.1 19.2 + - - +
1029C ASN* 3.7 4.0 - - - +
1030C LEU 3.1 0.6 - - - -
1031C MET* 1.3 72.9 - - - +
1033C SER* 1.3 67.7 + - - +
1034C VAL 2.9 2.6 + - - -
1035C LYS* 3.0 37.5 + - - +
1036C GLU* 2.7 48.1 + - - +
1039C ARG* 4.3 4.8 - - - +
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Residues in contact with SER1033 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984C VAL 3.4 8.4 + - - +
987C ARG* 3.9 20.2 + - - +
988C ILE* 3.9 16.0 - - - +
991C ILE* 3.1 26.4 - - - +
1029C ASN* 2.6 21.1 + - - +
1030C LEU* 3.5 4.3 - - - -
1032C GLN* 1.3 72.1 - - - +
1034C VAL* 1.3 53.1 + - - +
1036C GLU* 3.8 10.9 + - - +
1037C THR* 2.5 33.7 + - - -
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Residues in contact with VAL1034 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905C LEU* 3.3 31.9 - - + -
923C ALA* 4.1 16.8 - - + -
926C MET* 3.6 26.9 - - + -
958C SER* 5.2 0.2 - - - -
961C VAL* 4.6 13.2 - - + -
988C ILE* 3.8 21.5 - - + -
1030C LEU* 2.9 25.0 + - + +
1033C SER* 1.3 76.1 - - - +
1035C LYS* 1.3 64.1 + - - +
1036C GLU 3.1 2.0 - - - -
1037C THR* 3.3 6.8 + - - -
1038C VAL* 3.2 22.5 + - + +
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Residues in contact with LYS1035 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904C GLN* 3.7 39.9 + - + +
905C LEU* 3.8 11.0 - - + +
908C GLU* 3.6 32.1 + - + +
1031C MET 3.1 13.5 + - - +
1032C GLN* 3.4 28.3 - - - +
1034C VAL* 1.3 76.4 - - - +
1036C GLU* 1.3 64.1 + - - +
1038C VAL* 3.2 6.7 + - - +
1039C ARG* 2.8 58.5 + - - +
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Residues in contact with GLU1036 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984C VAL* 4.2 26.1 - - + +
987C ARG* 4.4 7.8 + - - -
1032C GLN* 2.7 50.5 + - - +
1033C SER* 4.0 9.7 - - - +
1035C LYS* 1.3 76.1 - - - +
1037C THR* 1.3 59.4 + - - +
1039C ARG* 3.0 31.4 + - - +
1040C GLU* 2.8 34.7 + - + +
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Residues in contact with THR1037 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C ILE* 5.0 3.7 - - + +
961C VAL* 4.6 12.1 - - + -
965C ALA* 3.7 22.7 - - + -
981C LEU* 3.5 9.8 - - + +
984C VAL* 3.3 17.8 + - + +
985C CYS* 3.6 22.9 - - + -
988C ILE* 3.5 9.1 - - - +
1033C SER 2.5 24.8 + - - -
1034C VAL* 3.3 8.2 + - - -
1036C GLU* 1.3 77.8 - - - +
1038C VAL* 1.3 58.3 + - - +
1041C ALA* 3.0 28.9 + - - +
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Residues in contact with VAL1038 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905C LEU* 5.1 2.5 - - + -
908C GLU* 3.7 26.2 - - + +
909C ALA* 4.9 1.3 - - + -
912C TRP* 4.5 2.6 + - + +
919C ILE* 4.0 21.1 - - + +
920C ILE* 3.9 24.2 - - + -
923C ALA* 4.3 20.4 - - + -
961C VAL* 6.0 0.7 - - + -
1034C VAL* 3.2 16.3 + - + +
1035C LYS* 3.4 9.6 - - - +
1036C GLU 3.1 0.6 - - - -
1037C THR* 1.3 75.8 - - - +
1039C ARG* 1.3 65.6 + - - +
1040C GLU 3.4 0.2 - - - -
1041C ALA* 4.4 3.6 - - - -
1042C GLU* 3.4 8.0 + - - +
1058C TRP* 3.3 28.4 - - + -
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Residues in contact with ARG1039 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908C GLU* 3.0 36.1 - - - +
911C LYS* 5.3 0.9 - - - +
1032C GLN* 4.3 5.5 - - - +
1035C LYS* 2.8 55.4 + - - +
1036C GLU* 3.0 34.9 + - - +
1038C VAL* 1.3 75.1 - - - +
1040C GLU* 1.3 64.2 + - + +
1042C GLU* 3.7 9.7 - - - +
1043C ALA* 3.3 20.1 + - - +
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Residues in contact with GLU1040 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976C ARG* 5.1 3.2 + - - -
977C ILE* 3.8 17.8 - - - +
980C ASN* 3.2 41.0 - - + +
981C LEU* 3.0 31.2 - - + +
984C VAL* 4.4 11.5 - - + +
1036C GLU* 2.8 21.4 + - + +
1037C THR* 4.7 0.4 - - - -
1039C ARG* 1.3 78.3 - - + +
1041C ALA* 1.3 52.1 + - - +
1043C ALA* 2.9 9.6 + - - +
1044C ALA* 2.7 35.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA1041 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919C ILE* 4.7 17.7 - - + -
965C ALA* 5.9 0.7 - - - -
968C VAL* 3.9 22.5 - - + +
981C LEU* 2.9 17.2 - - + +
1037C THR 3.0 19.1 + - - +
1038C VAL* 3.9 3.6 - - - +
1040C GLU* 1.3 74.3 - - - +
1042C GLU* 1.3 61.9 + - - +
1044C ALA* 3.5 5.5 + - - +
1045C SER* 3.3 14.2 + - - -
1056C LEU* 5.0 0.4 - - + -
1058C TRP* 3.6 22.6 + - + -
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Residues in contact with GLU1042 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912C TRP* 4.2 19.5 - - + -
1038C VAL 3.4 7.7 + - - +
1039C ARG* 3.7 9.8 - - - +
1040C GLU 3.2 0.6 - - - -
1041C ALA* 1.3 74.8 - - - +
1043C ALA* 1.3 66.2 + - - +
1045C SER* 2.7 34.3 + - - +
1046C ILE* 3.9 1.7 + - - +
1058C TRP* 3.2 54.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA1043 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976C ARG* 6.0 1.8 - - - +
977C ILE* 4.2 26.8 - - + +
1039C ARG 3.3 12.8 + - - +
1040C GLU* 2.9 15.8 + - - +
1042C GLU* 1.3 83.6 + - - +
1044C ALA* 1.3 56.1 + - - +
1045C SER 2.9 6.6 + - - -
1046C ILE* 3.2 24.2 + - - +
1047C LYS 4.1 1.6 + - - -
----------------------------------------------------------
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Residues in contact with ALA1044 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968C VAL* 3.7 24.8 - - + +
972C CYS* 3.5 28.2 - - + -
977C ILE* 3.8 10.4 - - + +
978C ARG 5.6 0.2 - - - +
981C LEU* 4.2 7.9 - - + -
1040C GLU 2.7 18.4 + - - +
1041C ALA 3.6 2.7 - - - +
1042C GLU 3.2 0.4 - - - -
1043C ALA* 1.3 69.5 - - - +
1045C SER* 1.3 50.3 + - - +
1046C ILE 3.4 1.1 - - - -
1047C LYS 4.2 2.9 - - - +
1048C ILE* 2.7 41.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il