Contacts of the helix formed by residues 1020 - 1048 (chain B) in PDB entry 3U5N
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B LEU* 3.3 7.0 - - - +
1018B TYR* 3.4 2.6 - - - +
1019B GLN* 1.3 88.8 - - + +
1021B PRO* 1.3 70.3 - - + +
1022B ASP* 2.8 40.2 - - + +
1023B ASP* 2.8 39.2 + - - +
1024B PHE 3.7 1.7 + - - -
1084B ARG* 4.9 4.5 - - - +
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Residues in contact with PRO1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B LEU* 3.2 11.9 - - + -
962B ASP* 3.5 31.0 - - - +
966B CYS* 4.1 12.1 - - - -
1020B ILE* 1.3 93.4 - - + +
1022B ASP* 1.3 65.8 + - - +
1024B PHE* 3.1 5.1 + - + +
1025B VAL* 3.0 26.9 + - + +
1081B TYR* 3.5 28.0 - - + +
1084B ARG* 3.8 17.5 - - - +
1086B PHE* 4.0 7.2 - - + -
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Residues in contact with ASP1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020B ILE* 2.8 19.4 - - + +
1021B PRO* 1.3 77.0 - - - +
1023B ASP* 1.3 61.6 + - - +
1025B VAL* 3.5 2.1 + - - +
1026B ALA* 3.0 28.9 + - - +
1084B ARG* 2.5 48.7 + - - -
1086B PHE* 3.7 19.1 - - + +
1087B ALA 5.1 9.2 + - - +
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Residues in contact with ASP1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018B TYR* 3.6 21.3 - - + -
1019B GLN* 3.7 10.7 + - - +
1020B ILE* 2.8 37.1 + - - +
1022B ASP* 1.3 80.3 - - - +
1024B PHE* 1.3 61.5 + - - +
1026B ALA* 3.6 6.3 + - - +
1027B ASP* 3.1 24.1 + - - +
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Residues in contact with PHE1024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958B LEU* 5.4 0.7 - - + -
966B CYS* 3.3 53.6 - - + -
969B LEU* 3.9 30.1 - - + -
970B LEU* 4.1 10.3 - - + -
973B LEU* 6.1 0.2 - - + -
1006B VAL* 3.5 31.4 - - + -
1010B LEU* 4.0 11.4 - - + -
1018B TYR* 3.8 28.2 - + + -
1020B ILE 3.7 1.6 + - - -
1021B PRO* 3.1 10.4 + - + +
1023B ASP* 1.3 75.3 - - - +
1025B VAL* 1.3 76.8 + - + +
1027B ASP* 3.2 3.5 + - - +
1028B VAL* 3.0 41.7 + - + +
1073B PHE* 4.4 5.2 - + - -
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Residues in contact with VAL1025 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969B LEU* 5.3 1.3 - - + -
1021B PRO* 3.0 20.6 + - + +
1022B ASP 3.8 4.3 - - - +
1024B PHE* 1.3 87.4 - - + +
1026B ALA* 1.3 57.5 + - - +
1028B VAL* 3.3 2.4 + - - +
1029B ARG* 3.0 61.0 + - + +
1073B PHE* 4.5 7.9 - - + -
1077B LEU* 3.9 30.7 - - + -
1081B TYR* 5.5 1.3 - - + -
1086B PHE* 3.9 31.9 - - + -
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Residues in contact with ALA1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022B ASP 3.0 17.4 + - - +
1023B ASP* 4.0 6.5 - - - +
1024B PHE 3.3 0.2 - - - -
1025B VAL* 1.3 77.2 - - - +
1027B ASP* 1.3 60.3 + - - +
1029B ARG* 3.7 7.9 + - - +
1030B LEU* 3.1 27.9 + - - +
1033B LYS* 5.0 3.0 - - - +
1087B ALA 5.5 6.1 - - - +
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Residues in contact with ASP1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B LYS* 4.3 6.2 + - - -
1001B MET* 3.3 36.1 - - - +
1006B VAL* 4.0 7.2 - - + -
1009B LYS* 2.8 28.8 + - - -
1018B TYR* 2.8 30.6 + - - +
1023B ASP 3.1 16.5 + - - +
1024B PHE 3.2 3.1 + - - +
1026B ALA* 1.3 77.2 - - - +
1028B VAL* 1.3 62.1 + - - +
1030B LEU* 3.3 18.1 + - - +
1031B ILE* 3.3 10.0 + - - +
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Residues in contact with VAL1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970B LEU* 5.3 2.9 - - + -
973B LEU* 3.7 20.0 - - + -
1003B LEU* 5.4 0.2 - - + -
1006B VAL* 4.4 11.0 - - + -
1024B PHE* 3.0 49.9 + - + +
1025B VAL 3.3 4.5 + - - +
1027B ASP* 1.3 76.8 - - - +
1029B ARG* 1.3 62.2 + - - +
1031B ILE* 3.2 20.6 + - + +
1032B PHE* 3.2 19.8 - - + -
1073B PHE* 3.5 38.8 - - + -
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Residues in contact with ARG1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025B VAL* 3.0 34.4 + - - +
1026B ALA* 4.1 5.6 - - - +
1028B VAL* 1.3 75.0 - - - +
1030B LEU* 1.3 57.7 + - - +
1032B PHE* 3.1 9.8 + - - +
1033B LYS* 2.9 54.0 + - + +
1073B PHE* 4.2 7.8 - - + -
1074B GLU* 2.8 41.7 + - - +
1077B LEU* 3.4 16.6 - - - +
1086B PHE* 2.8 39.8 + - - +
1087B ALA* 4.5 5.5 + - - +
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Residues in contact with LEU1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999B LYS* 3.3 55.2 - - + +
1001B MET* 3.6 20.9 - - + -
1026B ALA 3.1 18.4 + - - +
1027B ASP* 3.4 16.2 - - - +
1029B ARG* 1.3 72.5 - - - +
1031B ILE* 1.3 67.7 + - - +
1033B LYS* 4.0 17.0 - - + +
1034B ASN* 2.9 46.9 + - - +
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Residues in contact with ILE1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982B PHE* 3.9 23.2 - - + +
1001B MET* 3.6 31.9 - - + +
1002B ASP 3.6 17.5 - - - +
1003B LEU* 3.4 31.9 - - + +
1006B VAL* 4.2 7.6 - - + -
1027B ASP 3.3 13.0 + - - +
1028B VAL* 3.2 14.3 + - - +
1030B LEU* 1.3 80.8 - - - +
1032B PHE* 1.3 80.9 + - + +
1034B ASN* 3.5 6.2 + - - +
1035B CYS* 3.2 21.3 + - - +
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Residues in contact with PHE1032 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B LEU* 4.5 8.7 - - + -
982B PHE* 4.0 22.7 - + + -
1003B LEU* 5.3 2.5 - - + -
1028B VAL* 3.2 41.7 - - + -
1029B ARG* 3.1 8.4 + - - +
1031B ILE* 1.3 97.6 - - + +
1033B LYS* 1.3 63.7 + - - +
1035B CYS* 3.4 5.1 + - + +
1036B GLU* 3.2 24.6 + - - +
1066B GLY* 3.6 23.0 - - - +
1069B VAL* 3.5 36.6 - - + -
1070B ALA* 3.6 34.1 - - + -
1073B PHE* 4.9 3.1 - + + -
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Residues in contact with LYS1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B ALA* 5.0 2.7 - - - +
1029B ARG* 2.9 51.3 + - + +
1030B LEU* 3.7 17.9 - - + +
1032B PHE* 1.3 74.4 - - - +
1034B ASN* 1.3 61.8 + - - +
1036B GLU* 3.3 5.7 + - - +
1037B ARG* 2.9 31.0 + - - +
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Residues in contact with ASN1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993B TYR* 3.9 17.7 + - - +
997B ILE* 3.4 33.4 - - + +
999B LYS* 2.8 26.5 + - - +
1000B PRO* 3.7 7.7 - - - +
1001B MET* 3.8 6.6 + - - +
1030B LEU* 2.9 36.1 + - - +
1031B ILE* 3.6 6.4 - - - +
1033B LYS* 1.3 75.2 - - - +
1035B CYS* 1.3 65.0 + - - +
1037B ARG* 4.4 1.2 - - - +
1038B PHE* 3.0 27.0 + - - +
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Residues in contact with CYS1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982B PHE* 3.6 24.9 - - + -
993B TYR* 5.6 1.8 - - - -
1031B ILE 3.2 11.3 + - - +
1032B PHE* 3.5 11.7 - - - +
1033B LYS 3.2 0.4 - - - -
1034B ASN* 1.3 80.8 - - - +
1036B GLU* 1.3 59.8 + - - +
1038B PHE* 3.4 3.8 + - - +
1039B ASN* 3.1 29.5 + - - +
1062B VAL* 3.5 35.9 - - - -
1063B ALA* 3.9 13.2 - - - -
1066B GLY* 4.2 6.7 - - - -
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Residues in contact with GLU1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B PHE 3.2 14.7 + - - +
1033B LYS* 3.8 5.6 - - - +
1035B CYS* 1.3 82.7 - - - +
1037B ARG* 1.3 59.6 + - - +
1039B ASN* 3.5 15.9 + - - +
1040B GLU* 2.9 31.1 + - + +
1059B ASP* 4.9 2.1 - - - +
1063B ALA* 4.0 15.7 - - - +
1066B GLY 5.3 0.7 - - - -
1067B LYS* 3.4 36.0 + - - +
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Residues in contact with ARG1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B ILE* 4.4 12.4 + - + +
997B ILE* 4.0 17.5 - - + -
1033B LYS 2.9 18.1 + - - +
1034B ASN* 3.8 4.9 - - - +
1036B GLU* 1.3 75.3 - - - +
1038B PHE* 1.3 60.2 + - - +
1040B GLU* 2.7 37.5 + - - +
1041B MET* 2.9 49.4 + - - +
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Residues in contact with PHE1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
990B ILE* 3.9 27.1 - - + -
991B PRO* 4.2 3.8 - - + -
993B TYR* 3.4 45.1 - + + -
996B ILE* 3.6 30.1 - - + -
997B ILE* 4.2 3.1 - - + +
1034B ASN 3.0 18.3 + - - +
1035B CYS* 3.9 3.8 - - - +
1037B ARG* 1.3 73.5 - - - +
1039B ASN* 1.3 69.7 + - - +
1041B MET* 3.2 1.4 + - - -
1042B MET* 2.9 65.3 + - + +
1062B VAL* 6.3 2.5 - - + -
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Residues in contact with ASN1039 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035B CYS 3.1 16.9 + - - +
1036B GLU* 3.8 12.3 + - - +
1038B PHE* 1.3 80.3 - - - +
1040B GLU* 1.3 63.4 + - - +
1042B MET* 3.1 9.4 + - - +
1043B LYS* 3.1 31.5 + - - +
1058B ALA 4.7 1.4 - - - +
1059B ASP* 2.5 31.9 + - - +
1060B SER* 3.0 32.6 + - - +
1063B ALA* 3.4 20.7 - - + +
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Residues in contact with GLU1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B GLU 2.9 19.9 + - - +
1037B ARG* 2.7 46.7 + - - +
1039B ASN* 1.3 81.0 - - - +
1041B MET* 1.3 73.2 + - + +
1043B LYS* 3.4 12.1 + - - +
1044B VAL* 3.3 22.0 + - + +
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Residues in contact with MET1041 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996B ILE* 4.2 30.1 - - + -
1037B ARG* 2.9 43.4 + - - +
1038B PHE 3.2 3.3 + - - +
1040B GLU* 1.3 107.2 - - + +
1042B MET* 1.3 61.0 + - - +
1044B VAL* 3.2 27.4 + - + +
1045B VAL* 3.0 33.2 + - + +
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Residues in contact with MET1042 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991B PRO 4.2 9.6 - - - +
992B ASN* 4.5 8.5 - - + +
996B ILE* 3.6 18.4 - - + -
1038B PHE* 2.9 62.2 + - + +
1039B ASN* 3.1 8.7 + - - +
1041B MET* 1.3 78.5 - - - +
1043B LYS* 1.3 61.7 + - + +
1045B VAL* 3.2 32.2 + - + +
1046B GLN* 3.2 26.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS1043 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039B ASN* 3.1 20.7 + - - +
1040B GLU* 3.7 11.7 - - - +
1041B MET 3.2 0.2 - - - -
1042B MET* 1.3 73.9 - - + +
1044B VAL* 1.3 67.0 + - + +
1046B GLN* 3.2 29.4 + - - +
1047B VAL* 3.4 11.1 + - - +
1058B ALA* 3.2 40.4 - - - +
1059B ASP* 3.8 20.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL1044 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040B GLU* 3.3 16.1 + - + +
1041B MET* 3.2 32.4 + - + +
1043B LYS* 1.3 76.5 - - - +
1045B VAL* 1.3 64.0 + - + +
1047B VAL* 3.1 28.1 - - + +
1048B TYR* 3.3 25.5 - - + +
----------------------------------------------------------
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Residues in contact with VAL1045 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992B ASN* 5.6 5.4 - - - +
996B ILE* 5.9 1.6 - - + -
1041B MET* 3.0 21.6 + - + +
1042B MET* 3.2 30.9 + - + +
1044B VAL* 1.3 77.6 - - + +
1046B GLN* 1.3 66.5 + - + +
1047B VAL 3.4 0.3 + - - -
1048B TYR* 3.5 15.6 + - - +
1049B ALA* 3.9 10.4 + - + +
----------------------------------------------------------
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Residues in contact with GLN1046 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042B MET* 3.2 22.5 + - - +
1043B LYS* 3.2 23.3 + - - +
1044B VAL 3.2 0.8 - - - -
1045B VAL* 1.3 83.8 - - + +
1047B VAL* 1.3 56.3 + - - +
1049B ALA* 3.0 33.5 + - - +
1058B ALA 5.3 3.3 + - - +
----------------------------------------------------------
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Residues in contact with VAL1047 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043B LYS 3.4 6.7 + - - +
1044B VAL* 3.1 26.0 + - + +
1046B GLN* 1.3 78.4 - - - +
1048B TYR* 1.3 76.8 + - + +
1049B ALA 3.3 2.3 + - - -
----------------------------------------------------------
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Residues in contact with TYR1048 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1044B VAL* 3.3 43.7 - - + +
1045B VAL* 3.5 8.7 + - - +
1046B GLN 3.2 0.8 - - - -
1047B VAL* 1.3 87.4 - - + +
1049B ALA* 1.3 59.1 + - - +
----------------------------------------------------------
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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