Contacts of the helix formed by residues 1010 - 1043 (chain B) in PDB entry 5TWV
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B LEU* 3.7 17.0 - - + +
1006B SER* 5.1 3.4 - - - -
1009B GLY* 1.3 75.4 - - - -
1011B LEU* 1.3 63.6 + - - +
1012B LEU 3.6 0.7 - - - -
1013B LEU* 3.9 3.2 - - - +
1014B SER* 2.9 33.2 + - - -
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Residues in contact with LEU1011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B ILE* 1.3 76.2 - - - +
1012B LEU* 1.3 60.2 + - - +
1014B SER* 3.3 4.8 + - - -
1015B LEU* 2.9 41.1 + - + +
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Residues in contact with LEU1012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009B GLY* 5.9 1.3 - - - -
1010B ILE 4.7 1.0 - - - +
1011B LEU* 1.3 78.3 - - - +
1013B LEU* 1.3 58.4 + - - +
1015B LEU* 3.9 8.3 - - - +
1016B LEU* 2.9 30.5 + - - +
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Residues in contact with LEU1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008B ALA 5.0 5.2 - - - +
1009B GLY 4.2 16.9 - - - +
1010B ILE* 3.7 7.0 + - - +
1011B LEU 3.3 0.6 - - - -
1012B LEU* 1.3 75.7 - - - +
1014B SER* 1.3 61.1 + - - +
1016B LEU* 4.0 4.2 - - - +
1017B VAL* 2.9 33.4 + - - +
1085B THR* 4.9 6.8 - - - +
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Residues in contact with SER1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B ILE 2.9 21.9 + - - -
1011B LEU* 3.3 5.8 + - - -
1013B LEU* 1.3 77.6 - - - +
1015B LEU* 1.3 51.6 + - - +
1017B VAL* 4.6 1.7 - - - +
1018B PHE* 2.7 38.9 + - - +
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Residues in contact with LEU1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011B LEU* 2.9 28.1 + - + +
1012B LEU* 4.0 7.0 - - - +
1014B SER* 1.3 77.3 - - - +
1016B LEU* 1.3 60.8 + - - +
1018B PHE* 3.7 14.2 - - + +
1019B SER* 2.9 28.8 + - - -
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Residues in contact with LEU1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B LEU 2.9 19.3 + - - +
1013B LEU* 4.0 3.6 - - - +
1015B LEU* 1.3 75.6 - - - +
1017B VAL* 1.3 59.4 + - - +
1019B SER* 3.2 7.2 + - - -
1020B GLN* 2.9 25.8 + - - +
1081B VAL* 4.5 4.0 - - - +
1084B VAL* 4.8 6.8 - - + +
1085B THR* 3.8 29.2 - - - +
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Residues in contact with VAL1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013B LEU 2.9 18.7 + - - +
1014B SER* 4.6 2.0 - - - +
1016B LEU* 1.3 74.0 - - - +
1018B PHE* 1.3 60.5 + - - +
1020B GLN* 3.2 10.0 + - + +
1021B LEU* 2.9 27.9 + - - +
1085B THR* 3.9 12.7 - - - -
1144B SER* 6.3 2.9 - - - -
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Residues in contact with PHE1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014B SER 2.7 24.5 + - - +
1015B LEU* 3.7 17.7 - - + +
1016B LEU 3.2 0.2 - - - -
1017B VAL* 1.3 78.0 - - - +
1019B SER* 1.3 59.1 + - - +
1021B LEU* 3.3 9.8 + - + +
1022B LEU* 2.9 33.7 + - + +
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Residues in contact with SER1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015B LEU 2.9 19.0 + - - -
1016B LEU* 3.2 7.4 + - - -
1018B PHE* 1.3 75.9 - - - +
1020B GLN* 1.3 61.4 + - - +
1022B LEU* 3.8 7.7 - - - +
1023B LYS* 2.9 27.9 + - - +
1081B VAL* 3.3 17.9 - - - +
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Residues in contact with GLN1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016B LEU 2.9 13.8 + - - +
1017B VAL* 3.5 13.5 - - - +
1018B PHE 3.2 0.4 - - - -
1019B SER* 1.3 74.6 - - - +
1021B LEU* 1.3 58.6 + - - +
1023B LYS* 3.2 5.0 + - - +
1024B HIS* 2.9 27.7 + - - +
1081B VAL* 3.9 11.4 - - - +
1082B THR* 3.8 30.4 - - - +
1085B THR* 5.4 2.9 - - - -
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Residues in contact with LEU1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017B VAL 2.9 17.1 + - - +
1018B PHE* 3.3 11.2 + - + +
1020B GLN* 1.3 73.9 - - - +
1022B LEU* 1.3 58.8 + - - +
1024B HIS* 3.3 7.6 + - - +
1025B MET* 2.9 26.3 + - - +
1148B LEU* 5.8 7.6 - - + -
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Residues in contact with LEU1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018B PHE* 2.9 25.7 + - + +
1019B SER* 3.8 8.3 - - - +
1021B LEU* 1.3 76.3 - - - +
1023B LYS* 1.3 58.6 + - - +
1025B MET* 3.3 9.9 + - - +
1026B VAL* 2.9 26.2 + - - +
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Residues in contact with LYS1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019B SER 2.9 18.4 + - - +
1020B GLN* 3.2 7.6 + - - +
1022B LEU* 1.3 77.7 - - - +
1024B HIS* 1.3 56.8 + - - +
1026B VAL* 3.2 11.0 + - - +
1027B LEU* 2.9 23.0 + - - +
1074B LEU* 4.7 1.8 - - + +
1077B VAL* 4.6 2.0 - - + +
1078B LEU* 4.1 29.2 - - + +
1081B VAL* 4.1 15.3 - - + -
1082B THR* 4.9 3.4 - - - +
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Residues in contact with HIS1024 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020B GLN 2.9 16.0 + - - +
1021B LEU* 3.3 6.9 + - - +
1022B LEU 3.3 0.2 - - - -
1023B LYS* 1.3 74.1 - - - +
1025B MET* 1.3 61.5 + - - +
1027B LEU* 3.0 15.3 + - + +
1028B VAL* 2.9 28.1 + - + +
1078B LEU* 5.8 0.4 - - - -
1082B THR* 6.6 0.2 - - - -
1145B ARG 5.3 1.1 - - - -
1148B LEU* 3.7 29.4 - - + -
1149B LEU* 3.5 32.3 - - + -
1152B SER* 3.6 15.8 - - - -
1294B TYR* 5.6 1.3 - - - -
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Residues in contact with MET1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021B LEU 2.9 14.0 + - - +
1022B LEU* 3.5 12.8 - - - +
1024B HIS* 1.3 75.4 - - - +
1026B VAL* 1.3 57.7 + - - +
1028B VAL* 3.3 14.4 - - + +
1029B ALA* 2.9 26.0 + - - +
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Residues in contact with VAL1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022B LEU 2.9 13.8 + - - +
1023B LYS* 3.4 12.3 - - - +
1024B HIS 3.2 0.2 - - - -
1025B MET* 1.3 76.1 - - - +
1027B LEU* 1.3 59.0 + - - +
1029B ALA* 3.3 9.6 + - - +
1030B ILE* 2.9 31.4 + - - +
1074B LEU* 3.8 20.0 - - + -
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Residues in contact with LEU1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023B LYS 2.9 13.6 + - - +
1024B HIS* 3.0 27.1 + - + +
1026B VAL* 1.3 74.7 - - - +
1028B VAL* 1.3 61.0 + - - +
1030B ILE* 3.1 15.6 + - + +
1031B ASP* 2.9 23.2 + - - +
1074B LEU* 5.3 1.1 - - - +
1078B LEU* 5.2 9.4 - - + -
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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
----------------------------------------------------------
1024B HIS* 2.9 17.9 + - + +
1025B MET* 3.3 21.3 - - + +
1027B LEU* 1.3 73.0 - - - +
1029B ALA* 1.3 58.9 + - - +
1031B ASP* 3.5 13.5 - - + -
1032B TYR* 2.9 28.0 + - + +
1152B SER* 4.7 20.9 - - - +
1153B ALA* 5.3 2.0 - - + +
1156B VAL* 4.3 23.1 - - + -
1287B TYR* 5.1 5.6 - - + +
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Residues in contact with ALA1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025B MET 2.9 19.0 + - - +
1026B VAL* 3.4 11.9 - - - +
1028B VAL* 1.3 76.9 - - - +
1030B ILE* 1.3 59.4 + - + +
1032B TYR* 3.9 5.1 - - - +
1033B TRP* 2.9 31.4 + - - +
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Residues in contact with ILE1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B VAL 2.9 18.7 + - - +
1027B LEU* 3.1 12.5 + - - +
1029B ALA* 1.3 76.0 - - + +
1031B ASP* 1.3 59.6 + - - +
1033B TRP* 4.0 4.6 - - - +
1034B LEU* 2.9 32.0 + - + +
1070B LEU 5.2 2.2 - - - +
1071B LEU* 3.4 40.8 - - + +
1072B CYS* 5.1 0.2 - - - -
1073B SER* 4.7 1.1 - - - +
1074B LEU* 3.8 38.1 - - + +
1075B GLY* 4.5 2.2 - - - +
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Residues in contact with ASP1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027B LEU 2.9 11.9 + - - +
1028B VAL* 3.3 19.1 - - + +
1029B ALA 3.2 0.2 - - - -
1030B ILE* 1.3 78.5 - - - +
1032B TYR* 1.3 57.6 + - - +
1034B LEU* 3.8 4.1 - - - +
1035B ALA* 2.9 28.5 + - - +
1287B TYR* 3.2 27.8 - - + +
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Residues in contact with TYR1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B VAL* 2.9 18.0 + - + +
1029B ALA* 4.2 6.3 - - - +
1031B ASP* 1.3 73.9 - - - +
1033B TRP* 1.3 62.7 + - - +
1035B ALA* 4.0 10.1 - - + -
1036B LYS* 2.8 42.2 + - + +
1159B TYR* 6.4 2.5 - + - -
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Residues in contact with TRP1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029B ALA 2.9 20.0 + - - +
1030B ILE* 4.0 5.2 - - - +
1032B TYR* 1.3 78.1 - - + +
1034B LEU* 1.3 60.9 + - - +
1036B LYS* 4.0 4.3 - - - +
1037B TRP* 2.9 31.2 + - - +
1071B LEU* 5.5 9.0 - - + -
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Residues in contact with LEU1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B ALA* 5.4 3.1 - - + +
1030B ILE* 2.9 22.3 + - + +
1031B ASP* 3.9 4.9 - - - +
1033B TRP* 1.3 75.7 - - - +
1035B ALA* 1.3 58.2 + - - +
1037B TRP* 3.9 5.4 - - - +
1038B THR* 2.9 27.4 + - - -
1071B LEU* 5.6 8.4 - - + +
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Residues in contact with ALA1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B PHE* 5.1 15.9 - - + -
1031B ASP 2.9 18.6 + - - +
1032B TYR* 3.6 15.3 - - + +
1033B TRP 3.2 0.2 - - - -
1034B LEU* 1.3 76.4 - - - +
1036B LYS* 1.3 59.6 + - - +
1038B THR* 3.3 7.8 + - - -
1039B ASP* 2.9 24.6 + - - +
1279B GLY* 4.6 6.1 - - - -
1280B LEU* 5.0 11.4 + - + +
1283B LEU* 5.6 3.8 - - + -
----------------------------------------------------------
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Residues in contact with LYS1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032B TYR* 2.8 37.2 + - + +
1033B TRP* 4.1 4.5 - - - +
1035B ALA* 1.3 73.9 - - - +
1037B TRP* 1.3 61.5 + - - +
1039B ASP* 3.1 11.4 + - - +
1040B SER* 2.9 23.2 + - - -
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Residues in contact with TRP1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 6.0 1.9 - + - -
1033B TRP 2.9 18.3 + - - +
1034B LEU* 4.3 4.0 - - - +
1036B LYS* 1.3 73.8 - - - +
1038B THR* 1.3 61.2 + - - +
1040B SER* 3.1 24.7 + - - -
1041B ALA* 2.9 33.0 + - + +
1061B GLN* 3.6 26.5 - - + -
1062B SER* 4.0 6.3 - - - -
1063B VAL* 3.4 39.9 - - + -
1064B TYR* 3.6 15.0 - - + -
1067B VAL* 3.5 26.5 - - + -
1068B PHE* 3.3 33.0 - + - -
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Residues in contact with THR1038 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B SER 5.9 0.9 - - - -
573B PRO* 4.5 11.6 - - - +
576B ALA* 4.5 20.6 - - - -
577B PHE* 4.9 13.0 - - - -
1034B LEU 2.9 21.8 + - - -
1035B ALA* 3.3 9.6 - - - -
1037B TRP* 1.3 78.2 - - - +
1039B ASP* 1.3 57.6 + - - +
1041B ALA* 3.4 7.4 + - - +
1042B LEU* 2.9 27.0 + - - +
1278B ALA 5.3 0.4 - - - -
1279B GLY* 5.3 1.1 - - - -
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Residues in contact with ASP1039 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035B ALA 2.9 12.2 + - - +
1036B LYS* 3.1 13.2 + - - +
1038B THR* 1.3 75.5 - - - +
1040B SER* 1.3 58.9 + - - +
1042B LEU* 3.6 8.7 - - - +
1043B VAL* 2.9 27.0 + - - +
1278B ALA* 3.7 15.6 - - + +
1279B GLY* 3.6 23.5 - - - +
----------------------------------------------------------
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Residues in contact with SER1040 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036B LYS 2.9 11.4 + - - -
1037B TRP* 3.1 39.9 + - - -
1039B ASP* 1.3 77.6 - - - +
1041B ALA* 1.3 61.4 + - - +
1043B VAL* 3.3 18.1 + - - +
1044B LEU* 3.8 6.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA1041 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B PHE* 5.5 4.7 - - + -
571B LEU* 3.8 35.0 - - + +
572B SER 4.8 9.6 - - - +
1037B TRP* 2.9 23.8 + - + +
1038B THR* 3.8 7.2 - - - +
1040B SER* 1.3 74.9 - - - +
1042B LEU* 1.3 61.9 + - - +
1044B LEU* 3.5 19.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU1042 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B PRO* 4.1 25.7 - - + +
1038B THR 2.9 18.6 + - - +
1039B ASP 3.6 4.7 - - - +
1040B SER 3.3 0.4 - - - -
1041B ALA* 1.3 77.0 - - - +
1043B VAL* 1.3 58.2 + - - +
1044B LEU 3.2 6.0 + - - -
1278B ALA* 3.5 28.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL1043 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039B ASP 2.9 15.9 + - - +
1040B SER* 3.6 11.0 - - - +
1041B ALA 3.2 0.8 - - - -
1042B LEU* 1.3 76.7 - - - +
1044B LEU* 1.3 58.6 + - - +
1278B ALA* 5.3 5.8 - - + -
----------------------------------------------------------
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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