Contacts of the helix formed by residues 920 - 956 (chain A) in PDB entry 6PUO
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 LEU 920 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914A PHE* 3.5 52.0 - - + +
917A SER* 3.3 18.9 + - - +
918A LYS 3.5 0.6 - - - -
919A THR* 1.3 102.1 - - - +
921A GLY* 1.3 66.9 + - - +
922A PRO 3.5 1.3 - - - -
923A LYS* 3.1 25.2 + - + +
924A ILE* 3.3 11.6 - - + +
933D ASP* 5.4 8.1 - - + -
936D PHE* 4.3 38.8 - - + +
940D LEU* 5.6 4.0 - - + -
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Residues in contact with GLY 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914A PHE 3.4 13.3 + - - -
915A THR* 4.3 7.0 - - - -
917A SER 4.0 3.4 + - - -
920A LEU* 1.3 76.6 - - - +
922A PRO* 1.3 70.0 - - - +
924A ILE* 3.0 19.9 + - - +
925A ILE* 3.0 19.3 + - - +
1063A TRP* 4.3 16.8 - - - -
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Residues in contact with PRO 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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918A LYS* 4.3 15.7 - - - +
919A THR* 4.7 2.7 - - - -
920A LEU 3.9 2.5 - - - +
921A GLY* 1.3 87.9 - - - +
923A LYS* 1.3 66.7 + - + +
925A ILE* 3.2 11.6 + - + +
926A ILE* 2.9 34.9 + - + +
1059A THR* 4.0 20.0 + - + +
1060A ASP* 4.4 23.8 - - + -
1063A TRP* 4.1 19.7 - - + -
1050D TYR* 6.5 0.9 - - + -
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Residues in contact with LYS 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919A THR* 3.5 23.8 - - - +
920A LEU* 3.1 17.4 + - + +
922A PRO* 1.3 82.3 - - + +
924A ILE* 1.3 61.6 + - + +
926A ILE* 3.2 16.3 + - + +
927A VAL* 3.0 34.0 + - - +
933D ASP* 5.4 4.9 - - - -
1043D LEU* 4.8 17.7 - - + -
1046D ALA* 5.2 2.0 - - + -
1047D MET* 4.1 29.0 + - + +
1050D TYR* 3.3 47.3 - - - +
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Residues in contact with ILE 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A TRP* 4.9 16.6 - - + -
911A MET* 4.9 11.0 - - + +
914A PHE* 4.6 23.8 - - + -
915A THR* 4.8 18.6 - - + -
920A LEU* 3.3 17.3 - - + +
921A GLY* 3.0 12.7 + - - +
923A LYS* 1.3 79.0 - - + +
925A ILE* 1.3 63.0 + - + +
927A VAL* 3.3 14.9 - - + +
928A LYS* 3.0 37.6 + - + +
940D LEU* 6.0 3.6 - - + -
1043D LEU* 5.3 8.3 - - + -
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Residues in contact with ILE 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921A GLY 3.0 16.7 + - - +
922A PRO* 3.2 7.6 + - + +
924A ILE* 1.3 80.7 - - + +
926A ILE* 1.3 56.9 + - + +
928A LYS* 3.3 17.2 + - + +
929A ARG* 3.0 49.3 + - - +
1059A THR* 3.3 27.1 - - - +
1062A ILE* 5.4 13.2 - - + -
1063A TRP* 5.4 11.0 - - + +
1066A GLN* 6.1 5.2 - - + -
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Residues in contact with ILE 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922A PRO* 2.9 24.4 + - + +
923A LYS* 3.2 16.1 + - + +
925A ILE* 1.3 78.0 - - + +
927A VAL* 1.3 60.7 + - + +
929A ARG* 3.1 9.8 + - - +
930A MET* 2.9 42.7 + - + +
1051A THR 5.6 0.2 - - - +
1052A PHE* 4.5 13.9 - - + -
1055A VAL* 4.4 19.3 - - + -
1056A GLN* 4.3 26.2 - - + +
1059A THR* 4.8 11.7 - - + -
1046D ALA* 4.0 25.1 - - + -
1050D TYR* 5.8 2.7 - - + -
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Residues in contact with VAL 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923A LYS 3.0 15.6 + - - +
924A ILE* 3.3 26.9 - - + +
926A ILE* 1.3 81.1 - - + +
928A LYS* 1.3 63.1 + - + +
930A MET* 3.1 20.3 + - + +
931A MET* 3.1 16.3 + - - +
1039D LEU* 5.1 12.7 - - + +
1042D ASN* 6.0 0.4 - - + -
1043D LEU* 3.6 46.0 - - + +
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Residues in contact with LYS 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867A PHE* 3.3 57.9 - - + +
868A TRP* 3.8 16.5 - - - +
924A ILE* 3.0 26.0 + - + +
925A ILE* 3.6 17.8 - - + +
927A VAL* 1.3 78.0 - - + +
929A ARG* 1.3 63.7 + - - +
931A MET* 4.3 20.0 + - + +
932A LYS* 5.1 1.9 + - - +
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Residues in contact with ARG 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925A ILE* 3.0 36.1 + - - +
926A ILE* 3.3 11.9 - - - +
928A LYS* 1.3 81.0 + - - +
930A MET* 1.3 62.1 + - - +
931A MET 3.4 0.5 + - - -
932A LYS* 3.7 16.1 + - - +
933A ASP* 4.7 1.7 - - - +
1051A THR* 4.5 14.8 + - - +
1055A VAL* 3.5 38.0 - - + +
1062A ILE* 5.3 10.3 - - - +
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Residues in contact with MET 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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926A ILE* 2.9 32.3 + - + +
927A VAL* 3.1 11.1 + - - +
929A ARG* 1.3 73.1 - - + +
931A MET* 1.3 62.3 + - - +
932A LYS 3.1 2.7 - - - -
933A ASP* 2.8 24.5 - - - +
934A VAL* 3.2 18.7 + - + +
1048A PHE* 3.5 36.3 - - + +
1051A THR* 3.7 25.4 - - + +
1052A PHE* 3.7 18.8 - - + +
1042D ASN* 3.7 39.3 - - + +
1045D ILE* 5.7 1.8 - - + -
1046D ALA* 4.6 2.0 - - + +
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Residues in contact with MET 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867A PHE* 6.4 2.0 - - + -
927A VAL 3.1 14.3 + - - +
928A LYS* 4.4 16.4 - - + +
929A ARG 3.3 0.6 - - - -
930A MET* 1.3 77.4 - - - +
932A LYS* 1.3 68.5 + - + +
934A VAL* 3.3 10.3 + - + +
935A PHE* 3.1 28.9 + - + +
1039D LEU* 5.0 16.2 - - + -
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Residues in contact with LYS 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928A LYS 5.1 1.5 + - - +
929A ARG 3.7 12.2 + - - +
930A MET 3.1 1.0 - - - -
931A MET* 1.3 87.4 - - + +
933A ASP* 1.3 60.0 + - - +
935A PHE* 4.0 4.0 + - - +
936A PHE* 3.4 29.6 + - + -
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Residues in contact with ASP 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929A ARG 4.7 0.8 - - - +
930A MET* 2.8 23.9 - - - +
932A LYS* 1.3 74.3 - - + +
934A VAL* 1.3 63.3 + - - +
935A PHE 3.2 0.9 - - - -
936A PHE* 3.9 10.2 - - + +
937A PHE* 3.0 24.9 + - - +
1047A MET* 4.4 17.1 - - + +
1048A PHE* 4.4 12.0 - - - -
1051A THR* 4.3 19.3 - - - +
919B THR* 5.5 3.8 - - - +
920B LEU* 5.5 9.0 - - + -
923B LYS* 5.4 4.9 + - - -
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Residues in contact with VAL 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930A MET* 3.2 18.1 + - + +
931A MET* 3.3 13.2 + - + +
933A ASP* 1.3 78.0 + - - +
935A PHE* 1.3 63.5 + - - +
937A PHE* 3.3 7.7 + - - +
938A LEU* 3.0 25.7 + - + +
1048A PHE* 3.7 15.7 - - + -
1034D LEU* 5.3 3.6 - - + +
1038D ILE* 3.7 24.7 - - + -
1039D LEU* 4.4 19.3 - - + -
1042D ASN* 3.5 27.4 - - - +
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Residues in contact with PHE 935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931A MET* 3.1 21.4 + - + +
932A LYS* 4.1 6.5 - - - +
934A VAL* 1.3 78.1 - - - +
936A PHE* 1.3 78.2 + + - +
938A LEU* 3.1 38.4 + - + +
939A PHE* 3.1 13.2 + - + +
1034D LEU* 5.1 13.0 - - + -
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Residues in contact with PHE 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932A LYS* 3.4 21.7 + - + -
933A ASP* 3.5 9.2 + - + +
934A VAL 3.4 0.2 - - - -
935A PHE* 1.3 94.0 - + - +
937A PHE* 1.3 63.8 + - - +
939A PHE* 3.7 16.2 + + + +
940A LEU* 3.7 16.1 + - - +
753B LEU* 6.0 6.7 - - + -
914B PHE* 4.6 12.2 - + + -
920B LEU* 4.3 34.9 - - + +
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Residues in contact with PHE 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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933A ASP 3.0 18.4 + - - +
934A VAL* 3.7 6.3 - - - +
936A PHE* 1.3 73.9 - - - +
938A LEU* 1.3 65.9 + - - +
940A LEU* 3.2 22.6 + - + +
941A LEU* 3.1 41.4 + - + +
1040A LEU* 3.6 44.9 - - + -
1043A LEU* 3.6 33.9 - - + -
1044A LEU* 3.5 41.3 - - + -
1048A PHE* 5.7 1.3 - + + -
1038D ILE* 5.4 7.4 - - + -
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Residues in contact with LEU 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934A VAL* 3.0 16.8 + - + +
935A PHE* 3.1 31.3 + - + +
937A PHE* 1.3 77.6 - - - +
939A PHE* 1.3 65.5 + - + +
941A LEU* 3.3 22.3 - - + +
942A ALA* 3.0 28.1 + - + +
1030D CYS 5.2 1.3 - - - +
1033D LEU 5.1 1.6 - - - +
1034D LEU* 3.7 48.2 - - + +
1038D ILE* 5.6 6.3 - - + -
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Residues in contact with PHE 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935A PHE* 3.1 12.5 + - + +
936A PHE* 3.8 15.9 - + + +
937A PHE 3.2 0.4 - - - -
938A LEU* 1.3 82.2 - - + +
940A LEU* 1.3 61.6 + - - +
942A ALA* 3.3 7.8 + - + +
943A VAL* 3.1 36.2 + - + +
807B PHE* 5.7 9.2 - + - -
910B LEU* 6.3 3.6 - - + -
913B ILE* 5.5 9.4 - - + -
914B PHE* 3.6 33.7 - + - -
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Residues in contact with LEU 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936A PHE 3.7 14.8 + - - +
937A PHE* 3.2 41.7 + - + +
939A PHE* 1.3 79.3 - - - +
941A LEU* 1.3 67.9 + - - +
943A VAL* 3.3 12.3 - - + +
944A TRP* 3.0 24.5 + - + +
1040A LEU* 4.1 20.6 - - + -
1043A LEU* 5.1 12.8 - - + -
914B PHE* 3.9 31.9 - - + -
920B LEU* 5.6 4.0 - - + -
924B ILE* 6.0 3.8 - - + -
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Residues in contact with LEU 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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937A PHE* 3.1 34.6 + - + +
938A LEU* 3.3 35.2 - - + +
940A LEU* 1.3 77.4 - - - +
942A ALA* 1.3 62.1 + - + +
944A TRP* 3.4 3.2 + - + +
945A VAL* 2.9 42.4 + - + +
1040A LEU* 4.1 25.6 - - + -
1033D LEU* 6.4 3.6 - - + -
1038D ILE* 5.1 11.9 - - + -
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Residues in contact with ALA 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938A LEU* 3.0 23.7 + - + +
939A PHE* 3.6 7.9 - - + +
941A LEU* 1.3 83.4 - - + +
943A VAL* 1.3 57.3 + - - +
945A VAL* 3.4 4.4 + - - +
946A VAL* 3.0 31.5 + - - +
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Residues in contact with VAL 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939A PHE* 3.1 32.5 + - + +
940A LEU* 3.3 17.5 - - + +
942A ALA* 1.3 76.4 - - - +
944A TRP* 1.3 66.0 + - + +
946A VAL* 3.3 12.9 - - + +
947A SER* 3.0 26.2 + - - -
807B PHE* 5.5 8.3 - - + -
907B CYS* 5.9 5.6 - - + +
910B LEU* 4.7 25.6 - - + -
914B PHE* 6.5 0.2 - - + -
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Residues in contact with TRP 944 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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940A LEU* 3.0 19.0 + - + +
941A LEU* 3.6 4.5 - - + +
943A VAL* 1.3 79.6 - - + +
945A VAL* 1.3 79.6 + - + +
947A SER* 2.6 28.7 + - - -
948A PHE* 3.0 54.9 + + + +
1035A PHE* 3.5 43.1 - + + -
1036A THR* 3.7 28.3 - - + +
1040A LEU* 4.6 20.3 - - + +
908B LEU* 4.5 23.6 - - + -
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Residues in contact with VAL 945 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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941A LEU* 2.9 30.9 + - + +
942A ALA* 4.0 4.9 - - - +
944A TRP* 1.3 92.6 - - + +
946A VAL* 1.3 59.5 + - - +
948A PHE* 3.4 4.0 + - - +
949A GLY* 2.9 26.0 + - - -
974A SER* 4.7 16.5 - - - +
978A ILE* 4.6 24.9 - - + -
1036A THR* 6.2 0.9 - - + -
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Residues in contact with VAL 946 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942A ALA 3.0 22.2 + - - +
943A VAL* 3.3 18.8 - - + +
945A VAL* 1.3 78.9 - - - +
947A SER* 1.3 61.5 + - - +
949A GLY* 3.8 1.7 - - - +
950A VAL* 3.0 33.8 + - + +
974A SER* 6.5 0.2 - - - -
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Residues in contact with SER 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A VAL* 3.0 18.8 + - - -
944A TRP* 2.6 25.8 + - - -
946A VAL* 1.3 79.3 - - - +
948A PHE* 1.3 71.1 + - - +
950A VAL* 3.3 10.9 - - - +
951A ALA* 3.0 27.7 + - - +
903B PHE* 4.5 7.7 - - - -
904B ILE* 5.1 1.2 - - - +
907B CYS* 3.6 33.7 - - - -
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Residues in contact with PHE 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A TRP* 3.0 58.0 + + + +
945A VAL* 4.1 3.4 - - - +
947A SER* 1.3 83.8 + - - +
949A GLY* 1.3 56.3 + - - +
951A ALA* 3.6 5.3 - - + +
952A LYS* 2.9 30.0 + - - +
1028A LEU 5.5 1.6 - - - -
1031A LEU* 4.6 21.1 - - + -
1032A TYR* 4.7 15.3 - - + -
1035A PHE* 4.4 11.7 - + - -
1036A THR* 5.7 1.6 - - + -
904B ILE* 3.7 32.5 - - + -
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Residues in contact with GLY 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945A VAL 2.9 17.3 + - - -
946A VAL* 3.8 2.2 - - - -
947A SER 3.2 0.2 - - - -
948A PHE* 1.3 77.5 - - - +
950A VAL* 1.3 56.4 + - - +
952A LYS* 3.3 9.0 + - - +
953A GLN* 3.0 28.5 + - - +
970A ALA* 5.2 5.0 - - - +
974A SER* 4.6 19.3 - - - -
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Residues in contact with VAL 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A VAL* 3.0 20.0 + - + +
947A SER* 3.3 15.9 - - - +
949A GLY* 1.3 73.7 - - - +
951A ALA* 1.3 59.2 - - - +
953A GLN* 3.5 6.8 + - + +
954A ALA* 2.9 32.0 + - + +
814B ALA* 5.0 11.2 - - + -
817B LEU* 6.1 2.0 - - + -
818B MET* 4.1 32.5 - - + -
903B PHE* 3.6 28.5 - - + -
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Residues in contact with ALA 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A SER 3.0 18.7 + - - +
948A PHE* 3.6 9.6 - - + +
949A GLY 3.2 0.2 - - - -
950A VAL* 1.3 78.1 - - + +
952A LYS* 1.3 57.1 + - - +
954A ALA* 3.2 5.8 + - - +
955A ILE* 3.0 33.7 + - - +
900B SER* 5.1 8.1 - - - +
903B PHE* 5.5 3.8 - - + -
904B ILE* 3.7 34.1 - - + -
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Residues in contact with LYS 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A PHE 2.9 17.2 + - - +
949A GLY* 3.3 7.2 + - - +
951A ALA* 1.3 77.6 - - - +
953A GLN* 1.3 63.0 + - - +
954A ALA 3.4 0.2 + - - -
955A ILE* 3.5 18.0 - - - +
956A LEU* 3.5 25.7 + - + +
970A ALA* 5.9 0.4 - - + -
973A HIS* 4.3 34.6 + - - +
974A SER* 5.2 3.1 - - - +
977A THR* 4.9 9.7 - - - -
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Residues in contact with GLN 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949A GLY 3.0 15.9 + - - +
950A VAL* 4.0 7.6 - - + +
952A LYS* 1.3 79.7 - - - +
954A ALA* 1.3 65.6 + - - +
957A ILE* 3.6 32.3 + - + +
958A HIS 5.0 5.3 + - - -
960A GLU* 5.5 6.7 + - - +
966A LEU* 4.6 20.7 - - + +
967A PHE* 5.9 1.5 - - - +
970A ALA* 3.7 28.9 - - + +
818B MET* 3.5 35.7 - - - +
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Residues in contact with ALA 954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A VAL* 2.9 21.0 + - + +
951A ALA* 3.7 6.3 - - - +
953A GLN* 1.3 82.1 + - - +
955A ILE* 1.3 65.1 + - - +
957A ILE 3.3 7.5 - - - +
817B LEU* 3.7 30.3 - - + +
818B MET* 5.4 4.5 - - + +
893B TYR* 5.9 0.2 - - - -
896B ARG* 2.6 32.6 + - - +
900B SER* 4.8 6.5 - - - -
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Residues in contact with ILE 955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A ALA 3.0 17.6 + - - +
952A LYS* 3.5 13.2 - - - +
954A ALA* 1.3 81.0 - - - +
956A LEU* 1.3 73.1 + - + +
957A ILE 3.4 3.2 + - - +
893B TYR* 2.6 34.8 + - + +
896B ARG* 6.4 0.2 - - - -
897B VAL* 3.7 34.7 - - + +
900B SER* 4.7 13.2 - - - +
901B LEU* 4.9 10.1 - - + -
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Residues in contact with LEU 956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952A LYS* 3.5 26.4 + - + +
953A GLN 4.6 0.7 - - - -
954A ALA 3.5 0.4 - - - -
955A ILE* 1.3 95.4 - - + +
957A ILE* 1.3 59.7 + - - +
1024A LEU* 6.2 4.7 - - + -
893B TYR* 4.5 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