Contacts of the helix formed by residues 449 - 477 (chain A) in PDB entry 3OMA
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 PRO 449 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLN 4.3 0.4 - - - +
448A TYR* 1.3 86.4 - - + +
450A GLU* 1.3 64.6 + - - +
451A TRP* 3.3 22.9 - - + +
452A ALA* 3.1 22.4 + - + -
453A GLY 3.3 9.2 + - - -
514A VAL* 4.3 9.6 - - + -
517A TYR* 3.7 35.2 - - + +
518A THR* 3.6 12.3 - - - +
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Residues in contact with GLU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 3.4 32.3 + - + +
379A THR* 2.8 29.4 + - - -
448A TYR* 2.6 35.6 + - + +
449A PRO* 1.3 72.5 - - - +
451A TRP* 1.3 63.3 + - - +
453A GLY 3.4 1.2 + - - -
454A LYS* 2.8 53.9 + - + +
531A TRP* 5.1 0.2 - - - -
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Residues in contact with TRP 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A PRO* 4.1 19.0 - - + +
450A GLU* 1.3 78.6 - - - +
452A ALA* 1.3 78.2 + - + +
454A LYS* 3.6 10.2 + - - +
455A LEU* 3.1 46.5 + - + +
510A PHE* 4.2 11.0 - + - -
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Residues in contact with ALA 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A PRO* 3.1 24.4 + - + +
451A TRP* 1.3 98.9 - - + +
453A GLY* 1.3 59.4 + - - +
455A LEU* 3.3 0.4 + - - -
456A HIS* 2.9 27.3 + - - +
510A PHE* 3.3 19.5 - - + -
514A VAL* 3.6 27.6 - - + -
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Residues in contact with GLY 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR* 3.3 21.1 - - - +
383A TRP* 4.6 0.3 + - - -
437A TYR* 3.7 30.4 + - - -
448A TYR* 4.6 1.1 - - - -
449A PRO 3.3 9.0 + - - -
450A GLU 3.4 1.0 + - - -
452A ALA* 1.3 78.3 - - - +
454A LYS* 1.3 55.5 + - - +
456A HIS* 3.5 2.9 + - - +
457A PHE* 3.0 27.2 + - - +
514A VAL* 5.0 0.6 - - - +
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Residues in contact with LYS 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LEU 3.7 21.7 + - - -
378A LYS* 4.2 4.0 - - - +
379A THR* 3.2 8.6 + - - +
382A LEU* 4.0 17.5 - - + -
450A GLU* 2.8 50.0 + - + +
451A TRP* 3.7 11.2 - - - +
453A GLY* 1.3 72.6 - - - +
455A LEU* 1.3 60.8 + - - +
457A PHE* 3.3 6.9 + - - +
458A TRP* 2.9 42.1 + - + +
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A TRP* 3.1 31.5 + - + +
452A ALA* 3.3 5.4 + - - +
454A LYS* 1.3 72.4 - - - +
456A HIS* 1.3 65.7 + - - +
458A TRP* 3.3 7.3 + - + -
459A MET* 3.0 56.0 + - + +
510A PHE* 3.7 26.0 - - + -
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Residues in contact with HIS 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A TRP* 3.4 26.8 - + - -
433A PHE* 3.7 23.6 - + - -
437A TYR* 2.8 23.0 + + - +
452A ALA 2.9 17.4 + - - +
453A GLY 3.5 4.0 - - - +
455A LEU* 1.3 77.5 - - - +
457A PHE* 1.3 62.1 + - - +
459A MET* 3.4 11.1 + - - +
460A MET* 3.0 23.7 + - + +
507A SER* 3.3 29.1 + - - -
508A PHE* 4.9 0.8 - - - -
510A PHE* 4.1 8.1 - - + -
511A PHE* 3.3 35.2 - + + +
514A VAL* 5.5 0.4 - - + -
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Residues in contact with PHE 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A THR* 5.2 0.4 - - + -
382A LEU* 3.1 51.6 - - + -
383A TRP* 3.6 37.7 - + + +
386A GLY* 4.5 4.5 - - - -
430A PHE* 3.9 20.6 - + - -
453A GLY 3.0 15.2 + - - +
454A LYS* 3.5 9.0 - - - +
456A HIS* 1.3 77.8 - - - +
458A TRP* 1.3 102.6 + + - +
460A MET* 3.4 1.4 + - - +
461A PHE* 2.8 46.5 + + + +
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Residues in contact with TRP 458 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LEU* 4.2 19.0 - - + +
454A LYS* 2.9 35.8 + - + +
455A LEU* 3.3 8.3 + - + +
457A PHE* 1.3 102.9 - + - +
459A MET* 1.3 57.6 + - - +
461A PHE* 3.8 25.7 - + - +
462A VAL* 3.0 43.0 + - + +
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Residues in contact with MET 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A LEU* 3.0 45.5 + - + +
456A HIS* 3.7 5.8 - - - +
458A TRP* 1.3 76.0 - - - +
460A MET* 1.3 57.4 + - - +
462A VAL* 5.0 2.0 - - - -
463A GLY* 2.8 27.5 + - - -
503A LEU* 4.0 26.4 - - + +
504A SER* 4.9 0.2 - - - -
506A ALA* 5.2 3.4 - - - +
507A SER* 3.5 23.2 - - - -
510A PHE* 3.3 46.0 - - + -
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Residues in contact with MET 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 3.4 39.3 - - + -
383A TRP* 3.8 28.5 - - + -
425A SER 5.2 2.9 - - - +
430A PHE* 3.9 12.6 - - + -
433A PHE* 4.6 6.5 - - + -
456A HIS* 3.0 23.1 + - + +
457A PHE 3.7 2.9 - - - +
459A MET* 1.3 74.6 - - - +
461A PHE* 1.3 60.8 + - - +
463A GLY* 5.0 0.2 - - - -
464A ALA* 2.8 47.3 + - - +
504A SER* 3.3 20.9 - - - +
507A SER* 2.7 33.6 - - - +
508A PHE* 4.8 1.1 - - + +
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Residues in contact with PHE 461 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A GLY* 4.6 8.5 - - - -
389A PHE* 4.0 25.4 - + - -
390A LEU* 4.0 22.0 - - + -
430A PHE* 4.2 9.2 - + - -
457A PHE* 2.8 43.0 + + + +
458A TRP* 3.8 27.4 - + - +
459A MET 3.3 0.2 - - - -
460A MET* 1.3 80.0 - - - +
462A VAL* 1.3 67.9 + - + +
464A ALA* 4.6 0.6 - - - +
465A ASN* 2.7 50.7 + - - +
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A TRP* 3.0 28.9 + - + +
459A MET* 4.2 2.5 - - - +
461A PHE* 1.3 84.6 - - + +
463A GLY* 1.3 59.7 + - - +
465A ASN* 3.5 2.9 + - - +
466A LEU* 3.0 41.9 + - + +
503A LEU* 4.0 17.0 - - + -
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Residues in contact with GLY 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A MET 2.8 22.3 + - - -
462A VAL* 1.3 74.6 - - - +
464A ALA* 1.3 51.0 + - - +
466A LEU* 3.2 1.4 + - - -
467A THR* 2.7 35.9 + - - -
500A GLY* 3.2 12.8 - - - +
503A LEU* 3.7 15.4 - - - +
504A SER* 3.0 14.4 - - - -
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Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 5.3 2.5 - - + -
426A LEU* 3.7 32.0 - - + +
430A PHE* 5.1 2.5 - - + -
460A MET* 2.8 39.4 + - + +
461A PHE* 4.6 1.3 - - - +
463A GLY* 1.3 72.0 - - - +
465A ASN* 1.3 57.6 + - - +
467A THR* 3.4 4.2 + - - -
468A PHE* 3.1 38.3 + - + +
504A SER* 3.1 8.4 + - - +
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Residues in contact with ASN 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A PHE* 4.5 5.2 - - - -
390A LEU* 3.5 23.4 - - - +
422A TYR* 2.7 34.8 + - - +
426A LEU* 4.4 2.0 - - - +
461A PHE* 2.7 47.5 + - + +
462A VAL* 3.9 3.8 - - - +
463A GLY 3.3 0.6 - - - -
464A ALA* 1.3 74.8 - - - +
466A LEU* 1.3 61.6 + - - +
469A PHE* 3.0 33.8 + - + +
470A PRO* 3.7 0.5 - - - +
1009A TRD 4.3 13.1 - - + +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A VAL* 3.0 37.5 + - + +
463A GLY 3.2 4.7 + - - +
465A ASN* 1.3 75.0 - - - +
467A THR* 1.3 62.4 + - - +
470A PRO* 3.2 20.4 - - - +
496A VAL* 3.7 25.6 - - + +
497A SER* 3.5 9.2 - - - -
499A LEU* 5.5 3.4 - - + -
500A GLY* 3.6 18.6 - - - +
503A LEU* 4.7 8.5 - - + -
1009A TRD 4.5 20.4 - - + -
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Residues in contact with THR 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 3.8 18.6 - - + +
52A ARG* 4.8 0.9 - - - -
463A GLY 2.7 20.3 + - - -
464A ALA* 3.6 6.7 - - - -
465A ASN 3.3 0.2 - - - -
466A LEU* 1.3 76.4 - - - +
468A PHE* 1.3 92.8 + - + +
470A PRO* 3.8 1.6 - - - +
471A GLN* 3.6 7.5 + - - +
497A SER* 2.7 47.5 + - - +
500A GLY* 2.8 19.8 + - - -
501A ALA* 2.8 4.5 + - + -
504A SER* 3.6 4.0 + - - -
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Residues in contact with PHE 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 3.5 44.0 - + + -
417A VAL 4.8 0.4 - - - -
418A ALA* 3.6 11.7 - - - +
421A HIS* 3.2 50.3 - + + -
422A TYR* 3.6 22.9 - - + -
425A SER* 4.1 1.6 - - - -
426A LEU* 3.6 25.4 - - + -
464A ALA* 3.1 23.8 + - - +
467A THR* 1.3 94.3 - - + +
469A PHE* 1.3 67.6 + - - +
470A PRO* 3.3 2.5 - - - -
471A GLN* 3.0 39.8 + - - +
472A HIS* 3.9 0.2 + - - -
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Residues in contact with PHE 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TRD 3.9 36.3 - - + -
393A VAL* 4.7 7.0 - - + -
422A TYR* 3.3 24.2 + + - +
465A ASN* 3.0 14.9 + - + +
468A PHE* 1.3 73.5 - - - +
470A PRO* 1.3 68.5 - - + +
472A HIS* 2.9 43.1 + + - +
473A PHE* 3.8 32.3 + + - -
1009A TRD 4.0 24.0 - - + -
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Residues in contact with PRO 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ASN 3.7 2.0 - - - +
466A LEU 3.2 27.6 - - - +
467A THR 3.8 1.3 - - - +
468A PHE 3.4 3.1 - - - -
469A PHE* 1.3 93.6 - - + +
471A GLN* 1.3 57.2 + - - +
472A HIS 3.2 0.2 - - - -
473A PHE* 3.2 19.8 + - + +
474A LEU* 3.1 27.3 + - - +
493A TRP* 3.9 37.3 - - + +
496A VAL* 4.0 16.2 - - + -
497A SER* 4.7 2.2 - - - +
1009A TRD 4.3 12.6 - - + -
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Residues in contact with GLN 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A HEA 3.5 11.9 + - - -
52A ARG* 3.4 17.0 - - - +
414A TYR* 3.2 41.0 - - + +
417A VAL* 3.2 26.7 - - - +
418A ALA* 3.9 3.1 - - + -
467A THR* 3.6 11.6 + - - +
468A PHE* 3.0 35.5 + - - +
470A PRO* 1.3 75.3 - - - +
472A HIS* 1.3 59.1 + - - +
474A LEU* 4.2 12.8 - - + -
475A GLY 3.0 23.2 + - - -
497A SER* 3.1 22.8 + - - +
----------------------------------------------------------
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Residues in contact with HIS 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TRD 3.9 33.2 - - + +
393A VAL* 4.6 5.3 - - + +
394A GLY* 6.3 0.2 - - - -
397A THR* 3.7 21.1 + - + +
415A TYR* 3.8 28.8 - + + +
418A ALA* 3.6 29.5 - - + +
422A TYR* 3.8 26.2 - + - -
469A PHE* 2.9 40.0 + + - +
471A GLN* 1.3 77.2 - - - +
473A PHE* 1.3 59.0 + - + +
475A GLY 3.4 0.9 + - - -
476A ARG* 3.0 35.2 + - - +
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Residues in contact with PHE 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TRD 4.1 18.4 - - + -
469A PHE* 3.8 30.5 - + - -
470A PRO* 3.3 21.5 - - + +
472A HIS* 1.3 77.0 - - + +
474A LEU* 1.3 65.5 + - - +
476A ARG* 3.3 2.4 + - - +
477A GLN* 3.0 28.1 + - - +
493A TRP* 3.6 48.0 - + + -
1009A TRD 4.3 24.2 - - + -
40B GLY 3.6 16.6 - - - +
41B THR* 3.7 35.2 - - + -
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 5.9 0.2 - - - +
414A TYR* 4.1 10.1 - - + -
470A PRO 3.1 14.2 + - - +
471A GLN* 3.8 23.3 - - + +
473A PHE* 1.3 76.1 - - - +
475A GLY* 1.3 57.6 + - - +
477A GLN* 3.3 6.4 + - - +
478A GLY 3.0 9.9 + - - -
479A MET* 2.9 35.0 + - + +
490A PHE* 3.5 41.7 - - + +
493A TRP* 3.9 19.5 - - + +
494A ASN* 3.6 38.1 - - - +
497A SER* 5.1 1.3 - - - -
----------------------------------------------------------
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Residues in contact with GLY 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TYR* 3.6 9.0 - - - -
410A TYR* 4.4 0.9 - - - -
413A THR* 3.7 20.1 + - - -
414A TYR* 4.0 3.0 - - - +
415A TYR* 3.4 29.8 - - - -
471A GLN 3.0 10.7 + - - -
472A HIS 3.8 2.0 - - - -
474A LEU* 1.3 74.5 - - - +
476A ARG* 1.3 59.0 + - - +
478A GLY* 2.9 19.3 + - - -
479A MET 4.4 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TRD 3.3 56.5 - - - +
409A TYR* 2.6 30.8 + - - -
410A TYR* 2.9 44.5 + - + +
415A TYR* 4.1 7.1 + - + -
472A HIS 3.0 23.1 + - - +
473A PHE* 3.7 4.3 - - - +
475A GLY* 1.3 75.3 - - - +
477A GLN* 1.3 53.5 + - - +
478A GLY 3.2 0.2 - - - -
41B THR 2.8 21.8 + - - +
42B GLY* 3.2 26.0 - - - +
43B PHE* 3.3 20.7 - - + +
58B ASP* 2.9 19.8 + - - -
62B LEU* 4.2 10.1 - - - +
----------------------------------------------------------
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Residues in contact with GLN 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A TYR* 4.1 1.6 - - - -
473A PHE 3.0 18.3 + - - +
474A LEU* 3.5 1.8 - - + +
475A GLY 3.1 0.2 - - - -
476A ARG* 1.3 75.0 - - - +
478A GLY* 1.3 57.1 + - - +
479A MET 3.6 0.4 - - - -
490A PHE* 3.4 28.2 - - + -
35B ARG 5.1 0.6 + - - -
36B PRO* 3.3 7.8 - - - +
37B GLN* 2.7 46.7 + - - +
40B GLY* 3.7 27.5 - - - +
42B GLY 3.1 22.2 + - - +
43B PHE 3.7 14.5 + - - -
44B GLN* 2.9 32.3 + - - +
45B PRO* 5.8 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