Contacts of the helix formed by residues 664 - 701 (chain B) in PDB entry 3A8P
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 664 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B VAL* 3.6 3.0 - - + +
663B SER* 1.3 78.5 - - - +
665B PRO* 1.3 66.4 - - - +
666B LYS* 2.8 46.5 + - - +
667B ASN* 3.0 26.9 + - + +
668B ARG* 2.9 23.9 + - - +
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Residues in contact with PRO 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B SER 2.9 10.4 - - - +
664B ASP* 1.3 86.9 - - - +
666B LYS* 1.3 59.3 + - + +
668B ARG* 3.4 12.3 - - + +
669B LYS* 2.8 33.4 + - - +
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Residues in contact with LYS 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B ASP* 2.8 20.5 + - - +
665B PRO* 1.3 82.4 - - + +
667B ASN* 1.3 64.0 + - - +
669B LYS* 4.5 3.2 - - - +
670B ALA* 3.5 19.4 + - - +
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Residues in contact with ASN 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B VAL* 3.8 14.9 - - + +
664B ASP* 3.0 26.0 + - + +
666B LYS* 1.3 82.0 + - - +
668B ARG* 1.3 61.7 + - - +
670B ALA* 3.4 6.6 + - - +
671B ILE* 3.0 38.1 + - + +
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Residues in contact with ARG 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659B LEU* 2.7 52.6 + - + +
660B SER* 5.0 2.4 - - - +
662B VAL* 2.6 47.8 + - + +
663B SER 4.7 6.1 - - - -
664B ASP 2.9 12.0 + - - +
665B PRO* 3.1 14.3 + - + +
667B ASN* 1.3 78.4 - - - +
669B LYS* 1.3 57.1 + - - +
671B ILE* 3.1 3.5 + - - +
672B GLU* 2.8 46.3 + - - +
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Residues in contact with LYS 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B PRO 2.8 19.2 + - - +
666B LYS* 4.6 3.8 - - - +
668B ARG* 1.3 74.4 - - - +
670B ALA* 1.3 59.4 + - - +
672B GLU* 3.5 10.3 - - + +
673B ASN* 2.7 57.8 + - - +
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Residues in contact with ALA 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B LYS 3.5 15.5 + - - +
667B ASN* 3.5 13.0 - - - +
668B ARG 3.1 0.6 - - - -
669B LYS* 1.3 79.0 - - - +
671B ILE* 1.3 66.4 + - + +
673B ASN* 3.8 7.2 - - - +
674B GLN* 3.0 23.4 + - - +
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Residues in contact with ILE 671 (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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655B ALA* 3.5 28.7 - - + +
658B GLN* 3.9 23.8 - - + +
659B LEU* 4.1 12.3 - - + +
662B VAL* 3.9 30.7 - - + -
667B ASN* 3.0 18.8 + - + +
668B ARG 3.4 6.7 - - - +
670B ALA* 1.3 77.0 - - + +
672B GLU* 1.3 63.9 + - - +
674B GLN* 3.2 8.4 + - - +
675B ILE* 2.9 36.0 + - + +
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Residues in contact with GLU 672 (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 LEU* 3.0 34.2 - - + +
668B ARG* 2.8 45.2 + - - +
669B LYS* 3.5 14.8 + - + +
671B ILE* 1.3 75.4 - - - +
673B ASN* 1.3 65.7 + - - +
675B ILE* 3.0 12.5 + - - +
676B ARG* 2.9 22.5 + - - +
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Residues in contact with ASN 673 (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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669B LYS* 2.7 49.1 + - - +
670B ALA* 3.8 6.3 - - - +
672B GLU* 1.3 80.8 - - - +
674B GLN* 1.3 58.0 + - - +
676B ARG* 3.1 10.4 + - - +
677B GLN* 2.9 29.6 + - - +
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Residues in contact with GLN 674 (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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670B ALA 3.0 14.3 + - - +
671B ILE* 3.4 12.3 - - - +
673B ASN* 1.3 76.4 - - - +
675B ILE* 1.3 57.4 + - - +
677B GLN* 3.2 17.3 + - - +
678B TRP* 2.9 87.5 + - + +
681B ASN* 6.0 0.2 - - - +
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Residues in contact with ILE 675 (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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652B LYS* 4.4 13.5 - - + +
655B ALA* 4.0 14.8 - - + -
656B GLU* 3.6 36.1 - - + +
659B LEU* 4.5 12.1 - - + -
671B ILE* 2.9 33.3 + - + +
672B GLU* 3.0 10.1 + - - +
674B GLN* 1.3 74.8 - - - +
676B ARG* 1.3 65.7 + - - +
678B TRP* 3.1 13.2 + - + +
679B GLU* 2.9 39.2 + - + +
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Residues in contact with ARG 676 (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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672B GLU 2.9 11.7 + - - +
673B ASN* 3.3 15.5 - - - +
675B ILE* 1.3 79.8 - - - +
677B GLN* 1.3 62.5 + - - +
679B GLU* 3.3 20.2 + - - +
680B GLN* 3.2 43.7 + - - +
683B GLU* 5.8 0.6 + - - -
715B SER* 4.8 6.9 + - - -
717B PRO* 4.3 29.8 - - - +
718B SER* 5.8 0.4 + - - -
740B ARG* 5.5 4.9 - - - +
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Residues in contact with GLN 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B ASN 2.9 12.8 + - - +
674B GLN* 3.5 21.3 - - - +
676B ARG* 1.3 79.3 - - - +
678B TRP* 1.3 62.4 + - - +
680B GLN* 3.3 23.5 + - - +
681B ASN* 3.0 58.3 + - - +
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Residues in contact with TRP 678 (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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648B ASP* 3.6 39.7 + - + +
651B MET* 3.4 55.3 - - + +
652B LYS* 3.6 27.1 - - + -
655B ALA* 3.5 18.6 - - + -
674B GLN* 2.9 63.8 + - + +
675B ILE* 3.1 9.6 + - - +
677B GLN* 1.3 74.3 - - - +
679B GLU* 1.3 60.6 + - - +
681B ASN* 3.0 11.3 + - - +
682B LEU* 2.8 37.9 + - + +
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Residues in contact with GLU 679 (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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652B LYS* 3.5 25.3 + - - +
656B GLU* 5.6 0.2 - - - +
675B ILE* 2.9 29.0 + - - +
676B ARG* 3.6 19.6 + - - +
677B GLN 3.3 0.2 - - - -
678B TRP* 1.3 75.6 - - - +
680B GLN* 1.3 57.5 + - - +
682B LEU* 3.2 12.9 + - - +
683B GLU* 3.0 32.8 + - - +
713B ALA 4.8 2.6 - - - +
715B SER* 3.8 29.1 - - - -
716B ARG 5.1 1.3 + - - -
717B PRO* 4.7 6.1 - - - +
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Residues in contact with GLN 680 (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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676B ARG* 3.2 36.5 + - - +
677B GLN* 3.7 26.7 + - - +
678B TRP 3.2 0.6 - - - -
679B GLU* 1.3 76.4 - - - +
681B ASN* 1.3 66.1 + - - +
683B GLU* 3.2 19.9 + - - +
684B LYS* 3.3 12.6 + - - +
715B SER* 6.1 0.2 - - - -
740B ARG* 3.6 34.4 + - - +
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Residues in contact with ASN 681 (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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648B ASP* 3.3 26.8 + - - +
674B GLN* 6.0 0.2 - - - +
677B GLN* 3.0 46.6 + - - +
678B TRP* 3.5 15.0 - - - +
680B GLN* 1.3 77.0 - - - +
682B LEU* 1.3 57.6 + - - +
684B LYS* 3.3 7.8 + - - +
685B PHE* 2.9 43.5 + - + -
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Residues in contact with LEU 682 (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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645B ILE* 3.9 33.0 - - + +
648B ASP* 4.1 14.4 - - + -
649B SER* 3.7 30.7 - - - +
652B LYS* 3.8 28.7 - - + -
678B TRP 2.8 21.6 + - - +
679B GLU* 3.4 8.3 - - - +
681B ASN* 1.3 75.3 - - - +
683B GLU* 1.3 59.4 + - - +
685B PHE* 4.1 4.0 - - + -
686B HIS* 2.8 45.8 + - + +
713B ALA* 5.1 4.3 - - + +
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Residues in contact with GLU 683 (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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676B ARG* 5.8 0.7 + - - -
679B GLU 3.0 20.9 + - - +
680B GLN* 3.2 9.5 + - - +
682B LEU* 1.3 75.2 - - - +
684B LYS* 1.3 57.6 + - - +
686B HIS* 3.7 3.4 - - - +
687B MET* 2.8 32.4 + - - +
713B ALA* 3.5 17.7 - - - +
714B THR* 3.7 2.4 - - - -
715B SER* 2.8 30.1 + - - +
718B SER* 2.6 27.3 + - - -
733B PHE* 3.7 25.3 - - + -
737B VAL* 4.4 4.7 - - + +
740B ARG* 2.5 35.6 + - - +
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Residues in contact with LYS 684 (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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680B GLN 3.3 8.0 + - - +
681B ASN* 3.5 10.1 - - - +
682B LEU 3.2 0.2 - - - -
683B GLU* 1.3 79.7 - - - +
685B PHE* 1.3 70.4 + - + +
687B MET* 3.1 2.8 + - - +
688B ASP* 2.6 54.2 + - - +
737B VAL* 3.6 29.5 - - + +
740B ARG* 5.7 0.4 - - - +
741B ASP* 4.5 22.7 + - - -
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Residues in contact with PHE 685 (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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641B LEU* 4.1 22.0 - - + +
644B LYS* 3.4 51.6 - - + -
645B ILE* 3.4 24.1 - - + +
648B ASP* 3.5 25.8 - - - -
681B ASN* 2.9 34.8 + - + +
682B LEU* 3.9 9.0 - - + +
683B GLU 3.4 0.2 - - - -
684B LYS* 1.3 82.3 - - + +
686B HIS* 1.3 58.6 + - - +
688B ASP* 3.4 3.9 + - - +
689B LEU* 3.0 28.4 + - - +
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Residues in contact with HIS 686 (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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642B LEU* 6.3 0.4 - - + -
645B ILE* 3.7 35.7 - - + +
649B SER* 5.3 1.2 + - - -
682B LEU* 2.8 41.8 + - + +
683B GLU 3.8 2.2 - - - +
685B PHE* 1.3 70.4 - - - +
687B MET* 1.3 59.9 + - - +
689B LEU* 3.4 14.6 + - + +
690B PHE* 3.0 30.0 + - - +
709B SER 5.2 6.6 + - - -
710B LEU* 3.6 20.4 - - + +
713B ALA* 3.6 24.2 - - + +
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Residues in contact with MET 687 (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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572B ILE* 3.9 15.4 - - + +
683B GLU 2.8 16.6 + - - +
684B LYS 3.1 5.4 + - - +
686B HIS* 1.3 74.5 - - - +
688B ASP* 1.3 70.2 + - - +
690B PHE* 3.3 3.7 + - - +
691B ARG* 3.0 23.9 + - - +
710B LEU* 3.6 22.4 - - + +
730B VAL* 4.4 1.1 - - - +
733B PHE* 3.3 44.6 - - + +
734B HIS* 3.7 45.8 - - + +
737B VAL* 4.3 19.5 - - + -
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Residues in contact with ASP 688 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 3.8 25.7 - - + +
684B LYS* 2.6 55.6 + - - +
685B PHE* 3.9 3.6 - - - +
687B MET* 1.3 78.8 - - - +
689B LEU* 1.3 57.7 + - - +
691B ARG* 3.3 28.0 + - - +
692B MET* 2.9 36.0 + - + +
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Residues in contact with LEU 689 (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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638B THR* 3.9 35.4 - - - +
641B LEU* 3.6 10.4 - - + +
642B LEU* 3.7 25.1 - - + -
645B ILE* 3.8 17.3 - - + -
685B PHE 3.0 18.6 + - - +
686B HIS* 3.6 14.6 - - + +
688B ASP* 1.3 77.0 - - - +
690B PHE* 1.3 57.8 + - - +
692B MET* 3.3 3.0 + - - +
693B ARG* 2.9 72.8 + - - +
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Residues in contact with PHE 690 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ILE* 4.2 12.6 - - + -
574B GLN* 3.6 29.8 - - - -
686B HIS 3.0 17.5 + - - +
687B MET 3.3 4.9 + - - +
689B LEU* 1.3 74.4 - - - +
691B ARG* 1.3 61.0 + - - +
693B ARG* 3.2 8.2 + - - +
694B CYS* 2.9 50.0 + - - -
705B PRO* 3.5 40.8 - - + +
706B ASN 3.7 16.2 - - - -
707B PRO* 3.9 8.5 - - + -
710B LEU* 3.7 31.0 - - + -
730B VAL* 3.8 14.6 - - + -
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Residues in contact with ARG 691 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ASP* 2.9 51.7 + - - +
572B ILE* 3.7 29.2 - - + -
621B PHE* 4.3 9.1 - - - -
687B MET* 3.0 13.6 + - - +
688B ASP* 3.6 28.2 + - - +
690B PHE* 1.3 75.0 - - - +
692B MET* 1.3 80.4 + - + +
694B CYS* 3.1 3.9 + - - +
695B TYR* 3.0 73.0 + - + +
734B HIS* 4.6 6.4 + - - -
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Residues in contact with MET 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B PHE* 3.8 35.2 - - + -
634B LEU* 3.7 22.8 - - + +
637B GLN* 3.8 24.0 - - + -
638B THR* 3.4 22.7 - - + -
641B LEU* 4.0 17.5 - - + -
688B ASP* 2.9 23.1 + - + +
689B LEU 3.6 2.5 - - - +
691B ARG* 1.3 97.9 - - - +
693B ARG* 1.3 58.9 + - - +
695B TYR* 3.3 14.9 + - + +
696B LEU* 2.8 30.0 + - - +
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Residues in contact with ARG 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703A GLU* 4.6 13.8 + - - -
638B THR* 4.7 8.3 - - + +
642B LEU* 4.0 27.3 - - - +
689B LEU* 2.9 51.6 + - + +
690B PHE* 3.6 6.5 - - - +
691B ARG 3.2 0.2 - - - -
692B MET* 1.3 73.7 - - - +
694B CYS* 1.3 61.2 + - - +
696B LEU* 3.5 11.0 - - + +
697B ALA* 2.8 32.1 + - - +
705B PRO* 3.7 27.4 - - + +
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Residues in contact with CYS 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ILE* 4.6 6.1 - - + -
574B GLN* 4.0 10.8 - - - -
614B HIS* 3.6 24.5 - - + +
690B PHE* 2.9 48.8 + - - -
691B ARG* 3.4 9.0 - - - +
693B ARG* 1.3 75.0 - - - +
695B TYR* 1.3 62.8 + - + +
697B ALA* 3.3 1.9 + - - +
698B SER* 2.9 33.8 + - - -
704B LEU* 3.8 14.4 - - - +
705B PRO* 3.7 11.7 - - - -
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Residues in contact with TYR 695 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B ASP* 3.2 21.5 - - - -
571B SER 2.6 31.1 + - - -
614B HIS* 3.7 34.8 - + + -
617B CYS* 3.4 23.0 - - + +
618B ALA* 3.7 23.1 - - + -
621B PHE* 4.6 4.3 - - + -
634B LEU* 3.9 26.0 - - + -
691B ARG* 3.0 46.4 + - + -
692B MET* 3.6 12.6 - - + +
694B CYS* 1.3 76.5 - - + +
696B LEU* 1.3 64.2 + - - +
698B SER* 3.4 1.6 + - - -
699B LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B VAL* 3.9 28.3 - - + +
634B LEU* 3.5 30.5 - - + +
635B LYS* 4.1 22.4 - - + +
638B THR* 4.5 23.6 - - + +
692B MET 2.8 14.4 + - - +
693B ARG* 3.5 10.3 - - + +
695B TYR* 1.3 76.7 - - - +
697B ALA* 1.3 61.6 + - - +
699B LEU* 3.3 2.6 + - - -
700B GLN* 3.0 43.8 + - - +
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Residues in contact with ALA 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B ARG 2.8 21.8 + - - +
694B CYS 3.7 3.4 - - - +
696B LEU* 1.3 73.0 - - - +
698B SER* 1.3 57.3 + - - +
700B GLN* 3.2 1.3 + - - -
701B GLY* 2.8 28.2 + - - -
702B GLY* 2.9 23.3 + - - +
703B GLU 3.3 28.7 - - - +
704B LEU* 3.9 11.7 - - + -
705B PRO* 4.5 0.4 - - + -
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Residues in contact with SER 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B VAL* 4.3 2.4 - - - +
611B THR* 3.5 42.0 + - - +
614B HIS* 2.9 43.5 + - - +
615B SER* 4.2 4.2 + - - -
694B CYS 2.9 13.1 + - - -
695B TYR 3.9 2.2 - - - -
697B ALA* 1.3 75.7 - - - +
699B LEU* 1.3 60.2 + - - +
701B GLY* 3.9 6.5 + - - -
702B GLY 5.4 0.2 - - - -
704B LEU* 3.9 9.7 - - - +
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Residues in contact with LEU 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B SER* 3.9 28.9 - - - +
618B ALA* 3.9 9.4 - - + -
630B THR* 3.7 32.1 - - + -
631B VAL* 4.2 16.6 - - + -
634B LEU* 3.8 17.0 - - + -
695B TYR 3.0 15.0 + - - +
696B LEU* 3.8 3.8 - - - +
698B SER* 1.3 77.8 - - - +
700B GLN* 1.3 64.4 + - + +
701B GLY 3.5 0.4 + - - -
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Residues in contact with GLN 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631B VAL* 3.8 32.0 - - + +
635B LYS* 4.0 16.3 + - - +
696B LEU* 3.0 33.5 + - + +
697B ALA* 4.4 1.7 - - - +
699B LEU* 1.3 82.0 - - + +
701B GLY* 1.3 63.6 + - - +
702B GLY* 3.1 4.4 + - - +
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Residues in contact with GLY 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B ALA 2.8 5.8 + - - -
698B SER* 3.9 5.6 + - - -
699B LEU 3.5 3.6 + - - -
700B GLN* 1.3 78.6 - - - +
702B GLY* 1.3 63.4 + - - +
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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) + - + + + + + -
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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