Contacts of the helix formed by residues 459 - 491 (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 GLN 459 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C SER* 3.6 5.4 - - - -
458C TYR* 1.3 72.0 - - - +
460C LYS* 1.3 70.3 + - - +
461C TRP* 2.8 23.0 + - + +
462C GLN* 2.8 46.3 + - + +
463C MET 4.2 0.5 + - - -
643C LYS* 3.6 36.7 + - - +
646C ASP* 3.8 15.6 + - - +
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Residues in contact with LYS 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C SER* 4.1 15.0 - - - +
450C ASP* 3.4 49.8 + - - +
453C SER* 3.5 17.9 + - - +
454C GLN* 4.3 10.1 - - - +
458C TYR* 3.6 3.2 + - - -
459C GLN* 1.3 75.0 - - - +
461C TRP* 1.3 60.2 + - - +
462C GLN 3.3 0.4 + - - -
463C MET* 3.7 16.6 + - - +
464C MET 3.9 2.9 + - - -
642C PHE* 3.7 35.8 - - + +
643C LYS* 4.8 0.4 - - - +
645C ARG* 4.9 7.9 - - - +
646C ASP* 2.7 51.1 + - + +
649C ILE* 5.5 8.0 - - - +
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Residues in contact with TRP 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C VAL* 4.8 11.0 - - + -
368C LEU* 4.6 7.0 - - + -
459C GLN* 2.8 30.5 + - + -
460C LYS* 1.3 72.6 - - - +
462C GLN* 1.3 128.3 + - - +
463C MET 2.7 4.1 + - - -
464C MET* 2.8 14.9 + - + +
465C LEU* 2.8 39.4 + - + -
639C ILE* 3.4 45.5 - - + +
642C PHE* 3.8 10.4 - - + +
643C LYS* 4.0 33.6 - - + +
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Residues in contact with GLN 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C VAL* 4.2 17.7 - - - +
367C LYS* 4.7 14.2 - - + +
368C LEU* 3.0 31.6 + - + +
371C LEU* 3.8 18.2 - - + -
458C TYR* 3.8 7.9 - - + -
459C GLN* 2.8 48.5 + - + +
461C TRP* 1.3 132.8 - - - +
463C MET* 1.3 61.5 + - - +
465C LEU* 3.1 1.7 - - - +
466C ALA 3.0 16.1 + - - -
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Residues in contact with MET 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 5.6 1.8 - - + -
371C LEU* 3.9 13.2 - - + +
374C ARG* 4.5 9.0 - - - +
375C VAL* 3.9 12.6 - - + -
442C PHE* 4.5 7.2 - - + -
445C LEU* 3.4 52.0 - - + +
448C VAL* 4.2 8.7 - - + -
449C SER* 2.8 34.5 - - - +
458C TYR* 3.5 26.9 - - + +
459C GLN 4.2 0.2 + - - -
460C LYS 3.7 7.9 + - - +
461C TRP 2.7 3.8 + - - -
462C GLN* 1.3 75.0 - - - +
464C MET* 1.3 68.8 + - - +
466C ALA* 2.8 15.2 + - - +
467C TYR* 2.8 13.3 + - - +
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Residues in contact with MET 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C PHE* 4.1 14.8 - - + -
460C LYS 3.9 0.8 + - - -
461C TRP* 2.8 14.6 + - - +
463C MET* 1.3 75.6 - - - +
465C LEU* 1.3 69.8 + - - +
467C TYR* 3.5 0.3 + - - +
468C ALA* 3.0 16.8 + - - +
518C LEU* 3.3 30.7 - - + +
519C VAL* 4.5 4.7 - - + +
635C VAL* 3.9 14.4 - - + +
638C GLY* 3.5 26.5 - - - -
639C ILE* 3.7 25.1 - - + +
642C PHE* 3.5 49.3 - - + -
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Residues in contact with LEU 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU* 3.7 14.4 - - + -
461C TRP* 2.8 37.2 + - + +
462C GLN 3.1 10.5 - - - +
464C MET* 1.3 85.7 - - - +
466C ALA* 1.3 64.7 + - - +
468C ALA* 2.8 2.8 + - - +
469C LEU* 2.8 52.5 + - + +
635C VAL* 3.9 15.7 - - + -
639C ILE* 3.8 22.4 - - + -
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Residues in contact with ALA 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU* 3.9 7.2 - - + +
371C LEU* 4.3 7.2 - - + -
372C LEU* 3.6 33.7 - - - +
375C VAL* 4.3 9.2 - - + -
462C GLN 3.0 8.9 + - - +
463C MET* 2.8 17.1 + - - +
465C LEU* 1.3 74.7 - - - +
467C TYR* 1.3 66.7 + - - +
469C LEU* 2.8 24.4 + - - +
470C HIS* 3.1 11.0 + - - -
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Residues in contact with TYR 467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C VAL* 4.6 3.9 - - + +
389C ARG* 3.4 18.6 + - - -
437C ASN 3.9 1.9 + - - -
438C ALA* 3.2 18.6 + - + -
441C LEU* 4.1 17.0 - - + -
442C PHE* 3.4 40.8 - + + -
445C LEU* 4.8 13.5 - - + -
463C MET 2.8 10.8 + - - +
464C MET 3.9 2.7 - - - +
466C ALA* 1.3 74.9 - - - +
468C ALA* 1.3 70.1 + - - +
469C LEU 3.0 0.3 + - - -
470C HIS* 3.0 42.1 + + - -
471C VAL* 3.4 6.6 + - + +
514C GLU* 2.3 46.2 + - + -
518C LEU* 3.5 24.9 - - + -
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Residues in contact with ALA 468 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C MET 3.0 10.2 + - - +
465C LEU 2.8 12.2 + - - +
467C TYR* 1.3 85.3 - - - +
469C LEU* 1.3 60.3 + - + +
471C VAL* 2.9 20.8 - - - +
472C LEU* 3.7 4.3 - - - +
515C PHE* 3.4 36.8 - - + -
518C LEU* 3.8 7.4 - - + -
635C VAL* 4.0 17.9 - - + -
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Residues in contact with LEU 469 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU* 4.2 14.6 - - + -
372C LEU* 4.1 15.7 - - + -
465C LEU* 2.8 51.8 + - + +
466C ALA* 2.8 13.7 + - - +
468C ALA* 1.3 81.1 - - + +
470C HIS* 1.3 61.9 + - - +
472C LEU* 2.9 33.9 + - + +
473C PRO* 4.0 2.3 - - - +
635C VAL* 6.1 0.2 - - + -
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Residues in contact with HIS 470 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C LEU* 3.8 14.8 - - + +
375C VAL* 3.3 28.5 - - + +
376C THR* 3.8 24.2 - - - +
379C LEU* 2.8 37.8 - - + +
389C ARG* 3.4 14.1 - - - -
466C ALA 3.1 5.3 + - - -
467C TYR* 3.0 42.5 + + - -
469C LEU* 1.3 75.2 - - - +
471C VAL* 1.3 87.0 + - - +
472C LEU 2.9 1.9 + - - -
473C PRO* 2.9 21.9 - - - +
474C PHE* 3.5 13.5 - - + -
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Residues in contact with VAL 471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG* 3.0 28.9 - - - +
467C TYR* 3.4 5.1 + - + +
468C ALA* 2.9 31.2 - - - +
470C HIS* 1.3 89.1 + - + +
472C LEU* 1.3 67.5 + - - +
474C PHE* 2.8 16.8 + - - -
475C SER* 2.8 42.6 + - - +
511C LEU* 4.1 4.0 - - + -
514C GLU* 3.8 14.4 - - + +
515C PHE* 3.6 24.0 - - + -
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C ALA 3.7 9.4 - - - +
469C LEU* 2.9 35.2 - - + +
470C HIS 2.9 1.6 + - - -
471C VAL* 1.3 80.4 - - + +
473C PRO* 1.3 74.9 - - + +
475C SER* 4.2 0.2 - - - -
476C VAL* 2.8 27.9 + - - +
507C LEU* 5.2 1.7 - - + +
511C LEU* 4.4 28.0 - - + -
515C PHE* 4.9 6.7 - - + -
631C ILE* 5.7 3.6 - - + -
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Residues in contact with PRO 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469C LEU 4.0 2.9 - - - +
470C HIS* 2.9 24.5 - - + +
472C LEU* 1.3 86.0 - - + +
474C PHE* 1.3 70.2 + - + +
476C VAL* 2.8 27.9 - - + +
477C VAL* 2.8 15.7 + - - +
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Residues in contact with PHE 474 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C THR* 4.3 18.4 - - - -
379C LEU* 3.9 22.2 - - + -
380C VAL* 5.2 14.6 - - + -
386C VAL* 3.9 25.8 - - + -
389C ARG* 4.2 21.8 - - + +
390C LEU* 3.8 20.9 - - + -
470C HIS* 3.5 30.7 - - - -
471C VAL* 2.8 12.1 + - - +
473C PRO* 1.3 81.9 - - + +
475C SER* 1.3 66.6 + - - +
477C VAL* 2.7 30.1 + - - +
478C ALA* 2.8 7.7 + - - +
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Residues in contact with SER 475 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG* 5.1 1.7 + - - +
437C ASN* 3.7 5.4 + - - +
471C VAL* 2.8 39.2 + - - +
474C PHE* 1.3 71.5 - - - +
476C VAL* 1.3 56.1 + - - -
478C ALA* 2.8 12.6 + - - +
479C THR* 2.7 33.6 + - - -
507C LEU* 3.9 4.0 - - - -
510C HIS* 2.9 33.5 + - - -
511C LEU* 4.0 15.7 - - - -
514C GLU* 3.8 0.7 + - - -
----------------------------------------------------------
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Residues in contact with VAL 476 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LEU 2.8 21.9 + - - +
473C PRO* 2.8 25.6 - - + +
475C SER* 1.3 72.4 - - - +
477C VAL* 1.3 62.5 + - + +
479C THR* 3.7 2.1 + - - -
480C MET* 3.2 28.7 + - + +
507C LEU* 3.6 35.8 - - + +
----------------------------------------------------------
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Residues in contact with VAL 477 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU* 3.2 26.9 - - + -
473C PRO 2.8 16.3 + - - +
474C PHE* 2.7 27.8 + - - +
476C VAL* 1.3 74.8 - - + +
478C ALA* 1.3 50.4 + - - +
480C MET* 2.8 27.6 + - + +
481C ILE* 2.8 40.1 + - + -
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Residues in contact with ALA 478 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ARG 3.2 20.4 - - - +
390C LEU* 3.1 30.4 - - - +
393C ASN* 4.2 12.1 - - + +
474C PHE 2.8 8.1 + - - +
475C SER* 2.8 13.1 + - - +
477C VAL* 1.3 76.7 - - - +
479C THR* 1.3 54.7 + - - +
481C ILE* 3.2 3.6 + - - +
482C PHE* 2.8 37.2 + - - +
510C HIS* 4.5 4.3 - - + -
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Residues in contact with THR 479 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ASN* 4.0 13.6 + - - +
475C SER 2.7 15.6 + - - -
476C VAL* 3.8 6.5 - - - -
478C ALA* 1.3 75.2 - - - +
480C MET* 1.3 59.4 + - - +
482C PHE* 3.5 4.5 - - + +
483C SER* 2.8 32.9 + - - -
503C SER* 3.4 27.4 - - - +
506C LEU* 3.3 36.0 + - + +
507C LEU* 3.3 20.9 - - - +
510C HIS* 4.7 2.4 - - - +
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Residues in contact with MET 480 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C VAL* 3.2 22.0 + - + +
477C VAL* 2.8 12.8 + - + +
479C THR* 1.3 76.9 - - - +
481C ILE* 1.3 52.6 - - - +
483C SER* 2.9 12.2 + - - +
484C SER* 2.1 47.0 + - - +
499C PHE* 3.6 25.1 - - + -
503C SER* 3.7 23.3 - - - +
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Residues in contact with ILE 481 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU* 3.6 33.0 - - + +
391C LEU* 4.2 13.5 - - + -
394C LEU* 3.2 30.7 - - + -
477C VAL* 2.8 41.2 + - + +
478C ALA* 3.4 5.6 - - - +
480C MET* 1.3 70.4 - - + +
482C PHE* 1.3 67.4 + - - +
484C SER* 3.1 12.9 + - - -
485C VAL* 3.3 17.4 + - + +
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Residues in contact with PHE 482 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ASN* 3.2 40.8 - - + -
394C LEU* 3.6 22.2 - - - +
396C MET* 4.5 1.8 - - + -
397C GLY* 3.7 15.3 - - - -
426C PHE* 3.1 49.6 - + + -
430C THR* 5.2 1.8 - - + -
478C ALA 2.8 21.4 + - - +
479C THR* 3.5 10.3 - - + +
481C ILE* 1.3 75.9 - - - +
483C SER* 1.3 68.1 + - - +
485C VAL* 3.7 0.2 - - - +
486C CYS* 2.8 46.3 + - + -
502C PHE* 4.0 12.3 - + - -
506C LEU* 3.5 25.1 - - + -
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Residues in contact with SER 483 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C THR* 2.8 19.6 + - - -
480C MET* 2.9 15.2 + - - -
482C PHE* 1.3 83.4 - - - +
484C SER* 1.3 75.4 + - - +
486C CYS 4.5 0.2 - - - +
487C TYR* 2.8 31.2 + - - +
499C PHE* 3.5 10.3 - - - -
502C PHE* 4.2 14.8 - - - -
503C SER* 2.6 31.8 + - - -
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Residues in contact with SER 484 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C MET* 2.1 32.2 + - - -
481C ILE* 3.1 12.5 + - - -
483C SER* 1.3 77.6 + - - +
485C VAL* 1.3 65.9 + - - +
488C TRP* 3.4 20.2 - - - +
499C PHE* 3.5 20.6 - - - -
----------------------------------------------------------
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Residues in contact with VAL 485 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 3.7 15.0 - - + -
398C LEU* 3.8 28.3 - - + -
401C LEU* 5.0 4.3 - - + -
481C ILE* 3.3 19.2 + - + +
482C PHE 3.7 1.8 - - - +
483C SER 3.3 0.2 - - - -
484C SER* 1.3 85.3 + - - +
486C CYS* 1.3 60.6 + - - +
488C TRP* 4.6 0.9 - - - +
489C THR* 2.4 32.6 + - - +
----------------------------------------------------------
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Residues in contact with CYS 486 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C LEU* 4.4 1.8 - - - -
397C GLY* 3.5 37.5 - - - +
398C LEU* 4.1 5.2 - - - -
401C LEU* 4.9 3.6 - - + -
426C PHE* 5.0 2.9 - - + -
482C PHE* 2.8 42.2 + - + +
483C SER* 5.1 0.4 - - - -
485C VAL* 1.3 87.1 - - - +
487C TYR* 1.3 67.9 + - - +
489C THR* 2.8 19.7 + - - -
490C LEU* 2.8 32.0 + - + +
502C PHE* 6.2 0.2 - - + -
----------------------------------------------------------
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Residues in contact with TYR 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C SER* 2.8 22.7 + - - +
486C CYS* 1.3 72.6 - - - +
488C TRP* 1.3 66.1 + + - +
490C LEU* 3.5 6.0 + - - -
491C GLY 2.9 21.5 + - - -
492C LEU* 2.8 57.5 + - + +
493C HIS* 2.6 31.0 + - - +
494C PRO* 4.3 7.2 - - + -
498C ARG* 4.0 9.7 + - - +
499C PHE* 3.8 41.3 + + + -
502C PHE* 3.6 52.9 - + + -
578C ASN* 4.5 2.9 + - - -
579C GLU* 4.6 2.9 - - + +
----------------------------------------------------------
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Residues in contact with TRP 488 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C SER* 3.4 23.1 - - - +
485C VAL 4.1 0.9 + - - +
486C CYS 3.2 0.6 - - - -
487C TYR* 1.3 80.3 - + - +
489C THR* 1.3 63.5 + - - +
491C GLY* 2.8 21.9 + - - -
494C PRO* 3.0 39.9 - - + -
495C GLU* 5.0 0.2 - - - -
496C VAL* 4.1 32.1 - - + -
499C PHE* 3.5 32.1 - + + -
----------------------------------------------------------
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Residues in contact with THR 489 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401C LEU* 3.8 34.6 - - + +
406C ARG* 3.7 24.8 - - + +
485C VAL* 2.4 31.2 + - - +
486C CYS* 2.8 7.9 + - - -
488C TRP* 1.3 74.0 - - - +
490C LEU* 1.3 63.1 + - - +
491C GLY* 4.5 0.2 - - - -
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Residues in contact with LEU 490 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C GLY 5.0 5.8 - - - +
400C LEU* 5.9 0.7 - - + -
401C LEU* 3.9 21.5 - - + +
404C VAL* 4.2 6.3 - - + -
405C LEU 3.2 23.6 - - - +
406C ARG* 4.3 1.2 - - - +
407C VAL* 2.8 40.6 + - + +
422C LEU* 3.9 32.5 - - + -
426C PHE* 4.2 15.0 - - + -
486C CYS* 2.8 36.9 + - + +
487C TYR* 3.9 1.6 - - - +
489C THR* 1.3 77.6 - - - +
491C GLY* 1.3 58.8 + - - +
492C LEU* 3.3 18.2 - - + -
----------------------------------------------------------
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Residues in contact with GLY 491 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C VAL* 4.5 8.7 - - - +
409C SER* 5.3 4.0 + - - -
419C ARG* 5.2 4.0 + - - -
487C TYR 2.9 6.2 + - - -
488C TRP* 2.8 19.6 + - - -
489C THR 4.4 0.4 - - - -
490C LEU* 1.3 80.3 - - - +
492C LEU* 1.3 60.7 + - - +
493C HIS 4.0 1.0 + - - -
494C PRO* 5.4 3.0 - - - +
579C GLU* 4.9 0.2 - - - +
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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