Contacts of the helix formed by residues 615 - 649 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A CYS 3.1 0.8 + - - -
614A PRO* 1.3 83.3 - - - +
616A ALA* 1.3 57.5 + - - +
617A THR 3.7 0.2 - - - -
619A ARG* 2.6 46.8 + - - +
644C ILE* 5.2 1.1 - - - -
647C HIS* 3.3 37.5 + - - +
648C LEU* 6.1 0.2 - - - +
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Residues in contact with ALA 616 (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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573A GLU* 3.5 26.0 - - + +
577A VAL* 3.3 24.2 - - + -
609A ILE* 4.7 0.7 - - + -
613A CYS* 2.8 22.7 + - + +
614A PRO 3.0 0.2 - - - -
615A GLY* 1.3 74.7 - - - +
617A THR* 1.3 70.4 + - - +
618A SER 3.1 2.0 - - - -
619A ARG* 2.8 12.9 + - - +
620A PHE* 2.8 26.0 + - - +
623A ASN* 4.7 0.9 - - - +
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Residues in contact with THR 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A VAL* 3.6 20.7 - - - +
581A TYR* 5.4 6.9 + - - -
606A ILE* 6.3 1.8 - - - -
609A ILE* 4.5 11.7 - - + +
610A GLU* 4.1 13.0 - - - +
614A PRO 3.3 20.1 + - - +
616A ALA* 1.3 75.5 - - - +
618A SER* 1.3 76.6 + - - +
620A PHE* 3.8 12.1 - - - +
105C ARG* 6.0 3.4 - - - +
647C HIS* 4.6 5.4 - - + -
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Residues in contact with SER 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A GLY 4.1 0.6 + - - -
616A ALA 2.8 1.0 + - - -
617A THR* 1.3 82.7 + - - +
619A ARG* 1.3 65.4 + - - +
620A PHE* 3.2 1.9 + - - +
621A THR* 4.1 16.6 + - - +
647C HIS* 3.3 33.2 - - - -
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Residues in contact with ARG 619 (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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569A LYS* 4.3 2.6 - - - +
570A TYR* 5.5 1.4 - - - -
573A GLU* 2.3 38.4 + - - +
613A CYS 5.1 0.8 + - - -
615A GLY* 2.6 55.5 + - - +
616A ALA* 2.8 6.9 + - - +
618A SER* 1.3 80.2 - - - +
620A PHE* 1.3 65.7 + - - +
621A THR* 3.3 0.9 - - - -
622A MET* 2.8 54.2 + - + +
623A ASN* 3.0 34.8 + - - +
643C LYS* 5.7 3.4 - - + -
644C ILE* 3.3 45.3 - - - +
647C HIS* 5.5 2.0 - - + +
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Residues in contact with PHE 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ARG* 4.5 7.9 - - - -
501A TYR* 4.0 38.1 - + - -
573A GLU 4.9 0.2 - - - -
574A ILE* 3.8 24.2 - - + -
577A VAL* 3.7 24.0 - - + -
578A ASN* 3.8 22.2 - - + -
581A TYR* 5.5 4.5 - + + -
616A ALA 2.8 9.7 + - - +
617A THR 3.8 16.4 - - - +
618A SER 3.2 0.6 - - - +
619A ARG* 1.3 73.4 - - - +
621A THR* 1.3 76.4 + - + +
622A MET 3.3 0.2 - - - -
623A ASN* 2.8 28.7 + - - +
624A PHE* 3.6 32.7 + + - -
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Residues in contact with THR 621 (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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618A SER 4.1 11.8 + - - +
619A ARG* 3.0 4.2 + - - -
620A PHE* 1.3 86.0 - - + +
622A MET* 1.3 71.3 + - - +
624A PHE* 3.9 12.3 - - - +
625A LEU* 4.1 2.6 + - - +
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Residues in contact with MET 622 (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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619A ARG* 2.8 55.9 + - + +
621A THR* 1.3 75.4 + - - +
623A ASN* 1.3 56.2 + - - +
624A PHE 3.0 2.0 - - - -
625A LEU* 2.3 60.4 + - + +
626A ILE* 3.2 18.5 + - + -
640C VAL* 3.4 33.7 - - + +
643C LYS* 3.9 34.1 - - + -
644C ILE* 4.6 0.9 - - + -
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Residues in contact with ASN 623 (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 TYR* 3.7 24.4 - - - +
573A GLU* 3.4 40.0 + - - +
574A ILE* 3.5 17.3 - - + -
616A ALA* 4.7 1.4 - - - +
619A ARG* 3.0 39.5 + - - +
620A PHE* 2.8 22.7 + - - +
622A MET* 1.3 75.1 - - - +
624A PHE* 1.3 52.5 + - - +
626A ILE* 2.8 11.0 + - - +
627A LEU* 2.7 32.6 + - - +
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Residues in contact with PHE 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A TYR* 3.7 36.3 - + - -
504A ALA* 3.6 27.4 - - + -
505A ALA* 4.1 4.0 - - - -
574A ILE* 3.3 46.9 - - + +
620A PHE* 3.6 29.9 + + - -
621A THR 3.9 10.8 - - - +
622A MET 2.7 2.2 + - - -
623A ASN* 1.3 74.0 - - - +
625A LEU* 1.3 66.2 + - - +
627A LEU* 2.8 14.5 + - + -
628A TYR* 2.8 39.9 + + + +
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Residues in contact with LEU 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A THR 4.1 2.5 + - - +
622A MET* 2.3 47.3 + - + +
624A PHE* 1.3 70.4 - - - +
626A ILE* 1.3 62.1 + - + +
628A TYR* 3.7 3.4 + - - +
629A SER* 2.9 29.3 + - - +
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Residues in contact with ILE 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A TYR* 3.2 40.4 - - + -
622A MET* 3.7 26.5 - - + -
623A ASN* 2.8 14.5 + - - +
625A LEU* 1.3 77.6 - - + +
627A LEU* 1.3 58.2 + - - +
629A SER* 2.8 33.4 + - - -
630A PHE* 3.3 20.2 - - + -
640C VAL* 3.5 38.6 - - + -
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Residues in contact with LEU 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ALA* 3.8 23.1 - - - +
508A ALA* 3.7 21.6 - - + +
509A PRO* 4.9 1.8 - - + -
512A ILE* 4.0 11.7 - - + +
567A PHE* 3.9 26.9 - - + +
570A TYR* 3.9 9.6 - - - +
571A CYS* 3.6 40.6 - - + -
574A ILE* 3.8 12.1 - - + -
623A ASN 2.7 15.8 + - - +
624A PHE* 2.8 9.1 + - - +
626A ILE* 1.3 74.3 - - - +
628A TYR* 1.3 66.5 + - + +
630A PHE* 3.6 13.9 + - - +
631A ILE* 4.7 0.9 + - - +
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Residues in contact with TYR 628 (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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504A ALA* 2.3 42.1 + - + +
507A LEU* 3.6 24.5 - - + +
508A ALA* 3.8 21.5 - - + -
511A LEU* 5.1 0.7 - - + -
624A PHE* 2.8 42.2 + + - +
625A LEU* 3.7 3.4 - - - +
627A LEU* 1.3 80.4 - - + +
629A SER* 1.3 65.2 + - - +
630A PHE 3.2 1.6 + - - -
631A ILE* 3.3 30.8 - - + +
632A PRO* 3.0 19.4 - - - +
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Residues in contact with SER 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A LEU* 2.9 19.3 + - - -
626A ILE* 2.8 26.3 + - - -
628A TYR* 1.3 77.6 - - - +
630A PHE* 1.3 61.3 + - - +
632A PRO* 2.9 20.7 - - - +
633A ALA* 3.8 5.9 + - - +
636C ILE* 5.3 8.8 - - - +
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Residues in contact with PHE 630 (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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512A ILE* 4.1 9.0 - - + -
564A TYR 5.5 0.2 - - - -
565A PHE 3.7 19.7 - - - -
566A THR 3.6 6.7 - - - -
567A PHE* 3.3 49.6 - + + -
570A TYR* 4.8 3.1 - + - -
626A ILE* 3.3 40.6 - - + -
627A LEU* 3.6 10.5 - - - +
628A TYR 3.2 1.4 - - - -
629A SER* 1.3 76.4 - - - +
631A ILE* 1.3 58.5 + - - +
633A ALA* 2.8 26.4 + - + +
634A LEU* 2.8 31.7 + - + +
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Residues in contact with ILE 631 (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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472A LEU* 5.6 4.3 - - + -
508A ALA* 4.2 6.7 - - - +
511A LEU* 3.9 23.6 - - + -
512A ILE* 3.3 44.0 - - + +
515A PHE* 4.1 18.6 - - + -
627A LEU 4.8 2.9 - - - +
628A TYR* 3.3 39.5 - - + +
630A PHE* 1.3 73.7 - - + +
632A PRO* 1.3 73.2 - - + +
634A LEU* 4.2 5.6 - - - -
635A VAL* 3.3 22.2 + - - +
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Residues in contact with PRO 632 (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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628A TYR 3.0 17.7 - - - +
629A SER* 2.9 19.5 - - - +
631A ILE* 1.3 92.2 - - + +
633A ALA* 1.3 68.2 + - - +
635A VAL* 3.0 9.2 - - + +
636A ILE* 2.8 37.7 + - + +
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Residues in contact with ALA 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A SER 4.2 5.4 - - - +
630A PHE* 2.8 16.8 + - + +
632A PRO* 1.3 79.6 - - - +
634A LEU* 1.3 67.8 + - + +
636A ILE* 2.8 14.1 + - - +
637A LEU* 2.8 24.7 + - - +
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Residues in contact with LEU 634 (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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512A ILE* 3.9 35.4 - - + +
515A PHE* 3.9 15.7 - - + +
516A LEU* 3.4 44.6 - - + -
519A VAL* 3.0 16.4 - - + +
630A PHE* 2.8 39.6 + - + +
631A ILE* 4.2 4.7 - - - +
632A PRO 3.4 0.2 - - - -
633A ALA* 1.3 73.5 - - + +
635A VAL* 1.3 57.1 + - - +
637A LEU* 3.2 11.7 + - + +
638A GLY 2.8 23.2 + - - -
565C PHE* 6.1 1.1 - - + -
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Residues in contact with VAL 635 (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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464A MET* 4.0 16.8 - - - -
465A LEU* 3.9 28.9 - - + -
468A ALA* 4.0 14.1 - - + -
515A PHE* 4.5 15.4 - - + +
518A LEU* 5.4 0.9 - - + -
519A VAL* 5.1 0.7 - - - -
631A ILE 3.3 14.7 + - - +
632A PRO* 3.0 24.7 - - + +
634A LEU* 1.3 75.7 - - - +
636A ILE* 1.3 62.4 + - + +
638A GLY* 3.0 4.1 + - - +
639A ILE* 2.8 32.2 + - + +
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Residues in contact with ILE 636 (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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632A PRO* 2.8 41.9 + - + +
633A ALA* 2.8 14.5 + - - +
635A VAL* 1.3 76.7 - - + +
637A LEU* 1.3 65.8 + - + +
639A ILE* 3.3 14.2 + - + +
640A VAL* 3.3 17.3 + - + +
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Residues in contact with LEU 637 (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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519A VAL* 3.8 21.5 - - + -
633A ALA 2.8 11.0 + - - +
634A LEU* 3.3 13.7 - - + +
636A ILE* 1.3 76.6 - - + +
638A GLY* 1.3 69.4 + - - +
640A VAL* 2.4 41.9 + - + +
641A VAL* 2.8 20.2 + - + -
564C TYR* 4.6 6.7 - - + +
565C PHE* 3.5 35.4 - - + -
570C TYR* 4.4 12.1 - - - +
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Residues in contact with GLY 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A MET* 2.7 19.1 - - - -
519A VAL* 3.6 20.4 - - - -
634A LEU 2.8 10.7 + - - -
635A VAL* 3.0 2.6 + - - -
637A LEU* 1.3 76.3 - - - +
639A ILE* 1.3 68.5 + - - +
641A VAL* 2.8 14.3 + - - -
642A PHE* 2.8 17.4 + - - -
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Residues in contact with ILE 639 (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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461A TRP* 3.4 40.1 - - + +
464A MET* 2.8 28.6 - - + +
465A LEU* 3.8 36.8 - - + +
635A VAL* 2.8 22.4 + - + +
636A ILE* 3.5 14.4 - - + +
637A LEU 3.1 0.2 - - - -
638A GLY* 1.3 75.0 - - - +
640A VAL* 1.3 63.4 + - - +
642A PHE* 2.9 1.6 + - - +
643A LYS* 2.8 28.3 + - + +
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Residues in contact with VAL 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A ILE* 3.3 4.5 + - + +
637A LEU* 2.4 62.6 + - + +
639A ILE* 1.3 75.3 - - - +
641A VAL* 1.3 62.1 + - - +
643A LYS* 3.3 8.7 + - - +
644A ILE* 2.8 44.9 + - + +
570C TYR* 4.1 13.7 - - + +
619C ARG* 5.1 0.4 - - - +
622C MET* 3.5 32.3 - - + -
626C ILE* 4.7 10.1 - - + -
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Residues in contact with VAL 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A VAL* 3.9 11.4 - - + +
522A GLY* 3.8 23.1 - - - +
523A ILE* 3.4 45.5 - - + +
637A LEU* 2.8 26.2 + - + +
638A GLY* 2.8 14.1 + - - +
640A VAL* 1.3 72.4 - - - +
642A PHE* 1.3 56.1 + - + +
644A ILE* 3.2 10.5 - - - +
645A ARG* 2.7 32.7 + - + +
564C TYR* 3.7 19.1 + - + +
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Residues in contact with PHE 642 (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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442A PHE* 4.0 23.3 - + - -
446A ARG* 4.9 3.6 - - + -
449A SER* 6.4 1.6 - - - -
460A LYS* 3.7 26.9 - - + +
461A TRP* 3.7 18.6 - - + +
464A MET* 3.3 38.6 - - + -
518A LEU 3.9 11.9 - - - -
519A VAL* 4.3 6.5 - - - -
522A GLY* 3.5 33.2 - - - -
638A GLY 2.8 23.4 + - - -
639A ILE 2.9 5.5 + - - +
641A VAL* 1.3 78.5 - - + +
643A LYS* 1.3 58.4 + - - +
644A ILE 3.0 1.1 - - - -
645A ARG* 2.8 44.9 + - - +
646A ASP* 3.1 11.3 + - - +
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Residues in contact with LYS 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A GLN* 3.7 12.5 + - - +
461A TRP* 3.1 51.1 - - + +
639A ILE* 2.8 22.3 + - + +
640A VAL* 3.5 12.3 - - - +
642A PHE* 1.3 70.4 - - - +
644A ILE* 1.3 56.3 + - - +
646A ASP* 2.3 31.2 - - - +
647A HIS* 4.3 4.7 - - - -
619C ARG* 5.0 6.4 - - + +
622C MET* 4.3 30.3 - - - -
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Residues in contact with ILE 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A VAL* 2.8 43.2 + - + +
641A VAL 3.2 4.9 - - - +
643A LYS* 1.3 71.7 - - + +
645A ARG* 1.3 63.4 + - - +
646A ASP 3.1 0.2 - - - -
647A HIS* 2.8 31.9 + - + +
648A LEU* 3.8 4.4 + - + +
564C TYR* 3.5 44.6 - - + +
569C LYS* 4.7 6.3 - - - +
570C TYR* 4.6 4.5 - - + -
615C GLY* 5.4 5.2 - - - +
619C ARG* 3.2 43.7 - - - +
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Residues in contact with ARG 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ARG* 3.4 42.1 + - - +
449A SER* 5.7 0.6 - - - -
450A ASP* 2.5 45.5 + - - -
460A LYS* 4.8 8.3 - - - +
522A GLY* 3.3 32.0 + - - +
525A GLN* 3.5 24.7 - - - +
641A VAL* 2.7 21.8 + - + +
642A PHE* 2.8 29.6 + - - +
644A ILE* 1.3 73.8 - - + +
646A ASP* 1.3 56.5 + - - +
648A LEU* 2.8 41.6 + - + +
649A ILE* 3.6 10.5 + - + +
564C TYR* 5.8 0.9 - - - +
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Residues in contact with ASP 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 5.9 3.1 - - - +
453A SER* 5.3 1.0 + - - +
459A GLN* 3.7 18.5 + - - +
460A LYS* 3.3 53.0 + - + +
642A PHE 3.1 5.8 + - - +
643A LYS* 2.3 31.6 - - - +
644A ILE 2.9 1.0 + - - -
645A ARG* 1.3 76.3 - - - +
647A HIS* 1.3 66.9 + - + +
649A ILE 4.1 10.6 - - - +
----------------------------------------------------------
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Residues in contact with HIS 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.8 13.6 - - - +
643A LYS 4.3 4.5 - - - -
644A ILE* 2.8 22.5 + - + +
646A ASP* 1.3 82.2 - - - +
648A LEU* 1.3 65.6 + - - +
649A ILE* 3.5 3.7 + - - -
650A SER* 4.8 0.5 + - - -
610C GLU* 5.9 0.2 + - - -
614C PRO* 3.8 18.7 + - + +
615C GLY* 3.3 39.5 + - - +
617C THR* 4.4 3.8 - - - -
618C SER* 3.4 33.0 + - - -
619C ARG* 5.0 2.2 - - + +
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Residues in contact with LEU 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A GLY 4.8 1.1 - - - +
523A ILE* 4.3 19.1 - - - +
525A GLN* 3.9 25.8 - - - +
644A ILE* 3.8 4.8 + - + +
645A ARG* 2.8 36.1 + - + +
647A HIS* 1.3 75.3 - - - +
649A ILE* 1.3 65.5 + - + +
650A SER* 4.1 2.1 + - - -
553C GLN* 3.4 44.5 - - - +
560C LYS* 5.2 7.4 - - + +
564C TYR* 4.1 19.5 - - - +
614C PRO* 5.6 1.6 - - - -
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Residues in contact with ILE 649 (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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103A LEU* 4.8 2.1 - - - +
450A ASP* 4.6 12.1 - - + +
454A GLN* 4.7 5.2 + - - -
460A LYS* 4.5 19.4 + - - +
525A GLN* 4.1 24.9 - - - +
645A ARG* 3.6 7.2 + - - +
646A ASP 4.1 10.6 - - - +
647A HIS 3.5 2.2 - - - -
648A LEU* 1.3 86.5 - - + +
650A SER* 1.3 70.0 + - - +
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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
------------------------------------------------------------
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