Contacts of the helix formed by residues 1010 - 1042 (chain B) in PDB entry 2O8C
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 THR1010 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953B GLU* 6.0 3.1 - - + +
956B GLU* 3.5 24.8 + - - +
1007B TRP* 3.1 22.6 + - + +
1008B THR 3.2 0.8 - - - -
1009B LYS* 1.3 86.6 + - - +
1011B ILE* 1.3 63.2 + - + +
1012B GLU 3.6 1.3 - - - -
1013B LYS* 3.3 4.8 + - - +
1014B LYS* 2.8 63.6 + - + +
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Residues in contact with ILE1011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953B GLU* 4.1 16.7 - - + +
969B TYR* 4.3 16.8 - - + +
977B TYR* 3.9 26.0 - - + +
979B LEU* 5.2 1.1 - - + -
1005B ARG 5.2 2.5 - - - +
1006B TYR* 3.6 27.4 - - + -
1007B TRP* 3.2 61.3 + - + +
1010B THR* 1.3 75.2 - - + +
1012B GLU* 1.3 53.2 + - - +
1014B LYS* 3.1 2.6 + - - +
1015B LEU* 2.7 45.1 + - + +
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Residues in contact with GLU1012 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994B TYR* 4.9 9.9 - - - -
996B LEU* 5.1 4.5 - - - +
1006B TYR* 3.7 34.9 - - + -
1007B TRP 4.0 3.2 + - - -
1008B THR* 3.4 37.0 + - - +
1010B THR 3.6 0.4 - - - -
1011B ILE* 1.3 77.5 - - - +
1013B LYS* 1.3 62.2 + - + +
1015B LEU* 4.2 7.6 - - + +
1016B ALA* 3.3 23.0 + - - +
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Residues in contact with LYS1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008B THR* 3.4 24.0 - - - +
1009B LYS* 3.7 22.2 + - - +
1010B THR* 3.3 8.0 + - - +
1011B ILE 3.2 0.8 - - - -
1012B GLU* 1.3 78.9 - - + +
1014B LYS* 1.3 62.0 + - + +
1016B ALA* 4.1 4.7 - - - +
1017B ASN* 3.3 26.5 + - - +
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Residues in contact with LYS1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949B GLN* 3.1 22.0 - - + +
952B LEU* 3.4 37.2 - - + +
953B GLU* 3.9 21.8 - - + +
956B GLU* 3.8 19.6 + - - -
1010B THR* 2.8 37.3 + - + +
1013B LYS* 1.3 80.5 - - + +
1015B LEU* 1.3 58.0 + - - +
1016B ALA 3.3 1.3 - - - -
1017B ASN* 3.3 12.0 + - - +
1018B LEU* 2.8 23.8 + - - +
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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
----------------------------------------------------------
953B GLU* 4.6 3.6 - - - +
974B ARG 4.3 10.3 - - - +
976B ARG* 3.4 39.9 - - + +
977B TYR* 3.6 25.6 - - + -
1006B TYR* 3.5 15.9 - - + +
1011B ILE* 2.7 34.2 + - + +
1012B GLU* 4.2 6.5 - - + +
1013B LYS 3.6 0.2 - - - -
1014B LYS* 1.3 69.6 - - - +
1016B ALA* 1.3 56.7 + - - +
1017B ASN 3.0 1.6 - - - -
1018B LEU* 3.5 19.4 - - + +
1019B ILE* 2.7 48.5 + - + +
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Residues in contact with ALA1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B GLU 3.3 17.3 + - - +
1013B LYS* 4.1 7.6 - - - +
1015B LEU* 1.3 78.1 - - - +
1017B ASN* 1.3 60.9 + - - +
1019B ILE* 4.1 8.3 - - - +
1020B ASN* 3.0 33.7 + - - +
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Residues in contact with ASN1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945B ARG* 5.9 0.3 - - - +
949B GLN* 3.6 22.4 - - - +
1013B LYS 3.3 19.2 + - - +
1014B LYS* 3.3 14.9 + - - +
1015B LEU 3.0 0.2 - - - -
1016B ALA* 1.3 80.4 - - - +
1018B LEU* 1.3 60.1 + - - +
1019B ILE 3.3 0.2 - - - -
1020B ASN* 3.2 14.0 + - - +
1021B ALA* 3.0 28.6 + - - +
1024B ARG* 5.7 0.3 + - - -
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Residues in contact with LEU1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B GLU* 3.9 33.2 - - + +
949B GLN* 3.2 17.9 + - + +
950B SER* 4.2 10.8 - - - +
953B GLU* 4.7 4.9 - - - +
976B ARG* 4.6 5.2 - - - +
977B TYR* 3.8 34.1 - - + +
1014B LYS 2.8 16.4 + - - +
1015B LEU* 3.0 18.1 + - + +
1017B ASN* 1.3 76.6 - - - +
1019B ILE* 1.3 57.5 + - - +
1021B ALA* 3.4 3.6 + - - +
1022B GLU* 2.8 58.2 + - - +
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Residues in contact with ILE1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973B GLY 5.4 0.4 - - - +
974B ARG* 4.1 52.5 - - + +
976B ARG* 4.3 18.2 - - - +
1015B LEU* 2.7 33.6 + - + +
1016B ALA* 4.1 8.7 - - - +
1018B LEU* 1.3 71.4 - - - +
1020B ASN* 1.3 58.8 + - - +
1022B GLU* 3.1 7.2 + - + +
1023B GLU* 2.8 53.5 + - + +
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Residues in contact with ASN1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016B ALA* 3.0 23.3 + - - +
1017B ASN* 3.4 15.8 + - - +
1019B ILE* 1.3 76.2 - - - +
1021B ALA* 1.3 56.9 + - - +
1023B GLU* 3.1 16.8 + - - +
1024B ARG* 3.0 53.9 + - - +
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Residues in contact with ALA1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942B ALA* 3.6 27.5 - - - +
945B ARG* 4.2 17.9 - - + +
946B GLU* 2.9 22.7 - - + +
1017B ASN 3.0 15.9 + - - +
1018B LEU* 3.7 3.6 - - - +
1020B ASN* 1.3 75.9 - - - +
1022B GLU* 1.3 58.0 + - - +
1024B ARG* 3.4 15.0 + - - +
1025B ARG 3.2 21.1 + - - -
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Residues in contact with GLU1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946B GLU* 3.4 25.8 - - + +
950B SER* 5.5 0.2 + - - -
976B ARG* 3.0 41.9 + - - -
1018B LEU* 2.8 39.1 + - - +
1019B ILE* 3.1 8.1 + - + +
1021B ALA* 1.3 75.2 - - - +
1023B GLU* 1.3 59.6 + - + +
1025B ARG* 3.5 20.1 + - - +
1026B ASP* 3.1 30.5 - - - +
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Residues in contact with GLU1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B THR* 6.1 1.4 - - - +
490B GLU* 5.7 0.9 - - - +
974B ARG* 5.1 6.2 + - - -
1019B ILE* 2.8 38.3 + - + +
1020B ASN* 3.6 16.1 - - - +
1022B GLU* 1.3 81.3 - - + +
1024B ARG* 1.3 62.5 + - - +
1025B ARG 3.3 1.3 - - - -
1026B ASP* 3.4 8.2 + - - +
1027B VAL* 3.3 27.5 + - - +
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Residues in contact with ARG1024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938B ASP* 4.6 8.6 - - + +
941B LEU* 5.1 11.1 + - - +
942B ALA* 3.8 20.0 - - + +
945B ARG* 4.1 34.1 - - - +
1017B ASN 5.7 0.2 + - - -
1020B ASN* 3.0 43.3 + - + +
1021B ALA* 3.4 13.2 + - - +
1023B GLU* 1.3 76.1 - - - +
1025B ARG* 1.3 63.6 + - - +
1027B VAL* 3.6 7.9 + - - +
1028B SER* 3.3 23.4 + - - -
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Residues in contact with ARG1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939B GLN* 4.8 14.8 - - + +
942B ALA* 4.1 10.7 - - + +
943B ASP* 5.5 1.8 - - + +
946B GLU* 3.3 38.0 + - - +
1021B ALA 3.2 6.2 + - - +
1022B GLU* 3.5 26.0 + - - +
1024B ARG* 1.3 73.7 - - - +
1026B ASP* 1.3 77.3 + - - +
1027B VAL 3.1 0.4 - - - -
1028B SER* 3.0 7.2 + - - -
1029B LEU* 2.6 55.3 + - + +
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Residues in contact with ASP1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847B GLU* 5.8 8.2 - - + +
848B THR* 5.7 1.2 + - - -
1022B GLU 3.1 20.3 + - - +
1023B GLU* 3.4 10.2 + - - +
1024B ARG 3.3 0.6 - - - -
1025B ARG* 1.3 106.5 + - - +
1027B VAL* 1.3 58.2 + - + +
1029B LEU* 4.0 11.3 - - - +
1030B LYS* 3.1 26.9 + - - +
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Residues in contact with VAL1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023B GLU 3.3 16.5 + - - +
1024B ARG* 3.8 9.4 - - - +
1025B ARG 3.1 0.4 - - - -
1026B ASP* 1.3 77.2 - - + +
1028B SER* 1.3 60.3 + - - +
1030B LYS* 3.2 5.9 + - - +
1031B ASP* 3.0 29.8 + - + +
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Residues in contact with SER1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935B SER* 3.5 19.6 + - - -
938B ASP* 3.4 26.3 - - - +
939B GLN* 3.6 29.0 + - - +
1024B ARG 3.3 11.8 + - - -
1025B ARG 3.0 7.9 + - - -
1027B VAL* 1.3 79.3 - - - +
1029B LEU* 1.3 56.4 + - - +
1031B ASP* 3.4 3.1 + - - +
1032B CYS* 2.9 31.9 + - - +
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Residues in contact with LEU1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926B LEU 4.0 22.6 - - - +
927B ILE* 4.7 5.8 - - + -
928B THR* 4.1 8.3 - - - +
939B GLN* 4.1 24.7 - - - +
1025B ARG* 2.6 40.7 + - + +
1026B ASP* 4.1 21.1 - - - +
1028B SER* 1.3 73.0 - - - +
1030B LYS* 1.3 57.9 + - - +
1032B CYS* 4.0 3.4 - - - +
1033B MET* 3.2 38.1 + - + +
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Residues in contact with LYS1030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839B ASP 4.8 11.1 + - - -
840B SER* 5.7 3.2 - - - +
844B MET* 5.8 2.2 - - - +
847B GLU* 3.3 35.1 + - + +
851B SER* 6.0 1.3 - - - +
854B LYS* 4.0 20.4 - - - +
1026B ASP 3.1 20.2 + - - +
1027B VAL* 3.7 6.5 - - - +
1028B SER 3.2 0.4 - - - -
1029B LEU* 1.3 77.4 - - - +
1031B ASP* 1.3 58.5 + - - +
1033B MET* 3.7 6.4 + - + +
1034B ARG* 3.1 25.8 + - - +
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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
----------------------------------------------------------
935B SER* 3.8 22.0 + - - +
1027B VAL* 3.0 17.9 + - + +
1028B SER* 4.0 6.1 - - - +
1030B LYS* 1.3 74.3 - - - +
1032B CYS* 1.3 61.1 + - - +
1034B ARG* 3.3 29.3 + - - +
1035B ARG* 2.9 42.6 + - - +
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Residues in contact with CYS1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926B LEU 4.8 6.3 - - - -
928B THR* 3.0 34.1 - - + +
929B PRO* 5.8 0.4 - - - -
933B PHE* 3.8 33.9 - - + -
935B SER* 5.6 2.9 - - - -
1028B SER 2.9 17.2 + - - +
1029B LEU* 4.1 4.0 - - - +
1031B ASP* 1.3 78.1 - - - +
1033B MET* 1.3 58.2 + - - +
1035B ARG* 3.2 6.1 + - - +
1036B LEU* 3.0 42.3 + - - +
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Residues in contact with MET1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851B SER* 3.6 31.2 - - - +
854B LYS* 4.3 10.1 - - - -
855B ILE* 3.8 30.5 - - + -
925B GLY* 5.7 0.7 - - - -
926B LEU* 4.0 21.1 - - + +
1029B LEU* 3.2 25.0 + - + +
1030B LYS* 4.1 5.8 - - + +
1032B CYS* 1.3 77.0 - - - +
1034B ARG* 1.3 63.7 + - - +
1036B LEU* 3.4 8.8 + - - +
1037B PHE* 3.2 61.5 + - + -
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Residues in contact with ARG1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B VAL* 3.3 26.9 - - + +
829B GLY* 3.2 27.4 + - - +
830B SER 4.3 0.9 - - - -
831B PRO* 4.2 22.1 - - - +
834B SER* 3.4 35.8 + - - -
1030B LYS 3.1 16.8 + - - +
1031B ASP* 3.4 29.3 + - - +
1032B CYS 3.2 0.2 - - - -
1033B MET* 1.3 78.3 - - - +
1035B ARG* 1.3 77.9 + - - +
1037B PHE* 3.3 4.3 + - - -
1038B TYR* 3.0 34.6 + - - +
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Residues in contact with ARG1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933B PHE* 4.1 33.3 - - + +
935B SER* 5.4 7.5 - - - +
937B TYR* 5.9 0.8 + - - -
1031B ASP* 2.9 35.0 + - - +
1032B CYS* 3.4 9.0 - - - +
1034B ARG* 1.3 99.9 - - - +
1036B LEU* 1.3 60.2 + - + +
1038B TYR* 3.8 9.0 + - - +
1039B ASN* 3.3 20.6 + - - +
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Residues in contact with LEU1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858B PHE* 5.2 2.0 - - + -
912B TRP* 3.6 31.5 - - + -
915B ALA* 5.9 2.9 - - + -
916B PHE* 5.1 9.9 - - + -
926B LEU* 3.8 34.8 - - + -
933B PHE 5.2 9.2 - - - +
1032B CYS* 3.0 33.6 + - - +
1033B MET* 3.8 7.0 - - - +
1034B ARG 3.1 0.4 - - - -
1035B ARG* 1.3 75.0 - - + +
1037B PHE* 1.3 69.3 + - + +
1038B TYR 3.1 1.3 - - - -
1039B ASN* 3.0 17.4 + - + +
1040B PHE* 3.0 10.2 + - - +
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Residues in contact with PHE1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B ILE* 3.7 29.9 - - + +
828B VAL* 3.5 33.9 - - + -
829B GLY* 4.1 5.2 - - - +
854B LYS* 4.1 20.0 - - + -
855B ILE* 4.6 2.5 - - + -
858B PHE* 3.3 53.2 - + + -
926B LEU* 4.8 3.8 - - + -
1033B MET* 3.2 53.4 + - + +
1034B ARG* 3.3 3.5 + - - +
1036B LEU* 1.3 77.1 - - + +
1038B TYR* 1.3 56.3 + - - +
1040B PHE* 3.3 5.3 + - - +
1041B ASP* 2.9 28.2 + - - +
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Residues in contact with TYR1038 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B GLU* 2.7 36.7 + - + +
829B GLY* 3.4 21.7 - - - +
830B SER* 5.0 0.4 - - - -
831B PRO* 3.6 35.7 - - + -
1034B ARG* 3.0 19.8 + - - +
1035B ARG* 3.9 10.1 - - + +
1036B LEU 3.1 0.2 - - - -
1037B PHE* 1.3 78.7 - - - +
1039B ASN* 1.3 59.1 + - + +
1041B ASP* 3.4 18.4 + - - +
1042B LYS* 3.1 66.4 + - + +
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Residues in contact with ASN1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B GLU* 4.8 9.2 - - - +
912B TRP* 3.6 21.9 - - + -
1035B ARG 3.3 11.9 + - - +
1036B LEU* 3.0 14.4 + - + +
1038B TYR* 1.3 80.7 - - + +
1040B PHE* 1.3 63.1 + - - +
1042B LYS* 3.3 32.8 - - - +
1043B ASN* 4.3 1.6 + - - +
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Residues in contact with PHE1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822B LEU* 3.7 20.0 - - + -
825B ILE* 3.7 36.8 - - + -
858B PHE* 3.6 26.9 - + + -
861B ALA* 4.6 5.4 - - + -
862B LEU* 3.6 21.5 - - + -
865B PHE* 4.0 16.2 - + - -
908B GLU* 5.8 0.2 - - - -
912B TRP* 3.7 25.1 - + + +
1036B LEU 3.0 7.2 + - - +
1037B PHE* 3.6 7.4 - - - +
1039B ASN* 1.3 76.2 - - - +
1041B ASP* 1.3 63.8 + - - +
1042B LYS 3.3 0.3 + - - -
1043B ASN* 3.4 4.4 + - - +
1047B TRP* 3.0 64.4 + + - -
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Residues in contact with ASP1041 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B LYS* 3.9 17.8 + - - -
822B LEU 4.8 2.1 - - - +
825B ILE* 5.3 1.1 - - + -
826B HIS* 2.9 55.8 + - - +
1037B PHE 2.9 17.1 + - - +
1038B TYR* 3.5 21.9 - - + +
1040B PHE* 1.3 82.2 - - - +
1042B LYS* 1.3 56.6 + - - +
1044B TYR* 2.9 32.3 + - - +
1047B TRP* 5.3 1.1 - - - -
----------------------------------------------------------
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Residues in contact with LYS1042 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B GLU 5.7 3.8 - - - -
1038B TYR* 3.1 58.1 + - + +
1039B ASN* 3.3 29.7 - - - +
1041B ASP* 1.3 75.1 + - - +
1043B ASN* 1.3 55.6 + - + +
1044B TYR* 3.3 16.9 + - - -
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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