Contacts of the helix formed by residues 449 - 477 (chain F) in PDB entry 1FFT
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 ASN 449 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F SER* 4.2 1.9 + - - -
447F LYS 4.1 1.8 + - - -
448F LEU* 1.3 70.2 - - - +
450F GLU* 1.3 60.2 + - - +
451F THR* 2.7 47.8 + - - -
452F TRP* 2.9 19.7 + - - +
453F GLY* 3.5 15.1 + - - -
515F GLN* 3.6 23.5 + - + +
518F VAL* 6.0 4.6 - - - +
519F SER* 4.2 11.3 + - - +
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Residues in contact with GLU 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378F HIS* 3.0 31.9 + - + +
379F SER* 2.9 44.8 + - - -
448F LEU 2.9 9.8 + - - +
449F ASN* 1.3 69.9 - - - +
451F THR* 1.3 68.4 + - - +
453F GLY 4.0 0.7 - - - -
454F LYS* 2.8 49.0 + - - +
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Residues in contact with THR 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449F ASN* 2.7 21.8 + - - -
450F GLU* 1.3 79.8 - - - +
452F TRP* 1.3 83.8 + - + +
453F GLY 3.0 0.4 - - - -
454F LYS* 2.8 25.2 + - - +
455F ARG* 3.5 22.0 + - - +
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Residues in contact with TRP 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449F ASN* 2.9 16.7 + - - +
451F THR* 1.3 97.7 - - + +
453F GLY* 1.3 52.6 + - - +
454F LYS 3.0 0.4 - - - -
455F ARG* 2.6 48.8 + - + +
456F ALA* 2.6 37.2 + - + +
511F CYS* 4.3 31.2 - - + +
514F ILE* 5.4 8.3 - - + -
515F GLN* 3.9 25.8 - - + +
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Residues in contact with GLY 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379F SER* 4.1 18.6 + - - -
382F LEU* 5.0 1.9 - - - +
383F TRP* 5.4 5.2 + - - -
449F ASN 3.5 15.1 + - - -
451F THR 2.9 2.4 + - - -
452F TRP* 1.3 79.4 - - - +
454F LYS* 1.3 61.6 + - - +
456F ALA* 4.6 3.2 - - - +
457F PHE* 3.5 19.2 + - - +
515F GLN* 3.6 12.8 + - - -
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Residues in contact with LYS 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F PHE 4.2 14.2 + - - -
378F HIS* 4.5 7.4 + - - -
379F SER 5.1 0.4 - - - +
382F LEU* 3.7 22.0 - - + -
450F GLU* 2.8 47.8 + - + +
451F THR* 2.8 8.9 + - - +
453F GLY* 1.3 77.1 - - - +
455F ARG* 1.3 61.5 + - + +
457F PHE* 3.7 5.3 - - - +
458F TRP* 3.1 31.7 - - + +
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Residues in contact with ARG 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451F THR* 3.9 16.5 - - - +
452F TRP* 2.6 79.3 + - + +
454F LYS* 1.3 78.2 - - + +
456F ALA* 1.3 67.2 + - - +
457F PHE 3.0 2.0 + - - -
458F TRP* 3.3 13.9 + - - +
459F PHE* 3.6 14.7 + - - +
511F CYS* 5.2 1.3 - - - -
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Residues in contact with ALA 456 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383F TRP* 5.2 5.6 - - + -
452F TRP* 2.6 17.8 + - + +
453F GLY* 4.6 4.5 - - - +
455F ARG* 1.3 73.6 - - - +
457F PHE* 1.3 62.3 + - - +
459F PHE* 3.5 5.0 + - - +
460F TRP* 3.0 25.0 + - - +
508F GLY* 4.8 1.6 - - - +
511F CYS* 3.4 33.1 - - - -
512F LEU* 4.1 22.7 - - + +
515F GLN* 5.0 1.6 - - - +
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Residues in contact with PHE 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F LEU* 3.1 60.1 - - + -
383F TRP* 3.6 48.1 - + + -
385F ILE* 4.8 4.3 - - + -
386F GLY* 4.5 8.5 - - - -
430F PHE* 4.1 7.0 - + - -
453F GLY 3.5 19.1 + - - +
454F LYS* 3.7 6.7 - - - +
455F ARG 3.0 1.0 - - - -
456F ALA* 1.3 76.6 - - - +
458F TRP* 1.3 68.7 + + - +
460F TRP* 2.7 23.9 + - - +
461F ILE* 2.8 47.9 + - + +
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Residues in contact with TRP 458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F LEU* 5.7 4.8 - - + +
454F LYS* 3.1 28.1 + - + +
455F ARG* 3.3 6.6 + - - +
457F PHE* 1.3 89.6 - + - +
459F PHE* 1.3 62.8 + - + +
461F ILE* 2.8 21.7 + - + -
462F ILE* 2.6 62.5 + - + +
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Residues in contact with PHE 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455F ARG 3.6 10.2 + - - +
456F ALA* 3.5 9.1 + - - +
457F PHE 3.4 0.6 - - - -
458F TRP* 1.3 81.7 - - + +
460F TRP* 1.3 57.2 + - - +
462F ILE* 4.5 10.8 - - + -
463F GLY* 3.2 23.9 + - - -
504F LEU* 3.8 53.9 - - + +
505F ILE* 4.1 11.2 + - - +
507F LEU* 4.8 12.3 - - + -
508F GLY* 4.5 17.5 - - - -
511F CYS* 5.8 1.8 - - - -
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Residues in contact with TRP 460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F PHE* 3.7 13.9 - + - -
383F TRP* 3.5 22.8 - + + -
425F ILE* 4.2 19.1 - - + +
429F VAL* 4.2 23.1 - - + +
430F PHE* 3.4 33.5 - + - -
433F PHE* 4.4 11.5 - + - -
456F ALA 3.0 13.0 + - - +
457F PHE 2.7 13.8 + - - +
459F PHE* 1.3 77.6 - - - +
461F ILE* 1.3 62.2 + - - +
464F PHE* 3.7 17.8 + - - +
505F ILE* 3.5 36.6 - - + +
508F GLY* 4.9 4.3 - - - -
509F ILE* 3.1 49.8 - - + -
1001F HEM 5.2 2.2 - - + -
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Residues in contact with ILE 461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386F GLY* 5.4 3.8 - - - -
389F VAL* 6.4 1.8 - - + -
390F THR* 4.9 5.8 - - - +
430F PHE* 4.5 16.8 - - + -
457F PHE* 2.9 66.2 - - + +
458F TRP* 2.8 28.9 + - + +
460F TRP* 1.3 70.3 - - - +
462F ILE* 1.3 73.0 + - + +
464F PHE* 3.3 11.0 + - - +
465F PHE* 3.4 27.4 - - + -
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Residues in contact with ILE 462 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458F TRP* 2.6 57.6 + - + +
459F PHE* 4.2 12.1 - - + +
461F ILE* 1.3 76.6 - - + +
463F GLY* 1.3 66.4 + - - +
464F PHE 3.0 0.2 + - - -
465F PHE* 3.0 16.0 + - - +
466F VAL* 3.5 18.8 + - + +
504F LEU* 3.8 19.7 - - + -
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Residues in contact with GLY 463 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459F PHE 3.2 10.2 + - - -
462F ILE* 1.3 78.5 - - - +
464F PHE* 1.3 69.6 + - - +
466F VAL* 3.0 7.0 + - - -
467F ALA* 2.9 23.2 + - - +
501F GLY 3.4 18.9 - - - +
504F LEU* 4.2 6.0 - - - +
505F ILE* 3.3 15.7 - - - -
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Residues in contact with PHE 464 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F THR* 3.7 16.6 - - + -
418F ALA 5.4 0.4 - - - -
421F HIS 4.1 4.3 - - - -
422F ASN* 3.4 55.4 - - + -
425F ILE* 4.3 17.7 - - + -
426F GLY* 5.0 1.8 - - - -
430F PHE* 5.9 3.1 - + + -
460F TRP 3.7 11.4 + - - +
461F ILE* 3.3 11.1 + - - +
462F ILE 3.0 1.2 + - - -
463F GLY* 1.3 77.3 - - - +
465F PHE* 1.3 95.9 + + - +
467F ALA 2.9 11.4 + - - -
468F PHE* 2.9 66.4 + + + +
469F MET* 5.5 3.1 - - + -
505F ILE* 3.3 16.3 - - + +
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Residues in contact with PHE 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389F VAL* 5.5 4.3 - - + -
390F THR* 4.3 18.4 - - + -
393F VAL* 4.7 18.2 - - + -
461F ILE* 3.4 24.9 - - + -
462F ILE* 3.0 7.3 + - - +
464F PHE* 1.3 106.1 - + - +
466F VAL* 1.3 58.8 + - + +
467F ALA 2.8 10.2 + - - -
469F MET* 3.1 49.1 + - + +
470F PRO* 2.9 23.2 - - - +
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Residues in contact with VAL 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462F ILE* 3.8 26.9 - - + +
463F GLY* 3.0 4.3 + - - +
465F PHE* 1.3 75.3 - - + +
467F ALA* 1.3 55.0 + - - +
470F PRO* 4.2 7.2 - - - -
497F ILE* 2.7 49.7 - - + +
498F ALA* 3.3 0.5 + - - -
500F SER* 4.2 5.2 - - - +
501F GLY* 2.8 28.4 - - - +
504F LEU* 5.8 1.6 - - + -
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Residues in contact with ALA 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ARG* 2.5 30.8 + - - +
463F GLY 2.9 14.1 + - - +
464F PHE 2.9 3.3 + - - +
465F PHE 2.8 1.0 - - - -
466F VAL* 1.3 81.0 - - - +
468F PHE* 1.3 77.5 + - + +
470F PRO* 4.1 3.8 - - - -
471F LEU* 3.7 2.8 - - - +
498F ALA* 3.5 19.2 - - - +
501F GLY 3.7 10.5 - - - -
502F ALA* 3.7 5.6 - - + +
505F ILE* 4.2 5.2 - - + -
1001F HEM 5.6 0.7 - - + -
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Residues in contact with PHE 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ARG* 3.7 10.1 - - - -
417F ILE* 5.4 0.7 - - + -
418F ALA* 3.6 15.5 - - - +
421F HIS* 4.0 24.5 - + + -
425F ILE* 3.1 24.7 - - + -
464F PHE* 2.9 52.0 + + + +
465F PHE 3.3 0.2 + - - -
467F ALA* 1.3 102.5 - - + +
469F MET* 1.3 67.6 + - - +
470F PRO* 3.1 2.2 - - - +
471F LEU* 3.2 40.0 + - + +
472F TYR* 3.6 4.0 + - - -
505F ILE* 4.5 2.2 - - + -
1001F HEM 3.6 48.0 - + + -
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Residues in contact with MET 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F VAL* 4.9 14.1 - - + -
422F ASN* 5.8 2.2 - - - -
464F PHE* 5.5 4.0 - - + -
465F PHE* 3.1 53.5 + - + +
468F PHE* 1.3 75.3 - - - +
470F PRO* 1.4 68.6 - - + +
472F TYR* 3.2 43.6 + - - +
473F ALA* 4.0 1.9 + - - +
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Residues in contact with PRO 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465F PHE 2.9 17.3 - - - +
466F VAL* 4.1 5.6 - - - +
468F PHE 3.2 9.2 - - - +
469F MET* 1.4 91.3 - - + +
471F LEU* 1.3 61.5 + - - +
473F ALA* 2.9 22.9 + - - +
474F LEU* 3.4 6.8 + - - +
494F MET* 3.8 40.8 - - + +
497F ILE* 3.5 29.4 - - + -
498F ALA* 4.2 7.2 - - + +
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Residues in contact with LEU 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ARG* 4.1 15.5 - - - +
414F LEU* 3.3 41.1 - - + +
417F ILE* 4.0 16.2 - - + -
418F ALA* 4.0 11.0 - - + +
467F ALA 3.7 7.6 - - - +
468F PHE* 3.2 40.6 - - + +
470F PRO* 1.3 75.7 - - - +
472F TYR* 1.3 63.9 + - - +
474F LEU* 3.3 17.0 + - + -
475F GLY 3.2 15.8 + - - -
495F LEU* 5.3 3.6 - - + -
498F ALA* 3.7 24.7 - - + -
1001F HEM 6.4 0.2 - - + -
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Residues in contact with TYR 472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393F VAL* 6.2 1.3 - - + -
394F GLY* 4.5 3.7 - - - -
397F THR* 2.8 46.0 + - + +
415F PHE* 3.1 36.1 - + + +
418F ALA* 3.1 33.6 + - + +
419F HIS* 3.0 13.9 + - - -
422F ASN* 4.6 6.7 - - - +
468F PHE 3.6 4.2 + - - -
469F MET* 3.2 40.2 + - - +
470F PRO 3.1 0.4 - - - -
471F LEU* 1.3 79.2 - - - +
473F ALA* 1.3 65.0 + - - +
475F GLY* 3.0 10.2 + - - -
476F PHE* 3.2 21.0 - - + -
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Residues in contact with ALA 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469F MET 4.0 1.2 + - - +
470F PRO* 2.9 13.0 + - + +
472F TYR* 1.3 73.3 - - - +
474F LEU* 1.3 55.3 + - - +
475F GLY 2.5 17.2 + - - -
476F PHE* 2.6 23.6 + - - +
477F MET* 3.3 10.6 + - + +
494F MET* 3.4 30.1 - - + -
28G ALA 3.5 20.7 - - - +
29G LEU* 3.6 11.2 - - + +
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Residues in contact with LEU 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F LEU* 3.9 11.0 - - + -
470F PRO 3.8 4.0 - - - +
471F LEU* 3.3 26.9 + - + +
473F ALA* 1.3 77.8 - - - +
475F GLY* 1.3 57.6 + - - +
477F MET* 3.2 21.4 - - - +
479F MET* 2.9 37.2 + - + +
491F PHE* 3.4 29.8 - - + -
494F MET* 3.2 36.1 - - + -
495F LEU* 3.5 34.1 - - + +
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Residues in contact with GLY 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409F VAL 4.7 2.4 - - - +
410F LEU* 4.1 10.9 - - - +
413F SER* 3.4 20.4 + - - -
414F LEU* 3.9 1.3 - - - +
415F PHE* 3.7 17.9 - - - -
471F LEU 3.2 5.1 + - - -
472F TYR 3.0 8.4 + - - -
473F ALA 2.5 6.9 + - - -
474F LEU* 1.3 71.8 - - - +
476F PHE* 1.3 56.8 + - - +
478F GLY* 2.7 24.6 + - - -
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Residues in contact with PHE 476 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F LEU* 5.9 1.3 - - + -
409F VAL* 5.7 1.7 - - - +
410F LEU* 4.3 12.3 - - + -
415F PHE* 3.4 36.6 - + - -
472F TYR* 3.2 17.9 - - + -
473F ALA* 2.6 14.2 + - - +
475F GLY* 1.3 69.3 - - - +
477F MET* 1.3 57.7 + - - +
478F GLY* 2.8 10.8 + - - -
28G ALA 5.6 1.6 - - - +
29G LEU* 4.1 11.4 - - - -
30G LEU* 3.2 44.2 - - + +
31G ASP* 3.4 26.7 - - - +
32G PRO* 3.6 14.3 - - - +
46G THR* 5.8 2.9 - - + -
50G LEU* 5.4 12.8 - - + -
177G PRO* 5.3 0.2 - - - +
178G ARG* 3.2 14.7 + - - -
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Residues in contact with MET 477 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473F ALA* 3.7 2.0 - - + +
474F LEU* 3.2 38.4 - - + +
476F PHE* 1.3 77.3 - - - +
478F GLY* 1.3 65.0 + - - +
490F GLN* 3.7 19.7 - - + +
491F PHE* 3.2 50.9 - - + -
494F MET* 4.9 0.9 - - + -
27G SER 3.4 28.9 - - - +
28G ALA* 3.6 31.7 - - + +
30G LEU 5.0 0.2 + - - -
177G PRO* 4.2 9.9 - - - +
178G ARG* 3.6 18.6 + - - +
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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