Contacts of the helix formed by residues 615 - 649 (chain C) in PDB entry 5DO7
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 GLY 615 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A ILE* 5.1 4.9 - - - -
647A HIS* 3.3 35.5 + - - +
613C CYS 3.6 0.2 - - - -
614C PRO* 1.3 83.3 - - - +
616C ALA* 1.3 53.9 + - - +
617C THR 3.7 0.2 - - - -
619C ARG* 2.6 47.4 + - - +
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Residues in contact with ALA 616 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573C GLU* 3.5 26.9 - - + +
577C VAL* 3.3 22.9 - - + -
613C CYS* 3.4 19.7 - - + +
614C PRO 3.0 1.4 - - - -
615C GLY* 1.3 75.5 - - - +
617C THR* 1.3 70.1 + - - +
618C SER 3.1 2.5 - - - -
619C ARG* 2.8 24.3 + - - +
620C PHE* 2.8 14.9 + - - +
623C ASN* 4.7 0.4 - - - +
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Residues in contact with THR 617 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A HIS* 4.4 3.6 - - - -
577C VAL* 3.7 15.5 - - + +
581C TYR* 5.3 6.9 + - - -
606C ILE* 5.7 4.9 - - + -
609C ILE* 3.6 26.0 - - + -
610C GLU* 3.6 23.9 + - - +
614C PRO 3.9 8.5 + - - +
616C ALA* 1.3 76.6 - - - +
618C SER* 1.3 78.7 + - - +
620C PHE* 3.8 12.1 - - - +
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Residues in contact with SER 618 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A HIS* 3.4 28.0 - - - -
615C GLY 4.1 0.8 + - - -
616C ALA 2.9 1.2 + - - -
617C THR* 1.3 88.5 + - - +
619C ARG* 1.3 64.6 + - - +
620C PHE* 3.2 1.5 + - - +
621C THR* 4.1 16.1 + - - +
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Residues in contact with ARG 619 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A VAL* 5.1 0.2 - - - +
643A LYS* 5.0 5.6 - - + +
644A ILE* 3.2 49.8 - - - +
647A HIS* 5.0 5.2 - - + +
569C LYS* 4.9 1.3 - - - +
570C TYR* 4.2 12.7 - - - -
573C GLU* 1.9 50.3 + - - +
615C GLY* 2.6 30.4 + - - +
616C ALA* 2.8 9.1 + - - +
618C SER* 1.3 80.6 - - - +
620C PHE* 1.3 66.6 + - - +
621C THR* 3.3 1.1 + - - -
622C MET* 2.8 42.7 + - + +
623C ASN* 2.2 36.9 + - - +
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Residues in contact with PHE 620 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C ARG* 4.4 9.2 - - - -
501C TYR* 4.1 37.0 - + - -
573C GLU 4.7 0.4 - - - -
574C ILE* 3.5 36.6 - - + -
577C VAL* 3.8 23.1 - - + -
578C ASN* 3.8 15.3 - - + -
581C TYR* 5.5 5.4 - + + -
616C ALA 2.8 9.5 + - - +
617C THR 3.8 16.2 - - - +
618C SER 3.2 0.8 - - - +
619C ARG* 1.3 72.9 - - - +
621C THR* 1.3 76.2 + - + +
622C MET 3.3 0.2 - - - -
623C ASN* 2.8 26.5 + - - +
624C PHE* 3.6 29.7 + + - -
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Residues in contact with THR 621 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C SER 4.1 13.0 + - - +
619C ARG* 3.0 4.2 + - - -
620C PHE* 1.3 85.3 - - + +
622C MET* 1.3 72.6 + - - +
624C PHE* 3.9 12.2 - - - +
625C LEU* 4.2 2.1 + - - +
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Residues in contact with MET 622 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A VAL* 3.5 39.7 - - + -
643A LYS* 4.3 34.1 - - - -
619C ARG* 2.8 42.7 + - + +
621C THR* 1.3 77.0 + - - +
623C ASN* 1.3 61.3 + - - +
624C PHE 3.0 2.5 - - - -
625C LEU* 2.3 61.7 + - + +
626C ILE* 3.2 26.5 + - + -
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Residues in contact with ASN 623 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570C TYR* 3.7 16.4 + - - +
573C GLU* 3.4 31.3 + - - +
574C ILE* 3.5 17.5 - - + +
616C ALA* 4.7 0.8 - - - +
619C ARG* 2.2 54.1 + - - +
620C PHE* 2.8 23.1 + - - +
622C MET* 1.3 75.2 - - - +
624C PHE* 1.3 52.0 + - - +
626C ILE* 2.8 14.4 + - - +
627C LEU* 2.7 32.6 + - - +
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Residues in contact with PHE 624 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C TYR* 3.7 37.0 - + - -
504C ALA* 3.6 28.0 - - + -
505C ALA* 4.1 4.3 - - - -
574C ILE* 3.3 49.5 - - + +
620C PHE* 3.6 27.6 + + - -
621C THR 3.9 10.3 - - - +
622C MET 2.7 2.4 + - - -
623C ASN* 1.3 74.4 - - - +
625C LEU* 1.3 65.9 + - - +
627C LEU* 2.8 2.7 + - - +
628C TYR* 2.8 49.7 + + + +
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Residues in contact with LEU 625 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621C THR 4.2 1.9 + - - +
622C MET* 2.3 48.2 + - + +
624C PHE* 1.3 69.5 - - - +
626C ILE* 1.3 57.9 + - + +
628C TYR* 3.6 4.2 + - - +
629C SER* 2.9 37.5 + - - +
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Residues in contact with ILE 626 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A LEU* 5.6 3.1 - - + -
640A VAL* 4.7 13.7 - - + -
564C TYR 5.1 1.1 - - - +
570C TYR* 3.3 56.5 - - + +
622C MET* 3.7 18.6 - - + -
623C ASN* 2.8 37.5 + - - +
625C LEU* 1.3 74.7 - - + +
627C LEU* 1.3 58.6 + - - +
629C SER* 2.8 31.7 + - - +
630C PHE* 3.3 19.3 - - + -
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Residues in contact with LEU 627 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C ALA* 3.8 23.1 - - - +
508C ALA* 3.7 20.8 - - + +
509C PRO* 4.9 1.6 - - + -
512C ILE* 4.0 11.2 - - + +
567C PHE* 3.9 27.4 - - + +
570C TYR* 3.9 11.0 - - - +
571C CYS* 3.6 39.7 - - + -
574C ILE* 3.8 13.2 - - + -
623C ASN 2.7 16.5 + - - +
624C PHE* 2.8 9.4 + - - +
626C ILE* 1.3 73.3 - - - +
628C TYR* 1.3 66.2 + - + +
629C SER 3.5 0.2 + - - -
630C PHE* 3.6 13.8 + - - +
631C ILE* 4.7 0.7 + - - +
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Residues in contact with TYR 628 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C ALA* 2.4 43.6 + - + +
507C LEU* 3.6 24.8 - - + +
508C ALA* 3.8 21.5 - - + -
511C LEU* 5.1 0.9 - - + -
624C PHE* 2.8 43.0 + + - +
625C LEU* 3.7 3.6 - - - +
627C LEU* 1.3 78.6 - - + +
629C SER* 1.3 65.7 + - - +
630C PHE 3.2 1.7 + - - -
631C ILE* 3.3 30.9 - - + +
632C PRO* 3.0 18.9 - - - +
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Residues in contact with SER 629 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625C LEU* 2.9 27.4 + - - +
626C ILE* 2.8 25.3 + - - -
628C TYR* 1.3 78.8 - - - +
630C PHE* 1.3 60.4 + - - +
632C PRO* 3.0 20.2 - - - +
633C ALA* 3.8 6.2 + - - +
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Residues in contact with PHE 630 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512C ILE* 4.1 8.1 - - + -
564C TYR 5.6 0.2 - - - -
565C PHE 3.7 19.3 - - - -
566C THR 3.6 7.0 - - - -
567C PHE* 3.3 51.1 - + + -
570C TYR* 4.6 5.4 - + - -
626C ILE* 3.3 32.1 - - + -
627C LEU* 3.6 10.8 - - - +
628C TYR 3.2 1.4 - - - -
629C SER* 1.3 77.7 - - - +
631C ILE* 1.3 59.1 + - - +
633C ALA* 2.8 12.9 + - + +
634C LEU* 2.8 45.0 + - + +
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Residues in contact with ILE 631 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472C LEU* 5.7 4.5 - - + -
508C ALA* 4.2 6.1 - - - +
511C LEU* 3.9 24.0 - - + -
512C ILE* 3.3 43.5 - - + +
515C PHE* 4.1 18.7 - - + -
627C LEU 4.8 3.4 - - - +
628C TYR* 3.3 39.9 - - + +
630C PHE* 1.3 72.8 - - + +
632C PRO* 1.3 71.3 - - + +
634C LEU* 4.2 5.4 - - - -
635C VAL* 3.3 22.0 + - - +
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Residues in contact with PRO 632 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C TYR 3.0 26.2 - - - +
629C SER* 3.0 18.6 - - - +
631C ILE* 1.3 83.9 - - + +
633C ALA* 1.3 64.5 + - - +
635C VAL* 3.1 8.4 - - + +
636C ILE* 2.8 35.2 + - + +
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Residues in contact with ALA 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C SER 4.1 4.9 - - - +
630C PHE* 2.8 16.1 + - + +
632C PRO* 1.3 79.4 - - - +
634C LEU* 1.3 68.5 + - + +
636C ILE* 2.8 17.9 + - + +
637C LEU* 2.8 24.1 + - - +
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Residues in contact with LEU 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A PHE* 6.3 0.7 - - + -
512C ILE* 3.9 35.7 - - + +
515C PHE* 3.9 14.8 - - + +
516C LEU* 3.3 44.6 - - + -
519C VAL* 3.0 16.8 - - + +
630C PHE* 2.8 40.7 + - + +
631C ILE* 4.2 5.6 - - - +
632C PRO 3.4 0.2 - - - -
633C ALA* 1.3 72.2 - - + +
635C VAL* 1.3 57.4 + - - +
637C LEU* 3.3 11.1 + - + +
638C GLY 2.8 22.9 + - - -
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Residues in contact with VAL 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C MET* 3.9 18.2 - - - -
465C LEU* 3.9 27.8 - - + -
468C ALA* 4.0 14.8 - - + -
469C LEU* 6.1 0.7 - - + -
515C PHE* 4.5 16.7 - - + +
518C LEU* 5.4 0.2 - - + -
519C VAL* 5.1 0.2 - - - -
631C ILE 3.3 14.0 + - - +
632C PRO* 3.1 19.5 - - + +
634C LEU* 1.3 75.7 - - - +
636C ILE* 1.3 63.3 + - + +
638C GLY* 3.0 3.5 + - - +
639C ILE* 2.8 33.2 + - + +
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Residues in contact with ILE 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629A SER* 5.3 8.3 - - - +
632C PRO* 2.8 33.4 + - + +
633C ALA* 2.8 28.9 + - + +
635C VAL* 1.3 75.9 - - + +
637C LEU* 1.3 62.7 + - + +
639C ILE* 3.4 14.2 + - + +
640C VAL* 3.4 17.0 + - - +
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Residues in contact with LEU 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A TYR* 4.7 5.8 - - + +
565A PHE* 3.7 31.9 - - + -
570A TYR* 4.5 11.9 - - - +
519C VAL* 3.8 20.9 - - + -
633C ALA 2.8 11.2 + - - +
634C LEU* 3.3 15.7 - - + +
636C ILE* 1.3 76.4 - - + +
638C GLY* 1.3 67.4 + - - +
640C VAL* 2.4 41.9 + - + +
641C VAL* 2.8 20.5 + - + -
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Residues in contact with GLY 638 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464C MET* 3.5 24.2 - - - -
519C VAL* 3.6 15.0 - - - -
634C LEU 2.8 10.7 + - - -
635C VAL 3.0 5.3 + - - -
637C LEU* 1.3 72.5 - - - +
639C ILE* 1.3 70.7 + - - +
641C VAL* 2.8 14.1 + - - -
642C PHE* 2.8 16.2 + - - -
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Residues in contact with ILE 639 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C TRP* 3.4 42.6 - - + +
464C MET* 3.7 22.0 - - + -
465C LEU* 3.8 34.8 - - + -
635C VAL* 2.8 26.0 + - + +
636C ILE* 3.5 14.4 - - + +
638C GLY* 1.3 77.2 - - - +
640C VAL* 1.3 63.0 + - - +
642C PHE* 2.8 1.9 + - - +
643C LYS* 2.8 28.5 + - + +
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Residues in contact with VAL 640 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570A TYR* 4.1 7.0 - - + +
622A MET* 3.4 26.0 - - + -
626A ILE* 3.5 24.9 - - + -
636C ILE 3.4 5.5 + - - +
637C LEU* 2.4 61.4 + - + +
639C ILE* 1.3 74.8 - - - +
641C VAL* 1.3 62.8 + - - +
643C LYS* 3.5 7.5 - - - +
644C ILE* 2.8 43.2 + - + +
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Residues in contact with VAL 641 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A TYR* 3.7 18.6 + - + -
519C VAL* 3.9 11.7 - - + +
522C GLY* 3.8 22.7 - - - +
523C ILE* 3.4 44.0 - - + -
637C LEU* 2.8 25.9 + - + +
638C GLY* 2.8 13.9 + - - +
640C VAL* 1.3 72.4 - - - +
642C PHE* 1.3 57.7 + - + +
644C ILE* 3.2 10.5 - - + +
645C ARG* 2.7 31.6 + - + +
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Residues in contact with PHE 642 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C PHE* 4.0 24.2 - + - -
446C ARG* 4.9 3.4 - - + -
449C SER* 6.3 1.8 - - - -
460C LYS* 3.7 26.7 - - + +
461C TRP* 3.8 18.4 - - - +
464C MET* 3.5 41.1 - - + -
518C LEU 4.0 9.6 - - - -
519C VAL* 4.3 4.3 - - - -
522C GLY* 3.5 33.0 - - - -
638C GLY 2.8 20.5 + - - +
639C ILE 2.8 8.3 + - - +
641C VAL* 1.3 76.4 - - + +
643C LYS* 1.3 64.4 + - - +
644C ILE 3.1 1.3 - - - -
645C ARG* 2.8 38.6 + - - +
646C ASP 3.1 10.7 + - - -
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Residues in contact with LYS 643 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A ARG* 5.3 4.4 - - + +
622A MET* 3.9 32.1 - - + -
459C GLN* 3.6 32.0 + - - +
460C LYS* 5.3 0.4 - - - -
461C TRP* 4.0 29.3 - - + +
639C ILE* 2.8 21.4 + - + +
640C VAL* 3.5 11.4 - - - +
642C PHE* 1.3 70.8 - - - +
644C ILE* 1.3 60.5 + - - +
646C ASP* 3.7 15.6 - - - +
647C HIS* 4.3 7.3 - - - -
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Residues in contact with ILE 644 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A TYR* 3.6 45.1 - - + +
569A LYS* 4.8 6.1 - - - +
570A TYR* 4.6 7.4 - - + +
615A GLY* 5.5 1.6 - - - -
619A ARG* 3.3 47.3 - - - +
640C VAL* 2.8 41.4 + - + +
641C VAL 3.2 5.8 - - - +
643C LYS* 1.3 68.8 - - - +
645C ARG* 1.3 64.1 + - - +
646C ASP 3.0 1.8 - - - -
647C HIS* 2.8 33.1 + - + +
648C LEU* 3.8 10.5 + - + -
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Residues in contact with ARG 645 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C ARG* 3.4 44.9 + - - +
449C SER* 5.7 0.6 - - - -
450C ASP* 2.5 44.3 + - - -
460C LYS* 4.9 8.0 - - - +
522C GLY* 3.3 31.3 + - - +
525C GLN* 4.1 24.0 - - - +
641C VAL* 2.7 21.6 + - + +
642C PHE* 2.8 26.3 + - - +
644C ILE* 1.3 75.1 - - - +
646C ASP* 1.3 64.1 + - - +
647C HIS 3.1 0.2 - - - -
648C LEU* 2.8 35.0 + - + +
649C ILE* 3.6 11.2 + - + +
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Residues in contact with ASP 646 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 5.5 1.9 - - - +
453C SER* 4.4 4.4 + - - -
459C GLN* 3.8 24.3 + - - +
460C LYS* 2.7 53.2 + - + +
642C PHE 3.1 5.5 + - - +
643C LYS* 3.7 16.7 - - - +
645C ARG* 1.3 76.5 - - - +
647C HIS* 1.3 64.9 - - + +
649C ILE* 3.4 16.8 - - - +
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Residues in contact with HIS 647 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A PRO* 4.0 15.9 + - + +
615A GLY* 3.3 40.8 + - - +
617A THR* 4.6 3.6 - - + -
618A SER* 3.3 36.9 + - - -
619A ARG* 5.1 1.7 + - + +
103C LEU* 4.3 19.3 - - - +
643C LYS 4.3 11.2 - - - -
644C ILE* 2.8 21.8 + - + +
646C ASP* 1.3 77.6 - - + +
648C LEU* 1.3 67.2 + - + +
649C ILE 3.3 7.1 + - - -
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Residues in contact with LEU 648 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A GLN* 4.5 23.6 - - + +
560A LYS* 5.5 8.5 - - + +
564A TYR* 3.0 28.5 - - - +
614A PRO* 4.7 16.8 - - + -
103C LEU* 5.4 1.6 - - - +
522C GLY 5.4 0.7 - - - +
523C ILE* 5.3 8.7 - - - +
525C GLN* 5.4 8.5 - - - +
644C ILE* 4.4 8.7 - - + -
645C ARG* 2.8 41.0 + - + +
647C HIS* 1.3 73.0 - - + +
649C ILE* 1.3 56.8 + - - +
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Residues in contact with ILE 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C ARG* 4.0 28.6 + - - +
103C LEU* 3.5 26.5 - - + +
450C ASP* 5.1 15.3 - - + +
454C GLN* 4.7 11.1 - - + +
460C LYS* 5.5 7.9 - - - +
525C GLN* 5.3 12.9 - - - +
645C ARG* 3.6 12.1 + - + +
646C ASP 3.4 19.1 - - - +
647C HIS 3.3 6.3 - - - -
648C LEU* 1.3 79.4 - - - +
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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