Contacts of the helix formed by residues 664 - 701 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662A VAL* 3.6 11.2 - - - +
663A SER* 1.3 79.5 + - - +
665A PRO* 1.3 68.7 - - + +
667A ASN* 2.9 42.9 + - + +
668A ARG* 2.9 32.7 + - - +
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Residues in contact with PRO 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A SER 3.2 6.8 - - - +
664A ASP* 1.3 84.4 - - + +
666A LYS* 1.3 76.6 + - + +
667A ASN* 5.4 0.2 - - - +
668A ARG* 3.1 19.8 - - + +
669A LYS* 3.2 11.3 + - - +
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Residues in contact with LYS 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A ASP* 4.9 0.2 - - - +
665A PRO* 1.3 86.6 - - + +
667A ASN* 1.3 68.6 + - - +
669A LYS* 3.0 31.8 - - + +
670A ALA* 3.0 24.3 + - - +
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Residues in contact with ASN 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A VAL* 4.0 6.5 - - + -
664A ASP* 2.9 44.5 - - + +
665A PRO* 3.3 1.0 - - - +
666A LYS* 1.3 79.5 - - - +
668A ARG* 1.3 64.4 + - - +
670A ALA* 3.5 7.1 + - - +
671A ILE* 3.3 27.4 + - + +
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Residues in contact with ARG 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A LEU* 3.1 51.7 + - - +
660A SER* 4.1 12.1 + - - +
662A VAL* 2.7 31.7 + - + +
663A SER* 4.3 4.2 - - - +
664A ASP 2.9 23.4 + - - +
665A PRO* 3.1 8.5 - - + +
667A ASN* 1.3 74.7 - - - +
669A LYS* 1.3 66.4 + - - +
671A ILE* 3.0 14.4 + - - +
672A GLU* 3.0 31.0 + - - +
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Residues in contact with LYS 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A PRO* 3.2 5.9 + - - +
666A LYS* 3.0 56.2 - - + +
668A ARG* 1.3 78.9 - - - +
670A ALA* 1.3 58.2 + - + +
672A GLU* 3.1 19.4 + - - +
673A ASN* 2.8 48.8 + - - +
676A ARG* 6.3 0.4 - - - +
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Residues in contact with ALA 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666A LYS 3.0 18.8 + - - +
667A ASN* 3.6 9.9 - - - +
669A LYS* 1.3 80.9 - - + +
671A ILE* 1.3 62.3 + - + +
673A ASN* 3.5 11.9 + - - +
674A GLN* 3.4 17.5 + - - +
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Residues in contact with ILE 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A ALA* 3.8 27.6 - - + +
658A GLN* 4.7 6.5 - - + +
659A LEU* 3.9 23.3 - - + +
662A VAL* 3.7 30.1 - - + -
667A ASN* 3.4 13.7 - - + +
668A ARG 3.0 6.7 + - - +
670A ALA* 1.3 76.6 - - + +
672A GLU* 1.3 61.2 + - - +
674A GLN* 3.1 14.8 + - + +
675A ILE* 2.9 32.1 + - + +
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Residues in contact with GLU 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A LEU* 4.1 16.2 - - + +
668A ARG* 3.0 36.6 + - - +
669A LYS* 3.4 21.2 + - - +
671A ILE* 1.3 74.7 - - - +
673A ASN* 1.3 59.5 + - - +
675A ILE* 3.1 11.7 + - - +
676A ARG* 2.8 56.1 + - + +
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Residues in contact with ASN 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A LYS* 2.8 37.1 + - - +
670A ALA* 3.6 11.2 - - - +
672A GLU* 1.3 74.8 - - - +
674A GLN* 1.3 62.7 + - - +
676A ARG* 2.7 39.5 + - - +
677A GLN* 3.2 20.4 + - - +
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Residues in contact with GLN 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A ALA* 4.2 13.5 - - - +
670A ALA 3.4 8.8 + - - +
671A ILE* 3.1 18.4 + - - +
673A ASN* 1.3 78.1 - - - +
675A ILE* 1.3 64.8 + - + +
677A GLN* 3.0 10.4 + - + +
678A TRP* 3.0 56.4 + - + +
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Residues in contact with ILE 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A LYS* 4.1 21.7 - - + +
655A ALA* 3.9 18.8 - - + -
656A GLU* 3.7 35.4 - - + +
659A LEU* 3.8 28.5 - - + -
671A ILE* 2.9 23.9 + - + +
672A GLU* 3.4 11.0 - - - +
674A GLN* 1.3 75.5 - - - +
676A ARG* 1.3 59.5 + - + +
678A TRP* 3.2 11.8 + - - +
679A GLU* 2.9 28.5 + - + +
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Residues in contact with ARG 676 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669A LYS* 6.3 0.2 - - - +
672A GLU* 2.8 39.2 + - + +
673A ASN* 2.7 49.0 - - - +
675A ILE* 1.3 76.9 - - + +
677A GLN* 1.3 57.4 + - - +
679A GLU* 3.4 14.5 - - - +
680A GLN* 2.9 39.5 + - + +
717A PRO* 6.2 3.8 - - - -
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Residues in contact with GLN 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673A ASN 3.2 11.5 + - - +
674A GLN* 3.0 13.3 + - + +
676A ARG* 1.3 74.0 - - - +
678A TRP* 1.3 60.9 + - + +
680A GLN* 3.1 21.2 + - - +
681A ASN* 2.8 68.6 + - - +
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Residues in contact with TRP 678 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647A MET* 5.7 0.9 - - + -
648A ASP* 3.6 42.2 - - + +
651A MET* 3.5 40.0 + - + -
652A LYS* 4.0 26.9 - - + -
655A ALA* 4.2 8.1 - - + +
674A GLN* 3.0 58.6 + - + +
675A ILE* 3.4 11.4 - - - +
677A GLN* 1.3 77.0 - - + +
679A GLU* 1.3 58.2 + - - +
681A ASN* 3.4 11.9 + - - +
682A LEU* 3.0 35.4 + - - +
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Residues in contact with GLU 679 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A LYS* 3.8 28.5 + - - +
675A ILE* 2.9 15.2 + - - +
676A ARG* 3.4 17.5 - - - +
678A TRP* 1.3 75.7 - - - +
680A GLN* 1.3 66.8 + - + +
682A LEU* 3.4 7.3 + - - +
683A GLU* 3.2 24.9 + - + +
715A SER* 3.2 37.1 + - - -
717A PRO* 3.9 16.5 - - - +
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Residues in contact with GLN 680 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676A ARG* 2.9 27.3 + - + +
677A GLN* 3.7 23.3 + - - +
679A GLU* 1.3 75.3 - - + +
681A ASN* 1.3 66.9 + - - +
683A GLU* 3.1 13.0 + - - +
684A LYS* 3.1 22.0 + - - +
737A VAL* 5.9 0.2 - - - +
740A ARG* 3.8 51.0 + - - +
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Residues in contact with ASN 681 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A ASP* 3.7 20.9 + - - +
677A GLN* 2.8 51.8 + - - +
678A TRP* 3.6 15.5 - - - +
679A GLU 3.3 0.2 - - - -
680A GLN* 1.3 75.7 - - - +
682A LEU* 1.3 57.2 + - - +
684A LYS* 3.3 8.5 + - - +
685A PHE* 3.0 42.8 + - + -
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Residues in contact with LEU 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A ILE* 3.6 34.3 - - + +
648A ASP* 3.6 28.3 - - + +
649A SER* 3.7 20.2 - - - +
652A LYS* 4.0 24.0 - - + -
678A TRP 3.0 22.0 + - - +
679A GLU* 3.6 6.7 - - - +
680A GLN 3.1 0.4 - - - -
681A ASN* 1.3 74.9 - - - +
683A GLU* 1.3 59.6 + - + +
685A PHE* 3.3 5.3 + - + +
686A HIS* 2.9 42.7 + - + +
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Residues in contact with GLU 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679A GLU* 3.2 13.0 + - + +
680A GLN* 3.1 16.0 + - - +
682A LEU* 1.3 77.2 - - + +
684A LYS* 1.3 58.1 + - - +
686A HIS* 3.3 8.9 + - - +
687A MET* 2.8 29.6 + - - +
713A ALA 3.9 15.7 - - - +
715A SER* 2.9 30.8 + - - +
718A SER* 2.7 25.9 + - - -
733A PHE* 3.7 23.6 - - + -
737A VAL* 4.3 4.2 - - + +
740A ARG* 2.6 32.5 + - - +
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Residues in contact with LYS 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680A GLN 3.1 12.0 + - - +
681A ASN* 3.5 11.4 - - - +
683A GLU* 1.3 73.8 - - - +
685A PHE* 1.3 67.1 + - + +
687A MET* 3.1 3.4 + - + +
688A ASP* 2.8 62.0 + - - +
737A VAL* 3.3 30.0 - - + +
741A ASP* 3.6 29.6 - - - +
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Residues in contact with PHE 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A LEU* 3.9 25.7 - - + +
644A LYS* 4.0 46.4 - - + -
645A ILE* 3.5 21.4 - - + +
648A ASP* 3.3 31.2 - - - -
681A ASN* 3.0 34.7 + - + +
682A LEU* 3.8 8.3 - - + +
683A GLU 3.3 0.4 - - - -
684A LYS* 1.3 82.0 - - + +
686A HIS* 1.3 57.2 + - - +
688A ASP* 3.3 6.3 + - - +
689A LEU* 2.8 30.1 + - - +
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Residues in contact with HIS 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A ILE* 3.9 35.8 - - + +
682A LEU* 2.9 37.0 + - + +
683A GLU* 3.6 5.6 - - - +
685A PHE* 1.3 76.4 - - - +
687A MET* 1.3 58.7 + - - +
689A LEU* 3.4 12.4 + - + +
690A PHE* 3.0 27.7 + - - +
709A SER 5.8 1.6 + - - -
710A LEU* 3.6 18.5 - - + +
713A ALA* 3.7 28.7 - - + +
733A PHE* 5.6 0.2 - - + -
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Residues in contact with MET 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ILE* 3.7 25.4 - - + -
683A GLU 2.8 16.8 + - - +
684A LYS* 3.1 8.5 + - + +
686A HIS* 1.3 75.1 - - - +
688A ASP* 1.3 67.4 + - - +
690A PHE* 3.3 3.9 + - - +
691A ARG* 3.0 23.8 + - - +
710A LEU* 3.8 19.5 - - + +
730A VAL* 4.1 1.8 - - - +
733A PHE* 3.3 40.4 - - + +
734A HIS* 3.4 48.5 - - + +
737A VAL* 4.2 12.6 - - + -
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Residues in contact with ASP 688 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641A LEU* 3.6 26.7 - - + +
684A LYS* 2.8 53.6 + - - +
685A PHE* 3.7 5.0 - - - +
687A MET* 1.3 78.2 - - - +
689A LEU* 1.3 57.2 + - - +
691A ARG* 3.3 32.1 + - - +
692A MET* 2.8 35.9 + - + +
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Residues in contact with LEU 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A THR* 3.8 42.2 - - - +
641A LEU* 3.5 12.7 - - + +
642A LEU* 3.6 26.0 - - + -
645A ILE* 4.1 13.2 - - + -
685A PHE 2.8 17.2 + - - +
686A HIS* 3.6 12.3 - - + +
687A MET 3.2 0.2 - - - -
688A ASP* 1.3 78.2 - - - +
690A PHE* 1.3 62.9 + - - +
692A MET* 3.3 3.0 + - - +
693A ARG* 3.0 57.1 + - - +
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Residues in contact with PHE 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ILE* 4.2 9.9 - - + -
574A GLN* 3.5 28.7 - - - -
686A HIS 3.0 14.3 + - - +
687A MET 3.3 7.6 + - - +
689A LEU* 1.3 76.6 - - - +
691A ARG* 1.3 59.2 + - - +
693A ARG* 3.1 10.6 + - - +
694A CYS* 2.9 48.3 + - - -
705A PRO* 3.3 43.5 - - + +
706A ASN 3.7 13.9 - - - -
707A PRO* 3.8 9.4 - - + -
710A LEU* 3.5 32.1 - - + -
730A VAL* 3.7 18.6 - - + -
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Residues in contact with ARG 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A ASP* 2.8 58.9 + - - +
572A ILE* 3.7 30.7 - - + -
621A PHE* 4.7 8.1 - - - -
687A MET* 3.0 17.0 + - - +
688A ASP* 3.6 28.1 + - - +
690A PHE* 1.3 77.2 - - - +
692A MET* 1.3 76.6 + - + +
694A CYS* 3.1 8.5 + - - +
695A TYR* 3.0 61.3 + - + +
734A HIS* 4.6 5.3 + - - -
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Residues in contact with MET 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621A PHE* 3.9 23.3 - - + -
634A LEU* 3.8 17.4 - - + +
637A GLN* 3.8 24.5 - - + -
638A THR* 3.7 18.2 - - + -
641A LEU* 3.9 16.8 - - + -
688A ASP* 2.8 25.0 + - + +
689A LEU* 3.6 5.4 - - - +
691A ARG* 1.3 95.4 - - - +
693A ARG* 1.3 57.5 + - - +
695A TYR* 3.3 34.1 + - + +
696A LEU* 3.0 32.6 + - - +
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Residues in contact with ARG 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638A THR* 4.6 12.2 - - + +
642A LEU* 4.3 17.4 - - - +
689A LEU* 3.0 55.3 + - - +
690A PHE* 3.1 9.9 + - - +
692A MET* 1.3 73.7 - - - +
694A CYS* 1.3 61.4 + - - +
696A LEU* 3.4 9.6 + - + +
697A ALA* 2.8 31.5 + - - +
705A PRO* 3.9 26.2 - - + +
703B GLU* 5.4 7.2 + - - -
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Residues in contact with CYS 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572A ILE* 4.4 7.2 - - + -
574A GLN* 4.1 10.5 - - - -
614A HIS* 3.6 26.9 - - + +
690A PHE* 2.9 49.3 + - - -
691A ARG* 3.3 9.9 - - - +
693A ARG* 1.3 77.6 - - - +
695A TYR* 1.3 66.3 + - + +
697A ALA 3.4 0.3 + - - -
698A SER* 3.0 27.5 + - - -
704A LEU* 3.6 6.5 - - - +
705A PRO* 3.6 17.3 - - - -
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Residues in contact with TYR 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ASP* 3.3 11.4 - - - -
571A SER 2.7 30.1 + - - -
614A HIS* 3.9 31.1 - + - +
617A CYS* 3.4 23.2 - - + +
618A ALA* 3.8 24.0 - - + -
621A PHE* 4.7 5.4 - - + -
634A LEU* 3.7 18.6 - - + -
691A ARG* 3.0 46.4 + - + +
692A MET* 3.6 26.7 - - + +
694A CYS* 1.3 78.2 - - + +
696A LEU* 1.3 63.4 + - - +
698A SER* 3.2 3.3 + - - -
699A LEU* 3.0 27.2 + - - +
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Residues in contact with LEU 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631A VAL* 3.8 31.2 - - + +
634A LEU* 3.5 41.3 - - + +
635A LYS* 4.0 15.3 - - + -
638A THR* 4.0 20.9 - - + +
692A MET 3.0 16.9 + - - +
693A ARG* 3.7 9.4 - - + +
695A TYR* 1.3 76.3 - - - +
697A ALA* 1.3 61.9 + - - +
699A LEU* 3.3 3.6 + - - +
700A GLN* 3.0 46.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A ARG 2.8 21.6 + - - +
694A CYS 3.8 3.6 - - - +
696A LEU* 1.3 73.6 - - - +
698A SER* 1.3 57.1 + - - +
700A GLN* 3.3 2.4 + - - -
701A GLY* 2.9 26.9 + - - -
702A GLY* 3.0 24.3 + - - +
703A GLU 3.5 24.0 - - - +
704A LEU* 3.9 14.6 - - + -
705A PRO* 4.5 0.7 - - + -
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Residues in contact with SER 698 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A VAL* 4.0 2.6 + - - +
611A THR* 3.6 42.3 + - - +
614A HIS* 3.2 40.2 + - - +
615A SER* 4.1 4.0 + - - -
694A CYS 3.0 13.7 + - - -
695A TYR 3.2 2.9 + - - -
697A ALA* 1.3 77.1 - - - +
699A LEU* 1.3 61.3 + - - +
700A GLN 3.7 0.2 + - - -
701A GLY* 4.0 5.8 + - - -
702A GLY 5.4 0.2 - - - -
704A LEU* 3.9 7.2 - - - +
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Residues in contact with LEU 699 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A SER* 3.6 34.8 - - - +
618A ALA* 4.1 10.5 - - + -
630A THR* 3.7 35.0 - - + -
631A VAL* 4.3 14.8 - - + -
634A LEU* 4.1 11.0 - - + -
695A TYR 3.0 15.7 + - - +
696A LEU* 3.9 4.5 - - - +
697A ALA 3.3 0.2 - - - -
698A SER* 1.3 78.5 - - - +
700A GLN* 1.3 63.6 + - + +
701A GLY 3.5 0.4 - - - -
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Residues in contact with GLN 700 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A VAL* 3.9 27.4 - - + +
635A LYS* 4.2 16.3 - - - +
696A LEU* 3.0 35.4 + - - +
697A ALA* 4.3 2.1 - - - +
699A LEU* 1.3 84.8 - - + +
701A GLY* 1.3 61.6 + - - +
702A GLY* 3.2 4.0 + - - +
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Residues in contact with GLY 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A ALA 2.9 6.2 + - - -
698A SER* 4.0 5.5 + - - -
699A LEU 3.5 2.6 - - - -
700A GLN* 1.3 78.1 - - - +
702A GLY* 1.3 63.0 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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