Contacts of the helix formed by residues 840 - 863 (chain A) in PDB entry 4K6J
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 ASP 840 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A GLU* 1.3 76.7 - - - +
841A GLU* 1.3 68.7 + - - +
842A GLU* 3.6 11.6 + - - +
843A LYS* 3.0 38.8 + - - +
844A LEU* 2.8 21.1 + - - +
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Residues in contact with GLU 841 (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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840A ASP* 1.3 73.9 - - - +
842A GLU* 1.3 69.6 + - + +
844A LEU* 3.6 6.8 - - - +
845A VAL* 2.9 26.4 + - + +
898A TYR* 5.7 2.7 + - - -
918A VAL* 3.4 44.0 - - + +
921A HIS* 3.0 29.9 + - + +
922A VAL* 3.9 17.3 - - + -
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Residues in contact with GLU 842 (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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840A ASP* 3.3 9.9 + - - +
841A GLU* 1.3 83.3 - - + +
843A LYS* 1.3 59.3 + - + +
845A VAL* 3.6 4.4 + - - +
846A ALA* 3.1 29.1 + - - +
921A HIS* 5.9 3.6 - - + -
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Residues in contact with LYS 843 (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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839A GLU* 3.4 23.3 - - + +
840A ASP* 3.0 28.0 + - - +
842A GLU* 1.3 80.2 - - + +
844A LEU* 1.3 58.1 + - - +
846A ALA* 3.8 5.7 - - - +
847A SER* 2.8 32.4 + - - -
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Residues in contact with LEU 844 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LEU* 3.9 11.4 - - + +
839A GLU* 3.4 33.8 - - + +
840A ASP 2.8 18.6 + - - +
841A GLU* 3.6 4.3 - - - +
843A LYS* 1.3 75.1 - - - +
845A VAL* 1.3 60.2 + - - +
847A SER* 3.2 3.3 + - - -
848A LEU* 3.0 38.8 + - + +
894A LEU* 3.7 34.1 - - + -
898A TYR* 3.9 22.0 - - + +
922A VAL* 3.6 29.4 - - + -
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Residues in contact with VAL 845 (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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841A GLU 2.9 19.3 + - - +
842A GLU* 4.0 3.6 - - - +
844A LEU* 1.3 75.5 - - - +
846A ALA* 1.3 57.5 + - - +
848A LEU* 3.8 7.2 - - - +
849A TRP* 2.9 34.6 + - + +
921A HIS* 3.5 43.7 - - + +
922A VAL* 3.8 28.7 - - + -
925A ALA* 4.4 12.7 - - + +
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Residues in contact with ALA 846 (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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751A GLU* 4.4 18.8 - - - +
831A CYS* 4.7 0.5 - - - -
842A GLU 3.1 19.3 + - - +
843A LYS* 3.8 7.6 - - - +
844A LEU 3.2 0.2 - - - -
845A VAL* 1.3 75.4 - - - +
847A SER* 1.3 58.6 + - - +
849A TRP* 4.1 6.5 - - - +
850A GLY* 2.8 27.5 + - - -
853A ARG* 4.3 3.3 + - - -
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Residues in contact with SER 847 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A CYS* 3.3 36.3 - - - +
834A HIS* 3.3 17.3 + - - +
835A LEU* 3.9 7.0 - - - -
839A GLU* 3.3 20.9 + - - -
843A LYS 2.8 21.9 + - - -
844A LEU 3.2 5.4 + - - -
846A ALA* 1.3 76.6 - - - +
848A LEU* 1.3 61.9 + - - +
850A GLY 3.2 1.4 + - - -
851A ALA* 3.0 20.1 + - - +
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Residues in contact with LEU 848 (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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835A LEU* 3.7 23.3 - - + -
844A LEU* 3.0 37.8 + - + +
845A VAL* 3.8 4.3 - - - +
847A SER* 1.3 76.1 - - - +
849A TRP* 1.3 57.7 + - - +
851A ALA* 3.1 5.7 + - - +
852A GLU* 2.9 28.9 + - - +
891A CYS* 3.9 27.8 - - - -
894A LEU* 4.6 4.3 - - + -
922A VAL* 4.6 1.3 - - + +
925A ALA* 4.0 19.3 - - + +
926A VAL* 3.5 34.5 - - + +
929A CYS* 3.8 19.2 - - + -
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Residues in contact with TRP 849 (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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790A THR* 5.0 2.8 + - - -
792A GLY* 4.7 5.3 - - - -
793A HIS* 3.2 56.7 + + - -
796A MET* 4.0 17.5 - - + -
845A VAL* 2.9 25.6 + - + +
846A ALA* 4.1 4.7 - - - +
848A LEU* 1.3 77.3 - - - +
850A GLY* 1.3 62.1 + - - +
852A GLU* 3.3 40.6 - - + -
853A ARG* 3.0 71.5 + - + +
856A ARG* 4.2 6.1 - - - -
925A ALA* 5.6 3.3 - - + +
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Residues in contact with GLY 850 (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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751A GLU* 4.3 2.0 - - - -
827A LYS* 4.6 1.2 - - - +
831A CYS* 3.6 17.7 - - - -
846A ALA 2.8 17.0 + - - -
847A SER 3.6 1.8 - - - -
848A LEU 3.2 0.2 - - - -
849A TRP* 1.3 78.8 - - - +
851A ALA* 1.3 59.2 + - - +
853A ARG* 3.2 22.5 + - - +
854A CYS* 3.4 27.9 + - - -
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Residues in contact with ALA 851 (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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828A VAL* 4.2 10.0 - - + +
831A CYS* 3.8 13.8 - - + -
832A VAL* 4.4 17.3 - - + -
835A LEU* 6.0 1.8 - - + -
847A SER 3.0 12.5 + - - +
848A LEU* 3.5 8.5 - - - +
850A GLY* 1.3 74.1 - - - +
852A GLU* 1.3 54.6 + - - +
854A CYS* 3.2 3.6 + - - +
855A LEU* 2.7 48.3 + - + +
929A CYS* 4.1 15.0 - - - -
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Residues in contact with GLU 852 (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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848A LEU 2.9 15.0 + - - +
849A TRP* 3.3 29.0 - - + +
851A ALA* 1.3 72.9 - - - +
853A ARG* 1.3 67.0 + - - +
855A LEU* 2.9 9.5 + - - +
856A ARG* 2.8 60.0 + - - +
925A ALA* 4.7 3.6 - - - +
928A ASP* 3.4 46.6 - - - +
929A CYS* 4.2 9.3 + - - -
931A ARG* 5.6 1.2 + - - -
932A ALA* 3.8 7.0 - - + -
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Residues in contact with ARG 853 (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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748A LEU* 2.5 58.8 + - + +
749A GLU 4.3 0.8 - - - -
750A LEU 3.4 18.6 + - - -
751A GLU* 3.3 20.6 + - - -
792A GLY* 3.4 30.3 - - - +
796A MET* 3.7 30.7 - - + +
827A LYS* 4.6 1.6 - - - +
846A ALA* 4.3 1.8 + - - +
849A TRP* 3.0 49.2 + - + +
850A GLY* 3.2 30.7 - - - +
852A GLU* 1.3 79.4 - - - +
854A CYS* 1.3 61.3 + - - +
856A ARG* 3.7 0.9 + - - +
857A VAL* 3.6 15.9 + - - +
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Residues in contact with CYS 854 (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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748A LEU* 4.0 24.2 - - - -
749A GLU* 5.4 0.2 - - - -
824A ILE* 3.5 19.5 - - + +
827A LYS* 3.4 37.9 - - - -
828A VAL* 3.5 21.3 - - + -
850A GLY 3.4 10.1 + - - +
851A ALA 3.2 4.0 + - - +
852A GLU 3.1 0.8 - - - -
853A ARG* 1.3 77.9 - - - +
855A LEU* 1.3 66.1 + - - +
856A ARG 3.2 0.2 - - - -
857A VAL* 3.1 5.4 + - - +
858A LEU* 3.0 26.2 + - - +
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Residues in contact with LEU 855 (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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828A VAL* 4.2 15.3 - - + -
851A ALA* 2.7 42.5 + - + +
852A GLU* 3.5 4.3 - - - +
854A CYS* 1.3 72.9 - - - +
856A ARG* 1.3 57.4 + - - +
858A LEU* 3.2 3.8 + - + -
859A GLU* 2.8 25.9 + - - +
880A LEU* 4.1 24.5 - - + -
884A SER* 4.2 10.8 - - - +
929A CYS* 4.4 1.8 - - - +
932A ALA* 3.9 15.0 - - + -
933A ILE* 3.5 37.0 - - + +
936A VAL* 3.2 30.3 - - + +
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Residues in contact with ARG 856 (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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782A LYS* 5.7 2.6 - - - +
793A HIS* 5.4 2.2 + - - -
796A MET* 3.3 42.2 - - - +
797A GLU* 4.5 4.9 + - - -
800A LEU* 3.6 20.2 - - + +
849A TRP* 4.2 6.3 - - - -
852A GLU* 2.8 49.8 + - - +
853A ARG 3.9 4.7 - - - +
855A LEU* 1.3 76.5 - - - +
857A VAL* 1.3 58.7 + - - +
859A GLU* 3.5 10.0 + - + +
860A SER* 3.1 25.6 + - - -
932A ALA* 4.3 14.4 - - + +
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Residues in contact with VAL 857 (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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748A LEU* 4.6 4.9 - - + -
796A MET* 4.3 15.0 - - + +
799A LEU* 3.8 40.4 - - + +
800A LEU* 4.4 4.5 - - + -
815A LEU* 4.9 5.6 - - + -
821A LEU* 5.5 0.2 - - + -
824A ILE* 3.7 27.6 - - + -
853A ARG 3.6 13.6 + - - +
854A CYS* 3.1 9.4 + - - +
856A ARG* 1.3 77.1 - - - +
858A LEU* 1.3 58.7 + - + +
860A SER* 3.3 6.4 + - - -
861A VAL* 3.0 40.0 + - + +
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Residues in contact with LEU 858 (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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821A LEU* 4.2 16.6 - - + +
824A ILE* 3.7 29.2 - - + -
825A VAL* 4.1 9.6 - - + -
828A VAL* 4.1 11.0 - - + -
854A CYS 3.0 18.2 + - - +
855A LEU* 3.2 10.5 + - + +
857A VAL* 1.3 76.9 - - - +
859A GLU* 1.3 60.7 + - - +
861A VAL* 3.4 14.1 - - - +
862A THR* 2.9 21.0 + - - +
872A LEU* 4.1 26.6 - - + +
880A LEU* 3.6 35.2 - - + -
936A VAL* 4.3 9.4 - - + +
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Residues in contact with GLU 859 (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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800A LEU* 5.8 0.2 - - - +
855A LEU 2.8 17.3 + - - +
856A ARG* 3.6 11.1 - - + +
857A VAL 3.2 0.2 - - - -
858A LEU* 1.3 76.2 - - - +
860A SER* 1.3 71.2 + - - +
862A THR* 2.8 20.1 + - - -
863A VAL* 3.4 15.8 + - - +
932A ALA* 5.3 1.3 - - - +
935A GLY* 4.1 21.3 - - - +
936A VAL* 3.9 12.1 - - + +
939A ASN* 2.9 34.0 + - - +
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Residues in contact with SER 860 (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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800A LEU* 3.7 19.6 + - - +
803A THR* 2.7 36.9 + - - +
804A SER* 5.0 0.9 - - - -
812A LYS* 4.1 8.3 - - - +
856A ARG 3.1 12.2 + - - -
857A VAL* 3.5 8.7 - - - -
859A GLU* 1.3 86.3 + - - +
861A VAL* 1.3 58.8 + - - +
862A THR 3.0 5.0 + - - -
863A VAL* 3.1 22.2 + - - +
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Residues in contact with VAL 861 (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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803A THR* 4.0 15.9 - - + -
812A LYS* 3.6 15.4 - - + +
815A LEU* 3.9 28.3 - - + -
821A LEU* 4.1 22.7 - - + -
857A VAL* 3.0 21.2 + - + +
858A LEU* 3.4 21.8 - - - +
860A SER* 1.3 74.1 - - - +
862A THR* 1.3 62.4 + - + +
863A VAL 3.5 0.4 - - - -
865A ASN* 3.3 11.3 - - - +
868A ASN* 2.7 36.7 + - - +
872A LEU* 4.5 2.2 - - + -
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Residues in contact with THR 862 (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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858A LEU 2.9 15.8 + - - +
859A GLU* 2.8 20.1 + - - -
860A SER 3.1 0.2 - - - -
861A VAL* 1.3 79.5 - - - +
863A VAL* 1.3 63.3 + - - +
864A HIS 3.2 0.5 + - - -
865A ASN 3.3 8.1 + - - -
868A ASN 3.9 2.2 - - - -
869A GLN* 2.9 58.7 + - + +
872A LEU* 3.6 24.5 - - + -
936A VAL* 5.6 2.2 - - + +
939A ASN* 2.9 23.1 + - - +
940A LEU* 4.2 6.9 - - + +
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Residues in contact with VAL 863 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A LYS* 5.7 11.0 - - + -
812A LYS* 2.8 34.0 + - - +
859A GLU* 3.4 33.8 + - - +
860A SER* 3.1 13.6 + - - +
862A THR* 1.3 73.9 - - - +
864A HIS* 1.3 87.7 + - + +
865A ASN* 3.0 2.4 + - - +
939A ASN* 4.0 6.7 - - - +
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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