Contacts of the helix formed by residues 1009 - 1039 (chain H) in PDB entry 6BAA
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 GLY1009 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005H LEU 3.0 11.8 + - - +
1006H SER 3.8 6.2 + - - -
1007H SER 3.5 2.0 - - - -
1008H ALA* 1.3 85.9 - - - +
1010H ILE* 1.3 64.3 + - - -
1011H LEU 3.3 3.7 + - - -
1012H LEU 4.0 1.6 + - - -
1013H LEU* 3.6 17.7 + - - +
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Residues in contact with ILE1010 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009H GLY* 1.3 72.1 - - - -
1011H LEU* 1.3 59.4 + - - +
1013H LEU* 3.3 8.0 - - - +
1014H SER* 2.9 29.3 + - - -
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Residues in contact with LEU1011 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009H GLY* 3.3 1.0 - - - -
1010H ILE* 1.3 77.9 - - - +
1012H LEU* 1.3 58.2 + - - +
1014H SER* 3.2 8.4 + - - -
1015H LEU* 3.0 25.9 + - - +
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Residues in contact with LEU1012 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008H ALA* 4.7 14.6 + - + +
1009H GLY 4.0 1.6 + - - -
1010H ILE 3.5 0.2 - - - -
1011H LEU* 1.3 76.0 - - - +
1013H LEU* 1.3 60.1 + - - +
1015H LEU* 3.6 9.0 - - + +
1016H LEU* 2.9 30.7 + - - +
1085H THR* 5.2 6.1 - - - +
1089H THR* 4.7 22.1 - - - +
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Residues in contact with LEU1013 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005H LEU* 6.5 1.6 - - + -
1008H ALA* 5.9 4.0 - - + +
1009H GLY 3.6 13.7 + - - +
1010H ILE* 3.3 13.7 + - - +
1011H LEU 3.2 0.2 - - - -
1012H LEU* 1.3 79.8 - - - +
1014H SER* 1.3 56.8 + - - +
1016H LEU* 3.2 5.3 + - - +
1017H VAL* 2.9 33.7 + - - +
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Residues in contact with SER1014 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010H ILE 2.9 14.0 + - - -
1011H LEU* 3.2 10.5 + - - -
1013H LEU* 1.3 74.3 - - - +
1015H LEU* 1.3 63.7 + - - +
1017H VAL* 5.0 2.7 - - - -
1018H PHE* 3.0 30.1 + - - +
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Residues in contact with LEU1015 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011H LEU 3.0 13.6 + - - +
1012H LEU* 3.6 11.7 - - - +
1013H LEU 3.3 0.2 - - - -
1014H SER* 1.3 73.9 - - - +
1016H LEU* 1.3 58.1 + - - +
1018H PHE* 3.9 2.3 - - - +
1019H SER* 2.9 32.7 + - - -
1085H THR* 5.1 9.4 - - - -
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Residues in contact with LEU1016 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012H LEU 2.9 17.6 + - - +
1013H LEU* 3.7 6.3 - - - +
1015H LEU* 1.3 76.2 - - - +
1017H VAL* 1.3 57.1 + - - +
1019H SER* 3.3 3.5 + - - -
1020H GLN* 2.9 31.6 + - - +
1082H THR* 5.0 6.1 - - - +
1085H THR* 4.5 22.0 - - - -
1086H VAL* 5.5 2.0 - - - +
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Residues in contact with VAL1017 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013H LEU 2.9 16.4 + - - +
1014H SER* 4.4 2.5 - - - +
1016H LEU* 1.3 77.5 - - - +
1018H PHE* 1.3 58.7 + - - +
1020H GLN* 3.8 5.4 - - - +
1021H LEU* 3.0 31.0 + - - +
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Residues in contact with PHE1018 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014H SER 3.0 20.0 + - - +
1015H LEU* 4.2 2.0 - - - +
1017H VAL* 1.3 78.5 - - - +
1019H SER* 1.3 56.2 + - - +
1021H LEU* 3.6 5.3 + - - +
1022H LEU* 2.9 28.5 + - - +
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Residues in contact with SER1019 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015H LEU 2.9 21.0 + - - -
1016H LEU* 3.8 4.3 - - - -
1018H PHE* 1.3 74.8 - - - +
1020H GLN* 1.3 60.5 + - - +
1022H LEU* 3.3 7.5 - - - +
1023H LYS* 2.9 29.8 + - - +
1081H VAL* 4.8 11.7 - - - -
1082H THR* 4.6 21.4 - - - -
1085H THR* 6.0 0.4 - - - -
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Residues in contact with GLN1020 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016H LEU 2.9 18.7 + - - +
1017H VAL* 3.8 5.6 - - - +
1019H SER* 1.3 73.4 - - - +
1021H LEU* 1.3 59.2 + - - +
1023H LYS* 3.4 3.8 + - - +
1024H HIS* 2.9 31.4 + - - +
1082H THR* 4.7 13.6 - - - -
1144H SER* 5.9 3.8 - - - +
1148H LEU* 4.0 21.6 - - + +
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Residues in contact with LEU1021 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017H VAL 3.0 17.4 + - - +
1018H PHE* 4.0 5.4 - - - +
1020H GLN* 1.3 75.6 - - - +
1022H LEU* 1.3 57.5 + - - +
1024H HIS* 4.1 4.2 - - - +
1025H MET* 2.9 34.1 + - - +
1148H LEU* 4.6 7.3 - - + +
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Residues in contact with LEU1022 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018H PHE 2.9 20.1 + - - +
1019H SER* 3.3 11.2 - - - +
1020H GLN 3.2 0.2 - - - -
1021H LEU* 1.3 76.8 - - - +
1023H LYS* 1.3 58.2 + - - +
1025H MET* 3.8 3.1 - - - +
1026H VAL* 2.9 28.3 + - - +
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Residues in contact with LYS1023 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019H SER 2.9 15.7 + - - +
1020H GLN* 4.3 3.4 - - - +
1022H LEU* 1.3 76.2 - - - +
1024H HIS* 1.3 58.5 + - - +
1026H VAL* 3.3 8.8 + - - +
1027H LEU* 2.9 27.0 + - - +
1077H VAL 5.6 0.7 - - - +
1078H LEU* 4.6 24.0 - - + +
1079H CYS 4.9 9.2 - - - +
1082H THR* 6.3 2.2 - - - -
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Residues in contact with HIS1024 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020H GLN 2.9 19.2 + - - +
1021H LEU* 4.1 4.3 - - - +
1023H LYS* 1.3 75.2 - - - +
1025H MET* 1.3 59.9 + - - +
1027H LEU* 3.1 8.5 + - - +
1028H VAL* 3.0 26.6 + - - +
1148H LEU* 4.4 22.7 - - + -
1149H LEU* 6.2 4.3 - - + -
1152H SER* 4.4 15.5 + - - +
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Residues in contact with MET1025 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021H LEU 2.9 18.9 + - - +
1022H LEU* 4.0 3.1 - - - +
1024H HIS* 1.3 73.0 - - - +
1026H VAL* 1.3 60.7 + - - +
1028H VAL* 3.6 9.0 - - + +
1029H ALA* 2.8 30.3 + - - +
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Residues in contact with VAL1026 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022H LEU 2.9 18.6 + - - +
1023H LYS* 3.5 10.1 - - - +
1024H HIS 3.2 0.2 - - - -
1025H MET* 1.3 77.1 - - - +
1027H LEU* 1.3 57.6 + - - +
1029H ALA* 3.2 5.6 + - - +
1030H ILE* 2.8 29.7 + - - +
1074H LEU* 4.8 13.0 - - + +
1077H VAL* 4.7 19.1 - - + -
1078H LEU* 5.2 7.0 - - + +
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Residues in contact with LEU1027 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H ILE* 5.1 17.3 - - + -
1023H LYS 2.9 12.9 + - - +
1024H HIS* 3.1 11.4 + - - +
1026H VAL* 1.3 77.0 - - - +
1028H VAL* 1.3 62.0 + - - +
1030H ILE* 3.2 9.1 + - - +
1031H ASP* 3.1 22.7 + - - +
1149H LEU* 6.0 6.7 - - + -
1287H TYR* 4.4 5.3 + - - +
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Residues in contact with VAL1028 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024H HIS 3.0 12.8 + - - +
1025H MET* 3.6 12.1 - - + +
1027H LEU* 1.3 75.1 - - - +
1029H ALA* 1.3 58.5 + - - +
1031H ASP* 3.2 4.7 + - - +
1032H TYR* 2.9 28.4 + - - +
1152H SER* 5.2 12.3 - - - +
1156H VAL* 5.1 16.3 - - + +
1287H TYR* 4.6 9.4 + - - -
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Residues in contact with ALA1029 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025H MET 2.8 19.0 + - - +
1026H VAL* 3.7 7.0 - - - +
1028H VAL* 1.3 73.4 - - - +
1030H ILE* 1.3 60.8 + - - +
1032H TYR* 3.7 8.0 - - - +
1033H TRP* 2.9 32.1 + - - +
1074H LEU* 5.6 5.2 - - + -
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Residues in contact with ILE1030 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H ILE* 5.9 6.3 - - + -
1026H VAL 2.8 14.2 + - - +
1027H LEU* 3.2 13.2 + - - +
1029H ALA* 1.3 76.4 - - - +
1031H ASP* 1.3 57.7 + - - +
1033H TRP* 3.9 2.3 - - - +
1034H LEU* 2.9 28.5 + - - +
1071H LEU* 5.7 9.5 - - + +
1074H LEU* 4.9 18.1 - - + +
1075H GLY* 5.8 2.9 - - - +
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Residues in contact with ASP1031 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580H LEU* 5.6 6.3 - - + -
1027H LEU 3.1 9.2 + - - +
1028H VAL* 3.2 6.0 + - - +
1030H ILE* 1.3 77.6 - - - +
1032H TYR* 1.3 57.9 + - - +
1034H LEU* 3.3 8.4 + - - +
1035H ALA 2.9 22.5 + - - -
1156H VAL* 6.5 0.4 - - + -
1283H LEU* 3.3 33.7 - - + +
1287H TYR* 3.7 24.7 - - + +
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Residues in contact with TYR1032 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028H VAL 2.9 16.9 + - - +
1029H ALA* 3.7 9.2 - - - +
1031H ASP* 1.3 77.8 - - - +
1033H TRP* 1.3 57.4 + - - +
1035H ALA* 3.1 6.2 + - - +
1036H LYS* 2.9 25.1 + - - +
1283H LEU* 4.4 7.4 - - - -
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Residues in contact with TRP1033 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029H ALA 2.9 17.5 + - - +
1030H ILE* 4.4 2.0 - - - +
1032H TYR* 1.3 73.0 - - - +
1034H LEU* 1.3 60.4 + - - +
1036H LYS* 3.7 8.9 - - + +
1037H TRP* 2.8 26.7 + - - +
1067H VAL* 5.1 14.8 - - + +
1070H LEU* 5.8 6.5 - - + -
1071H LEU* 5.9 9.0 - - + -
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Residues in contact with LEU1034 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576H ALA* 6.6 0.2 - - + -
577H PHE* 4.5 16.1 - - + -
1030H ILE 2.9 19.7 + - - +
1031H ASP* 3.3 10.8 - - - +
1032H TYR 3.1 0.2 - - - -
1033H TRP* 1.3 75.9 - - - +
1035H ALA* 1.3 58.9 + - - +
1037H TRP* 3.2 7.6 + - - +
1038H THR* 3.0 29.5 + - - -
1071H LEU* 6.1 2.6 - - + +
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Residues in contact with ALA1035 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577H PHE* 4.2 8.0 - - - -
1031H ASP 2.9 6.7 + - - -
1032H TYR* 3.1 8.9 + - - +
1034H LEU* 1.3 76.4 - - - +
1036H LYS* 1.3 61.7 + - - +
1038H THR* 3.3 1.8 + - - +
1039H ASP* 3.3 27.0 + - - +
1279H GLY* 4.1 21.7 - - - -
1280H LEU* 4.5 10.5 - - + +
1283H LEU* 3.7 26.2 - - + -
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Residues in contact with LYS1036 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032H TYR 2.9 15.9 + - - +
1033H TRP* 4.1 8.1 - - - +
1035H ALA* 1.3 73.2 - - - +
1037H TRP* 1.3 65.6 + - - +
1039H ASP* 4.3 9.4 - - - +
1067H VAL* 5.9 1.9 - - - +
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Residues in contact with TRP1037 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571H LEU* 6.3 2.2 - - + -
1033H TRP 2.8 16.1 + - - +
1034H LEU* 3.2 13.0 - - - +
1035H ALA 3.1 0.2 - - - -
1036H LYS* 1.3 80.7 - - - +
1038H THR* 1.3 64.8 + - - +
1039H ASP 3.2 7.8 + - - +
1067H VAL* 5.1 15.0 - - + -
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Residues in contact with THR1038 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571H LEU* 3.2 31.8 - - - +
572H SER* 4.0 2.9 - - - -
573H PRO* 3.6 37.9 - - - +
576H ALA* 5.3 5.2 - - - -
577H PHE* 5.5 2.9 - - - -
1034H LEU 3.0 12.6 + - - -
1035H ALA* 3.3 3.7 + - - -
1037H TRP* 1.3 79.6 - - - +
1039H ASP* 1.3 60.4 + - - +
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Residues in contact with ASP1039 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573H PRO* 4.6 4.1 - - + +
1035H ALA 3.3 14.6 + - - +
1036H LYS* 4.3 7.7 - - - +
1037H TRP 3.2 10.0 + - - +
1038H THR* 1.3 82.8 - - - +
1277H SER* 4.5 21.3 - - - +
1278H ALA* 5.6 2.2 - - + +
1279H GLY* 5.2 6.5 - - - +
----------------------------------------------------------
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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