Contacts of the helix formed by residues 862 - 897 (chain B) in PDB entry 1ZUC
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 GLY 862 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B GLN 3.9 1.0 + - - -
861B LYS* 1.3 74.8 - - - +
863B VAL* 1.3 60.9 + - - -
864B VAL* 3.3 4.9 + - - -
865B SER* 3.6 3.1 + - - -
866B SER* 2.9 34.0 + - - -
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Residues in contact with VAL 863 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B GLY* 1.3 72.5 - - - -
864B VAL* 1.3 65.9 + - + +
866B SER* 3.6 6.6 + - - -
867B SER* 2.9 34.2 + - - -
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Residues in contact with VAL 864 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862B GLY* 5.3 2.0 - - - -
863B VAL* 1.3 84.2 - - + +
865B SER* 1.3 64.3 + - - +
867B SER* 3.7 4.1 - - - -
868B GLN* 3.0 56.2 + - + +
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Residues in contact with SER 865 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860B GLN* 3.0 27.6 + - - -
861B LYS 4.0 14.4 - - - -
862B GLY 3.6 6.0 + - - -
863B VAL 3.5 0.2 - - - -
864B VAL* 1.3 82.3 - - - +
866B SER* 1.3 58.8 + - - +
868B GLN* 3.4 9.0 + - - +
869B ARG* 2.9 30.3 + - - +
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Residues in contact with SER 866 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856B ILE* 3.8 16.3 - - - +
857B GLY* 5.2 3.8 - - - -
860B GLN* 3.4 27.4 - - - -
862B GLY 2.9 22.1 + - - -
863B VAL* 3.6 8.3 + - - -
865B SER* 1.3 78.6 - - - +
867B SER* 1.3 58.8 + - - +
869B ARG* 3.6 1.9 - - - +
870B PHE* 3.1 28.4 + - - +
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Residues in contact with SER 867 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863B VAL 2.9 21.4 + - - -
864B VAL* 3.7 5.8 - - - -
866B SER* 1.3 76.1 + - - +
868B GLN* 1.3 64.3 + - - +
870B PHE* 3.5 8.9 + - - +
871B TYR* 3.2 20.1 + - - +
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Residues in contact with GLN 868 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864B VAL* 3.0 42.1 + - + +
865B SER* 3.6 7.4 - - - +
867B SER* 1.3 73.4 - - - +
869B ARG* 1.3 60.1 + - - +
871B TYR* 3.2 9.3 + - - +
872B GLN* 2.9 40.1 + - + +
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Residues in contact with ARG 869 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B LEU* 2.7 47.3 + - - +
812B GLN 3.2 12.3 + - - -
813B VAL* 3.6 5.1 - - - +
817B GLU* 2.7 36.1 + - - -
856B ILE* 3.6 29.4 - - + -
860B GLN* 3.8 26.2 + - + +
865B SER 2.9 21.1 + - - +
866B SER 3.6 5.4 - - - +
867B SER 3.3 0.2 - - - -
868B GLN* 1.3 69.9 - - - +
870B PHE* 1.3 60.6 + - - +
872B GLN* 3.2 16.4 + - - +
873B LEU* 2.9 49.1 + - + +
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Residues in contact with PHE 870 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849B ILE* 3.9 23.6 - - + -
852B LEU* 4.5 8.1 - - + -
853B ILE* 3.6 35.2 - - + -
856B ILE* 3.5 17.7 - - + +
866B SER 3.1 17.3 + - - +
867B SER* 3.7 8.1 - - - +
869B ARG* 1.3 75.6 - - - +
871B TYR* 1.3 58.2 + - - +
873B LEU* 4.9 0.7 - - - -
874B THR* 2.6 66.5 + - + +
930B PHE* 5.1 6.5 - + + -
931B HIS* 4.8 9.9 - + - -
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Residues in contact with TYR 871 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867B SER 3.2 13.5 + - - +
868B GLN* 3.2 13.0 + - - +
870B PHE* 1.3 78.3 - - - +
872B GLN* 1.3 66.9 + - + +
874B THR* 3.1 5.0 + - - -
875B LYS* 2.8 69.0 + - + +
931B HIS* 3.5 36.8 + + + +
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Residues in contact with GLN 872 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B LEU* 3.7 36.1 - - + +
868B GLN* 2.9 23.0 + - + +
869B ARG* 3.2 28.4 + - - +
871B TYR* 1.3 86.8 - - + +
873B LEU* 1.3 60.8 + - + +
875B LYS* 3.7 4.4 - - - +
876B LEU* 2.9 28.1 + - - +
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Residues in contact with LEU 873 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B LEU* 4.1 22.4 - - + -
813B VAL* 4.2 15.3 - - + -
817B GLU* 3.5 41.5 - - + +
821B MET* 3.4 28.4 - - + +
852B LEU* 4.3 11.4 - - + -
856B ILE* 3.9 16.2 - - + -
869B ARG* 2.9 36.2 + - - +
870B PHE* 4.3 2.5 - - - +
872B GLN* 1.3 78.8 - - - +
874B THR* 1.3 59.9 + - - +
876B LEU* 3.4 6.8 - - + +
877B LEU* 3.2 23.6 + - - +
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Residues in contact with THR 874 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B LEU* 4.0 16.8 - - + -
870B PHE* 2.6 52.7 + - + +
871B TYR 3.1 0.7 + - - -
873B LEU* 1.3 74.5 - - - +
875B LYS* 1.3 58.6 + - - +
877B LEU* 3.1 7.7 + - + +
878B ASP* 2.9 30.3 + - - -
930B PHE* 3.6 35.7 - - + -
931B HIS* 2.7 28.8 + - - -
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Residues in contact with LYS 875 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871B TYR* 2.8 57.2 + - + +
872B GLN* 3.7 6.1 - - - +
874B THR* 1.3 72.3 + - - +
876B LEU* 1.3 56.0 + - - +
878B ASP* 3.2 12.4 + - + +
879B ASN* 2.9 59.2 + - - +
931B HIS* 3.8 19.8 + - + +
932B LYS 4.2 17.0 + - - -
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Residues in contact with LEU 876 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B PHE* 4.0 24.7 - - + -
804B ILE* 5.6 3.1 - - + -
807B GLU* 4.4 20.4 - - + +
808B PHE* 4.1 21.1 - - + -
811B LEU* 3.8 25.6 - - + -
813B VAL* 4.9 2.0 - - + -
821B MET* 4.2 13.2 - - + -
872B GLN 2.9 15.0 + - - +
873B LEU* 3.4 9.6 - - + +
874B THR 3.3 0.2 - - - -
875B LYS* 1.3 73.0 - - - +
877B LEU* 1.3 64.3 + - - +
879B ASN* 3.1 12.7 + - - +
880B LEU* 3.0 35.2 + - + +
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Residues in contact with LEU 877 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761B PHE* 4.0 17.9 - - + -
821B MET* 3.9 36.1 - - + +
824B LEU* 4.2 19.7 - - + -
825B LEU* 3.8 29.1 - - + +
828B ASN* 4.2 16.0 + - - +
852B LEU* 5.2 1.6 - - + -
873B LEU 3.2 12.3 + - - +
874B THR* 3.1 9.9 + - - +
876B LEU* 1.3 77.4 - - + +
878B ASP* 1.3 62.4 + - - +
880B LEU* 3.2 22.8 + - + +
881B HIS* 3.8 3.6 + - - -
930B PHE* 3.7 28.3 - - + -
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Residues in contact with ASP 878 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B ASN* 5.4 0.4 + - - +
874B THR 2.9 16.8 + - - -
875B LYS* 3.4 19.1 + - + +
877B LEU* 1.3 73.2 - - - +
879B ASN* 1.3 62.9 + - - +
881B HIS* 3.3 24.9 + - - +
882B ASP* 3.6 5.4 - - - +
928B LEU 4.3 1.2 - - - +
929B LEU* 3.3 28.8 - - + +
930B PHE* 2.8 29.9 + - - -
931B HIS* 3.0 40.4 + - - +
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Residues in contact with ASN 879 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875B LYS* 2.9 46.8 + - - +
876B LEU* 3.1 12.6 + - - +
878B ASP* 1.3 74.3 - - - +
880B LEU* 1.3 64.7 + - - +
881B HIS 3.3 0.4 - - - -
882B ASP* 3.4 20.5 + - - +
883B LEU* 3.5 10.3 + - - +
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Residues in contact with LEU 880 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757B SER* 4.9 7.6 - - - +
760B VAL* 4.9 4.9 - - + -
761B PHE* 3.8 17.3 - - + -
804B ILE* 3.8 33.9 - - + -
825B LEU* 3.6 40.4 - - + -
876B LEU* 3.0 26.8 + - + +
877B LEU* 3.2 14.1 + - + +
879B ASN* 1.3 75.5 - - - +
881B HIS* 1.4 56.5 + - - +
882B ASP 3.2 0.2 + - - -
883B LEU* 4.4 10.8 - - + -
884B VAL* 2.8 41.6 + - + +
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Residues in contact with HIS 881 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B LEU* 6.5 0.4 - - + -
828B ASN* 3.4 35.8 + - - +
829B THR* 3.7 9.8 + - - -
877B LEU 3.8 2.4 + - - -
878B ASP* 3.3 18.4 + - - +
880B LEU* 1.4 74.7 - - - +
882B ASP* 1.3 61.5 + - - +
884B VAL* 3.6 5.4 + - - +
885B LYS* 3.0 27.6 + - - +
927B PRO* 3.5 27.1 - - + +
928B LEU 3.0 29.1 + - - -
929B LEU* 3.9 12.5 - - + +
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Residues in contact with ASP 882 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878B ASP 3.6 11.6 - - - +
879B ASN* 3.5 16.5 - - - +
880B LEU 3.1 0.6 - - - -
881B HIS* 1.3 78.3 - - - +
883B LEU* 1.3 64.6 + - - +
885B LYS* 3.3 21.2 + - - +
886B GLN* 3.5 14.0 + - - +
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Residues in contact with LEU 883 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
760B VAL* 4.3 3.1 - - + -
800B THR* 3.5 41.3 - - + +
803B GLN* 3.7 21.3 - - + +
804B ILE* 3.9 35.2 - - + -
879B ASN 3.5 8.7 + - - +
880B LEU* 3.2 14.9 + - + +
882B ASP* 1.3 77.6 - - - +
884B VAL* 1.3 67.0 + - + +
886B GLN* 3.2 19.6 + - - +
887B LEU* 3.5 27.5 + - + +
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Residues in contact with VAL 884 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756B MET* 4.0 14.1 - - + -
757B SER* 3.8 33.9 - - - +
760B VAL* 4.1 16.2 - - + -
880B LEU* 2.8 28.1 + - + +
881B HIS* 3.9 5.4 - - - +
883B LEU* 1.3 73.2 - - + +
885B LYS* 1.3 59.6 + - - +
887B LEU* 3.2 7.8 + - + +
888B HIS* 2.8 57.2 + - + +
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Residues in contact with LYS 885 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A ALA* 2.8 43.0 + - - +
923A GLY* 5.0 1.2 - - - -
924A MET* 4.7 10.8 - - - -
881B HIS 3.0 15.0 + - - +
882B ASP* 3.5 14.1 - - - +
883B LEU 3.3 0.4 - - - -
884B VAL* 1.3 76.8 - - - +
886B GLN* 1.3 61.4 + - - +
888B HIS* 3.4 9.0 + - - +
889B LEU* 3.0 24.0 + - + +
921B LEU* 3.8 21.0 + - + +
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Residues in contact with GLN 886 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A MET* 6.6 0.2 - - + -
797B LEU* 4.2 8.6 - - + +
800B THR* 3.3 37.6 + - + +
882B ASP 3.5 12.9 + - - +
883B LEU* 3.2 9.6 + - - +
885B LYS* 1.3 76.4 - - + +
887B LEU* 1.3 63.2 + - + +
889B LEU* 3.5 5.2 + - - +
890B TYR* 3.2 24.3 + - - +
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Residues in contact with LEU 887 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B T98 3.8 11.6 - - + +
756B MET* 3.9 31.6 - - + -
760B VAL* 3.8 35.2 - - + -
797B LEU* 3.8 24.7 - - + -
800B THR* 4.6 9.9 - - + -
801B MET* 3.8 25.8 - - + -
883B LEU* 3.7 21.5 - - + +
884B VAL* 3.2 7.5 + - - +
886B GLN* 1.3 73.4 - - - +
888B HIS* 1.3 61.2 + - - +
890B TYR* 3.3 3.4 + - - +
891B CYS* 2.9 31.9 + - - +
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Residues in contact with HIS 888 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B TYR 4.5 11.4 + - - -
755B TRP* 5.0 4.5 + + - -
756B MET* 3.5 35.6 + - + +
884B VAL* 2.8 37.0 + - + +
885B LYS* 3.6 8.0 - - - +
887B LEU* 1.3 74.2 - - - +
889B LEU* 1.3 56.1 + - - +
891B CYS* 4.4 3.1 - - - -
892B LEU* 2.8 31.0 + - - +
917B LEU* 3.2 36.5 - - + +
920B ILE* 3.7 33.9 - - + +
921B LEU* 3.9 13.6 - - + +
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Residues in contact with LEU 889 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A PRO* 3.7 37.9 - - + +
919A LYS* 3.9 8.5 - - + +
922A ALA* 4.3 5.2 - - + -
924A MET* 4.2 29.4 - - + -
885B LYS* 3.0 16.7 + - + +
886B GLN* 3.9 5.6 - - - +
888B HIS* 1.3 75.6 - - - +
890B TYR* 1.3 58.2 + - - +
892B LEU* 3.4 1.0 + - - -
893B ASN* 2.9 52.2 + - - +
921B LEU* 3.9 17.0 - - + +
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Residues in contact with TYR 890 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B T98 3.5 20.9 - - - -
715B LEU* 3.6 30.9 - - + +
793B SER* 4.7 5.4 + - - -
794B PHE* 3.6 30.9 - - + +
797B LEU* 3.8 31.2 - - + -
886B GLN 3.2 17.9 + - - +
887B LEU 3.7 3.8 - - - +
889B LEU* 1.3 76.6 - - - +
891B CYS* 1.3 54.0 + - - +
893B ASN* 3.5 7.0 + - - +
894B THR* 2.7 54.4 + - - -
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Residues in contact with CYS 891 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B T98 3.7 28.9 - - + -
755B TRP* 4.1 13.5 - - - -
756B MET* 4.0 11.0 - - + -
887B LEU 2.9 19.1 + - - +
888B HIS 3.7 3.6 - - - +
890B TYR* 1.3 74.4 - - - +
892B LEU* 1.3 61.2 + - - +
894B THR* 3.2 2.4 + - - -
895B PHE* 2.8 29.8 + - - +
905B PHE* 4.2 4.8 - - - -
909B MET* 5.1 0.2 - - - -
913B ILE* 3.6 30.5 - - - -
917B LEU* 4.0 11.0 - - + -
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Residues in contact with LEU 892 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU* 4.0 24.5 - - + -
896A ILE* 4.4 17.9 - - + -
918A PRO* 4.1 9.4 - - + -
888B HIS 2.8 18.8 + - - +
889B LEU 3.9 3.1 - - - +
891B CYS* 1.3 78.1 - - - +
893B ASN* 1.3 62.1 + - - +
895B PHE* 3.2 4.5 + - + +
896B ILE* 3.0 40.8 + - + +
913B ILE* 4.2 19.1 - - + -
917B LEU* 4.0 9.8 - - + +
918B PRO* 4.2 19.3 - - + -
921B LEU* 3.7 23.6 - - + -
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Residues in contact with ASN 893 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A ALA 4.4 7.6 - - - +
915A ALA 5.7 0.3 - - - +
918A PRO* 3.5 24.6 - - - +
919A LYS* 5.2 2.5 + - - +
889B LEU* 2.9 42.6 + - - +
890B TYR* 3.9 6.7 - - - +
892B LEU* 1.3 75.3 - - - +
894B THR* 1.3 58.8 + - - +
896B ILE* 3.4 5.7 + - - +
897B GLN* 2.9 47.9 + - - +
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Residues in contact with THR 894 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B T98 3.5 24.5 - - - -
715B LEU* 4.4 7.0 - - + -
890B TYR* 2.7 42.3 + - - -
893B ASN* 1.3 78.2 - - - +
895B PHE* 1.3 50.5 + - - +
897B GLN 3.2 2.1 + - - -
898B SER* 2.8 36.7 + - - -
901B LEU* 4.2 18.1 - - + +
903B VAL* 4.0 26.2 - - + -
905B PHE* 3.9 7.0 - - + -
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Residues in contact with PHE 895 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896A ILE* 4.0 41.5 - - + -
891B CYS 2.8 20.1 + - - +
892B LEU* 3.5 5.6 - - + +
894B THR* 1.3 73.2 - - - +
896B ILE* 1.3 63.9 + - - +
898B SER* 3.1 19.3 + - - -
905B PHE* 3.5 36.5 - + + -
910B SER* 3.5 47.6 - - - -
913B ILE* 3.8 26.2 - - + -
914B ALA* 4.8 3.4 - - + -
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Residues in contact with ILE 896 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A LEU* 4.0 13.7 - - + -
895A PHE* 4.1 13.8 - - + -
896A ILE* 3.5 24.7 - - + -
914A ALA* 3.5 35.2 - - + +
918A PRO* 3.4 34.8 - - + -
892B LEU* 3.0 25.6 + - + +
893B ASN* 3.5 9.6 - - - +
895B PHE* 1.3 77.8 - - - +
897B GLN* 1.3 66.6 + - + +
898B SER* 3.4 0.9 + - - -
899B ARG 5.2 0.3 + - - -
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Residues in contact with GLN 897 (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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914A ALA* 4.7 13.1 - - + +
893B ASN* 2.9 34.8 + - - +
894B THR 3.3 2.2 - - - -
896B ILE* 1.3 87.0 - - + +
898B SER* 1.3 63.2 + - - +
899B ARG 3.2 3.4 + - - -
900B ALA* 3.3 12.0 + - + +
901B LEU* 3.0 46.4 + - + +
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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) + - + + + + + -
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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