Contacts of the helix formed by residues 1012 - 1044 (chain B) in PDB entry 3H2V
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 SER1012 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010B ASN 3.4 4.3 + - - -
1011B ILE* 1.3 77.7 - - - +
1013B ASP* 1.3 55.4 + - - +
1014B GLU* 3.2 8.8 + - - +
1015B GLU* 2.9 30.6 + - - +
1016B SER* 2.5 34.0 + - - -
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Residues in contact with ASP1013 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011B ILE 3.9 0.7 + - - +
1012B SER* 1.3 72.6 + - - +
1014B GLU* 1.3 76.1 + - - +
1016B SER* 3.3 7.2 + - - -
1017B GLU* 3.1 24.1 + - - +
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Residues in contact with GLU1014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B SER* 3.2 6.1 + - - +
1013B ASP* 1.3 92.1 - - - +
1015B GLU* 1.3 62.3 + - - +
1017B GLU* 3.6 7.8 + - - +
1018B GLN* 3.1 26.9 + - - +
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Residues in contact with GLU1015 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005B MET* 4.2 18.9 - - + +
1011B ILE* 3.3 28.0 - - + +
1012B SER* 2.9 25.6 + - - +
1013B ASP 3.2 0.2 - - - -
1014B GLU* 1.3 75.0 - - - +
1016B SER* 1.3 65.6 + - - +
1018B GLN* 3.2 6.1 + - - +
1019B ALA* 3.0 22.9 + - - +
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Residues in contact with SER1016 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002B LYS* 3.4 18.0 + - - -
1005B MET* 4.1 13.2 - - - -
1011B ILE* 3.9 10.1 + - - +
1012B SER 2.5 25.3 + - - -
1013B ASP* 3.3 8.2 + - - -
1015B GLU* 1.3 79.3 - - - +
1017B GLU* 1.3 61.5 + - - +
1019B ALA 3.3 0.9 + - - -
1020B THR* 3.2 19.9 + - - -
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Residues in contact with GLU1017 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013B ASP 3.1 15.4 + - - +
1014B GLU* 4.5 9.9 - - - +
1016B SER* 1.3 77.8 - - - +
1018B GLN* 1.3 57.7 + - - +
1020B THR* 3.7 18.7 + - - +
1021B GLU* 3.1 58.6 + - - +
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Residues in contact with GLN1018 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014B GLU 3.1 19.0 + - - +
1015B GLU* 3.7 5.8 - - - +
1016B SER 3.1 0.8 - - - -
1017B GLU* 1.3 77.7 - - - +
1019B ALA* 1.3 66.2 + - - +
1021B GLU* 3.2 20.5 + - - +
1022B MET* 2.8 47.4 + - + +
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Residues in contact with ALA1019 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998B LEU* 5.0 3.7 - - - +
1001B VAL* 4.1 15.0 - - + -
1002B LYS* 3.9 15.7 - - + +
1005B MET* 3.7 25.1 - - + -
1015B GLU 3.0 13.4 + - - +
1016B SER 3.3 8.3 + - - +
1018B GLN* 1.3 76.9 - - - +
1020B THR* 1.3 63.8 + - - +
1022B MET* 3.2 24.8 + - + +
1023B LEU* 3.3 13.7 + - - +
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Residues in contact with THR1020 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B ASN* 4.2 18.2 - - - +
937B VAL* 5.2 13.6 + - + +
1002B LYS* 3.2 31.5 + - - +
1016B SER 3.2 8.8 + - - -
1017B GLU* 3.7 27.8 + - - +
1019B ALA* 1.3 80.2 - - - +
1021B GLU* 1.3 58.6 + - + +
1023B LEU* 3.3 7.5 + - - +
1024B VAL* 3.1 28.7 + - + +
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Residues in contact with GLU1021 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017B GLU* 3.1 47.6 + - - +
1018B GLN* 3.2 23.1 + - - +
1020B THR* 1.3 78.5 - - + +
1022B MET* 1.3 57.9 + - - +
1023B LEU 3.2 0.2 - - - -
1024B VAL* 4.0 9.1 - - + +
1025B HIS* 3.3 23.9 + - - +
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Residues in contact with MET1022 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
998B LEU* 3.1 44.8 - - + +
1001B VAL* 5.7 4.3 - - + -
1018B GLN* 2.8 42.3 + - + +
1019B ALA* 3.2 15.9 + - + +
1021B GLU* 1.3 75.0 - - - +
1023B LEU* 1.3 64.4 + - - +
1025B HIS* 3.8 7.9 - - - +
1026B ASN* 3.2 13.9 + - - +
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Residues in contact with LEU1023 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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898B MET* 5.2 6.1 - - - -
933B MET* 5.1 7.6 - - - -
937B VAL* 4.5 17.7 - - + -
947B LEU* 5.3 3.1 - - + -
995B LEU* 3.4 35.9 - - + +
998B LEU* 3.7 23.3 - - + +
999B SER* 4.1 11.0 - - - +
1002B LYS* 3.7 39.7 - - + -
1019B ALA 3.3 6.1 + - - +
1020B THR* 3.3 10.7 + - - +
1022B MET* 1.3 77.8 - - - +
1024B VAL* 1.3 67.9 + - + +
1026B ASN* 3.0 4.2 + - - +
1027B ALA* 2.8 25.3 + - + +
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Residues in contact with VAL1024 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895B ASN* 3.7 30.5 - - - +
897B PRO* 3.7 22.0 - - + -
898B MET* 3.8 11.8 - - + -
937B VAL* 6.1 0.7 - - + -
1020B THR* 3.1 20.3 + - + +
1021B GLU* 4.0 9.0 - - + +
1023B LEU* 1.3 80.8 - - + +
1025B HIS* 1.3 59.0 + - - +
1027B ALA* 3.7 7.3 - - - +
1028B GLN* 2.9 50.5 + - + +
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Residues in contact with HIS1025 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021B GLU 3.3 17.4 + - - +
1022B MET* 3.9 8.1 - - - +
1023B LEU 3.0 0.8 - - - -
1024B VAL* 1.3 80.6 - - - +
1026B ASN* 1.3 66.9 + - + +
1028B GLN* 3.4 15.7 + - - +
1029B ASN* 2.8 56.6 + - - -
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Residues in contact with ASN1026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991B ILE* 2.7 34.5 - - - +
994B GLN* 2.5 42.1 + - - +
995B LEU* 3.6 14.5 + - + +
998B LEU* 3.3 18.9 - - + +
1022B MET 3.2 14.8 + - - +
1023B LEU 3.0 4.8 + - - +
1025B HIS* 1.3 83.2 - - - +
1027B ALA* 1.3 58.4 + - - +
1029B ASN* 3.5 2.3 + - - -
1030B LEU* 2.9 26.9 + - - +
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Residues in contact with ALA1027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B MET* 4.1 17.9 - - + -
901B ALA* 4.7 1.1 - - + -
930B MET* 4.0 25.6 - - + -
933B MET* 6.2 0.2 - - - -
995B LEU* 4.2 10.7 - - + +
1023B LEU* 2.8 16.5 + - + +
1024B VAL* 3.7 6.7 - - - +
1026B ASN* 1.3 75.9 - - - +
1028B GLN* 1.3 65.6 + - - +
1030B LEU* 3.2 6.8 + - - +
1031B MET* 3.0 31.1 + - - +
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Residues in contact with GLN1028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B PRO* 4.0 15.6 + - - +
901B ALA* 4.1 21.5 - - + +
1024B VAL* 2.9 43.8 + - + +
1025B HIS* 3.4 19.5 + - - +
1027B ALA* 1.3 74.7 - - - +
1029B ASN* 1.3 67.6 + - - +
1031B MET* 3.6 2.8 + - - +
1032B GLN* 3.0 30.2 + - - +
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Residues in contact with ASN1029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
991B ILE* 4.3 13.9 - - + -
1025B HIS* 2.8 45.5 + - - +
1026B ASN* 4.0 4.7 - - - +
1027B ALA 3.2 0.4 - - - -
1028B GLN* 1.3 84.5 + - - +
1030B LEU* 1.3 68.3 + - - +
1032B GLN* 3.6 7.1 - - - +
1033B SER* 2.9 30.6 + - - +
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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
----------------------------------------------------------
926B MET* 3.8 15.0 - - + -
930B MET* 5.0 0.9 - - + -
954B ILE* 3.5 32.3 - - + -
958B SER* 4.4 4.0 - - - +
988B ILE* 4.3 24.7 - - + +
991B ILE* 3.7 19.0 - - + +
992B SER* 4.3 8.7 - - - +
995B LEU* 4.0 16.2 - - + -
1026B ASN 2.9 19.2 + - - +
1027B ALA* 3.2 6.5 + - - +
1029B ASN* 1.3 78.1 - - - +
1031B MET* 1.3 70.1 + - + +
1033B SER* 3.1 3.1 + - - -
1034B VAL* 2.9 36.2 + - + +
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Residues in contact with MET1031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B ALA* 3.4 37.9 - - + +
902B ALA* 4.1 2.0 - - - -
904B GLN* 6.0 1.3 - - + -
905B LEU* 3.8 27.8 - - + +
926B MET* 3.7 31.0 - - + +
927B ALA* 4.6 1.1 - - - -
930B MET* 3.0 50.7 - - + -
1027B ALA 3.0 19.9 + - - +
1028B GLN 3.9 3.6 - - - +
1030B LEU* 1.3 84.7 - - + +
1032B GLN* 1.3 63.0 + - - +
1034B VAL* 3.1 6.2 + - - +
1035B LYS* 2.9 27.7 + - + +
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Residues in contact with GLN1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B GLN* 5.4 4.1 - - - +
1028B GLN 3.0 19.3 + - - +
1029B ASN* 3.6 9.4 - - - +
1030B LEU 3.2 0.2 - - - -
1031B MET* 1.3 75.5 - - - +
1033B SER* 1.3 58.8 + - - +
1035B LYS* 3.7 28.8 + - + +
1036B GLU* 2.3 75.9 + - - +
1039B ARG* 4.5 1.4 + - - -
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Residues in contact with SER1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
984B VAL* 4.4 4.4 - - - +
987B ARG* 3.2 26.6 + - - +
988B ILE* 4.2 20.4 - - - -
991B ILE* 3.8 14.0 - - - +
1029B ASN* 2.9 18.7 + - - +
1030B LEU* 3.6 4.9 - - - -
1032B GLN* 1.3 74.4 - - - +
1034B VAL* 1.3 67.5 + - - +
1036B GLU* 3.2 8.9 + - - +
1037B THR* 3.0 27.7 + - - -
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Residues in contact with VAL1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B LEU* 3.8 16.4 - - + -
923B ALA* 4.4 12.3 - - + -
926B MET* 3.2 42.8 - - + -
961B VAL* 4.2 20.9 - - + -
988B ILE* 4.2 15.5 - - + -
1030B LEU* 2.9 24.5 + - + +
1031B MET* 3.1 5.4 + - - +
1033B SER* 1.3 75.5 - - - +
1035B LYS* 1.3 63.3 + - - +
1037B THR* 3.0 6.4 + - - -
1038B VAL* 3.0 25.1 + - + +
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Residues in contact with LYS1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904B GLN* 4.1 40.3 + - + +
905B LEU* 3.5 19.8 - - + +
908B GLU* 4.0 23.6 + - + -
1031B MET* 2.9 11.4 + - + +
1032B GLN* 3.7 29.2 - - + +
1034B VAL* 1.3 78.6 - - - +
1036B GLU* 1.3 59.3 + - - +
1038B VAL* 3.7 7.9 + - - +
1039B ARG* 3.0 62.4 + - - +
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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
----------------------------------------------------------
984B VAL* 4.6 19.7 - - + -
987B ARG* 4.2 15.6 + - - -
1032B GLN* 2.3 58.3 + - - +
1033B SER* 3.2 9.6 + - - +
1035B LYS* 1.3 77.9 - - - +
1037B THR* 1.3 62.2 + - - +
1039B ARG* 3.5 25.1 + - - +
1040B GLU* 3.1 28.3 + - + +
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Residues in contact with THR1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919B ILE* 4.6 5.8 - - + -
961B VAL* 4.0 18.2 - - + -
965B ALA* 3.7 29.8 - - + -
981B LEU* 4.1 7.6 - - + +
984B VAL* 4.0 14.4 + - - +
985B CYS* 3.8 11.9 - - + +
988B ILE* 3.6 16.3 - - - +
1033B SER 3.0 12.0 + - - -
1034B VAL 3.0 8.7 + - - -
1036B GLU* 1.3 74.3 - - - +
1038B VAL* 1.3 57.6 + - - +
1039B ARG 3.1 0.2 + - - -
1040B GLU* 3.1 0.9 + - - +
1041B ALA* 2.7 37.6 + - + +
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Residues in contact with VAL1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905B LEU* 5.3 1.1 - - + -
908B GLU* 4.5 17.5 - - + +
909B ALA* 5.5 2.7 - - + +
912B TRP* 4.4 9.9 - - + +
919B ILE* 4.0 23.8 - - + -
920B ILE* 4.2 11.0 - - + -
923B ALA* 4.4 19.3 - - + -
961B VAL* 5.7 0.7 - - + -
1034B VAL* 3.0 21.3 + - + +
1035B LYS* 3.7 12.3 - - - +
1037B THR* 1.3 77.6 - - - +
1039B ARG* 1.3 63.0 + - + +
1041B ALA* 3.8 4.2 - - - +
1042B GLU* 3.2 17.8 + - - +
1058B TRP* 3.4 24.9 - - + -
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Residues in contact with ARG1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B GLU* 3.2 35.9 + - + +
1032B GLN* 4.5 1.2 + - - -
1035B LYS* 3.0 48.4 + - - +
1036B GLU* 3.5 34.5 + - - +
1037B THR 3.1 0.6 - - - -
1038B VAL* 1.3 77.7 - - + +
1040B GLU* 1.3 59.6 + - + +
1042B GLU* 3.3 7.4 + - - +
1043B ALA* 3.1 25.8 + - - +
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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
----------------------------------------------------------
977B ILE* 3.2 37.7 - - - +
980B ASN* 3.4 35.5 - - + +
981B LEU* 4.0 18.4 - - + +
984B VAL* 4.8 9.2 - - + -
1036B GLU* 3.1 17.8 + - + +
1037B THR* 4.0 2.7 - - - +
1039B ARG* 1.3 78.2 - - + +
1041B ALA* 1.3 60.0 + - - +
1042B GLU 3.2 0.2 - - - -
1043B ALA* 3.7 10.1 - - - +
1044B ALA* 3.1 27.0 + - - +
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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
----------------------------------------------------------
919B ILE* 4.3 19.3 - - + -
965B ALA* 5.3 0.7 - - - -
968B VAL* 3.8 13.1 - - + +
981B LEU* 3.9 14.3 - - + +
1037B THR* 2.7 24.9 + - + +
1038B VAL* 3.8 4.9 - - - +
1040B GLU* 1.3 70.7 - - - +
1042B GLU* 1.3 65.0 + - - +
1044B ALA* 3.4 6.4 + - - +
1045B SER* 2.8 27.5 + - - -
1056B LEU* 5.4 0.2 - - + -
1058B TRP* 4.1 11.4 - - + -
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Residues in contact with GLU1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912B TRP* 3.1 29.7 - - + -
1038B VAL 3.2 14.6 + - - +
1039B ARG* 3.6 7.4 - - - +
1041B ALA* 1.3 78.7 - - - +
1043B ALA* 1.3 75.3 + - - +
1045B SER* 3.0 18.0 + - - -
1058B TRP* 3.6 44.6 - - + +
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Residues in contact with ALA1043 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977B ILE* 4.4 18.4 - - + +
1039B ARG 3.1 15.0 + - - +
1040B GLU* 3.7 13.9 - - - +
1042B GLU* 1.3 88.9 + - - +
1044B ALA* 1.3 59.0 + - - +
1045B SER* 3.3 3.1 + - - -
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Residues in contact with ALA1044 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968B VAL* 3.7 20.7 - - + +
972B CYS* 4.1 30.6 + - + +
977B ILE* 3.8 18.4 - - + -
981B LEU* 4.1 9.6 - - + -
1040B GLU 3.1 17.7 + - - +
1041B ALA 3.7 6.1 - - - +
1042B GLU 3.1 0.4 - - - -
1043B ALA* 1.3 74.6 - - - +
1045B SER* 1.3 62.1 + - - +
----------------------------------------------------------
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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