Contacts of the helix formed by residues 771 - 796 (chain B) in PDB entry 3JWR
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* 4.1 28.0 - - - +
769B THR 4.4 1.8 - - - +
770B LYS* 1.3 94.6 - - + +
772B TRP* 1.3 67.5 + - - +
773B PRO* 3.3 10.5 - - + -
774B ILE* 2.9 24.4 + - + +
775B GLN 2.8 18.9 + - - -
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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 3.5 0.8 + - - -
771B PRO* 1.3 71.2 - - - +
773B PRO* 1.3 68.9 - - + +
775B GLN* 4.0 8.5 - - + -
776B GLN* 2.6 74.8 + - - +
849B ASN* 3.7 20.8 + - - +
852B LYS* 3.5 60.0 - - + +
853B TRP* 3.8 51.8 - + - -
856B LEU* 4.1 15.0 - - + -
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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 10.3 - - + -
772B TRP* 1.3 104.2 - - + +
774B ILE* 1.3 63.6 + - + +
776B GLN* 3.3 17.1 - - + +
777B ARG* 3.6 12.3 + - - +
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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 4.4 3.6 - - - +
561B PHE 4.3 5.8 - - - +
562B SER* 3.4 33.4 - - - +
770B LYS* 3.8 19.7 - - + -
771B PRO* 2.9 34.0 + - + +
773B PRO* 1.3 79.0 - - + +
775B GLN* 1.3 67.7 + - - +
777B ARG* 2.9 35.5 + - - +
778B ILE* 2.9 27.0 + - + +
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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* 3.0 29.6 + - - +
768B ILE* 3.4 20.6 - - - +
770B LYS* 3.8 2.2 - - - +
771B PRO 2.8 12.0 + - - +
772B TRP* 3.7 8.1 - - + +
774B ILE* 1.3 76.6 - - - +
776B GLN* 1.3 66.5 + - - +
778B ILE* 4.9 3.4 - - - +
779B ALA* 2.9 31.6 + - - +
817B GLN* 3.5 14.7 + - - -
849B ASN* 3.3 35.7 - - - +
853B TRP* 3.0 30.4 + - + +
901B IBM 4.9 2.9 + - - +
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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* 2.6 64.7 + - - +
773B PRO* 3.3 14.4 - - + +
775B GLN* 1.3 76.9 - - - +
777B ARG* 1.3 63.7 + - + +
779B ALA* 3.4 6.2 + - - +
780B GLU* 3.2 33.9 + - + +
853B TRP* 4.5 11.0 - - - -
856B LEU* 5.1 4.1 - - - +
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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
----------------------------------------------------------
562B SER* 3.8 10.5 + - - -
563B ASP* 4.5 9.5 + - - -
564B PHE* 3.0 60.3 - - + +
773B PRO 3.7 10.6 + - - +
774B ILE* 2.9 30.3 + - - +
776B GLN* 1.3 74.7 - - + +
778B ILE* 1.3 83.2 + - - +
779B ALA 3.2 1.8 - - - -
780B GLU* 2.9 32.9 + - + +
781B LEU* 3.5 21.9 + - + +
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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
----------------------------------------------------------
563B ASP* 5.0 1.1 - - - +
612B TYR* 3.6 31.6 - - + -
620B ASN* 3.8 25.8 - - - +
767B ALA* 4.1 24.5 - - + +
770B LYS* 5.7 1.8 - - + -
774B ILE* 2.9 31.4 + - + +
775B GLN* 4.3 5.2 - - - +
777B ARG* 1.3 93.6 - - - +
779B ALA* 1.3 64.3 + - - +
780B GLU 3.0 2.0 - - - -
781B LEU* 3.2 19.8 + - + +
782B VAL* 3.1 17.9 + - + +
901B IBM 5.7 0.2 - - - -
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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
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775B GLN* 2.9 28.7 + - - +
776B GLN 3.4 5.6 - - - +
778B ILE* 1.3 77.7 - - - +
780B GLU* 1.3 59.7 + - - +
782B VAL* 4.0 9.3 - - - +
783B ALA* 3.1 27.9 + - - +
813B LEU* 5.2 3.9 - - + +
817B GLN* 4.0 10.8 - - - +
853B TRP* 3.8 27.6 - - + -
901B IBM 5.5 1.1 - - - +
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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* 3.2 31.3 + - + +
777B ARG* 2.9 22.7 + - + +
779B ALA* 1.3 82.6 - - - +
781B LEU* 1.3 62.1 + - + +
783B ALA* 3.2 6.4 - - - +
784B THR* 2.8 31.8 + - + +
787B TRP* 5.2 0.9 - - - -
810B ARG* 5.6 3.6 + - - -
813B LEU* 4.5 14.9 - - - +
853B TRP* 5.1 1.6 - - - -
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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* 3.8 25.4 - - + +
612B TYR* 4.0 16.6 - - + -
614B ASN* 5.9 1.1 - - - +
777B ARG* 3.5 28.5 - - + +
778B ILE* 3.2 21.7 + - + +
780B GLU* 1.3 80.2 - - + +
782B VAL* 1.3 69.0 + - - +
783B ALA 2.9 1.1 - - - -
784B THR* 2.9 26.1 + - + +
785B GLU* 2.9 9.7 + - - +
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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* 3.8 34.0 - - + +
778B ILE* 3.1 20.6 - - + +
779B ALA* 4.0 7.6 - - - +
781B LEU* 1.3 75.0 - - - +
783B ALA* 1.3 66.0 + - - +
785B GLU* 3.3 2.5 + - - +
786B PHE* 3.0 53.9 + - + -
901B IBM 3.7 38.8 - - + +
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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 3.1 21.9 + - - +
780B GLU* 3.2 12.8 - - - +
782B VAL* 1.3 79.4 - - - +
784B THR* 1.3 65.3 + - - +
786B PHE* 3.1 8.0 + - - +
787B TRP* 3.0 53.2 + - + -
813B LEU* 4.9 10.1 - - + -
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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* 3.1 17.2 - - - +
780B GLU* 2.8 20.4 - - + +
781B LEU* 2.9 14.4 + - + +
783B ALA* 1.3 74.8 - - + +
785B GLU* 1.3 67.2 + - - +
787B TRP* 3.0 21.0 + - + +
788B GLU* 2.8 39.1 + - - +
807B ARG* 4.9 0.2 + - - -
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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* 3.5 6.1 - - - +
611B ALA* 3.5 17.3 - - + +
612B TYR* 2.9 25.2 + - - +
613B HIS* 2.9 37.9 + - - -
657B HIS* 4.0 1.6 - - - -
659B GLY* 3.2 38.5 - - - +
660B VAL* 4.0 0.5 + - - -
781B LEU 2.9 7.9 + - - +
782B VAL* 3.8 5.2 - - - +
784B THR* 1.3 82.1 + - - +
786B PHE* 1.3 72.1 + - + +
788B GLU* 3.3 9.2 - - + +
789B GLN* 3.1 18.5 + - - +
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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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613B HIS* 5.8 0.9 - + - -
661B ASN* 6.3 3.6 - - + -
782B VAL* 3.0 28.9 + - + -
783B ALA* 3.4 10.1 - - - +
785B GLU* 1.3 87.4 - - + +
787B TRP* 1.3 63.1 + - - +
789B GLN* 2.9 21.6 + - - +
790B GLY 2.9 10.6 + - - -
804B MET* 3.4 55.9 - - + +
805B MET* 3.6 24.5 - - + +
901B IBM 3.5 51.8 - + + -
85D GLY* 5.8 1.8 - - - -
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Residues in contact with TRP 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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780B GLU* 5.2 0.9 - - - -
783B ALA* 3.0 45.6 + - + +
784B THR* 3.5 20.0 - - + +
786B PHE* 1.3 76.1 - - - +
788B GLU* 1.3 57.9 + - - +
790B GLY* 3.2 2.1 + - - -
791B ASP* 3.0 34.0 + - - +
803B PRO 5.1 0.8 + - - -
804B MET 4.2 10.0 + - - -
805B MET* 3.6 12.2 - - - +
806B ASP 3.7 8.9 + - - -
807B ARG* 3.1 64.8 + - + +
809B LYS 5.4 0.4 - - - -
810B ARG* 3.5 51.7 - - + +
813B LEU* 5.0 11.7 - - + -
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Residues in contact with GLU 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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609B ASN 5.6 2.4 - - - +
611B ALA* 5.1 5.2 - - - +
659B GLY 5.7 1.6 - - - +
784B THR* 2.8 22.3 + - - +
785B GLU* 3.3 15.2 - - - +
787B TRP* 1.3 76.7 - - - +
789B GLN* 1.3 58.5 + - - +
791B ASP* 3.5 13.7 + - - +
792B LEU* 2.9 31.6 - - + +
807B ARG* 3.8 13.9 + - - +
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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 3.1 + - - +
660B VAL* 3.5 27.4 - - + -
661B ASN* 3.0 45.2 + - - +
664B TYR* 3.1 19.8 - - + +
667B ARG* 4.7 0.2 - - - +
785B GLU* 3.1 8.5 + - - +
786B PHE* 2.9 14.5 + - - +
788B GLU* 1.3 76.0 - - - +
790B GLY* 1.3 66.6 + - - +
792B LEU* 3.0 13.4 + - - +
793B GLU* 2.9 40.2 + - - +
805B MET* 3.6 19.1 - - + +
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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 2.9 10.5 + - - -
787B TRP 3.2 1.3 + - - -
789B GLN* 1.3 75.0 - - - +
791B ASP* 1.3 64.9 + - - +
793B GLU* 3.3 10.3 + - - -
794B ARG* 3.3 10.4 + - - +
801B PRO* 3.3 31.3 - - - +
805B MET* 3.1 26.9 - - - +
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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 TRP 3.0 12.8 + - - +
788B GLU* 3.5 14.6 - - - +
790B GLY* 1.3 77.4 - - - +
792B LEU* 1.3 60.1 + - + +
794B ARG* 3.2 14.8 + - - +
795B THR* 2.8 41.0 + - + +
807B ARG* 2.7 44.1 + - - +
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Residues in contact with LEU 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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660B VAL* 4.6 9.9 - - + -
664B TYR* 3.6 28.7 - - + +
788B GLU* 2.9 23.8 - - + +
789B GLN* 3.0 13.2 + - - +
791B ASP* 1.3 77.8 - - + +
793B GLU* 1.3 62.2 + - - +
795B THR* 3.2 8.7 - - - +
796B VAL* 2.9 38.4 + - + +
797B LEU 3.2 5.0 + - - -
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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 TYR* 3.8 16.1 - - + -
667B ARG* 3.3 28.2 + - - +
789B GLN* 2.9 29.4 + - - +
790B GLY* 3.5 8.7 - - - +
791B ASP 3.2 0.4 - - - -
792B LEU* 1.3 76.2 - - - +
794B ARG* 1.3 58.3 + - - +
797B LEU* 2.9 13.6 - - + +
798B GLN 2.8 21.3 + - - -
799B GLN* 2.9 15.1 + - + +
800B GLN 4.1 2.6 - - - +
801B PRO* 3.0 32.2 - - + +
802B ILE 4.2 1.6 + - - -
805B MET* 3.1 28.7 - - - +
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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 3.4 14.9 + - - +
791B ASP* 3.2 15.3 + - - +
793B GLU* 1.3 77.2 - - - +
795B THR* 1.3 64.8 + - + +
798B GLN* 3.6 22.7 + - - +
799B GLN 3.3 16.2 - - - +
800B GLN* 3.1 29.8 - - + +
801B PRO* 3.9 11.5 - - + +
805B MET 5.1 0.4 + - - -
806B ASP* 2.8 30.4 + - - +
807B ARG* 3.7 17.2 - - - +
808B ASN* 3.6 19.5 + - - -
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Residues in contact with THR 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791B ASP* 2.8 30.4 + - + +
792B LEU* 3.2 12.5 - - - +
794B ARG* 1.3 84.8 - - + +
796B VAL* 1.3 70.7 + - - +
798B GLN* 3.3 15.6 + - - +
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Residues in contact with VAL 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B TYR* 3.4 20.9 - - - +
668B SER* 5.7 1.6 - - - -
792B LEU* 2.9 23.0 + - + +
795B THR* 1.3 87.6 - - - +
797B LEU* 1.3 79.4 + - + +
798B GLN* 3.5 6.2 - - - +
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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