Contacts of the helix formed by residues 1010 - 1040 (chain F) in PDB entry 5WUA
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 ILE1010 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005F LEU* 3.8 27.1 - - + +
1008F ALA* 3.1 10.2 + - + +
1009F GLY* 1.3 72.7 - - - +
1011F LEU* 1.3 57.6 + - - +
1012F LEU 3.0 0.9 - - - -
1013F LEU* 2.9 28.5 + - + +
1014F SER* 3.2 7.8 + - - -
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Residues in contact with LEU1011 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009F GLY 2.6 8.4 + - - +
1010F ILE* 1.3 75.1 - - - +
1012F LEU* 1.3 56.0 + - - +
1014F SER* 2.9 32.3 + - - -
1015F LEU* 3.6 6.4 + - - +
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Residues in contact with LEU1012 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009F GLY* 2.7 22.9 + - - +
1011F LEU* 1.3 72.3 - - - +
1013F LEU* 1.3 59.5 + - - +
1015F LEU* 4.5 1.7 + - - +
1016F LEU* 4.3 15.6 + - - +
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Residues in contact with LEU1013 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010F ILE* 2.9 15.8 + - + +
1012F LEU* 1.3 76.2 - - - +
1014F SER* 1.3 68.2 + - - +
1016F LEU* 4.4 3.4 - - - +
1017F VAL* 3.4 19.8 + - - +
1085F THR* 4.9 24.1 - - - +
1089F THR* 5.6 7.6 - - - -
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Residues in contact with SER1014 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010F ILE 3.2 5.3 + - - -
1011F LEU* 2.9 24.2 + - - -
1013F LEU* 1.3 81.2 - - - +
1015F LEU* 1.3 65.4 + - - -
1017F VAL* 3.0 12.5 + - - +
1018F PHE* 3.1 10.7 + - - +
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Residues in contact with LEU1015 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011F LEU 3.6 6.4 + - - +
1012F LEU 4.5 1.7 + - - +
1014F SER* 1.3 79.1 - - - +
1016F LEU* 1.3 51.1 + - - +
1018F PHE* 2.9 11.9 + - - +
1019F SER* 2.5 35.4 + - - -
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Residues in contact with LEU1016 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012F LEU 4.3 14.9 + - - +
1013F LEU* 4.0 4.2 + - - +
1014F SER 3.1 0.8 + - - -
1015F LEU* 1.3 77.2 - - - +
1017F VAL* 1.3 63.8 + - - +
1019F SER* 2.9 21.2 + - - -
1020F GLN* 3.0 10.2 + - - +
1078F LEU* 5.4 0.7 - - - -
1081F VAL* 4.0 31.4 - - + +
1085F THR* 5.6 4.0 - - - -
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Residues in contact with VAL1017 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013F LEU 3.4 11.2 + - - +
1014F SER* 3.0 10.8 + - - +
1016F LEU* 1.3 78.6 - - - +
1018F PHE* 1.3 58.0 + - - +
1020F GLN* 2.9 29.6 + - - +
1021F LEU* 3.2 5.2 + - - +
1081F VAL 6.0 0.2 - - - -
1082F THR* 5.8 8.3 - - - +
1085F THR* 6.5 1.1 - - - -
1144F SER* 5.4 12.8 - - - -
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Residues in contact with PHE1018 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014F SER 3.1 9.0 + - - +
1015F LEU* 2.9 18.3 + - - +
1017F VAL* 1.3 73.1 - - - +
1019F SER* 1.3 55.5 + - - +
1020F GLN 2.9 4.9 - - - -
1021F LEU* 2.9 24.8 + - + +
1022F LEU* 3.1 16.8 + - - +
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Residues in contact with SER1019 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015F LEU 2.5 16.2 + - - -
1016F LEU* 2.9 17.2 + - - -
1018F PHE* 1.3 71.6 - - - +
1020F GLN* 1.3 55.5 + - - +
1022F LEU* 5.2 2.6 - - - +
1023F LYS* 3.2 22.6 + - - +
1074F LEU 4.9 0.3 - - - +
1078F LEU* 4.3 6.9 + - - +
1081F VAL* 6.1 1.3 - - - -
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Residues in contact with GLN1020 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016F LEU 3.0 6.0 + - - +
1017F VAL* 2.9 21.0 + - - +
1019F SER* 1.3 76.3 - - - +
1021F LEU* 1.3 63.9 + - - +
1023F LYS* 2.9 13.5 + - - +
1024F HIS* 3.0 13.6 + - - +
1078F LEU* 3.4 32.3 - - + +
1082F THR* 5.5 5.8 - - - -
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Residues in contact with LEU1021 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017F VAL 3.2 6.1 + - - +
1018F PHE* 2.9 18.1 + - + +
1020F GLN* 1.3 73.4 - - - +
1022F LEU* 1.3 65.2 + - - +
1024F HIS* 2.9 17.2 + - - +
1025F MET* 3.0 14.1 + - - +
1148F LEU* 4.9 21.8 - - + +
1152F SER* 6.5 0.9 - - - -
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Residues in contact with LEU1022 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018F PHE 3.1 11.5 + - - +
1019F SER* 5.2 2.7 - - - +
1021F LEU* 1.3 77.8 - - - +
1023F LYS* 1.3 64.6 + - - +
1025F MET* 3.0 7.7 + - - -
1026F VAL* 2.8 30.4 + - + +
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Residues in contact with LYS1023 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019F SER 3.2 17.9 + - - +
1020F GLN* 2.9 16.2 + - - +
1022F LEU* 1.3 77.8 - - - +
1024F HIS* 1.3 60.1 + - - +
1026F VAL* 4.4 3.1 - - - +
1027F LEU* 3.0 24.8 + - - +
1074F LEU* 3.7 41.6 - - + +
1075F GLY* 5.4 0.7 - - - -
1078F LEU* 4.5 1.8 - - + -
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Residues in contact with HIS1024 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020F GLN 3.0 8.4 + - - +
1021F LEU* 2.9 11.9 + - - +
1023F LYS* 1.3 76.0 - - - +
1025F MET* 1.3 64.2 + - - +
1027F LEU* 2.9 22.5 + - - +
1028F VAL* 3.1 8.3 + - - +
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Residues in contact with MET1025 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021F LEU 3.0 12.9 + - - +
1022F LEU* 3.7 9.4 - - - +
1024F HIS* 1.3 75.4 - - - +
1026F VAL* 1.3 64.3 + - - +
1028F VAL* 2.9 11.2 + - - +
1029F ALA* 2.9 20.6 + - - +
1152F SER* 5.9 8.7 - - - -
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Residues in contact with VAL1026 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022F LEU* 2.8 21.2 + - + +
1023F LYS* 4.4 2.5 - - - +
1025F MET* 1.3 73.6 - - - +
1027F LEU* 1.3 62.1 + - - +
1029F ALA* 2.9 20.8 + - + +
1030F ILE* 3.1 17.2 + - - +
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Residues in contact with LEU1027 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F ILE* 6.3 3.4 - - + -
1023F LYS 3.0 16.6 + - - +
1024F HIS* 2.9 17.8 + - - +
1026F VAL* 1.3 76.5 - - - +
1028F VAL* 1.3 58.6 + - - +
1030F ILE* 5.0 1.5 - - - +
1031F ASP* 3.3 20.8 + - - +
1067F VAL* 5.7 1.4 - - - +
1071F LEU* 4.1 33.8 - - + +
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Residues in contact with VAL1028 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024F HIS 3.1 8.4 + - - +
1025F MET* 2.9 11.2 + - - +
1027F LEU* 1.3 76.2 - - - +
1029F ALA* 1.3 51.6 - - - +
1031F ASP* 2.9 8.6 + - - +
1032F TYR* 2.2 40.5 + - + +
1283F LEU* 6.2 3.8 - - + -
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Residues in contact with ALA1029 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025F MET 2.9 12.0 + - - +
1026F VAL* 2.9 14.4 + - + +
1028F VAL* 1.3 75.2 - - - +
1030F ILE* 1.3 51.8 + - - +
1032F TYR* 2.8 12.7 - - - +
1033F TRP* 2.6 33.9 + - - +
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Residues in contact with ILE1030 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026F VAL 3.1 12.4 + - - +
1027F LEU* 5.0 0.9 - - - +
1029F ALA* 1.3 72.5 - - - +
1031F ASP* 1.3 61.5 + - - +
1032F TYR 3.0 0.9 - - - -
1033F TRP* 2.9 7.4 + - - +
1034F LEU* 2.5 41.9 + - + +
1067F VAL* 4.1 20.0 - - + -
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Residues in contact with ASP1031 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027F LEU 3.3 16.9 + - - +
1028F VAL* 2.9 11.6 + - - +
1030F ILE* 1.3 78.0 - - - +
1032F TYR* 1.3 59.1 + - - +
1035F ALA* 3.3 27.2 - - + +
1036F LYS* 3.9 2.9 + - - +
1067F VAL* 4.7 8.2 - - + +
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Residues in contact with TYR1032 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028F VAL 2.2 27.2 + - - +
1029F ALA* 2.8 19.5 - - - +
1031F ASP* 1.3 71.3 - - - +
1033F TRP* 1.3 56.4 + - - +
1036F LYS* 3.2 19.1 - - - +
1279F GLY* 4.2 16.9 - - - +
1283F LEU* 4.1 26.9 - - + +
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Residues in contact with TRP1033 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029F ALA 2.6 15.7 + - - +
1030F ILE* 2.9 6.7 + - - +
1032F TYR* 1.3 74.4 - - - +
1034F LEU* 1.3 58.3 + - - +
1035F ALA 3.1 1.3 - - - -
1036F LYS 2.9 2.1 + - - -
1037F TRP* 2.2 45.8 + - + +
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Residues in contact with LEU1034 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030F ILE* 2.5 21.6 + - + +
1033F TRP* 1.3 74.6 - - - +
1035F ALA* 1.3 60.5 + - - +
1037F TRP* 4.0 6.4 - - - +
1038F THR* 3.1 21.3 + - - -
1060F ASP* 5.4 2.8 - - - +
1063F VAL* 4.8 15.4 - - + +
1064F TYR* 4.8 12.0 - - - +
1067F VAL* 4.6 14.8 - - + -
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Residues in contact with ALA1035 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571F LEU* 5.1 3.4 - - - +
1030F ILE 3.4 3.0 + - - -
1031F ASP* 3.3 24.7 - - + +
1033F TRP 3.1 0.4 - - - -
1034F LEU* 1.3 75.7 - - - +
1036F LYS* 1.3 61.4 + - - +
1038F THR* 2.9 11.4 + - - -
1039F ASP* 2.8 24.5 + - - +
1064F TYR* 5.2 10.2 - - + +
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Residues in contact with LYS1036 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573F PRO* 5.8 7.2 - - + -
1031F ASP 3.9 3.0 + - - +
1032F TYR* 3.2 25.1 - - - +
1033F TRP 2.9 4.4 + - - -
1035F ALA* 1.3 77.0 - - - +
1037F TRP* 1.3 50.7 + - - +
1039F ASP* 3.1 14.0 + - + +
1040F SER* 2.7 32.4 + - - -
1278F ALA 5.3 2.5 - - - +
1279F GLY* 5.0 13.2 - - - -
1282F GLY* 6.6 0.2 - - - -
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Residues in contact with TRP1037 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033F TRP* 2.2 40.7 + - + +
1034F LEU* 4.1 5.2 - - - +
1036F LYS* 1.3 69.0 - - - +
1038F THR* 1.3 56.3 + - - +
1040F SER* 3.0 31.3 - - - -
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Residues in contact with THR1038 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571F LEU* 5.1 9.1 + - - +
1034F LEU 3.1 14.6 + - - -
1035F ALA* 2.9 12.1 + - - -
1037F TRP* 1.3 72.2 - - - +
1039F ASP* 1.3 65.0 + - - +
1040F SER 2.9 8.7 + - - +
1060F ASP* 4.8 22.7 - - - -
1061F GLN* 5.8 1.6 - - - -
1064F TYR* 6.0 3.1 - - - -
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Residues in contact with ASP1039 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571F LEU* 3.5 31.5 - - + +
572F SER 5.0 0.4 - - - -
573F PRO* 4.7 15.9 - - + -
1035F ALA 2.8 11.5 + - - +
1036F LYS* 3.2 22.0 - - + +
1038F THR* 1.3 71.1 - - - +
1040F SER* 1.3 57.4 + - - +
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Residues in contact with SER1040 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036F LYS 2.7 15.8 + - - -
1037F TRP* 3.0 24.2 - - - -
1038F THR* 2.9 7.2 - - - +
1039F ASP* 1.3 77.0 - - - +
1278F ALA* 6.3 3.1 - - - -
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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