Contacts of the helix formed by residues 1020 - 1047 (chain E) in PDB entry 3U5P
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 ILE1020 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E LEU* 3.4 6.0 - - - +
959E SER* 6.4 0.7 - - - -
962E ASP* 4.7 6.5 - - - +
1018E TYR* 3.3 5.8 - - - +
1019E GLN* 1.3 86.0 - - + +
1021E PRO* 1.4 73.2 - - + +
1022E ASP* 2.9 35.2 - - + +
1023E ASP* 2.8 58.4 + - - +
1024E PHE* 3.3 4.9 + - - +
1084E ARG* 5.3 1.8 - - - +
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Residues in contact with PRO1021 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E LEU* 4.0 8.1 - - + -
959E SER 6.0 0.4 - - - +
962E ASP* 3.3 38.8 - - + +
966E CYS* 4.6 7.2 - - - -
1020E ILE* 1.4 97.8 - - + +
1022E ASP* 1.3 64.6 + - - +
1023E ASP 3.1 1.1 - - - -
1024E PHE* 3.9 9.8 - - + +
1025E VAL* 3.2 18.0 + - - +
1081E TYR* 3.5 16.4 - - + +
1084E ARG* 4.8 4.0 - - - +
1086E PHE* 3.1 32.2 - - + -
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Residues in contact with ASP1022 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020E ILE* 2.9 32.0 - - + +
1021E PRO* 1.3 76.7 - - - +
1023E ASP* 1.3 59.6 + - - +
1025E VAL* 4.0 2.3 - - - +
1026E ALA* 3.2 27.4 + - - +
1084E ARG* 2.7 38.2 + - - -
1086E PHE* 3.7 11.3 - - + +
1087E ALA* 4.9 12.2 + - + +
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Residues in contact with ASP1023 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018E TYR* 3.9 25.9 - - + -
1019E GLN* 4.2 7.6 + - - +
1020E ILE* 2.8 40.6 + - - +
1022E ASP* 1.3 77.7 - - - +
1024E PHE* 1.3 66.4 + - - +
1026E ALA* 3.4 6.8 + - - +
1027E ASP* 3.2 16.8 + - - +
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Residues in contact with PHE1024 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958E LEU* 6.1 0.2 - - + -
966E CYS* 3.3 46.9 - - + -
969E LEU* 3.5 33.0 - - + -
970E LEU* 4.0 6.5 - - + -
973E LEU* 6.4 0.2 - - + -
1006E VAL* 3.8 13.7 - - + -
1010E LEU* 3.3 28.5 - - + -
1018E TYR* 3.4 35.8 - + + -
1020E ILE 3.3 4.3 + - - +
1021E PRO* 4.0 6.7 - - + +
1022E ASP 3.5 0.2 - - - -
1023E ASP* 1.3 77.0 - - - +
1025E VAL* 1.3 75.9 + - + +
1027E ASP* 2.9 16.8 + - - +
1028E VAL* 3.1 29.2 + - + +
1073E PHE* 4.6 3.6 - + - -
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Residues in contact with VAL1025 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969E LEU* 5.0 0.7 - - + -
1021E PRO* 3.2 18.4 + - + +
1022E ASP 4.1 1.3 - - - +
1024E PHE* 1.3 92.3 - - + +
1026E ALA* 1.3 60.7 + - - +
1028E VAL* 3.8 6.7 + - - +
1029E ARG* 3.2 57.6 + - + +
1073E PHE* 4.5 4.0 - - + -
1077E LEU* 3.5 34.3 - - + -
1081E TYR* 5.7 1.1 - - + -
1086E PHE* 3.7 26.2 - - + -
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Residues in contact with ALA1026 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022E ASP 3.2 17.5 + - - +
1023E ASP* 3.7 9.0 - - - +
1024E PHE 3.0 1.2 + - - -
1025E VAL* 1.3 74.8 - - - +
1027E ASP* 1.3 67.6 + - - +
1029E ARG* 3.2 10.5 + - - +
1030E LEU* 3.0 20.9 + - - +
1033E LYS* 5.3 1.6 + - - +
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Residues in contact with ASP1027 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999E LYS* 4.8 6.2 + - - -
1001E MET* 3.6 20.1 - - + +
1006E VAL* 4.1 5.4 - - + -
1009E LYS* 2.7 35.5 + - - -
1018E TYR* 2.9 31.5 + - - +
1023E ASP 3.2 6.0 + - - +
1024E PHE 2.9 5.6 + - - +
1026E ALA* 1.3 77.4 - - - +
1028E VAL* 1.3 59.5 + - - +
1030E LEU* 2.6 39.5 + - - +
1031E ILE* 3.1 9.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL1028 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970E LEU* 5.7 0.7 - - + -
973E LEU* 3.8 27.1 - - + -
1003E LEU* 5.6 1.6 - - + -
1006E VAL* 4.8 11.0 - - + -
1024E PHE* 3.1 44.3 + - + +
1025E VAL 4.1 2.0 - - - +
1027E ASP* 1.3 77.2 - - - +
1029E ARG* 1.3 60.3 + - - +
1030E LEU 3.4 0.3 + - - -
1031E ILE* 3.4 18.2 - - + +
1032E PHE* 3.1 24.5 - - + -
1073E PHE* 3.7 34.5 - - + -
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Residues in contact with ARG1029 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025E VAL* 3.2 35.0 + - - +
1026E ALA* 3.2 8.9 + - - +
1027E ASP 3.0 0.4 - - - -
1028E VAL* 1.3 76.8 - - - +
1030E LEU* 1.3 60.3 + - - +
1031E ILE 3.2 0.2 - - - -
1032E PHE* 3.4 7.4 + - + +
1033E LYS* 3.0 52.7 + - - +
1073E PHE* 4.5 12.1 - - + -
1074E GLU* 2.7 30.4 + - - +
1077E LEU* 3.4 19.6 - - - +
1086E PHE* 3.5 24.5 + - - +
1087E ALA 4.8 4.0 - - - -
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Residues in contact with LEU1030 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999E LYS* 3.3 63.0 - - + +
1000E PRO 4.5 1.3 - - - +
1001E MET* 3.7 20.4 - - + -
1026E ALA 3.0 12.4 + - - +
1027E ASP* 2.6 18.6 + - - +
1029E ARG* 1.3 76.7 - - - +
1031E ILE* 1.3 65.7 + - - +
1033E LYS* 3.2 12.7 + - + +
1034E ASN* 2.8 40.9 + - - +
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Residues in contact with ILE1031 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982E PHE* 3.8 34.7 - - + -
1001E MET* 3.4 33.9 - - + +
1002E ASP* 3.4 30.5 - - - +
1003E LEU* 3.6 20.0 - - + +
1006E VAL* 4.2 12.1 - - + -
1027E ASP 3.1 5.8 + - - +
1028E VAL* 3.4 15.3 - - + +
1030E LEU* 1.3 79.1 - - - +
1032E PHE* 1.3 64.9 + - + +
1034E ASN* 3.4 5.6 + - - +
1035E CYS* 3.2 22.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE1032 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973E LEU* 4.5 8.3 - - + -
982E PHE* 3.9 35.7 - + + -
1003E LEU* 5.4 4.3 - - + -
1028E VAL* 3.1 41.3 - - + -
1029E ARG* 3.4 7.3 + - - +
1030E LEU 3.2 0.4 - - - -
1031E ILE* 1.3 85.0 - - + +
1033E LYS* 1.3 63.3 + - - +
1035E CYS* 3.6 4.4 - - - +
1036E GLU* 3.1 24.7 + - - +
1066E GLY* 3.8 15.8 - - - +
1069E VAL* 3.3 38.4 - - + -
1070E ALA* 3.6 34.8 - - + -
1073E PHE* 5.0 2.7 - + + -
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Residues in contact with LYS1033 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026E ALA* 5.3 1.8 + - - +
1029E ARG* 3.0 44.4 + - - +
1030E LEU* 3.7 12.3 - - + +
1032E PHE* 1.3 72.6 - - - +
1034E ASN* 1.3 69.4 + - - +
1036E GLU* 3.0 13.9 + - - +
1037E ARG* 2.8 27.2 + - + +
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Residues in contact with ASN1034 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993E TYR* 4.0 15.3 + - - +
997E ILE* 3.6 28.6 - - + +
999E LYS* 3.1 24.3 + - - +
1000E PRO* 3.6 14.3 - - - +
1001E MET* 3.7 9.2 + - - +
1030E LEU* 2.8 33.8 + - - +
1031E ILE* 3.5 5.8 - - - +
1033E LYS* 1.3 76.6 - - - +
1035E CYS* 1.3 58.1 + - - +
1037E ARG* 3.6 2.5 - - - +
1038E PHE* 2.8 33.5 + - - +
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Residues in contact with CYS1035 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982E PHE* 3.6 30.7 - - + -
993E TYR* 5.4 0.4 - - - -
1031E ILE 3.2 13.7 + - - +
1032E PHE* 3.6 9.4 - - - +
1034E ASN* 1.3 79.1 - - - +
1036E GLU* 1.3 63.5 + - - +
1038E PHE* 3.4 2.3 + - - +
1039E ASN* 3.3 22.3 + - - +
1062E VAL* 3.7 19.7 - - - -
1063E ALA* 3.9 12.3 - - - -
1066E GLY* 4.2 6.7 - - - -
18M ALY 3.8 22.4 - - + +
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Residues in contact with GLU1036 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032E PHE 3.1 13.4 + - - +
1033E LYS* 3.0 11.7 + - - +
1035E CYS* 1.3 78.6 - - - +
1037E ARG* 1.3 74.5 + - - +
1039E ASN* 3.4 7.7 + - - +
1040E GLU* 2.8 37.9 + - + +
1063E ALA* 5.4 4.7 - - - +
1067E LYS* 6.5 1.1 - - + -
----------------------------------------------------------
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Residues in contact with ARG1037 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996E ILE* 4.6 4.4 - - + +
997E ILE* 4.0 16.4 - - + -
1033E LYS* 2.8 18.7 + - + +
1034E ASN* 3.6 6.1 - - - +
1036E GLU* 1.3 93.0 + - - +
1038E PHE* 1.3 62.2 + - - +
1040E GLU* 3.2 29.8 + - - +
1041E MET* 3.0 43.9 + - + +
----------------------------------------------------------
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Residues in contact with PHE1038 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990E ILE* 3.9 25.8 - - + -
991E PRO 3.9 5.6 - - - -
992E ASN 4.1 0.7 - - - -
993E TYR* 3.5 50.9 - + + -
996E ILE* 4.0 29.6 - - + -
997E ILE* 4.3 4.9 - - + -
1034E ASN 2.8 17.7 + - - +
1035E CYS 4.0 3.8 - - - +
1036E GLU 3.2 0.2 - - - -
1037E ARG* 1.3 77.4 - - - +
1039E ASN* 1.3 59.2 + - + +
1041E MET* 3.1 2.9 + - - -
1042E MET* 2.9 62.8 + - + +
18M ALY 4.4 16.4 - - + +
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Residues in contact with ASN1039 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035E CYS 3.3 7.5 + - - +
1036E GLU* 3.7 7.7 + - - +
1038E PHE* 1.3 78.6 - - + +
1040E GLU* 1.3 65.2 + - - +
1042E MET* 3.9 8.5 - - - +
1043E LYS* 3.2 52.1 + - - +
1060E SER* 3.3 29.4 + - - +
1063E ALA* 3.4 33.6 - - + +
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Residues in contact with GLU1040 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036E GLU* 2.8 27.3 + - + +
1037E ARG* 3.4 37.7 + - - +
1039E ASN* 1.3 80.2 + - - +
1041E MET* 1.3 62.9 + - + +
1043E LYS* 2.3 48.8 + - - +
1044E VAL* 3.4 12.1 + - - +
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Residues in contact with MET1041 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996E ILE* 3.4 37.7 - - + -
1037E ARG* 3.0 46.0 + - + +
1038E PHE 3.1 3.8 + - - +
1040E GLU* 1.3 74.1 - - - +
1042E MET* 1.3 60.2 + - - +
1044E VAL* 2.7 40.2 + - + +
1045E VAL* 2.9 19.5 + - + +
----------------------------------------------------------
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Residues in contact with MET1042 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991E PRO* 4.9 3.4 - - + +
992E ASN* 4.8 12.8 - - - +
996E ILE* 4.6 7.2 - - - -
1038E PHE* 2.9 55.8 + - + +
1039E ASN* 3.9 10.8 - - - +
1041E MET* 1.3 74.8 - - - +
1043E LYS* 1.3 52.7 + - + +
1045E VAL* 3.7 23.2 - - + +
1046E GLN* 2.8 41.1 + - + +
----------------------------------------------------------
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Residues in contact with LYS1043 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039E ASN* 3.2 37.9 + - - +
1040E GLU* 2.3 46.4 + - - +
1041E MET 3.0 0.8 - - - -
1042E MET* 1.3 76.8 - - + +
1044E VAL* 1.3 62.6 + - + +
1046E GLN* 3.5 10.3 + - + +
1047E VAL* 3.4 17.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL1044 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040E GLU* 3.7 13.5 - - - +
1041E MET* 2.7 28.2 + - + +
1043E LYS* 1.3 73.9 - - + +
1045E VAL* 1.3 60.1 + - + +
1047E VAL* 3.0 33.4 - - + +
1048E TYR* 3.8 9.8 - - + +
----------------------------------------------------------
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Residues in contact with VAL1045 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992E ASN* 4.6 16.2 - - - +
996E ILE* 4.9 6.1 - - + -
1041E MET* 2.9 29.3 + - + +
1042E MET* 3.7 28.5 - - + +
1044E VAL* 1.3 74.6 - - + +
1046E GLN* 1.3 62.5 + - - +
1048E TYR* 3.4 28.8 + - - +
----------------------------------------------------------
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Residues in contact with GLN1046 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042E MET* 2.8 23.3 + - + +
1043E LYS* 3.6 11.0 - - + +
1044E VAL 3.2 0.2 - - - -
1045E VAL* 1.3 74.4 - - - +
1047E VAL* 1.3 56.1 + - - +
1048E TYR* 2.8 19.7 + - - +
1049E ALA* 4.2 12.0 + - - +
----------------------------------------------------------
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Residues in contact with VAL1047 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043E LYS 3.4 9.5 + - - +
1044E VAL* 3.0 26.7 + - + +
1046E GLN* 1.3 75.1 - - - +
1048E TYR* 1.3 83.4 + - + +
1049E ALA 4.0 2.1 + - - -
----------------------------------------------------------
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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