Contacts of the helix formed by residues 490 - 518 (chain A) in PDB entry 1KLN
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 ALA 490 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A TYR* 3.7 17.7 - - + +
488A GLN 3.6 3.4 + - - -
489A ILE* 1.3 73.0 - - - +
491A LEU* 1.3 67.2 + - - +
492A GLU* 3.3 3.8 - - + +
493A GLU* 3.0 20.9 + - + +
494A ALA* 2.9 21.5 + - - +
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Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A THR* 4.5 4.2 + - + -
334A LEU* 4.3 27.4 - - + -
382A TYR* 4.0 7.1 - - - -
384A PRO* 3.9 15.0 - - + -
387A HIS* 3.6 24.7 - - + -
389A TYR* 2.9 26.6 + - + +
393A PRO* 3.6 33.4 - - + -
395A GLN* 3.6 28.0 - - + +
489A ILE 3.4 2.0 + - - -
490A ALA* 1.3 70.3 - - - +
492A GLU* 1.3 66.2 + - + +
494A ALA* 3.6 2.8 - - - +
495A GLY* 3.0 23.7 + - - -
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Residues in contact with GLU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 2.9 67.4 - - + +
332A THR* 4.4 21.1 + - - +
334A LEU* 5.4 3.5 - - - +
490A ALA* 3.1 3.5 + - + +
491A LEU* 1.3 81.0 - - + +
493A GLU* 1.3 60.3 + - + +
495A GLY* 3.8 2.8 - - - +
496A ARG* 3.2 15.9 + - - +
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Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 3.1 24.3 + - - +
476A ILE* 3.9 25.5 - - + +
489A ILE* 4.4 7.6 - - + -
490A ALA* 3.0 20.4 + - + +
492A GLU* 1.3 73.8 - - + +
494A ALA* 1.3 69.9 + - - +
495A GLY 3.2 0.2 - - - -
496A ARG* 2.9 44.2 + - - +
497A TYR* 3.2 9.0 + - - +
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Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A TYR* 4.0 5.2 - - + -
387A HIS* 3.3 34.1 - - + -
476A ILE* 5.0 0.2 - - - -
486A PHE* 3.6 24.2 - - + -
489A ILE* 4.0 10.0 - - + +
490A ALA 2.9 11.6 + - - +
491A LEU 3.6 3.8 - - - +
493A GLU* 1.3 77.7 - - - +
495A GLY* 1.3 57.9 + - - +
497A TYR* 3.1 6.2 + - - +
498A ALA* 2.9 29.1 + - - +
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Residues in contact with GLY 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TYR* 5.4 1.8 - - - -
332A THR* 4.3 6.3 - - - -
382A TYR* 3.4 29.5 - - - -
491A LEU 3.0 11.0 + - - -
492A GLU* 4.1 2.2 - - - -
493A GLU 3.2 0.2 - - - -
494A ALA* 1.3 79.1 - - - +
496A ARG* 1.3 55.4 + - - +
499A ALA* 2.8 38.0 + - - +
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Residues in contact with ARG 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A VAL* 4.0 13.9 - - - +
325A ILE* 2.9 19.5 + - - +
326A SER* 3.2 36.9 - - - +
327A TYR* 3.4 22.0 - - + +
330A TYR* 4.3 6.1 - - - -
471A ILE* 3.4 35.6 - - + +
475A GLU* 5.1 4.9 + - - -
476A ILE* 4.2 13.1 - - + +
492A GLU 3.2 16.5 + - - +
493A GLU* 2.9 31.3 + - - +
495A GLY* 1.3 74.2 - - - +
497A TYR* 1.3 61.0 + - - +
500A GLU* 3.1 26.2 + - - +
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Residues in contact with TYR 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A GLU* 3.3 26.5 - - - -
471A ILE* 3.3 39.4 - - + +
473A PHE* 4.0 29.0 - + + +
476A ILE* 3.9 22.6 - - + +
486A PHE* 3.7 22.0 - + - -
493A GLU 3.2 2.9 + - - +
494A ALA 3.1 6.5 + - - +
496A ARG* 1.3 77.0 - - - +
498A ALA* 1.3 71.0 + - - +
500A GLU* 3.1 4.7 + - - +
501A ASP* 2.8 57.4 + - - +
14B C 2.5 36.3 + - - -
929B ZN 4.0 0.5 - - - -
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Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A GLU* 3.7 24.5 - - + +
372A SER* 3.0 26.9 + - - +
382A TYR* 3.7 23.8 - - + -
486A PHE* 4.7 0.7 - - + -
494A ALA 2.9 18.5 + - - +
495A GLY 4.1 0.2 - - - +
497A TYR* 1.3 81.0 - - + +
499A ALA* 1.3 62.6 + - - +
501A ASP* 3.4 5.1 - - - +
502A ALA 3.2 14.9 + - - -
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Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A TYR* 2.8 51.2 - - + -
372A SER* 4.2 8.5 - - - -
380A ALA* 3.7 2.9 - - + +
381A ALA 4.2 15.3 - - - -
382A TYR* 4.6 0.9 - - - +
495A GLY 2.8 18.1 + - - +
498A ALA* 1.3 70.9 - - - +
500A GLU* 1.3 63.9 - - - +
502A ALA* 3.1 6.0 + - - +
503A ASP* 3.0 19.2 + - - +
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Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 2.9 37.1 - - + +
330A TYR* 2.9 17.9 - - - +
468A HIS* 3.0 33.7 + - + -
469A LYS 3.9 0.7 - - - +
470A THR* 3.4 21.1 - - + +
471A ILE* 3.0 30.8 + - - +
496A ARG 3.1 14.3 + - - +
497A TYR 3.1 2.2 + - - +
499A ALA* 1.3 73.5 - - - +
501A ASP* 1.3 73.4 + - - +
503A ASP* 3.3 1.9 + - - +
504A VAL* 3.0 25.2 + - + +
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Residues in contact with ASP 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ALA* 5.2 6.1 - - + -
357A GLU* 4.7 4.4 - - - +
458A MET* 3.5 26.3 - - + +
470A THR* 5.5 0.5 - - - +
471A ILE 4.7 1.0 - - - +
497A TYR* 2.8 58.5 + - - +
498A ALA* 3.4 12.1 - - - +
500A GLU* 1.3 86.7 - - - +
502A ALA* 1.3 59.3 + - - +
504A VAL* 3.8 1.6 - - - +
505A THR* 2.8 34.2 + - - +
14B C 4.4 5.0 + - - -
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Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 4.1 8.2 - - + +
354A PHE 5.2 2.5 - - - +
355A ALA* 5.1 5.6 - - + +
372A SER* 4.1 15.3 - - - +
373A PHE 4.0 16.8 - - - +
374A ALA* 3.7 21.2 - - + +
498A ALA 3.2 9.5 + - - +
499A ALA 3.1 8.9 + - - +
501A ASP* 1.3 80.2 - - - +
503A ASP* 1.3 64.6 + - - +
505A THR* 3.3 8.1 - - - -
506A LEU* 3.2 17.0 + - - +
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Residues in contact with ASP 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 5.3 0.2 - - - +
329A ASN* 5.7 0.9 + - - -
330A TYR* 2.4 46.1 + - + +
374A ALA* 3.7 8.9 - - - +
376A GLU 4.1 1.9 - - - +
377A PRO* 3.3 6.1 - - - +
378A GLY* 2.9 32.3 + - - -
380A ALA* 4.2 1.8 - - + -
499A ALA 3.0 4.2 + - - -
500A GLU 3.5 1.3 - - - +
502A ALA* 1.3 77.3 - - - +
504A VAL* 1.3 59.1 + - - +
506A LEU* 3.1 6.8 + - - +
507A GLN* 3.0 48.9 + - - -
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Residues in contact with VAL 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A MET* 4.1 12.3 - - + -
462A ALA* 4.3 16.4 - - + -
466A LEU* 3.9 15.3 - - + -
468A HIS* 3.4 33.2 - - + +
470A THR* 4.1 7.6 - - + -
500A GLU* 3.0 21.6 + - + +
501A ASP 3.8 2.5 - - - +
503A ASP* 1.3 72.8 - - + +
505A THR* 1.3 57.6 + - - +
507A GLN* 3.0 15.0 + - - +
508A LEU* 2.8 50.5 + - + +
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Residues in contact with THR 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ALA* 4.7 3.6 - - + -
354A PHE 5.6 0.9 - - - +
417A VAL* 4.2 8.3 - - + +
418A GLY* 3.6 38.8 - - - +
419A GLN* 4.2 6.6 + - - +
442A THR* 3.4 15.4 - - + +
458A MET* 3.3 15.1 - - - +
501A ASP* 2.8 22.5 + - - +
502A ALA* 3.3 8.7 - - - +
504A VAL* 1.3 75.7 - - - +
506A LEU* 1.3 63.8 + - - +
508A LEU* 3.1 13.6 + - - +
509A HIS* 2.9 20.0 + - - +
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 5.2 8.5 - - + +
352A PHE* 5.3 1.3 - - - -
353A ALA* 4.6 19.7 - - + +
374A ALA* 3.9 13.9 - - + +
375A ILE 3.6 11.4 - - - +
376A GLU* 3.6 36.8 - - - +
377A PRO* 4.2 4.5 - - + -
417A VAL* 4.8 7.2 - - + -
502A ALA 3.2 7.9 + - - +
503A ASP* 3.1 11.6 + - - +
505A THR* 1.3 79.2 - - - +
507A GLN* 1.3 65.4 + - + +
509A HIS* 2.8 28.0 + - + +
510A LEU* 2.9 33.1 + - + +
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Residues in contact with GLN 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PRO* 3.9 28.0 - - + +
466A LEU* 3.7 22.8 - - + +
503A ASP* 3.0 57.1 + - - +
504A VAL* 3.6 12.0 - - - +
506A LEU* 1.3 74.2 - - - +
508A LEU* 1.3 61.7 + - - +
510A LEU* 2.9 21.4 + - + +
511A LYS* 3.0 15.9 + - - +
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Residues in contact with LEU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A THR* 4.0 7.4 - - + -
458A MET* 3.9 20.4 - - + -
461A LEU* 3.4 47.3 - - + +
462A ALA 4.2 0.4 - - - +
465A TRP* 3.6 20.2 - - + -
466A LEU* 3.8 14.8 - - + -
504A VAL* 2.8 38.7 + - + +
505A THR* 3.4 12.3 - - - +
507A GLN* 1.3 72.2 - - - +
509A HIS* 1.3 63.5 + - - +
511A LYS* 3.1 2.3 + - - +
512A MET* 3.0 39.4 + - + +
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Residues in contact with HIS 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 4.7 9.8 - - + +
417A VAL* 3.8 32.5 - - + +
440A PHE* 3.4 36.4 - + - +
442A THR* 4.1 2.4 - - + +
445A GLU* 3.0 25.7 + - - +
505A THR 2.9 11.1 + - - +
506A LEU* 2.8 14.6 + - + +
508A LEU* 1.3 77.3 - - - +
510A LEU* 1.3 74.9 + - + +
513A TRP* 3.0 60.5 + + + +
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Residues in contact with LEU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL* 6.3 1.1 - - + -
377A PRO* 4.0 30.5 - - + -
506A LEU* 2.9 27.8 + - + +
507A GLN* 3.2 14.1 - - + +
509A HIS* 1.3 97.5 - - + +
511A LYS* 1.3 56.1 + - + +
514A PRO* 3.1 25.2 - - - +
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Residues in contact with LYS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A TRP* 3.3 52.6 + - + +
466A LEU* 3.8 13.9 - - + -
507A GLN 3.0 15.4 + - - +
508A LEU 3.1 5.6 + - - +
510A LEU* 1.3 78.9 - - + +
512A MET* 1.3 61.9 + - + +
514A PRO* 3.4 6.6 - - - +
515A ASP* 2.8 25.6 - - - +
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Residues in contact with MET 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A THR* 3.9 20.9 - - - +
445A GLU* 3.4 20.9 - - + +
446A SER* 3.8 26.2 - - - -
449A LEU* 3.8 11.1 - - + +
461A LEU* 4.8 2.9 - - + -
465A TRP* 3.5 49.6 - - + +
508A LEU* 3.0 36.3 + - + +
511A LYS* 1.3 76.5 - - - +
513A TRP* 1.3 67.2 + - - +
514A PRO 3.1 0.5 - - - -
515A ASP* 3.1 6.2 + - - +
516A LEU* 3.0 23.1 + - - +
----------------------------------------------------------
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Residues in contact with TRP 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A PHE* 3.5 38.6 - + - -
445A GLU* 3.9 7.0 + - - -
509A HIS* 3.0 42.9 + + + +
512A MET* 1.3 71.6 - - - +
514A PRO* 1.3 66.5 - - + +
516A LEU* 3.3 15.1 + - + +
517A GLN* 3.0 54.1 + - + +
523A LEU* 3.5 30.5 - - + -
526A PHE* 3.6 17.0 - + - -
527A GLU* 4.1 17.7 - - + -
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Residues in contact with PRO 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A HIS 3.9 0.2 - - - +
510A LEU* 3.1 27.1 - - - +
511A LYS 3.4 8.5 - - - +
513A TRP* 1.3 94.1 - - + +
515A ASP* 1.3 65.7 + - - +
517A GLN* 3.0 30.0 + - + +
518A LYS* 3.4 7.2 + - - +
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Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 4.5 14.8 - - + -
465A TRP* 4.4 17.1 - - - -
511A LYS* 2.8 24.9 - - - +
512A MET 3.1 6.8 + - - +
514A PRO* 1.3 76.6 - - - +
516A LEU* 1.3 63.4 + - - +
518A LYS* 3.1 27.1 - - - +
519A HIS* 3.4 10.7 - - - -
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Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A GLU* 3.9 33.0 - - + +
448A ILE* 4.1 18.6 - - + -
449A LEU* 3.7 21.3 - - + +
512A MET 3.0 9.7 + - - +
513A TRP* 3.4 32.1 - - + +
514A PRO 3.1 0.2 - - - -
515A ASP* 1.3 79.8 - - - +
517A GLN* 1.3 61.8 + - - +
518A LYS 3.0 1.2 + - - -
519A HIS* 3.5 13.7 + - - -
522A PRO* 4.1 4.0 - - + -
523A LEU* 3.6 41.2 - - + +
526A PHE* 4.0 15.7 - - + -
----------------------------------------------------------
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Residues in contact with GLN 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A TRP* 3.0 56.7 + - + +
514A PRO* 3.0 15.1 + - - +
516A LEU* 1.3 73.1 - - - +
518A LYS* 1.3 66.0 + - - +
519A HIS* 3.2 3.7 + - - -
520A LYS 4.6 1.2 + - - -
523A LEU* 4.1 14.1 - - + +
----------------------------------------------------------
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Residues in contact with LYS 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A PRO 3.4 7.4 + - - +
515A ASP* 3.1 23.2 + - - +
517A GLN* 1.3 79.5 - - - +
519A HIS* 1.3 75.6 + - + +
520A LYS 4.2 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