Contacts of the helix formed by residues 469 - 491 (chain A) in PDB entry 1F4L
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 ARG 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A ARG* 5.3 1.3 - - - -
458A GLN* 6.2 0.4 - - - +
462A VAL* 5.4 2.4 - - - +
463A VAL* 3.7 40.8 - - + +
466A GLN* 2.9 42.1 + - - +
467A GLU* 2.7 38.2 + - - +
468A GLY* 1.3 73.6 - - - +
470A ASP* 1.3 64.4 + - - +
471A ALA 3.2 2.2 - - - -
472A ASP* 2.9 37.9 + - - +
473A LEU* 2.9 20.2 + - - +
476A ILE* 5.6 1.2 - - - +
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Residues in contact with ASP 470 (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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403A ARG* 2.4 40.9 + - - +
404A PHE* 3.1 31.5 - - + -
468A GLY* 3.3 7.4 - - - -
469A ARG* 1.3 77.1 + - - +
471A ALA* 1.3 61.8 + - - +
473A LEU* 3.2 1.6 + - - +
474A GLN 2.9 19.6 + - - -
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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
----------------------------------------------------------
404A PHE* 5.4 0.2 - - - -
468A GLY 4.8 4.4 + - - +
469A ARG 3.2 0.4 - - - -
470A ASP* 1.3 80.5 - - - +
472A ASP* 1.3 60.5 + - - +
474A GLN* 3.5 9.5 + - - +
475A ALA* 3.0 28.9 + - - +
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Residues in contact with ASP 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A VAL* 3.9 11.4 - - + -
469A ARG* 2.9 47.4 + - - +
471A ALA* 1.3 81.3 - - - +
473A LEU* 1.3 64.9 + - - +
475A ALA* 3.1 7.3 + - - +
476A ILE* 2.9 32.7 + - + +
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Residues in contact with LEU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A PHE* 3.7 23.1 - - + -
403A ARG* 3.4 44.0 - - - +
404A PHE* 4.1 5.6 - - + -
460A PRO* 3.9 27.1 - - + +
463A VAL* 3.9 7.1 - - + +
464A ALA* 4.0 15.7 - - + +
469A ARG 2.9 13.6 + - - +
470A ASP* 3.2 9.4 + - - +
472A ASP* 1.3 78.5 - - - +
474A GLN* 1.3 64.7 + - - +
476A ILE* 3.3 3.0 + - + +
477A CYS* 3.0 49.9 + - - -
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Residues in contact with GLN 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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400A ILE* 5.0 2.4 - - + +
404A PHE* 3.7 44.3 - - + +
407A VAL* 2.9 31.2 + - - +
408A LEU 3.7 3.4 + - - -
409A ALA* 3.7 21.3 - - - +
470A ASP 2.9 10.6 + - - +
471A ALA* 3.9 7.1 - - - +
473A LEU* 1.3 77.4 - - - +
475A ALA* 1.3 61.6 + - - +
477A CYS* 4.8 2.5 - - - -
478A SER* 2.7 40.3 + - - +
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Residues in contact with ALA 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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409A ALA* 4.4 14.1 - - + +
411A GLU 5.6 1.7 - - - +
413A ALA* 3.9 23.0 + - + +
471A ALA 3.0 17.9 + - - +
472A ASP* 3.1 7.6 + - - +
474A GLN* 1.3 77.7 - - - +
476A ILE* 1.3 62.9 + - + +
478A SER* 3.8 1.6 - - - -
479A MET* 3.0 24.9 + - - +
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Residues in contact with ILE 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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396A ASN* 4.6 1.6 - - - +
413A ALA* 5.8 0.7 - - + -
454A TYR* 3.9 16.1 - - + +
455A VAL* 5.0 6.4 - - + +
458A GLN* 3.5 59.2 - - + +
460A PRO* 3.9 27.4 - - + -
463A VAL* 3.9 20.0 - - + -
469A ARG* 5.6 1.3 - - - +
472A ASP* 2.9 26.4 + - + +
473A LEU* 3.8 4.7 - - - +
475A ALA* 1.3 76.5 - - + +
477A CYS* 1.3 59.6 + - - +
479A MET* 3.3 4.0 + - - +
480A GLY* 3.0 24.3 + - - -
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Residues in contact with CYS 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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396A ASN* 3.6 36.4 - - - +
399A PHE* 3.7 24.7 - - + -
400A ILE* 3.8 14.4 - - + -
404A PHE* 6.1 0.2 - - + -
460A PRO* 4.5 5.8 - - - -
473A LEU* 3.0 41.8 + - - +
474A GLN* 4.2 1.3 - - - +
476A ILE* 1.3 74.3 - - - +
478A SER* 1.3 66.1 + - - +
480A GLY 3.3 1.0 + - - -
481A ILE* 3.1 27.9 + - - +
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Residues in contact with SER 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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400A ILE* 3.8 3.1 - - - +
408A LEU* 3.4 27.3 - - - +
409A ALA* 2.9 36.2 + - - -
411A GLU 5.6 1.1 - - - -
474A GLN* 2.7 24.3 + - - +
475A ALA 3.8 3.1 - - - -
477A CYS* 1.3 77.1 - - - +
479A MET* 1.3 58.1 + - - +
481A ILE* 3.3 2.9 + - - +
482A ASN* 2.9 38.7 + - - -
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Residues in contact with MET 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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412A LEU* 3.9 16.6 - - - +
413A ALA* 3.8 12.1 - - + +
414A ASP* 3.2 44.9 - - + +
417A LEU* 4.2 4.9 - - + -
418A TYR* 3.9 16.4 - - + +
454A TYR* 3.5 32.1 - - + +
475A ALA 3.0 17.8 + - - +
476A ILE 3.4 5.6 - - - +
477A CYS 3.2 0.2 - - - -
478A SER* 1.3 77.0 - - - +
480A GLY* 1.3 61.6 + - - +
482A ASN* 3.1 6.1 + - - +
483A LEU* 3.0 55.9 + - + +
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Residues in contact with GLY 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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392A LEU* 4.0 9.6 - - - +
396A ASN* 3.7 23.3 - - - -
454A TYR* 4.6 1.2 - - - -
455A VAL* 4.5 12.6 - - - -
476A ILE 3.0 12.7 + - - -
477A CYS 3.3 0.6 + - - -
479A MET* 1.3 75.0 - - - +
481A ILE* 1.3 56.6 + - - +
483A LEU* 3.2 11.7 + - - +
484A PHE* 3.0 26.7 + - - +
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Residues in contact with ILE 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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392A LEU 4.5 3.8 - - - +
393A ALA* 4.8 2.0 - - - -
396A ASN* 3.8 18.4 - - + -
397A ALA* 4.0 13.5 - - - +
400A ILE* 2.9 39.3 - - + -
408A LEU* 3.9 21.5 - - + -
477A CYS 3.1 14.1 + - - +
478A SER 3.7 4.0 - - - +
480A GLY* 1.3 75.0 - - - +
482A ASN* 1.3 57.8 + - - +
484A PHE* 3.3 9.3 - - + +
485A ARG* 3.0 25.6 + - - +
505A PHE* 4.2 19.3 - - + -
506A LEU* 3.8 25.7 - - + +
519A LEU* 5.5 1.3 - - + -
524A VAL* 4.7 1.3 - - + -
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Residues in contact with ASN 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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408A LEU* 4.8 4.2 - - - +
412A LEU* 4.1 15.6 - - + +
418A TYR* 3.8 19.0 + - + -
478A SER* 2.9 28.1 + - - +
479A MET* 3.1 4.6 + - - +
481A ILE* 1.3 76.3 - - - +
483A LEU* 1.3 64.3 + - - +
485A ARG* 3.2 9.5 + - - +
486A VAL* 3.2 24.9 + - - +
518A PRO* 3.6 11.6 - - - +
519A LEU* 2.8 56.0 + - - +
520A LEU* 4.7 2.0 - - - +
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Residues in contact with LEU 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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392A LEU* 4.5 0.7 - - + -
417A LEU* 4.0 20.0 - - + -
418A TYR* 4.2 13.5 - - + -
421A PHE* 3.8 34.9 - - + -
451A ALA* 3.7 38.8 - - + +
454A TYR* 4.5 11.2 - - + -
479A MET* 3.0 39.6 + - + +
480A GLY* 3.2 10.1 + - - +
482A ASN* 1.3 74.5 - - - +
484A PHE* 1.3 64.1 + - - +
486A VAL* 3.1 6.9 + - - +
487A LEU* 3.0 27.0 + - - +
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Residues in contact with PHE 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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389A VAL* 3.4 28.5 - - + -
390A VAL* 4.2 10.1 - - + -
392A LEU* 4.1 15.8 - - + +
393A ALA* 3.8 32.1 - - + +
480A GLY 3.0 13.1 + - - +
481A ILE* 3.3 13.0 - - - +
483A LEU* 1.3 73.2 - - - +
485A ARG* 1.4 68.8 + - - +
487A LEU* 3.2 2.6 + - - +
488A MET* 2.9 53.9 + - + +
498A LEU* 5.5 1.1 - - + -
502A ALA* 3.7 25.6 - - + -
505A PHE* 4.1 17.7 - + - -
506A LEU* 4.2 10.8 - - + -
530A LEU* 4.0 10.1 - - + -
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Residues in contact with ARG 485 (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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418A TYR* 4.4 3.8 + - - -
481A ILE 3.0 12.9 + - - +
482A ASN* 3.3 16.1 + - - +
484A PHE* 1.4 79.1 - - - +
486A VAL* 1.3 63.8 + - - +
488A MET* 3.5 3.7 + - - +
489A THR* 2.8 33.6 + - - -
506A LEU* 4.1 21.1 - - + -
508A THR* 4.9 10.6 + - + +
509A GLU 5.0 4.8 + - - -
510A LEU* 3.8 24.0 - - + +
511A THR 5.3 2.0 + - - +
514A GLY* 3.1 33.1 + - - -
515A ILE* 4.2 11.2 - - - +
517A GLN* 3.1 24.9 + - - +
518A PRO* 4.1 2.8 - - - +
519A LEU* 3.8 36.5 - - + +
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Residues in contact with VAL 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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418A TYR* 3.4 33.9 - - + +
421A PHE* 4.1 24.2 - - + +
422A THR* 4.6 1.8 - - + -
482A ASN 3.2 13.2 + - - +
483A LEU* 3.1 8.8 + - - +
485A ARG* 1.3 75.3 - - - +
487A LEU* 1.3 64.2 + - - +
489A THR* 3.0 13.7 + - - -
490A TYR* 3.1 45.4 + - + +
515A ILE* 4.1 23.6 - - + -
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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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389A VAL* 4.8 15.5 - - + -
392A LEU* 3.4 32.8 - - + -
421A PHE* 4.1 11.4 - - + -
444A ILE* 3.6 33.8 - - + +
447A LEU* 3.8 23.6 - - + -
448A ALA* 3.7 23.6 - - + +
483A LEU 3.0 15.2 + - - +
484A PHE* 3.2 4.5 + - - +
486A VAL* 1.3 77.1 - - - +
488A MET* 1.3 58.2 + - - +
490A TYR* 3.2 9.6 + - + +
491A LEU* 3.0 32.5 + - + +
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Residues in contact with MET 488 (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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389A VAL* 3.8 24.0 - - + -
484A PHE* 2.9 50.3 + - + +
485A ARG* 4.0 1.1 - - - +
487A LEU* 1.3 72.9 - - - +
489A THR* 1.3 60.9 + - - +
491A LEU* 3.7 10.3 - - + +
492A LYS* 3.0 28.6 + - - +
495A LEU* 4.7 5.4 - - + +
498A LEU* 3.6 37.5 - - + +
499A THR* 3.6 31.8 + - - +
502A ALA* 4.1 2.7 - - + -
510A LEU* 3.7 20.5 - - + +
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Residues in contact with THR 489 (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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40A MET* 3.8 12.8 - - + +
485A ARG* 2.8 19.9 + - - -
486A VAL 3.0 10.0 + - - -
488A MET* 1.3 78.4 - - - +
490A TYR* 1.3 65.6 + - + +
492A LYS* 3.3 18.9 + - - +
493A PRO* 3.9 2.3 - - - +
510A LEU* 3.7 20.9 - - + +
511A THR 3.4 26.0 + - - +
512A TRP* 3.9 20.5 - - + +
515A ILE* 3.6 21.2 - - + +
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Residues in contact with TYR 490 (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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421A PHE 2.6 26.4 + - - -
422A THR 3.8 0.2 + - - -
425A ALA* 3.3 39.0 + - + +
428A ILE* 3.6 28.0 - - + -
432A TRP* 3.0 31.0 + - - -
444A ILE* 3.7 20.4 - - + -
447A LEU* 3.9 13.0 - - + -
486A VAL* 3.1 31.4 + - + +
487A LEU* 3.2 9.8 + - + +
489A THR* 1.3 77.9 - - + +
491A LEU* 1.3 61.4 + - - +
493A PRO* 3.6 3.9 - - - +
512A TRP* 3.7 26.7 - + - -
515A ILE* 3.5 18.3 - - + +
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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
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357A TYR* 4.7 15.7 - - + -
389A VAL* 3.8 38.4 - - + -
432A TRP* 4.9 0.4 - - + -
441A VAL* 5.1 4.3 - - + -
444A ILE* 3.8 32.3 - - + -
445A MET* 4.3 4.3 - - + -
487A LEU 3.0 20.1 + - - +
488A MET* 3.7 9.9 - - + +
489A THR 3.2 0.4 - - - -
490A TYR* 1.3 75.4 - - - +
492A LYS* 1.3 64.0 + - - +
493A PRO* 3.2 4.9 - - - -
494A VAL* 2.9 29.9 + - + +
495A LEU* 3.0 35.0 + - + +
499A THR* 4.5 0.7 - - - -
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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