Contacts of the helix formed by residues 738 - 778 (chain E) in PDB entry 1NLW
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 SER 738 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737E ALA* 1.3 76.3 - - - +
739E ARG* 1.3 65.3 + - - +
740E ALA* 3.5 10.4 + - - +
741E GLN* 2.7 38.9 + - - +
742E ILE* 2.9 22.2 + - - +
807J G 4.1 27.1 + - - -
808J C 3.1 19.1 - - - -
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Residues in contact with ARG 739 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D LEU* 4.1 21.8 - - + -
715E ARG* 4.8 2.6 + - - +
718E ILE* 4.1 8.9 - - - +
719E LYS* 3.7 29.7 - - - +
722E PHE* 3.6 54.6 - - + +
738E SER* 1.3 74.7 - - - +
740E ALA* 1.3 58.0 + - - +
742E ILE* 3.3 5.1 + - + +
743E LEU* 3.0 34.2 + - - +
808J C 3.2 29.2 + - - +
809J A 3.3 26.8 + - - -
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Residues in contact with ALA 740 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513D ARG* 6.3 0.4 - - - +
516D HIS* 4.4 17.7 - - + +
517D LEU* 3.5 23.6 - - + +
520D SER* 5.4 0.4 - - - -
738E SER* 3.7 9.0 - - - +
739E ARG* 1.3 80.8 - - - +
741E GLN* 1.3 60.8 + - + +
743E LEU* 3.5 2.9 + - - +
744E ASP* 2.8 37.1 + - - +
807J G 5.8 3.8 - - - +
808J C 4.8 0.6 + - - -
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Residues in contact with GLN 741 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732E LEU* 4.3 5.9 - - + +
736E LYS 4.4 2.4 + - - +
737E ALA* 3.2 18.2 - - + +
738E SER* 2.7 45.6 + - - +
740E ALA* 1.3 74.3 - - + +
742E ILE* 1.3 60.1 + - - +
744E ASP* 4.6 3.4 - - - -
745E LYS* 2.9 41.9 + - + +
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Residues in contact with ILE 742 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722E PHE* 3.6 37.7 - - + +
723E HIS* 5.0 4.7 - - + -
725E LEU* 3.9 23.1 - - + -
726E ARG* 3.4 45.3 - - + +
732E LEU* 3.5 10.9 - - + +
737E ALA* 3.9 15.0 - - + +
738E SER 2.9 19.1 + - - +
739E ARG* 3.6 9.4 - - + +
741E GLN* 1.3 77.2 - - - +
743E LEU* 1.3 57.4 + - - +
746E ALA* 2.9 34.6 + - + +
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Residues in contact with LEU 743 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517D LEU* 3.9 21.1 - - + +
520D SER* 3.7 32.8 - - - +
521D LEU* 3.8 30.1 - - + +
524D LEU* 4.1 22.2 - - + +
543D LEU* 4.1 7.9 - - + -
722E PHE* 3.9 24.0 - - + -
725E LEU* 4.6 3.1 - - + -
739E ARG 3.0 20.2 + - - +
740E ALA 4.0 1.8 - - - +
742E ILE* 1.3 78.2 - - - +
744E ASP* 1.3 53.8 + - - +
746E ALA* 3.9 3.6 - - - +
747E THR* 2.6 38.0 + - - -
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Residues in contact with ASP 744 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516D HIS* 4.0 14.0 + - - -
520D SER* 2.8 27.2 + - - -
740E ALA* 2.8 23.1 + - - +
741E GLN* 4.2 3.2 - - - +
743E LEU* 1.3 75.4 - - - +
745E LYS* 1.3 60.7 + - + +
747E THR* 3.3 6.8 + - - -
748E GLU* 3.0 33.3 + - - +
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Residues in contact with LYS 745 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729E VAL* 3.8 4.1 - - + +
731E SER* 4.0 16.8 + - - +
732E LEU* 3.5 33.9 - - + -
741E GLN* 2.9 26.8 + - + +
744E ASP* 1.3 76.0 - - + +
746E ALA* 1.3 58.8 + - - +
748E GLU* 2.9 43.6 + - - +
749E TYR* 3.0 29.6 + - - +
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Residues in contact with ALA 746 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D LEU* 4.7 8.7 - - + -
546D ALA* 5.9 0.2 - - + -
550D ILE* 4.3 3.5 - - + +
725E LEU* 4.0 25.8 - - + -
729E VAL* 3.8 24.4 - - + +
742E ILE* 2.9 20.8 + - + +
743E LEU* 3.9 3.8 - - - +
745E LYS* 1.3 76.1 - - - +
747E THR* 1.3 58.5 + - - +
749E TYR* 3.4 1.9 + - - +
750E ILE* 3.0 36.6 + - - +
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Residues in contact with THR 747 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520D SER 4.7 2.8 + - - -
523D LYS* 4.0 32.5 - - + +
524D LEU* 4.0 22.9 + - - +
527D LEU* 3.4 25.5 - - + +
743E LEU 2.6 22.9 + - - -
744E ASP* 3.4 9.1 - - - -
745E LYS 3.2 0.2 - - - -
746E ALA* 1.3 77.1 - - - +
748E GLU* 1.3 61.9 + - - +
750E ILE* 3.3 4.1 + - - +
751E GLN* 3.0 31.7 + - - +
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Residues in contact with GLU 748 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731E SER* 5.9 0.4 - - - +
744E ASP* 3.0 16.2 + - - +
745E LYS* 2.9 58.1 + - + +
747E THR* 1.3 77.4 - - - +
749E TYR* 1.3 57.5 + - - +
751E GLN* 3.4 9.7 + - - +
752E TYR* 2.8 29.6 + - - +
755E ARG* 4.7 0.5 + - - -
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Residues in contact with TYR 749 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D ILE* 3.5 31.2 - - + -
554D GLU* 2.7 31.0 + - - +
728E SER 4.4 0.7 - - - -
729E VAL* 4.0 9.6 - - + -
730E PRO* 3.4 40.5 - - + +
745E LYS 3.0 19.3 + - - +
746E ALA* 3.8 3.8 - - - +
747E THR 3.2 0.4 - - - -
748E GLU* 1.3 75.5 - - - +
750E ILE* 1.3 61.5 + - - +
752E TYR* 3.1 22.2 + + - +
753E MET* 2.8 67.8 + - + +
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Residues in contact with ILE 750 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524D LEU* 3.7 27.4 - - + -
527D LEU* 4.1 27.6 - - + +
528D VAL* 4.9 3.6 - - + -
546D ALA* 4.7 6.5 - - + +
549D HIS* 4.2 13.7 - - + +
550D ILE* 3.5 29.8 - - + -
553D LEU* 3.7 23.7 - - + +
746E ALA* 3.0 22.1 + - + +
747E THR* 3.3 4.2 + - - +
749E TYR* 1.3 76.6 - - - +
751E GLN* 1.3 59.7 + - - +
753E MET* 3.3 4.6 + - - +
754E ARG* 3.0 35.1 + - + +
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Residues in contact with GLN 751 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523D LYS* 4.6 13.1 - - - +
527D LEU* 3.4 25.0 - - + +
747E THR* 3.0 26.2 + - - +
748E GLU* 3.7 7.3 - - - +
750E ILE* 1.3 74.6 - - - +
752E TYR* 1.3 62.1 + - - +
754E ARG* 3.2 29.8 + - - +
755E ARG* 2.7 61.0 + - - +
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Residues in contact with TYR 752 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748E GLU 2.8 18.1 + - - +
749E TYR* 3.5 24.7 - + - +
751E GLN* 1.3 75.5 - - - +
753E MET* 1.3 88.5 + - + +
755E ARG* 3.2 15.3 + - + +
756E LYS* 2.9 48.8 + - + +
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Residues in contact with MET 753 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550D ILE* 5.8 0.9 - - + +
553D LEU* 4.1 25.1 - - + -
554D GLU* 4.6 15.3 - - + -
557D ASP* 4.6 8.1 - - - +
749E TYR* 2.8 56.3 + - + +
750E ILE* 3.6 4.9 - - - +
752E TYR* 1.3 105.1 - - + +
754E ARG* 1.3 61.1 + - - +
756E LYS* 3.1 27.9 - - + +
757E ASN* 3.0 37.7 + - - +
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Residues in contact with ARG 754 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D LEU* 3.0 50.4 + - - +
529D PRO* 5.7 4.6 - - - +
549D HIS* 5.9 1.0 + - - -
553D LEU* 4.9 14.1 - - + +
750E ILE* 3.0 20.8 + - + +
751E GLN* 3.2 32.6 + - - +
753E MET* 1.3 77.7 - - - +
755E ARG* 1.3 60.1 + - + +
757E ASN* 4.1 4.6 - - - +
758E HIS* 3.2 24.4 + - - +
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Residues in contact with ARG 755 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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748E GLU 4.7 0.4 + - - -
751E GLN* 2.7 73.4 + - - +
752E TYR* 3.2 14.6 - - + +
753E MET 3.2 0.2 - - - -
754E ARG* 1.3 79.7 - - + +
756E LYS* 1.3 59.0 + - - +
757E ASN 3.2 0.4 - - - -
758E HIS* 3.6 6.2 - - - +
759E THR* 3.0 34.7 + - - +
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Residues in contact with LYS 756 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557D ASP* 3.0 39.0 - - - +
561D VAL* 5.5 1.8 - - - +
752E TYR* 2.9 40.5 + - + +
753E MET* 3.1 27.8 + - + +
755E ARG* 1.3 75.8 - - - +
757E ASN* 1.3 59.0 + - - +
759E THR* 3.6 5.0 + - - -
760E HIS* 3.2 49.5 + - + +
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Residues in contact with ASN 757 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D LEU* 3.5 33.2 + - + +
556D SER* 3.4 14.0 - - - +
557D ASP* 3.3 34.0 + - - +
560D ALA* 4.3 6.4 - - - +
753E MET* 3.0 28.2 + - - +
754E ARG* 4.1 5.2 - - - +
756E LYS* 1.3 76.7 - - - +
758E HIS* 1.3 59.7 + - - +
760E HIS* 3.3 6.4 + - - +
761E GLN* 2.9 28.1 + - - +
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Residues in contact with HIS 758 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754E ARG 3.2 17.3 + - - +
755E ARG* 3.6 8.7 - - - +
757E ASN* 1.3 74.9 - - - +
759E THR* 1.3 68.7 + - - +
761E GLN* 3.2 11.2 + - + +
762E GLN* 3.0 30.7 + - + +
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Residues in contact with THR 759 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755E ARG* 3.0 18.2 + - - +
756E LYS* 3.7 8.0 - - - -
758E HIS* 1.3 79.8 - - - +
760E HIS* 1.3 63.8 + - + +
762E GLN* 3.0 15.2 + - + +
763E ASP* 2.7 40.9 + - - +
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Residues in contact with HIS 760 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D ASP* 3.2 29.0 + - - -
560D ALA* 3.8 30.0 - - + +
561D VAL* 3.4 26.6 - - + +
564D ILE* 4.0 13.2 - - + +
756E LYS* 3.2 33.6 + - + +
757E ASN* 3.3 9.5 + - - +
759E THR* 1.3 82.2 - - + +
761E GLN* 1.3 52.6 + - - +
763E ASP* 3.0 15.9 + - - +
764E ILE* 2.7 41.3 + - - +
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Residues in contact with GLN 761 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757E ASN 2.9 14.2 + - - +
758E HIS* 3.4 17.0 - - + +
759E THR 3.2 0.2 - - - -
760E HIS* 1.3 76.2 - - - +
762E GLN* 1.3 62.7 + - - +
764E ILE* 3.4 24.3 + - - +
765E ASP* 2.9 51.0 + - - +
768E LYS* 5.7 1.8 - - - +
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Residues in contact with GLN 762 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758E HIS* 3.0 20.8 + - + +
759E THR* 3.0 15.0 + - - +
761E GLN* 1.3 76.9 - - - +
763E ASP* 1.3 64.7 + - - +
765E ASP* 3.9 3.4 + - - +
766E ASP* 2.6 47.4 + - - +
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Residues in contact with ASP 763 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D ILE* 3.7 18.0 - - + +
759E THR* 2.7 40.5 + - - +
760E HIS* 3.0 16.4 + - - +
762E GLN* 1.3 80.7 + - - +
764E ILE* 1.3 60.0 + - - +
766E ASP* 3.1 7.7 + - - +
767E LEU* 2.9 40.3 + - + +
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Residues in contact with ILE 764 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560D ALA* 4.1 21.1 - - + -
563D GLN* 3.4 50.0 - - + +
564D ILE* 3.7 14.4 - - + -
567D LEU* 3.6 11.1 - - + +
760E HIS 2.7 24.4 + - - +
761E GLN* 3.6 27.1 - - - +
763E ASP* 1.3 71.4 - - - +
765E ASP* 1.3 63.9 + - - +
767E LEU* 3.1 7.0 + - - +
768E LYS* 3.0 34.8 + - - +
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Residues in contact with ASP 765 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761E GLN* 2.9 35.4 + - - +
762E GLN* 4.4 3.6 - - - +
764E ILE* 1.3 75.7 - - - +
766E ASP* 1.3 67.1 + - - +
768E LYS* 3.5 25.8 + - - +
769E ARG* 3.4 26.8 + - - +
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Residues in contact with ASP 766 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762E GLN* 2.6 42.8 + - - +
763E ASP* 3.1 8.6 + - - +
765E ASP* 1.3 77.8 - - - +
767E LEU* 1.3 69.0 + - + +
769E ARG* 3.1 22.5 + - - +
770E GLN* 3.2 21.2 + - + +
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Residues in contact with LEU 767 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564D ILE* 3.5 47.6 - - + +
567D LEU* 3.8 22.0 - - + -
568D GLN* 3.8 16.6 - - + +
571D GLN* 4.8 5.8 - - - +
763E ASP* 2.9 20.2 + - + +
764E ILE 3.4 6.7 - - - +
766E ASP* 1.3 80.7 - - + +
768E LYS* 1.3 54.8 + - - +
770E GLN* 3.2 24.2 + - - +
771E ASN* 3.1 36.7 + - - +
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Residues in contact with LYS 768 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563D GLN* 4.5 11.9 - - - +
567D LEU* 4.2 16.6 - - + -
761E GLN* 5.7 1.4 - - - +
764E ILE* 3.0 33.9 + - - +
765E ASP* 3.7 28.4 + - - +
766E ASP 3.1 0.4 - - - -
767E LEU* 1.3 74.8 - - - +
769E ARG* 1.3 55.7 + - + +
771E ASN* 3.3 6.7 + - - +
772E ALA* 2.7 36.8 + - - +
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Residues in contact with ARG 769 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765E ASP* 3.4 17.8 + - - +
766E ASP* 3.1 13.5 + - - +
768E LYS* 1.3 76.4 - - - +
770E GLN* 1.3 65.4 + - + +
772E ALA* 2.9 17.8 + - - +
773E LEU* 3.0 26.0 + - + +
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Residues in contact with GLN 770 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571D GLN* 2.8 38.6 + - - +
766E ASP* 3.2 15.9 + - + +
767E LEU* 3.2 28.1 - - - +
769E ARG* 1.3 75.4 - - + +
771E ASN* 1.3 61.0 + - - +
773E LEU* 3.6 11.1 + - - +
774E LEU* 3.3 26.7 + - + +
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Residues in contact with ASN 771 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567D LEU* 3.3 36.2 + - - +
570D GLU* 3.3 27.5 + - - +
571D GLN* 3.1 37.9 + - - +
574D LEU* 3.6 10.2 - - + +
767E LEU* 3.1 18.3 + - - +
768E LYS* 3.8 4.7 - - - +
770E GLN* 1.3 74.0 - - - +
772E ALA* 1.3 64.2 + - - +
773E LEU 3.2 0.2 - - - -
774E LEU* 3.3 1.3 + - - +
775E GLU* 2.9 36.8 + - - +
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Residues in contact with ALA 772 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768E LYS 2.7 22.1 + - - +
769E ARG* 2.9 9.4 + - - +
771E ASN* 1.3 73.5 - - - +
773E LEU* 1.3 61.9 + - + +
775E GLU* 3.6 14.0 + - - +
776E GLN* 3.2 24.9 + - - +
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Residues in contact with LEU 773 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769E ARG* 3.0 27.2 + - + +
770E GLN* 3.9 8.3 - - - +
771E ASN 3.2 0.2 - - - -
772E ALA* 1.3 78.1 - - + +
774E LEU* 1.3 67.2 + - + +
775E GLU 3.1 1.8 - - - -
776E GLN* 3.0 24.6 + - - +
777E GLN* 2.9 31.8 + - + +
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Residues in contact with LEU 774 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D GLN* 3.6 35.7 - - + +
574D LEU* 3.5 26.2 - - + -
575D LYS* 3.9 29.8 - - + -
578D LEU* 4.0 16.7 - - + +
770E GLN 3.3 13.8 + - - +
771E ASN* 3.3 3.1 + - - +
773E LEU* 1.3 79.0 - - + +
775E GLU* 1.3 57.0 + - - +
777E GLN* 3.5 21.2 + - - +
778E VAL* 2.9 33.3 + - - +
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Residues in contact with GLU 775 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D GLU* 4.7 6.0 - - - +
574D LEU* 3.7 19.7 - - + -
771E ASN* 2.9 32.5 + - - +
772E ALA* 3.7 11.8 + - - +
773E LEU 3.1 0.4 - - - -
774E LEU* 1.3 74.4 - - - +
776E GLN* 1.3 66.6 + - - +
777E GLN 2.9 1.6 - - - -
778E VAL* 2.9 28.5 + - - +
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Residues in contact with GLN 776 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772E ALA 3.2 11.0 + - - +
773E LEU* 3.0 27.9 + - - +
775E GLU* 1.3 79.6 - - - +
777E GLN* 1.3 64.3 + - - +
778E VAL 4.6 1.4 - - - -
----------------------------------------------------------
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Residues in contact with GLN 777 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D LEU* 4.3 12.3 - - + +
773E LEU* 2.9 16.2 + - + +
774E LEU* 3.5 37.1 + - - +
776E GLN* 1.3 81.9 - - + +
778E VAL* 1.3 69.9 + - - +
----------------------------------------------------------
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Residues in contact with VAL 778 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D LEU* 4.3 17.0 - - + +
577D GLN* 5.6 6.5 - - + +
578D LEU* 3.3 35.0 - - + -
774E LEU 2.9 24.0 - - - +
775E GLU* 2.9 18.4 + - - +
776E GLN 4.6 1.3 - - - -
777E GLN* 1.3 83.8 - - - +
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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