Contacts of the helix formed by residues 834 - 860 (chain B) in PDB entry 1ED8
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 ASN 834 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B LEU* 5.2 0.2 - - - -
770B GLY 2.9 30.9 + - - +
771B PRO 3.7 10.9 + - - +
772B LYS* 3.8 6.4 - - + +
829B GLN* 3.0 32.7 + - - +
832B ALA* 4.3 8.3 - - + +
833B ALA* 1.3 75.1 - - - +
835B PRO* 1.3 67.8 - - - +
836B CYS* 3.5 6.9 + - - +
837B GLY* 2.8 25.5 + - - -
838B GLN* 2.9 22.7 + - - +
902B TYR* 3.9 3.1 + - - -
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Residues in contact with PRO 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B PRO 4.2 3.8 - - - +
773B ALA 4.3 1.1 - - - +
833B ALA 3.2 12.8 - - - +
834B ASN* 1.3 83.7 - - - +
836B CYS* 1.3 57.9 + - - +
838B GLN* 3.2 3.4 + - + +
839B ILE* 2.8 36.9 + - - +
888B GLN* 3.1 41.5 - - + +
890B LEU* 3.9 22.7 - - + -
900B MET* 4.2 10.8 - - + -
902B TYR* 3.5 26.7 - - + +
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Residues in contact with CYS 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768B TRP* 3.6 12.5 - - + +
769B LEU 3.6 24.9 - - - +
770B GLY* 3.8 8.3 - - - +
784B VAL* 3.8 20.0 - - - -
786B CYS* 2.0 57.7 - - + -
834B ASN* 3.4 1.4 + - - +
835B PRO* 1.3 76.0 - - - +
837B GLY* 1.3 67.7 + - - +
839B ILE* 4.7 1.6 - - - -
840B GLY 3.0 18.7 + - - -
888B GLN* 4.6 2.2 + - - -
890B LEU* 4.0 5.4 - - - -
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Residues in contact with GLY 837 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766B VAL* 4.8 3.6 - - - -
768B TRP 3.7 16.4 + - - -
829B GLN* 3.6 28.5 - - - -
834B ASN* 2.8 17.1 + - - -
836B CYS* 1.3 76.4 - - - +
838B GLN* 1.3 61.5 + - - +
840B GLY* 3.5 0.5 + - - -
841B GLU* 3.2 28.9 + - - +
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Residues in contact with GLN 838 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B GLU* 3.7 14.7 - - + +
560B ALA* 4.9 1.6 - - - +
826B ILE* 4.0 24.6 - - + +
829B GLN* 3.4 15.1 - - + +
830B ASP* 3.0 38.3 + - - +
834B ASN 2.9 14.6 + - - +
835B PRO 3.5 2.5 - - - +
837B GLY* 1.3 76.7 - - - +
839B ILE* 1.3 65.4 + - + +
841B GLU* 3.4 4.9 + - - +
842B THR* 3.0 23.2 + - - +
874B SER* 3.3 16.4 + - - -
900B MET* 3.5 13.4 - - - +
902B TYR* 3.0 24.2 + - - -
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Residues in contact with ILE 839 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B GLU 5.5 0.4 - - - +
560B ALA* 4.0 7.0 - - + +
561B ALA* 4.0 31.2 - - + +
564B TYR* 3.8 34.1 - - + -
768B TRP* 3.6 21.8 - - + -
786B CYS* 5.6 0.4 - - - -
835B PRO 2.8 26.3 + - - +
836B CYS* 4.3 2.7 - - - +
838B GLN* 1.3 80.2 - - + +
840B GLY* 1.3 62.5 + - - +
842B THR* 2.9 18.7 + - - -
843B VAL* 3.0 16.1 + - + +
890B LEU* 4.9 5.4 - - + -
898B MET* 4.5 2.2 - - + -
900B MET* 4.0 24.7 - - - -
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Residues in contact with GLY 840 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B ARG* 3.6 9.1 - - - -
768B TRP* 3.6 34.5 - - - -
836B CYS 3.0 14.7 + - - -
837B GLY 4.0 0.7 - - - -
839B ILE* 1.3 75.9 - - - +
841B GLU* 1.3 63.9 + - - +
843B VAL* 3.5 2.3 + - - +
844B ASP* 3.0 27.2 + - - +
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Residues in contact with GLU 841 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B THR* 4.7 9.5 + - - +
764B MET 5.7 0.3 - - - +
765B PRO 4.8 2.3 - - - +
766B VAL* 3.4 19.4 - - + +
767B ARG* 2.7 38.7 + - - +
768B TRP 4.6 0.2 + - - -
823B GLY* 5.2 4.9 - - - -
825B SER* 3.9 30.5 + - - +
826B ILE* 3.6 28.0 - - + +
837B GLY 3.2 18.7 + - - +
838B GLN 4.0 1.1 - - - +
839B ILE 3.1 1.0 - - - -
840B GLY* 1.3 74.5 - - - +
842B THR* 1.3 59.3 + - - +
844B ASP* 3.6 18.4 - - - +
845B LEU* 3.1 24.3 + - - +
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Residues in contact with THR 842 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B MET* 4.1 16.6 - - + -
557B GLU* 4.5 9.0 + - - +
558B ILE* 4.7 2.7 - - - -
561B ALA* 3.7 27.0 - - + +
572B PHE* 4.6 5.2 - - + -
575B ILE* 3.7 20.1 - - + +
826B ILE* 3.7 18.7 - - - +
838B GLN* 3.0 16.0 + - - +
839B ILE 2.9 7.5 + - - -
841B GLU* 1.3 76.1 - - - +
843B VAL* 1.3 61.2 + - - +
844B ASP 3.1 0.2 - - - -
845B LEU* 3.1 4.1 + - - +
846B ASP* 2.9 26.7 + - - +
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Residues in contact with VAL 843 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B ALA* 3.8 30.7 - - + -
572B PHE* 4.2 14.1 - - + -
767B ARG* 4.4 20.4 - - - +
768B TRP* 4.2 17.5 - - + -
839B ILE* 3.0 16.6 + - + +
840B GLY* 3.7 8.1 - - - +
842B THR* 1.3 80.4 - - - +
844B ASP* 1.3 62.4 + - - +
846B ASP* 3.2 17.8 + - + +
847B GLU* 3.3 18.3 + - + +
958B SO4 4.8 1.6 - - - +
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Residues in contact with ASP 844 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B THR* 4.4 7.3 - - - +
767B ARG* 3.0 32.9 + - - +
798B THR* 4.4 6.1 - - - +
799B LEU* 3.5 39.0 + - - +
800B ALA 5.1 1.4 + - - -
823B GLY* 5.5 1.2 - - - -
840B GLY 3.0 18.8 + - - +
841B GLU* 3.6 23.8 - - - +
843B VAL* 1.3 76.3 - - - +
845B LEU* 1.3 61.5 + - - +
847B GLU* 3.3 16.3 + - - +
848B ALA* 3.5 10.0 + - - +
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Residues in contact with LEU 845 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B LEU* 4.2 23.3 - - + -
549B ILE 4.1 3.1 - - - +
550B GLY* 3.4 35.7 - - - +
553B MET* 3.8 22.0 - - + -
575B ILE* 4.9 3.4 - - + -
799B LEU* 3.9 24.2 - - + -
821B VAL 5.0 1.1 - - - +
822B GLU 4.9 0.2 - - - -
823B GLY* 4.0 13.0 - - - +
826B ILE* 4.1 4.3 - - + -
841B GLU 3.1 15.0 + - - +
842B THR* 3.1 8.5 + - - +
844B ASP* 1.3 73.4 + - - +
846B ASP* 1.4 67.6 + - - +
848B ALA* 3.1 3.5 + - + +
849B VAL* 2.8 30.5 + - + +
866B VAL* 5.3 3.4 - - + -
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Residues in contact with ASP 846 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B GLU* 5.1 2.3 - - - +
572B PHE* 3.3 28.7 - - + +
573B LYS 4.0 3.1 + - - -
574B GLY 2.7 27.1 + - - -
575B ILE* 2.9 30.1 + - + +
842B THR 2.9 12.4 + - - +
843B VAL* 3.2 12.8 + - + +
845B LEU* 1.4 77.6 - - - +
847B GLU* 1.3 56.7 + - - +
849B VAL* 3.3 2.7 + - - +
850B GLN* 2.8 54.9 + - - +
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Residues in contact with GLU 847 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B ARG* 2.5 41.1 + - - -
798B THR* 5.2 5.2 + - - +
800B ALA* 4.1 16.3 - - + +
843B VAL* 3.3 13.0 + - + +
844B ASP* 3.3 9.4 + - - +
845B LEU 3.2 0.8 - - - -
846B ASP* 1.3 77.4 - - - +
848B ALA* 1.3 62.8 + - - +
850B GLN* 3.1 12.0 + - - +
851B ARG* 2.7 46.4 + - - +
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Residues in contact with ALA 848 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B LEU* 4.1 12.3 - - + +
799B LEU* 3.9 23.8 - - + -
800B ALA* 4.0 14.5 - - - +
803B THR* 3.8 24.5 - - - +
844B ASP 3.5 4.9 + - - +
845B LEU* 3.1 8.9 + - - +
847B GLU* 1.3 79.3 - - - +
849B VAL* 1.3 62.4 + - - +
851B ARG* 3.2 6.1 + - - +
852B ALA* 3.0 22.0 + - - +
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Residues in contact with VAL 849 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B LEU* 3.8 24.0 - - + -
574B GLY* 3.3 33.0 - - - +
575B ILE* 3.7 6.1 - - + +
578B LEU* 4.4 0.9 - - + -
845B LEU* 2.8 27.5 + - + +
846B ASP 3.6 4.5 - - - +
848B ALA* 1.3 76.7 - - - +
850B GLN* 1.3 58.0 + - - +
852B ALA* 3.2 4.8 + - + +
853B LEU* 2.9 35.2 + - + +
864B VAL* 5.6 0.9 - - + -
866B VAL* 4.0 35.7 - - + -
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Residues in contact with GLN 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LYS* 3.7 34.1 + - + +
574B GLY* 3.5 18.2 - - - +
846B ASP* 2.8 43.7 + - - +
847B GLU* 3.1 20.9 + - - +
849B VAL* 1.3 78.6 - - - +
851B ARG* 1.3 83.5 + - - +
853B LEU* 3.4 4.7 + - - +
854B GLU* 3.1 23.7 + - - +
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Residues in contact with ARG 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800B ALA* 4.0 21.6 - - + +
803B THR* 4.5 9.0 - - + -
804B ASP* 3.5 36.0 + - - +
807B ILE* 4.3 3.9 - - + +
847B GLU* 2.7 51.9 + - - +
848B ALA* 3.2 6.9 + - - +
850B GLN* 1.3 102.1 + - - +
852B ALA* 1.3 64.6 + - - +
854B GLU* 3.4 22.2 + - - +
855B PHE* 3.2 23.7 + - - +
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Residues in contact with ALA 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ILE* 4.0 22.6 - - + +
548B LEU* 4.0 24.5 - - + -
803B THR* 4.8 2.6 - - + +
807B ILE* 4.1 13.0 - - + +
848B ALA 3.0 12.5 + - - +
849B VAL 3.6 7.6 - - - +
851B ARG* 1.3 80.2 - - - +
853B LEU* 1.3 56.3 + - - +
855B PHE* 3.4 2.8 + - - +
856B ALA* 3.0 29.0 + - - +
864B VAL* 4.1 9.4 - - + +
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Residues in contact with LEU 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B VAL* 4.1 19.1 - - + -
573B LYS 4.2 6.1 - - - +
574B GLY* 3.8 22.9 - - - +
577B ALA* 4.0 18.4 - - + +
578B LEU* 4.5 14.6 - - + -
849B VAL* 2.9 24.8 + - + +
850B GLN* 3.8 4.9 - - - +
851B ARG 3.2 0.2 - - - -
852B ALA* 1.3 75.6 - - - +
854B GLU* 1.3 57.3 + - - +
856B ALA* 3.6 1.6 - - - +
857B LYS* 2.7 40.9 + - + +
864B VAL* 4.7 8.7 - - + -
922B TYR* 4.0 38.8 - - + -
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Residues in contact with GLU 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804B ASP* 5.5 1.4 - - - +
850B GLN 3.1 16.4 + - - +
851B ARG* 3.5 27.7 + - - +
853B LEU* 1.3 74.8 - - - +
855B PHE* 1.3 64.4 + - - +
857B LYS* 3.2 18.8 + - - +
858B LYS* 3.1 51.5 + - + +
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Residues in contact with PHE 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LYS* 5.9 0.9 - - - -
544B ASN* 4.2 2.0 - - - -
546B ILE* 4.2 15.0 - - + -
807B ILE* 3.6 30.3 - - + -
811B SER* 4.5 12.6 - - - -
817B PHE* 4.2 29.2 - + - -
851B ARG 3.2 9.4 + - - +
852B ALA 3.6 7.0 - - - +
854B GLU* 1.3 82.2 - - - +
856B ALA* 1.3 57.3 + - - +
858B LYS* 3.1 22.8 + - + +
859B GLU* 2.7 59.9 + - + +
862B THR* 3.4 22.9 - - + -
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Residues in contact with ALA 856 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B ALA 3.0 18.3 + - - +
853B LEU* 3.2 4.5 + - - +
855B PHE* 1.3 83.5 - - - +
857B LYS* 1.3 61.8 + - - +
859B GLU 4.6 0.2 - - - +
860B GLY* 3.1 22.9 + - - -
862B THR* 3.8 21.3 + - + +
864B VAL* 3.5 24.7 - - + -
922B TYR* 4.0 20.9 + - + -
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Residues in contact with LYS 857 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B THR 5.5 0.3 - - - +
502B PRO* 4.8 23.5 - - + +
504B MET 4.5 3.6 - - - +
506B VAL* 3.6 37.8 - - + +
508B GLU* 3.7 18.3 + - - +
853B LEU* 2.7 19.6 + - + +
854B GLU* 3.5 22.2 - - - +
855B PHE 3.2 0.2 - - - -
856B ALA* 1.3 75.2 - - - +
858B LYS* 1.3 66.3 - - + +
860B GLY* 4.0 5.4 + - - -
922B TYR* 3.8 16.9 + - + +
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Residues in contact with LYS 858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B GLU* 3.1 41.8 + - + +
855B PHE* 4.3 24.0 - - + +
857B LYS* 1.3 82.3 - - + +
859B GLU* 1.3 63.5 + - - +
860B GLY* 3.4 1.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 859 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B LYS* 3.7 22.1 + - - +
544B ASN* 3.6 9.0 + - - +
855B PHE* 2.7 50.9 + - + +
856B ALA 4.5 0.4 - - - +
858B LYS* 1.3 73.0 - - - +
860B GLY* 1.3 55.1 + - - +
861B ASN* 2.3 57.3 + - - +
862B THR* 2.7 22.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 860 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B MET* 4.4 18.6 - - - +
856B ALA 3.1 17.2 + - - -
857B LYS 4.5 4.0 - - - -
858B LYS 3.4 4.0 - - - -
859B GLU* 1.3 73.7 + - - +
861B ASN* 1.3 68.5 + - - +
862B THR 3.5 2.2 + - - -
924B PRO* 4.7 1.3 - - - +
----------------------------------------------------------
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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