Contacts of the helix formed by residues 865 - 896 (chain G) 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 ASN 865 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861G PHE* 2.8 52.7 + - - +
862G TYR 2.9 6.7 + - - +
864G LYS* 1.3 86.8 - - - +
866G SER* 1.3 63.9 + - - +
867G ARG* 3.1 4.2 + - - -
868G TRP* 3.1 15.4 + - + -
869G THR* 3.1 20.1 + - - -
924G LYS* 2.4 46.8 + - - +
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Residues in contact with SER 866 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776G GLN* 3.3 31.1 + - - -
779G LEU* 3.8 16.2 - - - -
862G TYR 3.0 8.4 + - - -
863G ALA 3.4 7.4 + - - -
864G LYS 3.5 1.0 + - - -
865G ASN* 1.3 75.8 - - - +
867G ARG* 1.3 63.6 + - - +
869G THR* 3.8 1.5 - - - -
870G GLU* 2.9 42.7 + - - +
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Residues in contact with ARG 867 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865G ASN 3.2 1.8 - - - -
866G SER* 1.3 81.9 + - - +
868G TRP* 1.3 67.0 + - - +
870G GLU* 3.2 13.8 + - - +
871G GLY* 3.0 19.8 + - - -
923G VAL* 6.3 0.6 - - - +
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Residues in contact with TRP 868 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845G GLN* 3.9 24.0 - - + -
848G ILE* 3.7 34.8 - - + -
849G VAL* 4.1 3.1 - - + -
861G PHE* 3.8 23.6 - + - -
862G TYR* 4.1 14.8 - + - -
865G ASN* 3.1 11.3 + - + +
867G ARG* 1.3 78.7 - - - +
869G THR* 1.3 79.3 + - - +
871G GLY* 3.0 4.7 + - - -
872G LEU* 3.0 48.0 + - + +
920G ALA 3.2 27.5 + - - +
921G SER 3.2 12.9 + - - -
923G VAL* 3.5 24.5 - - + -
924G LYS* 3.4 37.3 - - + +
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Residues in contact with THR 869 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779G LEU* 4.0 28.3 - - + -
783G VAL* 4.0 19.5 - - + -
862G TYR* 3.2 51.3 + - + -
865G ASN 3.1 7.3 + - - -
866G SER* 3.8 7.4 - - - -
867G ARG 3.2 0.2 - - - -
868G TRP* 1.3 80.1 - - - +
870G GLU* 1.3 61.7 + - - +
872G LEU* 3.0 11.9 + - - +
873G ILE* 3.0 27.0 + - + +
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Residues in contact with GLU 870 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773G ASP* 4.6 12.1 - - - +
774G VAL* 4.9 11.2 + - + +
776G GLN* 6.0 0.9 - - - +
779G LEU* 4.1 20.1 - - + +
866G SER* 2.9 33.9 + - - +
867G ARG* 3.7 15.7 - - - +
869G THR* 1.3 76.0 - - - +
871G GLY* 1.3 57.0 + - - +
873G ILE* 3.3 10.2 + - + +
874G SER* 3.0 30.3 + - - -
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Residues in contact with GLY 871 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867G ARG 3.0 14.1 + - - -
868G TRP* 3.0 5.1 + - - -
870G GLU* 1.3 77.8 - - - +
872G LEU* 1.3 57.0 + - - +
874G SER* 3.5 7.0 + - - -
875G ALA* 3.0 31.0 + - - +
920G ALA* 3.5 13.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 872 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783G VAL* 4.3 17.0 - - + -
787G MSE 5.3 1.8 - - - -
845G GLN* 3.6 38.6 - - + +
862G TYR* 4.7 3.8 - - + -
868G TRP* 3.0 46.4 + - + +
869G THR* 3.0 10.1 + - - +
871G GLY* 1.3 74.8 - - - +
873G ILE* 1.3 60.5 + - - +
875G ALA* 3.9 1.4 - - - +
876G SER* 2.9 34.3 + - - -
917G LEU* 4.5 5.0 - - + +
920G ALA* 3.5 34.3 - - + +
921G SER* 3.8 12.3 - - - +
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Residues in contact with ILE 873 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774G VAL* 4.5 4.7 - - + -
779G LEU* 3.8 25.6 - - + -
782G VAL* 3.8 25.8 - - + -
783G VAL* 4.0 26.0 - - + +
786G GLU* 3.7 25.0 - - + +
787G MSE 6.1 0.2 - - - -
869G THR* 3.0 17.5 + - + +
870G GLU* 3.3 10.1 + - - +
872G LEU* 1.3 76.4 - - - +
874G SER* 1.3 58.2 + - - +
876G SER* 3.8 4.0 - - - -
877G LYS* 3.0 28.7 + - + +
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Residues in contact with SER 874 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870G GLU 3.0 14.9 + - - -
871G GLY* 3.5 10.2 + - - -
873G ILE* 1.3 76.3 - - - +
875G ALA* 1.3 68.8 + - - +
877G LYS* 3.4 6.5 + - - +
878G ALA* 3.1 21.8 + - - +
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Residues in contact with ALA 875 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871G GLY 3.0 15.6 + - - +
872G LEU 4.2 1.3 - - - +
874G SER* 1.3 82.1 + - - +
876G SER* 1.3 62.0 + - - +
878G ALA* 3.4 8.4 + - - +
879G VAL* 3.2 26.0 + - - +
913G SER 4.4 1.2 - - - +
916G GLN* 3.9 20.2 - - + +
917G LEU* 3.6 32.8 - - + +
920G ALA* 4.1 5.4 - - + -
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Residues in contact with SER 876 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786G GLU* 3.6 9.4 + - - -
787G MSE 3.4 29.2 - - - +
790G THR* 2.7 43.0 + - - +
872G LEU 2.9 20.3 + - - -
873G ILE* 3.8 4.9 - - - -
875G ALA* 1.3 75.2 - - - +
877G LYS* 1.3 66.2 + - - +
879G VAL* 3.1 7.7 + - - +
880G GLY 3.1 11.8 + - - -
917G LEU* 4.3 9.7 - - - +
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Residues in contact with LYS 877 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786G GLU* 3.7 27.6 + - - +
790G THR* 4.5 1.1 - - - -
873G ILE* 3.0 18.9 + - + +
874G SER* 3.7 7.4 - - - +
876G SER* 1.3 75.1 - - - +
878G ALA* 1.3 63.4 + - - +
880G GLY* 3.1 6.2 + - - -
881G TRP* 2.9 87.8 + - + +
----------------------------------------------------------
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Residues in contact with ALA 878 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874G SER 3.1 10.1 + - - +
875G ALA* 3.6 12.1 - - - +
876G SER 3.2 0.2 - - - -
877G LYS* 1.3 80.8 - - - +
879G VAL* 1.3 57.7 + - - +
881G TRP* 3.4 15.4 + - + +
882G GLY* 2.9 25.1 + - - -
913G SER* 3.7 22.6 + - - +
916G GLN* 6.5 0.7 - - + -
----------------------------------------------------------
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Residues in contact with VAL 879 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790G THR* 4.0 16.6 - - + -
794G ILE* 4.3 4.3 - - + -
834G ILE* 4.1 26.5 - - + -
838G VAL* 4.2 6.7 - - + -
875G ALA 3.2 14.1 + - - +
876G SER* 3.1 9.2 + - - +
878G ALA* 1.3 75.3 - - - +
880G GLY* 1.3 62.6 + - - +
882G GLY* 3.1 3.0 + - - -
883G ALA* 3.0 21.5 + - - +
910G ILE* 4.4 5.4 - - + +
913G SER* 3.6 31.9 - - - +
914G THR* 4.0 12.3 - - + +
917G LEU* 4.3 15.0 - - + -
----------------------------------------------------------
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Residues in contact with GLY 880 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790G THR* 4.2 12.3 - - - +
793G ALA* 4.3 20.1 - - - +
794G ILE* 6.0 0.4 - - - -
876G SER 3.1 12.5 + - - -
877G LYS* 3.1 8.0 + - - -
879G VAL* 1.3 78.5 - - - +
881G TRP* 1.3 63.2 + - - +
883G ALA* 3.2 6.1 + - - +
884G THR* 3.2 23.5 + - - -
----------------------------------------------------------
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Residues in contact with TRP 881 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877G LYS* 2.9 66.1 + - + +
878G ALA* 3.9 12.6 - - + +
880G GLY* 1.3 76.4 - - - +
882G GLY* 1.3 57.9 + - - +
884G THR* 3.2 11.4 + - + -
885G GLN* 2.9 40.4 + - + +
----------------------------------------------------------
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Residues in contact with GLY 882 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878G ALA 2.9 16.1 + - - -
879G VAL 3.1 5.6 + - - -
881G TRP* 1.3 77.7 - - - +
883G ALA* 1.3 56.1 + - - +
885G GLN* 3.6 13.2 + - - +
886G LEU* 3.1 28.2 + - - +
906G CYS 4.9 1.4 - - - +
909G GLU* 5.9 0.7 - - - -
910G ILE* 3.6 25.0 - - - +
913G SER* 5.4 1.1 - - - -
----------------------------------------------------------
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Residues in contact with ALA 883 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793G ALA* 4.3 15.0 - - + +
794G ILE* 4.6 5.4 - - + -
797G ALA* 4.2 7.6 - - + -
831G MSE 3.7 27.6 - - + -
879G VAL 3.0 10.8 + - - +
880G GLY* 3.2 8.5 + - - +
882G GLY* 1.3 75.4 - - - +
884G THR* 1.3 64.4 + - - +
886G LEU* 3.4 2.8 + - - +
887G VAL* 3.0 30.6 + - - +
910G ILE* 3.6 8.9 - - + +
----------------------------------------------------------
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Residues in contact with THR 884 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793G ALA* 5.1 6.6 - - - +
880G GLY 3.2 13.4 + - - -
881G TRP* 3.2 14.9 + - + -
883G ALA* 1.3 77.2 - - - +
885G GLN* 1.3 64.1 + - + +
887G VAL* 3.4 5.3 + - - +
888G GLU* 3.1 24.7 + - + +
----------------------------------------------------------
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Residues in contact with GLN 885 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881G TRP* 2.9 24.1 + - + +
882G GLY* 3.7 11.9 + - - +
883G ALA 3.2 0.2 - - - -
884G THR* 1.3 79.4 - - + +
886G LEU* 1.3 63.9 + - - +
888G GLU* 3.2 7.6 + - - +
889G ALA* 2.9 23.2 + - - +
906G CYS* 3.9 23.9 + - - +
909G GLU* 3.1 30.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 886 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801G ILE* 4.1 25.1 - - + -
827G CYS* 4.3 17.9 - - + -
830G LEU* 3.9 22.4 - - + -
831G MSE 4.5 10.5 - - - -
882G GLY 3.1 14.4 + - - +
883G ALA* 3.9 5.8 - - - +
885G GLN* 1.3 80.0 - - - +
887G VAL* 1.3 59.9 + - + +
889G ALA* 3.3 2.3 + - - +
890G ALA* 2.9 27.2 + - + +
903G LEU* 4.0 9.1 - - + +
906G CYS* 4.0 16.1 - - + +
907G SER* 3.8 32.1 - - - +
910G ILE* 4.2 7.6 - - + -
----------------------------------------------------------
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Residues in contact with VAL 887 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797G ALA* 3.4 35.2 - - + +
800G ARG* 3.9 30.1 - - + +
801G ILE* 4.4 9.9 - - + -
804G MSE 3.4 24.1 - - + +
883G ALA 3.0 18.7 + - - +
884G THR* 3.8 5.4 - - - +
886G LEU* 1.3 78.1 - - + +
888G GLU* 1.3 58.1 + - - +
890G ALA* 3.3 2.0 + - - -
891G ASP* 2.9 27.2 + - + +
----------------------------------------------------------
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Residues in contact with GLU 888 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884G THR* 3.1 20.6 + - + +
885G GLN* 3.2 6.5 + - - +
887G VAL* 1.3 78.7 - - - +
889G ALA* 1.3 57.9 + - - +
891G ASP* 3.5 8.5 + - - +
892G LYS* 2.9 68.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 889 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885G GLN 2.9 15.6 + - - +
886G LEU 3.7 4.3 - - - +
888G GLU* 1.3 72.8 - - - +
890G ALA* 1.3 66.5 + - - +
892G LYS* 3.5 5.4 + - - +
893G VAL* 3.2 25.5 + - - +
899G LYS 4.9 2.1 - - - +
902G GLU* 4.0 18.8 - - + +
903G LEU* 3.9 31.0 - - + +
906G CYS* 4.1 9.0 - - - -
----------------------------------------------------------
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Residues in contact with ALA 890 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
801G ILE* 5.3 3.6 - - + -
804G MSE 3.9 15.7 - - + -
824G LEU* 4.7 10.3 - - + -
827G CYS* 4.9 3.8 - - - -
886G LEU* 2.9 22.8 + - + +
887G VAL* 3.7 5.4 - - - +
889G ALA* 1.3 79.4 - - - +
891G ASP* 1.3 62.1 + - - +
893G VAL* 4.2 6.3 - - - -
894G VAL* 3.0 31.0 + - + +
903G LEU* 4.1 19.9 - - + +
----------------------------------------------------------
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Residues in contact with ASP 891 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804G MSE 3.6 21.0 - - + +
807G GLN* 5.3 0.2 - - - +
887G VAL* 2.9 18.8 + - + +
888G GLU* 3.6 10.4 - - - +
890G ALA* 1.3 75.7 - - - +
892G LYS* 1.3 70.5 + - - +
895G LEU* 2.8 56.9 + - - +
896G HIS* 3.2 22.7 + - - -
----------------------------------------------------------
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Residues in contact with LYS 892 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888G GLU* 2.9 51.4 + - + +
889G ALA* 3.8 5.6 - - - +
890G ALA 3.3 0.2 - - - -
891G ASP* 1.3 90.0 + - - +
893G VAL* 1.3 57.5 + - - +
896G HIS* 2.8 56.2 + - + -
898G GLY* 3.0 18.7 + - - +
----------------------------------------------------------
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Residues in contact with VAL 893 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816G LYS* 5.2 4.7 + - - -
820G ASN* 4.5 4.3 + - - -
889G ALA 3.2 16.5 + - - +
890G ALA* 3.6 8.3 - - - +
892G LYS* 1.3 79.6 - - - +
894G VAL* 1.3 70.8 + - + +
896G HIS 4.0 7.8 - - - +
898G GLY* 3.2 28.9 - - - +
899G LYS 3.9 6.5 - - - +
900G TYR* 3.6 58.0 + - + +
903G LEU* 4.5 10.1 - - + -
----------------------------------------------------------
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Residues in contact with VAL 894 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804G MSE 4.9 3.8 - - - +
808G ALA* 4.0 19.3 - - + +
811G ALA* 5.8 1.2 - - - +
812G SER* 5.5 2.3 + - - -
816G LYS* 4.3 12.0 + - - -
820G ASN* 3.8 42.3 + - + +
823G ILE* 5.3 6.7 - - + -
824G LEU* 4.2 27.6 - - + -
890G ALA* 3.0 21.3 + - + +
891G ASP 4.3 0.2 - - - +
893G VAL* 1.3 88.4 - - + +
895G LEU* 1.3 78.8 + - + +
896G HIS 5.0 0.2 - - - -
900G TYR* 5.4 0.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU 895 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804G MSE 4.2 11.0 - - + +
807G GLN* 3.7 37.0 - - + +
808G ALA* 3.9 25.6 - - - +
811G ALA* 4.6 15.7 - - + +
816G LYS* 6.1 1.1 - - - -
891G ASP* 2.8 35.3 + - - +
894G VAL* 1.3 94.9 - - + +
896G HIS* 1.3 80.6 + - + +
----------------------------------------------------------
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Residues in contact with HIS 896 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816G LYS* 5.1 7.3 + - - -
891G ASP* 3.2 34.6 + - - -
892G LYS* 2.8 39.7 + - + +
893G VAL 4.0 8.3 - - - +
894G VAL 5.0 0.5 - - - +
895G LEU* 1.3 96.0 + - + +
897G THR* 1.3 70.7 + - + +
----------------------------------------------------------
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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).
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