Contacts of the helix formed by residues 463 - 486 (chain A) in PDB entry 1MWR
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 463 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LYS* 4.0 1.6 - - - -
427A ILE* 3.5 8.8 - - - +
445A ARG* 2.8 39.3 + - - -
447A GLU 4.3 3.8 - - - +
449A VAL* 4.1 10.7 - - - +
453A ILE* 4.5 3.3 - - + +
458A ALA* 3.0 19.6 + - + -
461A SER* 3.3 6.2 + - - +
462A SER* 1.3 70.7 - - - +
464A ASN* 1.3 65.8 + - - +
465A ILE* 3.0 19.8 + - - +
466A PHE* 2.9 39.1 + - + -
467A PHE* 3.2 22.3 - - - -
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Residues in contact with ASN 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 2.8 28.2 + - - -
443A VAL* 4.3 1.1 - - + -
444A THR 3.1 29.2 + - - +
445A ARG* 3.9 9.2 - - - +
446A TYR* 3.1 38.5 + - - -
462A SER 3.3 3.0 + - - -
463A ASP* 1.3 72.8 + - - +
465A ILE* 1.3 56.1 + - - +
467A PHE 3.7 0.2 + - - -
468A ALA* 3.0 28.6 + - - +
519A TYR* 3.2 44.2 - - + +
521A GLN* 4.2 3.2 + - - -
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Residues in contact with ILE 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 3.8 32.3 - - + -
429A GLY 4.7 0.4 - - - +
430A LYS 3.9 12.6 - - - +
431A GLY 3.8 9.4 - - - +
432A TRP* 3.7 41.3 - - + -
443A VAL* 3.6 32.3 - - + +
445A ARG* 4.1 13.0 - - + +
463A ASP* 3.0 7.6 + - - +
464A ASN* 1.3 73.4 - - - +
466A PHE* 1.3 67.9 + - - +
468A ALA* 3.0 7.2 + - - +
469A ARG* 2.8 30.7 + - - +
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Residues in contact with PHE 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 4.0 13.9 - - + -
423A THR* 4.1 9.4 - - + -
425A TYR* 3.6 24.3 - + - -
427A ILE* 3.6 8.6 - - + +
453A ILE* 3.1 36.6 - - + -
454A ASP 3.8 4.0 - - - -
455A LEU* 3.5 36.1 - - + -
458A ALA* 3.2 32.3 - - + -
463A ASP* 2.9 21.1 + - + +
465A ILE* 1.3 76.1 - - - +
467A PHE* 1.3 68.6 + + - +
469A ARG* 3.4 4.6 + - - +
470A VAL* 3.1 37.4 + - + +
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Residues in contact with PHE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 3.7 53.8 - - + -
407A ILE* 6.0 0.9 - - + -
409A THR* 4.0 11.2 - - + +
410A ALA* 4.2 10.8 - - + -
419A LEU* 6.4 0.4 - - + -
455A LEU* 3.8 31.4 - - + -
458A ALA* 3.7 31.2 - - + -
459A ILE* 4.2 12.3 - - + -
463A ASP 3.2 21.2 + - - +
464A ASN 4.4 1.6 - - - +
465A ILE 3.2 0.2 - - - -
466A PHE* 1.3 83.6 - + - +
468A ALA* 1.3 67.0 + - - +
469A ARG 3.0 2.0 - - - -
470A VAL* 3.0 8.5 + - + +
471A ALA* 2.9 25.1 + - - +
518A GLY* 3.7 20.6 - - - +
519A TYR* 4.6 0.9 - - + -
597A LYS* 5.3 1.3 - - - -
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Residues in contact with ALA 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 5.3 3.4 - - + -
443A VAL* 3.9 26.9 - - + -
464A ASN 3.0 20.8 + - - +
465A ILE* 3.0 6.7 + - + +
467A PHE* 1.3 76.8 - - - +
469A ARG* 1.3 60.4 + - + +
471A ALA* 3.5 3.5 + - - +
472A LEU* 3.1 31.0 + - - +
515A ALA* 3.6 28.4 - - + +
518A GLY* 4.6 0.9 - - - -
519A TYR* 3.9 2.4 - - + -
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Residues in contact with ARG 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A TYR* 3.4 55.8 - - + +
426A LYS* 3.9 18.4 + - - +
427A ILE* 5.4 0.4 - - - +
432A TRP* 3.6 57.4 - - + +
465A ILE* 2.8 25.8 + - - +
466A PHE 3.7 4.7 - - - +
468A ALA* 1.3 75.1 - - - +
470A VAL* 1.3 54.5 + - - +
471A ALA 3.1 1.8 - - - -
472A LEU* 2.9 7.2 + - + +
473A GLU* 2.7 36.7 + - - +
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 3.7 25.1 - - + +
410A ALA* 5.2 1.3 - - - -
413A GLY* 4.6 7.9 - - - -
418A THR* 5.1 1.3 - - - +
419A LEU* 4.0 24.5 - - + -
425A TYR* 4.0 13.9 - - + +
466A PHE* 3.1 40.7 + - + +
467A PHE* 3.0 14.5 + - + +
469A ARG* 1.3 76.5 - - - +
471A ALA* 1.3 58.4 + - - +
473A GLU* 3.3 3.3 + - - +
474A LEU* 3.0 39.0 + - + +
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 4.3 1.3 - - + -
467A PHE 2.9 7.3 + - - +
468A ALA 3.7 4.3 - - - +
470A VAL* 1.3 76.3 - - - +
472A LEU* 1.3 63.0 - - - +
474A LEU* 3.4 11.1 + - - +
475A GLY 3.2 11.6 + - - -
479A PHE* 4.2 10.2 - - + +
514A LEU* 3.1 43.4 - - + +
518A GLY* 3.6 28.7 - - - -
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A TRP* 3.7 35.9 - - + -
434A LYS* 4.9 7.9 - - + +
438A TRP* 4.0 16.4 - - + -
468A ALA 3.1 19.6 + - - +
469A ARG* 2.9 9.2 + - + +
471A ALA* 1.3 75.9 - - - +
473A GLU* 1.3 63.1 + - - +
475A GLY* 3.6 9.9 + - - -
511A GLU* 3.7 47.3 - - + +
514A LEU* 4.0 11.3 - - + +
515A ALA* 4.2 6.7 - - + -
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Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A THR* 4.2 30.3 - - + +
423A THR* 5.7 0.3 - - - +
425A TYR* 2.9 34.2 + - - +
469A ARG 2.7 15.9 + - - +
470A VAL* 3.5 5.8 - - - +
472A LEU* 1.3 79.6 - - - +
474A LEU* 1.3 63.1 + - - +
475A GLY* 3.4 0.5 + - - -
478A LYS* 5.3 0.5 - - - +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A THR* 4.2 3.6 - - + +
412A ILE* 3.9 18.8 - - + +
413A GLY* 3.9 19.5 - - - +
416A ASN* 3.8 30.1 - - + +
418A THR* 3.2 26.9 - - + +
470A VAL* 3.0 31.8 + - + +
471A ALA* 3.8 4.5 - - - +
472A LEU 3.4 0.2 - - - -
473A GLU* 1.3 78.1 - - - +
475A GLY* 1.3 62.2 + - - +
478A LYS* 3.0 39.5 + - + +
479A PHE* 4.4 16.6 - - + +
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Residues in contact with GLY 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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471A ALA 3.2 9.2 + - - -
472A LEU 3.6 6.2 + - - -
473A GLU 3.3 3.4 - - - -
474A LEU* 1.3 77.3 - - - +
476A SER* 1.3 67.2 + - - -
477A LYS* 2.9 5.5 + - - -
478A LYS 3.0 13.2 + - - -
479A PHE* 3.0 10.7 + - - +
514A LEU* 4.0 8.1 - - - -
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Residues in contact with SER 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLY* 1.3 69.4 - - - -
477A LYS* 1.3 65.8 + - - +
479A PHE* 3.8 4.6 - - - +
480A GLU* 2.9 32.4 + - - +
508A LEU* 3.3 33.6 - - - +
509A ASP* 3.2 24.4 + - - -
514A LEU* 3.6 13.5 - - - +
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Residues in contact with LYS 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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475A GLY 2.9 5.4 + - - -
476A SER* 1.3 84.6 + - - +
478A LYS* 1.3 61.2 + - + +
480A GLU* 3.6 5.6 - - - +
481A LYS* 2.8 67.1 + - - +
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Residues in contact with LYS 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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412A ILE* 3.7 5.9 - - - +
416A ASN* 3.8 28.3 + - + +
418A THR* 4.9 7.9 - - + -
473A GLU 5.3 0.9 - - - +
474A LEU* 3.0 45.5 + - + +
475A GLY 3.0 1.8 + - - -
477A LYS* 1.3 85.3 - - + +
479A PHE* 1.3 53.5 + - - +
481A LYS* 3.6 6.0 - - - +
482A GLY* 2.6 34.1 + - - -
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Residues in contact with PHE 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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405A GLN* 3.7 23.3 - - - -
409A THR* 3.7 28.5 - - + -
412A ILE* 3.9 17.6 - - + +
471A ALA* 4.2 13.2 - - + -
474A LEU* 4.4 16.7 - - + +
475A GLY 3.0 17.7 + - - +
476A SER* 3.8 6.1 - - - +
478A LYS* 1.3 78.0 - - - +
480A GLU* 1.3 59.2 + - - +
483A MSE 2.8 40.7 + - + +
508A LEU* 5.0 11.2 - - + -
514A LEU* 4.2 16.6 - - + -
517A SER* 4.1 31.6 - - - -
518A GLY* 4.4 0.9 - - - -
524A ILE* 4.6 13.9 - - + -
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Residues in contact with GLU 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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476A SER 2.9 21.7 + - - +
477A LYS* 3.6 5.0 - - - +
479A PHE* 1.3 71.8 - - - +
481A LYS* 1.3 77.4 + - - +
483A MSE 3.1 8.0 + - - +
484A LYS* 2.9 28.0 + - + +
503A ILE* 5.4 10.4 - - + +
508A LEU* 4.7 23.6 - - + +
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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 LYS* 2.8 49.4 + - - +
478A LYS* 3.6 6.2 - - - +
480A GLU* 1.3 79.5 - - - +
482A GLY* 1.3 51.1 + - - +
484A LYS* 2.8 14.6 + - + +
485A LYS* 2.8 34.8 + - + +
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Residues in contact with GLY 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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412A ILE* 3.5 24.1 - - - +
415A ASN* 5.7 1.6 - - - -
416A ASN* 5.1 3.8 - - - +
478A LYS 2.6 21.5 + - - -
481A LYS* 1.3 73.9 - - - +
483A MSE 1.3 62.0 + - - +
485A LYS* 2.9 21.2 + - - +
486A LEU* 3.2 17.5 + - - +
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Residues in contact with MSE 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN* 2.8 42.6 - - - +
408A LEU* 3.4 26.0 - - + -
412A ILE* 3.3 16.9 - - - +
479A PHE* 2.8 29.3 + - + +
480A GLU* 3.4 7.9 - - - +
482A GLY* 1.3 72.4 - - - +
484A LYS* 1.3 58.4 + - - +
486A LEU* 3.7 4.3 + - - +
488A VAL* 2.9 40.5 + - + +
503A ILE* 3.7 25.1 - - + -
524A ILE* 4.7 11.7 - - + -
526A ILE* 3.6 19.5 - - + -
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Residues in contact with LYS 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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480A GLU* 2.9 15.5 + - + +
481A LYS* 2.8 15.8 + - + +
483A MSE 1.3 75.8 - - - +
485A LYS* 1.3 62.9 + - - +
486A LEU 3.2 1.8 - - - -
487A GLY* 3.0 13.0 + - - -
488A VAL 3.8 15.7 + - - +
489A GLY 5.4 3.4 - - - -
490A GLU* 3.6 35.0 + - + +
559A LYS* 4.3 0.9 + - - -
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Residues in contact with LYS 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ASN* 3.6 37.1 + - - +
481A LYS* 2.8 13.1 + - + +
482A GLY* 3.4 13.2 - - - +
484A LYS* 1.3 78.1 - - - +
486A LEU* 1.3 65.6 + - + +
487A GLY 3.1 0.7 + - - -
559A LYS* 3.7 21.2 + - - +
560A LYS 5.2 1.4 + - - -
561A ASN 3.3 24.5 + - - -
562A ILE* 4.1 15.7 + - + +
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Residues in contact with LEU 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A LEU* 4.1 28.9 - - + +
411A MSE 4.2 16.2 - - + -
412A ILE* 3.9 29.8 - - + -
482A GLY 3.2 8.5 + - - +
483A MSE 3.9 8.7 - - - +
484A LYS 3.2 0.8 - - - -
485A LYS* 1.3 80.5 - - + +
487A GLY* 1.3 58.8 + - - +
488A VAL* 3.5 1.7 + - + -
530A GLN* 5.0 1.4 + - - -
534A ILE* 4.2 19.8 - - + +
544A ILE* 3.5 21.4 - - + +
558A TRP* 5.4 1.9 - - - -
559A LYS* 3.9 5.9 - - - +
562A ILE* 3.6 46.9 - - + +
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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