Contacts of the helix formed by residues 473 - 512 (chain A) in PDB entry 2Y48
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 473 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472A ARG* 1.3 79.3 - - - +
474A ILE* 1.3 65.9 + - - +
475A THR* 2.9 29.4 + - - +
476A ALA* 3.0 10.1 + - - +
477A GLU* 3.3 17.4 + - - +
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Residues in contact with ILE 474 (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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473A ASP* 1.3 77.5 + - - +
475A THR* 1.3 66.8 + - + +
477A GLU* 2.9 18.3 + - + +
478A PHE* 2.7 27.7 + - - +
386B GLU* 4.1 35.9 - - + +
389B LEU* 4.0 38.1 - - + -
390B LEU* 4.5 8.5 - - + -
393B GLN* 3.4 21.3 - - - +
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Residues in contact with THR 475 (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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473A ASP* 2.9 18.1 + - - +
474A ILE* 1.3 80.0 - - + +
476A ALA* 1.3 61.3 + - - +
478A PHE* 3.3 3.0 + - - +
479A LEU* 2.9 30.1 + - - +
393B GLN* 3.5 25.8 - - - +
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Residues in contact with ALA 476 (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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465A ALA 5.0 1.2 - - - +
468A VAL* 5.0 8.3 - - + -
472A ARG* 3.8 26.0 - - + -
473A ASP* 3.0 18.0 + - - +
475A THR* 1.3 82.3 + - - +
477A GLU* 1.3 59.5 + - - +
479A LEU* 3.8 8.3 - - - +
480A VAL* 3.6 22.5 + - - +
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Residues in contact with GLU 477 (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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470A PRO* 5.9 0.3 - - - +
472A ARG* 2.9 45.5 + - - +
473A ASP 3.3 11.3 + - - +
474A ILE* 2.9 20.7 + - + +
476A ALA* 1.3 75.2 - - - +
478A PHE* 1.3 65.0 + - - +
479A LEU 3.3 0.2 - - - -
480A VAL* 3.4 8.1 + - - +
481A LYS* 3.1 44.0 + - + +
386B GLU* 4.3 18.8 - - - +
390B LEU* 5.0 2.5 - - + -
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Residues in contact with PHE 478 (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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474A ILE 2.7 13.5 + - - +
475A THR* 3.4 6.1 - - - +
477A GLU* 1.3 68.7 - - - +
479A LEU* 1.3 61.1 + - + +
481A LYS* 2.9 3.0 + - - -
482A SER* 2.5 45.4 + - - -
390B LEU* 3.8 18.2 - - + +
393B GLN* 3.2 59.2 - - + +
394B ALA* 3.6 23.1 - - - -
397B LYS* 3.9 28.3 - - + -
398B TYR* 4.7 0.9 - + - -
408B VAL* 3.8 24.9 - - + -
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Residues in contact with LEU 479 (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 GLN 5.4 1.3 - - - +
465A ALA* 3.5 28.7 - - + -
475A THR 2.9 19.8 + - - +
476A ALA* 3.8 9.4 - - - +
477A GLU 3.3 0.4 - - - -
478A PHE* 1.3 76.6 - - + +
480A VAL* 1.3 65.0 + - - +
482A SER* 4.5 5.2 - - - +
483A LYS* 2.9 50.9 + - + +
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Residues in contact with VAL 480 (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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462A TYR* 3.6 24.1 - - + +
465A ALA* 3.1 43.5 - - + +
466A SER* 3.9 9.0 - - - +
472A ARG* 4.0 22.9 - - - +
476A ALA 3.6 9.3 + - - +
477A GLU* 3.4 11.1 + - - +
478A PHE 3.3 0.4 - - - -
479A LEU* 1.3 77.4 - - - +
481A LYS* 1.3 67.2 + - + +
483A LYS* 3.7 0.4 + - - -
484A HIS* 3.0 27.1 + - + +
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Residues in contact with LYS 481 (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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477A GLU* 3.1 33.5 + - + +
478A PHE* 2.9 12.0 + - - +
480A VAL* 1.3 79.7 - - + +
482A SER* 1.3 70.0 + - - +
484A HIS* 3.0 15.4 + - + +
485A ARG* 3.0 13.3 + - - +
377B GLN* 6.0 1.7 - - - +
386B GLU* 4.9 5.9 + - - -
390B LEU* 3.8 25.7 - - + +
408B VAL* 3.8 32.6 + - + +
409B ILE 4.3 6.9 + - - -
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Residues in contact with SER 482 (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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478A PHE* 2.5 44.5 + - - -
479A LEU* 3.7 4.7 - - - +
481A LYS* 1.3 70.5 - - - +
483A LYS* 1.3 74.5 + - - +
484A HIS 2.7 2.3 + - - -
485A ARG* 2.8 15.1 + - - +
486A ASP* 3.0 14.3 + - - -
397B LYS* 3.5 23.9 + - - -
398B TYR* 3.7 7.3 + - - -
408B VAL* 4.0 13.3 - - - +
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Residues in contact with LYS 483 (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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458A LEU* 4.2 18.6 - - + +
461A GLN* 3.3 36.3 + - + +
462A TYR* 3.8 33.2 - - + +
465A ALA* 5.2 0.4 - - + -
479A LEU* 2.9 47.5 + - + +
480A VAL 4.0 2.0 - - - +
482A SER* 1.3 79.3 + - - +
484A HIS* 1.3 56.4 + - - +
486A ASP* 4.0 10.9 + - - +
487A LEU* 3.0 30.2 + - - +
397B LYS* 4.6 15.2 - - - +
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Residues in contact with HIS 484 (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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462A TYR* 3.7 23.5 - + + -
480A VAL* 3.0 16.8 + - + +
481A LYS* 3.1 15.3 - - + +
482A SER 2.7 5.5 + - - -
483A LYS* 1.3 71.7 - - - +
485A ARG* 1.3 68.1 + - - +
487A LEU* 3.2 3.8 + - - +
488A THR* 3.1 34.7 + - + -
372B LEU* 3.3 36.0 - - + +
373B PRO 4.6 4.4 + - - -
375B VAL* 4.3 25.3 - - + +
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Residues in contact with ARG 485 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A LYS 3.0 5.4 + - - +
482A SER 2.8 11.7 + - - +
484A HIS* 1.3 70.3 + - - +
486A ASP* 1.3 91.5 + - - +
488A THR* 2.9 20.6 + - - +
489A ALA* 3.0 39.1 + - + +
398B TYR* 3.5 22.6 + - - -
401B ASP* 4.3 6.8 + - - -
403B GLN* 5.9 1.0 - - - +
404B ALA* 3.2 44.2 - - - +
407B ASP* 3.9 26.5 + - + +
408B VAL* 3.9 17.7 - - + +
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Residues in contact with ASP 486 (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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458A LEU* 3.8 19.8 - - + +
482A SER* 3.0 14.3 + - - +
483A LYS* 4.0 9.3 + - - +
485A ARG* 1.3 91.3 + - - +
487A LEU* 1.3 60.5 + - - +
489A ALA* 3.7 2.1 + - - +
490A LEU* 3.3 28.7 + - + +
397B LYS* 3.7 17.7 + - - -
398B TYR* 2.5 32.6 + - - -
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Residues in contact with LEU 487 (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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455A ILE* 4.0 11.0 - - + +
458A LEU* 3.5 24.4 - - + +
459A HIS* 3.5 36.1 - - + +
462A TYR* 5.2 3.1 - - + -
483A LYS 3.0 19.6 + - - +
484A HIS 3.7 3.4 - - - +
485A ARG 3.0 0.2 - - - -
486A ASP* 1.3 78.4 - - - +
488A THR* 1.3 57.9 + - + +
490A LEU* 3.4 4.9 + - + +
491A CYS* 3.0 34.8 + - - -
370B TYR* 3.2 27.1 - - + +
372B LEU* 3.6 29.6 - - + +
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Residues in contact with THR 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A HIS* 3.1 32.0 + - + +
485A ARG* 2.9 16.0 + - - +
487A LEU* 1.3 72.9 - - + +
489A ALA* 1.3 54.6 + - - +
491A CYS* 3.1 10.8 + - + +
492A LYS* 2.8 32.2 + - - +
372B LEU* 4.4 25.1 - - + +
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Residues in contact with ALA 489 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A ARG* 3.0 42.5 + - + +
486A ASP 3.8 4.9 - - - +
488A THR* 1.3 73.3 + - - +
490A LEU* 1.3 62.0 + - + +
491A CYS 3.0 4.5 - - - -
492A LYS* 3.0 28.6 + - - +
493A GLU* 3.1 12.2 + - - +
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Residues in contact with LEU 490 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 3.8 16.2 - - + +
454A LYS* 4.2 29.8 - - + +
455A ILE* 3.1 35.4 - - + +
458A LEU* 4.8 11.2 - - + -
486A ASP* 3.3 18.8 + - + +
487A LEU* 3.7 6.3 - - - +
489A ALA* 1.3 82.7 - - + +
491A CYS* 1.3 58.2 + - - +
493A GLU* 4.1 18.6 - - - +
494A TYR 3.5 12.3 + - - -
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Residues in contact with CYS 491 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A ILE* 4.0 14.1 - - - -
487A LEU* 3.0 37.7 + - - +
488A THR* 3.4 12.3 - - + +
489A ALA 3.0 0.6 - - - -
490A LEU* 1.3 75.3 - - - +
492A LYS* 1.3 65.4 + - - +
494A TYR 4.3 1.5 - - - +
495A ASP* 3.2 29.1 + - - +
367B ILE* 3.8 25.5 - - + +
370B TYR 4.2 10.1 - - - -
371B ARG* 4.7 13.2 - - + +
372B LEU 5.9 0.4 - - - -
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Residues in contact with LYS 492 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A THR 2.8 11.6 + - - +
489A ALA* 3.0 15.0 - - - +
491A CYS* 1.3 77.3 - - - +
493A GLU* 1.3 62.1 + - + +
495A ASP* 2.9 24.2 + - - +
496A GLU* 3.1 33.7 + - - +
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Residues in contact with GLU 493 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LEU* 3.8 27.0 - - + +
489A ALA 3.1 12.0 + - - +
490A LEU* 4.1 11.5 - - - +
492A LYS* 1.3 78.0 - - + +
494A TYR* 1.3 55.2 + - - +
495A ASP 2.5 17.5 + - - -
496A GLU* 2.8 24.4 + - - +
497A LEU* 3.0 20.9 + - + +
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Residues in contact with TYR 494 (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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448A MET* 3.7 57.0 - - + +
451A LEU* 3.3 21.1 - - + +
452A LYS* 4.0 20.8 - - + +
455A ILE* 4.1 7.0 - - + -
490A LEU 3.5 11.1 + - - +
491A CYS 4.3 0.2 - - - -
492A LYS 3.5 0.2 - - - -
493A GLU* 1.3 74.4 - - - +
495A ASP* 1.3 60.6 + - - +
497A LEU* 4.1 8.2 - - - +
498A ALA* 3.6 17.1 + - + +
363B LEU* 4.0 18.2 + - + +
366B GLY* 3.8 17.9 - - - -
367B ILE* 3.8 40.4 - - + -
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Residues in contact with ASP 495 (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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491A CYS 3.2 14.9 + - - +
492A LYS* 2.9 15.8 + - - +
493A GLU 2.5 7.1 + - - -
494A TYR* 1.3 84.6 - - - +
496A GLU* 1.3 61.3 + - + -
497A LEU 3.2 1.1 - - - -
498A ALA* 3.4 8.4 + - - +
499A GLU* 3.3 20.8 + - - +
367B ILE* 4.8 0.4 - - - -
371B ARG* 2.7 39.5 + - - -
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Residues in contact with GLU 496 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A LYS* 3.1 35.7 + - + +
493A GLU* 2.8 18.4 + - - +
495A ASP* 1.3 70.5 - - - +
497A LEU* 1.3 62.8 + - + +
499A GLU* 3.0 25.0 - - - +
500A THR* 3.1 13.0 + - - -
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Residues in contact with LEU 497 (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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444A LEU* 3.9 17.6 - - + +
447A LYS* 3.7 40.4 - - + +
448A MET* 3.7 35.1 - - + +
451A LEU* 5.0 11.0 - - + -
493A GLU* 3.0 26.3 + - + +
494A TYR* 4.4 3.6 - - - -
496A GLU* 1.3 80.3 - - + +
498A ALA* 1.3 60.4 + - - +
499A GLU 3.0 1.8 - - - -
500A THR* 3.4 6.9 + - - +
501A GLN* 2.7 30.5 + - - +
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Residues in contact with ALA 498 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A MET* 4.1 14.1 - - + -
494A TYR* 3.6 22.0 + - + +
495A ASP* 3.4 11.5 + - - +
496A GLU 3.4 0.4 - - - -
497A LEU* 1.3 76.8 - - - +
499A GLU* 1.3 60.4 + - - +
501A GLN* 3.8 12.5 - - - +
502A GLY* 3.2 17.3 + - - -
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Residues in contact with GLU 499 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A ASP 3.3 10.4 + - - +
496A GLU* 3.0 18.6 - - - +
498A ALA* 1.3 74.6 - - - +
500A THR* 1.3 58.7 + - - +
502A GLY* 2.8 23.7 + - - -
503A LYS* 3.2 29.9 + - + +
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Residues in contact with THR 500 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A GLU* 6.0 0.4 - - - +
444A LEU* 3.7 28.0 - - + -
496A GLU 3.1 9.6 + - - -
497A LEU* 3.7 8.8 - - - +
499A GLU* 1.3 78.6 - - - +
501A GLN* 1.3 63.9 + - - +
503A LYS* 2.8 24.0 + - - +
504A LEU* 3.2 26.9 + - + +
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Residues in contact with GLN 501 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A LEU* 4.5 10.0 - - + +
444A LEU* 3.5 15.2 - - + +
445A LEU* 4.0 28.3 - - + +
448A MET* 3.2 22.8 - - - +
497A LEU 2.7 21.5 + - - +
498A ALA* 3.8 9.7 - - - +
500A THR* 1.3 72.6 - - - +
502A GLY* 1.3 56.9 + - - +
504A LEU* 4.1 0.9 - - - +
505A GLU* 2.9 58.9 + - - +
360B LYS* 4.2 19.2 - - - +
363B LEU* 4.9 3.1 - - - +
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Residues in contact with GLY 502 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A ALA 3.2 11.2 + - - -
499A GLU 2.8 17.3 + - - -
501A GLN* 1.3 72.9 - - - +
503A LYS* 1.3 60.4 + - - +
505A GLU* 3.9 11.3 + - - +
506A GLU* 3.6 25.2 + - - +
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Residues in contact with LYS 503 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A GLU* 3.2 25.9 + - + +
500A THR* 2.8 14.8 + - + +
502A GLY* 1.3 72.2 - - - +
504A LEU* 1.3 72.5 + - + +
506A GLU* 3.2 19.9 + - - +
507A LYS* 2.9 23.3 + - - +
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Residues in contact with LEU 504 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A THR* 4.4 8.7 - - + +
440A GLU* 3.6 33.9 - - + +
441A LEU* 3.6 46.4 - - + +
444A LEU* 4.9 3.6 - - + -
500A THR* 3.2 26.1 + - + +
501A GLN 4.2 1.1 - - - +
503A LYS* 1.3 79.9 - - + +
505A GLU* 1.3 55.4 + - - +
506A GLU 2.7 13.5 + - - -
507A LYS* 2.8 29.8 + - + +
508A LEU* 3.1 21.4 + - + +
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Residues in contact with GLU 505 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A LEU* 4.5 13.2 - - + +
501A GLN* 2.9 54.6 + - + +
502A GLY* 4.0 9.4 - - - +
503A LYS 3.3 0.2 - - - -
504A LEU* 1.3 72.0 - - - +
506A GLU* 1.3 57.7 + - + +
508A LEU* 4.0 17.6 - - - +
509A GLN* 4.0 16.3 + - - +
360B LYS* 4.2 20.4 + - + +
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Residues in contact with GLU 506 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A GLY 3.6 14.4 + - - +
503A LYS* 3.2 22.5 + - - +
504A LEU 2.7 4.2 + - - -
505A GLU* 1.3 75.2 - - + +
507A LYS* 1.3 56.4 + - + +
508A LEU 2.8 6.1 + - - -
509A GLN* 2.7 33.0 + - + +
510A GLU* 2.8 13.7 + - - +
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Residues in contact with LYS 507 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A THR* 3.9 27.5 + - + +
503A LYS 2.9 18.1 + - - +
504A LEU* 2.8 18.3 + - + +
506A GLU* 1.3 76.7 - - + +
508A LEU* 1.3 58.0 + - - +
510A GLU* 3.5 23.5 - - + +
511A LEU* 3.6 26.3 - - + +
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Residues in contact with LEU 508 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ILE* 4.0 27.9 - - + +
437A THR* 3.3 33.9 - - + +
438A GLN* 3.0 38.1 - - - +
441A LEU* 4.1 19.1 - - + -
504A LEU* 3.1 16.9 + - + +
505A GLU* 4.0 8.5 - - - +
506A GLU 2.8 0.6 - - - -
507A LYS* 1.3 78.1 - - - +
509A GLN* 1.3 59.4 + - - +
510A GLU 3.1 1.6 - - - -
511A LEU* 4.0 4.9 - - + +
512A GLU* 3.2 33.2 + - - +
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Residues in contact with GLN 509 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A GLU 4.0 13.9 + - - +
506A GLU* 2.7 16.0 + - + +
508A LEU* 1.3 76.7 - - - +
510A GLU* 1.3 68.5 + - - +
512A GLU* 4.2 7.2 - - + +
513A ALA* 3.1 21.8 + - - +
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Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A GLU 2.8 8.1 + - - +
507A LYS* 3.5 24.5 - - + +
509A GLN* 1.3 81.8 - - - +
511A LEU* 1.3 78.8 + - + +
513A ALA* 3.0 8.9 + - - +
514A ASN* 3.3 28.6 + - - +
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Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A HIS* 2.9 29.8 + - + +
433A LYS* 3.8 52.3 - - + +
434A ILE* 4.0 16.8 - - + -
437A THR* 5.3 7.0 - - + +
507A LYS* 3.6 27.0 + - + +
508A LEU* 3.9 3.5 + - + +
510A GLU* 1.3 94.2 - - + +
512A GLU* 1.3 62.6 + - - +
513A ALA 3.1 1.7 + - - -
514A ASN* 3.6 18.7 + - - +
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Residues in contact with GLU 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A HIS* 4.9 2.9 - - - -
431A TRP* 4.4 16.5 - - + -
434A ILE* 4.0 28.6 - - + +
438A GLN* 5.6 0.7 - - - +
508A LEU* 3.2 22.9 + - - +
509A GLN* 4.7 5.7 - - + +
511A LEU* 1.3 77.2 - - - +
513A ALA* 1.3 58.3 - - - +
515A PRO* 4.6 8.6 - - - +
349B ILE* 5.1 5.2 - - - +
353B LYS* 3.4 32.2 + - - +
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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