Contacts of the helix formed by residues 778 - 809 (chain H) in PDB entry 1R0D
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 GLU 778 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774H VAL* 4.2 6.5 - - + -
775H ARG* 2.8 41.1 + - + +
777H GLU* 1.3 101.1 - - - +
779H LEU* 1.3 65.2 + - - +
780H GLY 3.2 3.1 - - - -
781H ALA* 3.2 14.7 + - + +
782H VAL* 3.1 25.6 + - + +
859H GLN* 4.3 3.8 + - - +
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Residues in contact with LEU 779 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774H VAL* 3.7 27.1 - - + +
775H ARG 3.2 9.4 + - - +
776H GLN* 3.2 26.1 + - + +
778H GLU* 1.3 78.5 - - - +
780H GLY* 1.3 58.1 + - - +
782H VAL* 3.2 2.4 + - - +
783H VAL* 2.8 32.1 + - - +
862H TYR* 4.1 8.5 - - + +
866H SER* 3.5 42.4 - - - +
869H THR* 3.7 15.2 - - + +
870H GLU* 3.9 20.4 - - + +
873H ILE* 3.7 20.7 - - + +
----------------------------------------------------------
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Residues in contact with GLY 780 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776H GLN 4.9 0.2 + - - -
777H GLU 5.2 1.2 + - - -
778H GLU* 3.2 1.2 - - - +
779H LEU* 1.3 79.1 - - - +
781H ALA* 1.3 62.5 + - - +
783H VAL* 3.2 4.6 - - - +
784H ASP* 3.1 30.4 + - - -
859H GLN* 4.8 13.0 + - - +
862H TYR* 3.4 33.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 781 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778H GLU* 3.2 19.2 + - + +
780H GLY* 1.3 74.1 - - - +
782H VAL* 1.3 60.6 + - + +
784H ASP* 3.4 8.0 + - - +
785H LYS* 3.0 29.7 + - - +
859H GLN* 6.2 0.8 - - - +
----------------------------------------------------------
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Residues in contact with VAL 782 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774H VAL* 3.7 32.1 - - + -
778H GLU* 3.1 17.3 + - + +
779H LEU 3.7 6.3 - - - +
781H ALA* 1.3 75.1 - - + +
783H VAL* 1.3 60.4 + - - +
785H LYS* 3.3 6.3 + - + +
786H GLU* 2.8 34.2 + - + +
873H ILE* 3.8 28.3 - - + -
----------------------------------------------------------
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Residues in contact with VAL 783 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779H LEU 2.8 18.1 + - - +
780H GLY* 3.2 11.9 - - - +
782H VAL* 1.3 74.3 - - - +
784H ASP* 1.3 66.1 + - - +
786H GLU* 3.8 1.7 - - + +
787H MSE 3.0 33.3 + - + +
845H GLN* 4.3 9.4 - - - +
862H TYR* 3.7 33.4 - - + +
869H THR* 3.9 4.9 - - + +
872H LEU* 3.8 37.5 - - + -
873H ILE* 3.8 21.5 - - + +
----------------------------------------------------------
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Residues in contact with ASP 784 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780H GLY 3.1 23.8 + - - +
781H ALA* 3.6 6.9 - - - +
782H VAL 3.2 0.2 - - - -
783H VAL* 1.3 85.3 - - - +
785H LYS* 1.3 61.7 + - - +
787H MSE 4.0 5.4 - - - +
788H ALA* 3.2 22.5 + - - +
846H LYS* 4.5 15.5 - - - -
858H GLN* 4.9 8.5 + - - +
862H TYR* 4.1 14.5 + - - -
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Residues in contact with LYS 785 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
781H ALA 3.0 17.7 + - - +
782H VAL* 3.7 7.4 - - + +
784H ASP* 1.3 73.9 - - - +
786H GLU* 1.3 60.2 + - + +
788H ALA* 3.2 9.0 + - + +
789H ALA* 2.9 32.0 + - + +
----------------------------------------------------------
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Residues in contact with GLU 786 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782H VAL* 2.8 28.2 + - + +
783H VAL* 3.8 7.0 - - + +
785H LYS* 1.3 75.5 - - - +
787H MSE 1.3 62.5 + - - +
789H ALA* 3.2 11.3 + - - +
790H THR* 2.9 29.8 + - - -
873H ILE* 3.8 28.5 - - + +
876H SER* 3.9 12.8 - - - +
877H LYS* 3.8 32.3 + - - +
----------------------------------------------------------
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Residues in contact with MSE 787 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783H VAL* 3.0 27.7 + - + +
784H ASP* 4.0 5.2 - - - +
786H GLU* 1.3 76.7 - - - +
788H ALA* 1.3 57.9 + - - +
790H THR* 3.5 1.9 + - - -
791H SER* 3.0 32.1 + - - -
838H VAL* 3.9 25.6 - - + +
841H SER* 4.0 6.5 - - - +
842H THR* 3.2 36.8 - - + +
845H GLN* 3.5 38.4 - - - +
872H LEU 4.8 2.7 - - - +
876H SER* 3.1 33.7 - - - +
917H LEU* 4.1 12.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 788 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
784H ASP 3.2 13.8 + - - +
785H LYS* 3.5 13.9 - - + +
786H GLU 3.2 0.6 - - - -
787H MSE 1.3 74.7 - - - +
789H ALA* 1.3 55.7 + - - +
791H SER* 3.2 7.0 + - - -
792H ALA* 2.8 36.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 789 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785H LYS* 2.9 22.0 + - + +
786H GLU* 3.7 14.8 - - - +
788H ALA* 1.3 76.5 - - - +
790H THR* 1.3 55.9 + - - +
792H ALA* 3.6 7.2 - - - +
793H ALA* 2.8 30.5 + - - +
----------------------------------------------------------
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Residues in contact with THR 790 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786H GLU* 2.9 16.6 + - - -
787H MSE 3.8 3.8 - - - -
789H ALA* 1.3 72.9 - - - +
791H SER* 1.3 60.8 + - - +
793H ALA* 3.2 6.6 + - - +
794H ILE* 2.9 50.7 + - + +
838H VAL* 4.0 11.2 - - + -
876H SER* 2.8 40.7 + - - +
877H LYS* 4.7 0.2 - - - -
879H VAL* 3.8 21.3 - - + -
880H GLY* 4.0 9.8 + - - +
917H LEU* 5.7 0.4 - - + -
----------------------------------------------------------
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Residues in contact with SER 791 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787H MSE 3.0 14.7 + - - -
788H ALA* 3.6 6.7 - - - -
790H THR* 1.3 77.5 - - - +
792H ALA* 1.3 58.0 + - - +
794H ILE* 3.4 10.2 + - - +
795H GLU* 3.1 30.5 + - - +
835H ARG* 5.4 6.0 + - - +
838H VAL* 3.3 22.6 - - - +
839H THR* 4.6 10.4 + - - -
842H THR* 5.2 1.9 + - - -
----------------------------------------------------------
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Residues in contact with ALA 792 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788H ALA 2.8 18.1 + - - +
789H ALA* 3.6 8.3 - - - +
791H SER* 1.3 74.7 - - - +
793H ALA* 1.3 59.1 + - - +
795H GLU* 3.2 7.1 + - - +
796H ASP* 2.9 39.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 793 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
789H ALA 2.8 18.6 + - - +
790H THR* 3.6 7.6 - - - +
792H ALA* 1.3 74.8 - - - +
794H ILE* 1.3 58.9 + - - +
796H ASP* 3.5 12.1 + - - +
797H ALA* 3.0 27.5 + - - +
800H ARG* 5.8 0.5 + - - -
880H GLY* 4.4 21.8 - - - +
883H ALA* 4.4 6.1 - - + +
884H THR* 5.0 6.5 - - - +
----------------------------------------------------------
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Residues in contact with ILE 794 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790H THR* 2.9 30.0 + - + +
791H SER* 3.6 6.5 - - - +
792H ALA 3.2 0.2 - - - -
793H ALA* 1.3 75.7 - - + +
795H GLU* 1.3 60.1 + - - +
797H ALA* 3.3 7.1 + - - +
798H VAL* 2.9 28.1 + - + +
831H MSE 3.5 31.6 - - + +
834H ILE* 3.6 18.8 - - + +
835H ARG* 3.6 20.6 - - + +
838H VAL* 3.3 38.1 - - + -
879H VAL* 4.2 3.4 - - + +
883H ALA* 4.5 14.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 795 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791H SER 3.1 15.4 + - - +
792H ALA* 3.2 10.5 + - - +
794H ILE* 1.3 73.2 - - - +
796H ASP* 1.3 67.9 + - - +
798H VAL* 3.2 4.6 + - - +
799H ARG* 3.0 62.0 + - - +
835H ARG* 2.2 52.0 + - + -
----------------------------------------------------------
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Residues in contact with ASP 796 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792H ALA* 2.9 29.3 + - - +
793H ALA* 3.7 9.4 - - - +
795H GLU* 1.3 77.1 - - - +
797H ALA* 1.3 53.4 + - - +
799H ARG* 3.3 14.1 + - - +
800H ARG* 2.8 66.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 797 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793H ALA 3.0 18.6 + - - +
794H ILE* 3.4 5.8 - - - +
796H ASP* 1.3 74.0 - - - +
798H VAL* 1.3 66.4 + - - +
800H ARG* 4.4 4.7 - - - +
801H ILE* 2.9 31.6 + - - +
831H MSE 3.7 22.2 - - + -
883H ALA* 4.4 5.6 - - + -
887H VAL* 3.5 28.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL 798 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794H ILE* 2.9 21.1 + - + +
795H GLU* 3.2 10.5 + - - +
797H ALA* 1.3 75.2 - - - +
799H ARG* 1.3 66.5 + - + +
801H ILE* 3.9 3.1 - - - +
802H GLU* 3.0 53.7 + - + +
828H THR* 4.6 3.6 - - + +
831H MSE 3.7 27.8 - - + +
832H LYS* 4.0 30.3 - - + -
835H ARG* 4.4 15.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 799 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795H GLU* 3.0 47.7 + - - +
796H ASP* 3.6 13.1 + - - +
798H VAL* 1.3 79.0 - - + +
800H ARG* 1.3 63.9 + - + +
802H GLU* 3.4 8.5 + - - +
803H ASP* 3.0 25.5 + - - +
----------------------------------------------------------
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Residues in contact with ARG 800 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793H ALA 5.8 0.6 + - - -
796H ASP* 2.8 44.9 + - - +
797H ALA* 3.9 4.1 - - - +
799H ARG* 1.3 72.4 - - + +
801H ILE* 1.3 58.1 + - - +
803H ASP* 3.4 4.8 + - - +
804H MSE 2.9 35.5 + - + +
884H THR* 5.2 15.2 + - - +
887H VAL* 4.1 28.5 - - + +
----------------------------------------------------------
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Residues in contact with ILE 801 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797H ALA 2.9 24.3 + - - +
798H VAL* 3.9 3.4 - - - +
800H ARG* 1.3 75.3 - - - +
802H GLU* 1.3 63.9 + - - +
804H MSE 3.2 19.4 + - - +
805H MSE 3.2 14.4 + - - +
824H LEU* 3.3 30.0 - - + +
827H CYS* 3.9 30.7 - - + +
828H THR* 3.3 22.4 - - - +
831H MSE 4.5 10.5 - - + -
886H LEU* 4.4 10.3 - - + -
887H VAL* 4.1 26.7 - - + -
890H ALA* 5.5 3.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 802 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
798H VAL* 3.0 31.7 + - - +
799H ARG* 3.8 6.7 - - - +
801H ILE* 1.3 75.8 - - - +
803H ASP* 1.3 61.7 + - - +
805H MSE 3.4 26.7 - - - +
806H ASN* 3.7 5.2 + - - +
809H ARG* 5.5 0.3 + - - -
828H THR* 3.5 31.8 - - + +
832H LYS* 3.7 17.5 + - - -
----------------------------------------------------------
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Residues in contact with ASP 803 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799H ARG 3.0 17.8 + - - +
800H ARG* 4.0 4.0 - - - +
802H GLU* 1.3 73.2 - - - +
804H MSE 1.3 65.9 + - - +
805H MSE 3.0 2.0 - - - -
806H ASN* 3.1 14.9 + - - +
807H GLN* 3.0 55.3 + - - +
----------------------------------------------------------
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Residues in contact with MSE 804 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800H ARG* 2.9 23.4 + - + +
801H ILE* 3.2 11.2 + - - +
803H ASP* 1.3 76.6 - - - +
805H MSE 1.3 57.5 + - - +
807H GLN* 3.7 13.4 + - - +
808H ALA* 2.9 28.1 + - - +
824H LEU* 3.8 27.4 - - + -
887H VAL* 4.0 15.5 - - + +
890H ALA* 3.9 5.2 - - - +
891H ASP* 3.1 60.3 - - + +
894H VAL* 4.6 2.7 - - + -
895H LEU* 3.8 19.0 - - + +
----------------------------------------------------------
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Residues in contact with MSE 805 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801H ILE 3.3 9.6 - - - +
802H GLU* 3.4 15.7 - - - +
804H MSE 1.3 75.7 - - - +
806H ASN* 1.3 66.2 + - - +
808H ALA 3.0 7.3 + - - -
809H ARG* 3.2 22.0 + - - +
821H GLU* 2.8 59.7 - - + +
824H LEU* 3.3 31.4 - - + -
825H ASN* 4.0 32.3 - - + +
828H THR* 4.3 10.1 - - - -
----------------------------------------------------------
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Residues in contact with ASN 806 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802H GLU 3.7 5.0 + - - +
803H ASP* 3.1 21.4 + - - +
805H MSE 1.3 78.7 - - - +
807H GLN* 1.3 64.8 + - - +
809H ARG* 3.2 39.7 + - - +
810H HIS* 3.7 28.5 + - - -
----------------------------------------------------------
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Residues in contact with GLN 807 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
803H ASP* 3.0 37.2 + - - +
804H MSE 3.8 14.1 + - - +
806H ASN* 1.3 75.5 - - + +
808H ALA* 1.3 60.8 + - - +
809H ARG 3.3 0.2 - - - -
810H HIS* 3.2 12.4 + - - +
811H ALA* 3.0 29.4 + - - +
895H LEU* 4.5 18.0 - - + +
----------------------------------------------------------
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Residues in contact with ALA 808 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804H MSE 2.9 15.4 + - - +
805H MSE 3.0 11.6 + - - +
807H GLN* 1.3 73.7 - - - +
809H ARG* 1.3 53.4 + - - +
810H HIS 2.7 15.2 + - - -
811H ALA* 2.9 11.9 + - - +
812H SER* 3.2 23.6 + - - +
817H LEU* 3.8 5.3 - - + +
820H ASN* 5.3 5.4 - - + -
821H GLU* 3.4 11.4 - - - +
824H LEU* 4.7 2.2 - - + -
894H VAL* 4.2 20.0 - - + -
895H LEU* 4.3 8.3 - - - -
----------------------------------------------------------
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Residues in contact with ARG 809 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802H GLU 5.5 0.2 + - - -
805H MSE 3.2 30.7 + - - +
806H ASN* 3.2 28.7 + - - +
808H ALA* 1.3 75.1 - - - +
810H HIS* 1.3 70.5 + - + +
812H SER 4.1 2.9 - - - +
817H LEU* 3.5 26.3 - - + +
821H GLU* 3.4 36.3 + - - +
----------------------------------------------------------
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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