Contacts of the helix formed by residues 771 - 798 (chain B) in PDB entry 5JO3
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 PRO 771 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B SER* 3.8 38.1 - - - +
769B THR 4.5 1.1 - - - +
770B LYS* 1.4 85.0 - - + +
772B TRP* 1.3 66.2 + - - +
773B PRO* 3.3 10.3 - - + -
774B ILE* 2.9 34.7 + - + +
775B GLN 2.9 9.4 + - - -
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Residues in contact with TRP 772 (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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770B LYS 3.3 1.6 + - - -
771B PRO* 1.3 70.7 - - - +
773B PRO* 1.4 73.5 - - + +
775B GLN* 3.2 25.5 + - - -
776B GLN* 2.7 70.3 + - + +
849B ASN* 3.4 23.4 + - - +
852B LYS* 3.5 55.9 - - + +
853B TRP* 3.6 45.3 - + - -
856B LEU* 4.0 17.0 - - + -
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Residues in contact with PRO 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B PRO* 3.4 12.3 - - + +
772B TRP* 1.4 102.9 - - + +
774B ILE* 1.3 58.3 + - + +
776B GLN* 3.6 9.6 + - + +
777B ARG* 3.1 27.7 + - - +
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Residues in contact with ILE 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B SER 3.7 17.9 - - - +
561B PHE 4.7 3.6 - - - +
562B SER* 3.7 33.2 - - - +
770B LYS* 3.7 20.6 - - + -
771B PRO* 2.9 26.7 + - + +
773B PRO* 1.3 77.6 - - + +
775B GLN* 1.3 64.7 - - - +
777B ARG* 3.2 14.2 + - - +
778B ILE* 3.0 40.7 + - + +
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Residues in contact with GLN 775 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767B ALA 3.2 27.8 - - - +
768B ILE* 3.8 8.5 - - - +
770B LYS* 3.7 8.0 - - - +
771B PRO 2.9 7.4 + - - +
772B TRP* 3.2 28.4 - - - +
774B ILE* 1.3 77.0 - - - +
776B GLN* 1.3 61.7 + - - +
778B ILE* 3.3 3.0 + - - -
779B ALA* 2.8 26.2 + - - +
817B GLN* 3.4 17.8 - - - +
849B ASN* 3.3 28.5 - - - +
853B TRP* 2.8 29.0 + - - +
903B 6LK 3.5 15.4 - - - +
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Residues in contact with GLN 776 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B TRP* 2.7 63.0 + - + +
773B PRO* 3.9 8.7 - - - +
775B GLN* 1.3 80.1 + - - +
777B ARG* 1.3 62.0 + - - +
779B ALA* 3.3 6.8 + - - +
780B GLU* 3.1 34.7 + - + +
853B TRP* 4.9 8.4 - - + -
856B LEU* 5.3 4.0 - - - +
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Residues in contact with ARG 777 (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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562B SER* 5.1 1.6 + - - -
563B ASP* 3.7 22.2 + - - -
564B PHE* 3.4 60.2 - - - +
620B ASN* 5.4 0.2 - - - +
773B PRO 3.1 18.3 + - - +
774B ILE* 3.2 13.2 + - - +
776B GLN* 1.3 76.0 - - - +
778B ILE* 1.3 83.2 + - - +
780B GLU* 3.3 27.1 + - - +
781B LEU* 3.4 35.6 + - + +
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Residues in contact with ILE 778 (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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563B ASP* 5.4 0.4 - - - +
612B TYR* 3.6 31.6 - - + -
620B ASN* 5.0 14.6 - - - +
767B ALA* 3.6 31.2 - - + -
770B LYS* 4.9 3.4 - - + -
774B ILE* 3.0 38.3 + - + +
775B GLN 3.9 3.4 - - - +
777B ARG* 1.3 94.7 - - - +
779B ALA* 1.3 67.0 + - - +
781B LEU* 3.0 22.2 + - + +
782B VAL* 3.0 14.2 + - + +
903B 6LK 4.3 0.7 - - - -
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Residues in contact with ALA 779 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
775B GLN 2.8 22.0 + - - +
776B GLN 3.3 5.8 + - - +
778B ILE* 1.3 73.1 - - - +
780B GLU* 1.3 54.5 + - + +
782B VAL* 3.3 6.9 + - - +
783B ALA* 3.0 28.6 + - - +
813B ILE* 5.9 2.1 - - + +
817B GLN* 3.8 18.2 - - + +
853B TRP* 3.8 19.1 - - + -
903B 6LK 3.7 17.8 - - - -
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Residues in contact with GLU 780 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B GLN* 3.1 24.5 + - + +
777B ARG* 3.4 16.7 - - - +
778B ILE 3.1 0.4 - - - -
779B ALA* 1.3 77.9 - - - +
781B LEU* 1.3 58.6 + - + +
783B ALA* 3.4 6.6 + - - +
784B THR* 2.8 34.2 + - - +
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Residues in contact with LEU 781 (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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611B ALA* 3.6 36.9 - - + +
612B TYR* 3.8 11.6 - - + +
614B ASN* 5.6 1.6 - - - +
777B ARG* 3.4 37.4 + - + +
778B ILE* 3.0 18.2 + - + +
780B GLU* 1.3 76.5 - - + +
782B VAL* 1.3 64.4 + - - +
784B THR* 3.2 8.1 + - - +
785B GLU* 3.0 21.0 + - - +
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Residues in contact with VAL 782 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B TYR* 3.6 44.4 - - + -
778B ILE* 3.0 14.7 + - + +
779B ALA* 3.6 8.5 - - - +
781B LEU* 1.3 73.8 - - - +
783B ALA* 1.3 63.4 + - - +
785B GLU* 3.3 4.7 + - - +
786B PHE* 3.0 53.4 + - + -
903B 6LK 3.9 37.7 - - + +
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Residues in contact with ALA 783 (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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779B ALA 3.0 17.4 + - - +
780B GLU* 3.6 8.1 - - - +
782B VAL* 1.3 74.7 - - - +
784B THR* 1.3 59.5 + - - +
786B PHE* 3.2 8.8 + - - +
787B PHE* 2.8 48.7 + - + -
804B LEU 5.7 0.2 - - - -
813B ILE* 4.0 27.6 - - + -
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Residues in contact with THR 784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611B ALA* 3.7 18.6 - - + -
780B GLU* 2.8 23.1 + - - +
781B LEU* 3.2 8.9 + - - +
783B ALA* 1.3 75.7 - - - +
785B GLU* 1.3 57.7 + - - +
787B PHE* 3.4 7.3 + - - +
788B ASP* 2.9 31.0 + - + +
807B ARG* 4.9 1.6 + - - +
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Residues in contact with GLU 785 (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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610B VAL* 3.2 14.7 - - + +
611B ALA* 3.9 9.8 - - + +
612B TYR* 2.9 27.8 + - + +
613B HIS* 2.6 40.6 + - - -
657B HIS* 3.8 1.9 - - - -
659B GLY* 3.4 30.8 - - - +
781B LEU 3.0 12.3 + - - +
782B VAL 3.6 7.4 - - - +
784B THR* 1.3 77.4 - - - +
786B PHE* 1.3 70.4 + - + +
788B ASP* 3.2 8.5 + - + +
789B GLN* 3.0 21.5 + - - +
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Residues in contact with PHE 786 (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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612B TYR* 6.5 0.4 - + - -
613B HIS* 5.7 9.6 - + - -
661B SER* 6.2 1.8 - - - -
782B VAL* 3.0 42.8 + - + +
783B ALA* 3.7 6.5 - - - +
785B GLU* 1.3 82.8 - - + +
787B PHE* 1.3 58.9 + - - +
789B GLN* 3.2 8.0 + - + +
790B GLY 3.0 22.2 + - - -
804B LEU* 3.4 52.9 - - + +
805B MET* 3.4 35.5 - - + +
903B 6LK 3.8 34.5 - + + -
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Residues in contact with PHE 787 (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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783B ALA* 2.8 38.6 + - + +
784B THR* 3.9 5.4 - - - +
786B PHE* 1.3 70.2 - - - +
788B ASP* 1.3 60.4 + - - +
790B GLY* 3.2 1.6 + - - -
791B ASP* 3.0 32.7 + - - +
803B ASP 4.2 3.6 - - - -
804B LEU 3.5 17.3 - - - -
805B MET 3.6 11.5 - - - +
806B ASN 3.5 16.4 - - - -
807B ARG* 3.4 51.9 + - + +
810B LYS* 3.8 36.1 - - + -
813B ILE* 3.8 17.9 - - + -
816B MET* 6.0 0.4 - - + -
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Residues in contact with ASP 788 (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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659B GLY 4.9 5.5 - - - +
660B VAL* 5.5 0.3 - - - +
784B THR* 2.9 20.4 + - + +
785B GLU* 3.5 7.9 - - - +
787B PHE* 1.3 76.8 - - - +
789B GLN* 1.3 63.2 + - - +
791B ASP* 3.2 16.6 + - - +
792B ARG* 3.2 37.9 + - - +
807B ARG* 3.8 3.5 + - - +
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Residues in contact with GLN 789 (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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659B GLY 4.4 1.6 + - - +
660B VAL* 3.3 16.2 - - + -
661B SER* 2.9 46.4 + - - -
663B GLN* 5.8 0.4 - - - +
664B PHE* 3.5 20.2 - - + +
785B GLU 3.0 12.3 + - - +
786B PHE* 3.2 13.3 + - + +
788B ASP* 1.3 78.2 + - - +
790B GLY* 1.3 56.6 + - - +
792B ARG* 3.0 10.8 + - - +
793B GLU* 2.9 50.3 + - - +
805B MET* 3.2 25.8 - - - +
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Residues in contact with GLY 790 (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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786B PHE 3.0 10.9 + - - -
787B PHE 3.2 1.0 + - - -
789B GLN* 1.3 75.3 - - - +
791B ASP* 1.3 63.1 + - - +
793B GLU* 3.2 6.9 + - - +
794B ARG* 3.0 22.3 + - - +
801B PRO* 3.4 26.3 - - - +
805B MET* 3.2 24.6 - - - +
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Residues in contact with ASP 791 (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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787B PHE 3.0 14.9 + - - +
788B ASP* 3.4 15.7 - - - +
789B GLN 3.2 0.2 - - - -
790B GLY* 1.3 76.0 - - - +
792B ARG* 1.3 62.3 + - + +
794B ARG* 3.4 15.8 + - - +
795B LYS* 3.2 30.3 + - + +
807B ARG* 2.8 42.2 + - - +
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Residues in contact with ARG 792 (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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658B PRO* 4.5 10.7 + - - +
660B VAL* 3.8 23.1 - - - +
664B PHE* 3.6 33.1 - - + -
788B ASP* 3.3 27.7 + - - +
789B GLN* 3.0 11.7 + - - +
791B ASP* 1.3 73.8 - - + +
793B GLU* 1.3 56.0 + - - +
795B LYS* 4.5 4.3 - - - +
796B GLU* 2.7 68.1 + - - +
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Residues in contact with GLU 793 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B PHE* 3.7 22.4 - - + +
667B ASN* 5.7 1.7 + - - -
789B GLN* 2.9 44.6 + - - +
790B GLY* 3.2 8.2 + - - +
792B ARG* 1.3 72.9 - - - +
794B ARG* 1.3 66.8 + - - +
797B LEU* 2.9 34.1 + - + +
798B ASN 3.1 5.9 + - - -
799B ILE* 3.5 27.6 + - + +
801B PRO* 3.6 26.8 - - + +
802B THR 4.7 1.2 + - - -
805B MET* 3.9 9.3 - - - +
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Residues in contact with ARG 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B GLY 3.0 16.3 + - - +
791B ASP* 3.6 16.3 + - - +
792B ARG 3.3 0.2 - - - -
793B GLU* 1.3 77.2 - - - +
795B LYS* 1.3 63.5 + - + +
798B ASN* 3.2 23.7 + - - +
799B ILE 3.4 16.8 + - - +
800B GLU* 3.7 23.0 + - - +
801B PRO* 3.4 19.8 - - + +
806B ASN* 3.1 32.3 + - - +
808B GLU* 3.8 25.1 + - - +
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Residues in contact with LYS 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B ASP* 3.2 18.8 + - + +
792B ARG* 3.9 4.7 - - - +
794B ARG* 1.3 85.5 - - + +
796B GLU* 1.3 66.0 + - + +
798B ASN* 4.5 2.4 + - - +
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Residues in contact with GLU 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B PHE* 3.5 18.7 - - + -
668B THR* 3.6 21.1 - - + +
792B ARG* 2.7 56.6 + - - +
795B LYS* 1.3 80.6 - - + +
797B LEU* 1.3 65.7 + - + +
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Residues in contact with LEU 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B PHE* 4.5 10.8 - - + -
667B ASN* 3.4 51.8 - - + +
668B THR* 4.1 11.7 - - + -
793B GLU* 2.9 30.3 + - + +
796B GLU* 1.3 85.5 - - + +
798B ASN* 1.3 71.2 + - - +
799B ILE* 3.3 34.6 + - + +
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Residues in contact with ASN 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B GLU 3.1 3.2 + - - -
794B ARG* 3.2 17.4 + - - +
795B LYS 4.4 2.3 + - - +
796B GLU 3.7 1.0 - - - -
797B LEU* 1.3 80.2 - - - +
799B ILE* 1.3 61.2 + - - +
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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