Contacts of the helix formed by residues 436 - 459 (chain C) in PDB entry 1JFZ
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 TYR 436 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LYS 3.2 8.0 + - - +
424C ALA* 3.3 32.8 - - - +
426C THR 3.0 23.9 + - - -
427C HIS* 3.2 46.3 - + + -
428C VAL 5.4 0.4 - - - -
435C HIS* 1.3 73.9 - + - +
437C GLU* 1.3 62.1 + - + +
438C THR 3.1 2.7 - - - -
439C LEU* 2.9 9.9 + - - -
440C GLU* 2.8 45.3 + - + +
493C ILE* 5.3 0.4 - - + -
504C ILE* 3.6 19.9 - - + +
507C ASP* 3.8 26.3 + - + +
508C VAL* 3.4 22.2 - - + -
511C ALA* 3.9 5.2 - - + -
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Residues in contact with GLU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C VAL* 6.0 0.5 - - - +
435C HIS* 3.4 33.0 + - + +
436C TYR* 1.3 87.1 - - + +
438C THR* 1.3 60.0 + - - +
440C GLU* 3.3 6.4 + - - +
441C PHE 3.2 10.4 + - - -
662D LYS 5.1 0.2 - - - -
663D ARG* 3.1 22.5 - - - +
664D GLU* 2.7 71.5 + - + +
665D GLY 4.5 0.3 + - - -
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Residues in contact with THR 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423C LYS* 5.7 6.1 - - - -
435C HIS 4.6 3.8 + - - -
436C TYR 2.9 1.0 + - - -
437C GLU* 1.3 75.0 - - - +
439C LEU* 1.3 67.3 + - + +
440C GLU 3.0 1.6 - - - -
441C PHE* 3.2 15.3 + - - +
442C LEU* 3.3 12.0 + - - +
656D VAL* 3.6 27.4 - - + +
662D LYS* 2.3 56.0 + - + +
663D ARG* 4.6 0.5 - - - -
664D GLU* 4.4 0.2 - - - -
667D LEU* 4.5 6.5 - - + -
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Residues in contact with LEU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 4.2 13.9 - - + +
423C LYS* 3.3 42.4 - - + +
424C ALA* 3.7 21.5 - - + +
435C HIS 5.4 0.4 + - - +
436C TYR* 2.9 6.8 + - - +
438C THR* 1.3 78.3 - - + +
440C GLU* 1.3 57.2 + - - +
442C LEU* 4.5 2.7 - - + +
443C GLY 2.7 25.3 + - - -
511C ALA* 3.4 15.5 - - + +
514C ALA* 3.0 22.7 - - + +
515C ALA* 4.5 9.6 - - + +
518C ILE* 3.8 28.5 - - + -
656D VAL* 6.1 1.8 - - + -
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Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C TYR* 2.8 23.1 + - + +
437C GLU* 3.4 11.1 - - - +
438C THR 3.0 0.4 - - - -
439C LEU* 1.3 80.2 - - - +
441C PHE* 1.3 55.3 + - - +
443C GLY 3.7 0.2 - - - -
444C ASP* 2.8 31.5 + - + +
507C ASP* 2.7 35.7 - - - +
510C GLU* 3.0 14.2 - - - +
511C ALA* 3.7 9.8 - - + +
763C MN 1.8 35.3 + - - +
664D GLU* 3.5 14.9 - - - +
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Residues in contact with PHE 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C GLU 3.2 3.4 + - - -
438C THR* 3.4 11.9 - - - +
440C GLU* 1.3 78.3 - - - +
442C LEU* 1.3 60.4 + - - +
444C ASP* 3.5 15.4 - - + +
445C ALA* 3.8 1.6 + - - +
652D VAL* 3.4 23.7 - - + +
655D LEU* 4.0 16.8 - - + -
656D VAL* 3.9 12.3 - - + -
664D GLU* 2.8 37.2 + - + +
667D LEU* 3.7 38.6 - - + -
668D SER* 3.6 21.1 - - - -
671D LYS* 3.5 40.6 - - + -
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Residues in contact with LEU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C THR 3.3 8.5 + - - +
439C LEU* 3.9 7.6 - - + +
440C GLU 3.2 0.2 - - - -
441C PHE* 1.3 77.0 - - - +
443C GLY* 1.3 67.2 + - - +
444C ASP 3.0 1.6 - - - -
445C ALA* 2.9 13.3 + - - +
446C LEU* 3.0 13.9 + - + +
514C ALA* 3.9 17.5 - - + -
517C TYR* 4.0 18.6 - - + -
518C ILE* 4.1 19.7 - - + -
522C ARG* 4.3 2.9 - - - +
649D PHE* 4.7 11.9 - - + -
652D VAL* 3.8 11.9 - - + +
653D ASP* 3.7 45.1 - - + +
656D VAL* 4.2 14.4 - - + -
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Residues in contact with GLY 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C LEU 2.7 17.5 + - - -
442C LEU* 1.3 73.4 - - - +
444C ASP* 1.3 60.1 + - - +
446C LEU* 4.4 3.6 - - - -
447C VAL* 2.8 33.3 + - - +
510C GLU* 2.9 34.7 - - - +
514C ALA* 3.4 9.3 - - - +
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Residues in contact with ASP 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C GLU* 2.8 18.4 + - + +
441C PHE* 3.5 12.6 - - + +
442C LEU 3.0 0.2 + - - -
443C GLY* 1.3 79.9 - - - +
445C ALA* 1.3 63.5 + - - +
447C VAL* 4.3 0.9 - - - +
448C ASN* 3.3 23.0 + - - +
480C PHE* 6.0 1.4 - - - -
510C GLU* 3.8 14.9 - - - +
763C MN 4.1 14.7 + - - -
648D ASN* 5.5 1.7 + - - -
671D LYS* 5.8 5.8 + - - -
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441C PHE 4.3 0.4 - - - +
442C LEU 2.9 7.2 + - - +
444C ASP* 1.3 79.9 + - - +
446C LEU* 1.3 66.4 + - - +
448C ASN* 3.4 5.6 + - - +
449C PHE* 3.1 21.5 + - - +
645D ALA 4.5 0.7 - - - +
648D ASN* 3.6 19.1 + - - +
649D PHE* 3.9 13.8 - - + +
652D VAL* 3.3 43.5 - - + -
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Residues in contact with LEU 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LEU* 3.0 16.4 + - + +
443C GLY* 4.1 1.8 - - - +
445C ALA* 1.3 79.8 - - - +
447C VAL* 1.3 64.0 + - + +
449C PHE* 3.0 10.2 + - + +
450C PHE* 3.0 62.9 + - + -
513C TRP* 3.6 40.4 - - + +
514C ALA* 4.2 3.1 - - - +
517C TYR* 4.1 29.6 - - + -
524C ALA* 5.0 2.0 - - + -
527C THR* 4.3 1.8 - - + -
649D PHE* 4.1 27.9 - - + +
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Residues in contact with VAL 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C GLY 2.8 26.9 + - - +
444C ASP 4.3 1.6 - - - +
446C LEU* 1.3 76.6 - - + +
448C ASN* 1.3 63.8 + - - +
450C PHE* 3.0 18.7 + - + +
451C ILE* 3.1 15.6 + - + +
480C PHE* 3.6 33.0 - - + -
509C PHE* 4.5 3.6 - - + -
510C GLU* 4.4 10.1 - - - -
513C TRP* 4.0 30.5 - - + -
531C PHE* 3.7 27.8 - - + -
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Residues in contact with ASN 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C ASP* 3.3 21.1 + - - +
445C ALA* 3.5 4.9 + - - +
447C VAL* 1.3 78.5 - - - +
449C PHE* 1.3 57.6 + - - +
451C ILE* 3.9 1.0 - - - +
452C VAL* 2.9 36.0 + - - +
471C LYS* 3.0 37.5 + - - +
475C ILE* 3.8 24.7 - - + +
480C PHE* 5.4 0.8 - - - -
644D ASP* 5.7 2.0 + - - -
645D ALA* 3.8 24.5 - - - +
648D ASN* 4.4 12.1 - - - +
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Residues in contact with PHE 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ALA 3.1 12.4 + - - +
446C LEU* 3.0 9.5 + - + +
448C ASN* 1.3 74.1 - - - +
450C PHE* 1.3 88.9 + + - +
453C ASP* 3.0 26.2 + - + +
524C ALA* 4.8 2.0 - - + -
528C ARG* 4.6 5.2 - - - -
642D LEU* 4.3 11.4 - - + -
645D ALA* 3.8 23.1 - - - +
646D LEU* 4.0 22.4 - - + -
649D PHE* 4.1 26.9 - + + -
717D TYR* 3.5 43.3 - + - -
724D ALA* 4.0 23.8 - - + -
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Residues in contact with PHE 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LEU* 3.0 59.5 + - + -
447C VAL* 3.0 12.5 + - + +
449C PHE* 1.3 90.7 - + - +
451C ILE* 1.3 57.4 + - - +
453C ASP* 4.7 0.7 - - - -
454C LEU 3.2 7.8 + - - -
513C TRP* 4.6 1.3 - + + -
524C ALA 3.9 5.4 - - - -
527C THR* 3.8 16.8 - - + -
528C ARG* 3.3 50.3 - - + -
531C PHE* 3.6 40.6 - + + -
532C TYR* 2.5 35.9 + - + -
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Residues in contact with ILE 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447C VAL* 3.1 12.3 + - + +
448C ASN 4.2 1.8 - - - +
450C PHE* 1.3 73.8 - - - +
452C VAL* 1.3 65.5 + - + +
453C ASP 3.2 1.3 - - - -
454C LEU* 3.9 6.1 - - - +
455C LEU* 2.9 30.6 + - + +
471C LYS* 5.5 1.3 - - + +
474C LEU* 3.3 54.0 - - + +
475C ILE* 4.2 12.6 - - + -
479C PHE* 4.4 12.6 - - + -
480C PHE* 4.0 14.6 - - + -
483C LEU* 5.0 0.2 - - + -
531C PHE* 4.1 20.6 - - + -
532C TYR* 5.3 0.2 - - - -
539C ILE* 3.9 21.9 - - + +
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Residues in contact with VAL 452 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C ASN* 2.9 29.0 + - - +
449C PHE 3.2 0.9 + - - +
451C ILE* 1.3 78.7 - - + +
453C ASP* 1.3 57.8 + - - +
455C LEU* 3.6 5.6 - - - +
456C VAL* 2.9 31.4 + - - +
471C LYS* 3.7 39.3 - - + -
641D PHE* 3.9 20.1 - - + +
642D LEU* 3.8 23.8 - - + -
645D ALA* 3.7 24.9 - - + -
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Residues in contact with ASP 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449C PHE* 3.0 19.7 + - + +
450C PHE* 4.3 0.4 - - - -
452C VAL* 1.3 76.1 - - - +
454C LEU* 1.3 63.3 + - - +
456C VAL* 3.1 15.7 - - - +
457C GLN* 3.0 19.8 + - - +
528C ARG* 3.9 5.2 + - - -
532C TYR* 3.4 15.1 + - - +
642D LEU* 3.6 10.5 - - + +
717D TYR* 2.3 39.6 + - - -
722D ARG* 2.7 36.4 + - - -
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Residues in contact with LEU 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450C PHE 3.2 15.1 + - - +
451C ILE* 3.3 7.1 + - - +
453C ASP* 1.3 78.1 - - - +
455C LEU* 1.3 53.5 + - - +
457C GLN* 3.3 5.5 + - - +
458C TYR* 2.9 65.7 + - + +
532C TYR* 3.4 28.7 + - + +
536C LYS* 3.7 43.3 - - + +
539C ILE* 3.9 24.9 - - + -
540C LEU* 3.9 16.2 - - + -
543C ILE* 5.0 0.9 - - - -
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C ILE* 2.9 17.6 + - + +
452C VAL* 3.6 5.6 - - - +
454C LEU* 1.3 73.0 - - - +
456C VAL* 1.3 61.7 + - - +
457C GLN 3.1 1.8 - - - -
459C SER* 2.7 46.0 + - - +
466C PHE* 5.4 0.4 - - + -
467C LEU* 3.9 18.2 - - + +
470C LEU* 3.8 26.2 - - + -
471C LYS* 3.7 33.7 - - + +
474C LEU* 3.6 24.0 - - + +
543C ILE* 3.9 19.0 - - + +
641D PHE* 4.8 4.7 - - + -
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Residues in contact with VAL 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C VAL 2.9 20.6 + - - +
453C ASP* 3.1 17.9 - - - +
455C LEU* 1.3 74.0 - - - +
457C GLN* 1.3 61.2 + - - +
462C LYS* 2.9 31.5 - - + -
467C LEU* 4.5 11.2 - - + +
638D THR* 3.4 37.5 - - + +
641D PHE* 4.8 10.5 - - + -
642D LEU* 3.8 26.2 - - + -
718D ILE* 6.3 1.6 - - + -
722D ARG* 4.3 6.1 - - - +
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Residues in contact with GLN 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C ASP* 3.0 31.0 + - - +
454C LEU* 3.3 21.4 + - - +
455C LEU 3.1 0.4 - - - -
456C VAL* 1.3 82.6 - - - +
458C TYR* 1.3 77.7 + - + +
459C SER 4.0 0.2 - - - +
462C LYS* 2.9 20.0 + - - +
532C TYR* 4.6 5.5 + - - -
536C LYS* 5.8 0.2 - - - +
722D ARG* 3.4 42.6 + - - +
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Residues in contact with TYR 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LYS* 5.8 0.7 + - - -
454C LEU* 2.9 43.5 + - + +
457C GLN* 1.3 94.7 + - + +
459C SER* 1.3 68.6 + - - +
460C PRO* 3.4 2.3 - - - +
536C LYS* 2.5 35.2 + - - -
540C LEU* 3.3 39.7 - - + -
543C ILE* 3.9 12.4 - - + +
544C LYS* 5.2 10.0 - - - -
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Residues in contact with SER 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LYS* 4.8 5.0 + - - -
455C LEU* 2.7 35.3 + - - +
456C VAL 4.7 0.4 - - - -
457C GLN 3.5 1.0 - - - +
458C TYR* 1.3 73.7 - - - +
460C PRO* 1.3 63.9 - - - +
461C ASN 2.3 27.5 + - - -
462C LYS* 2.5 29.5 + - - -
466C PHE* 3.0 25.1 - - - -
467C LEU* 4.4 6.8 - - - +
543C ILE* 3.9 7.1 - - - +
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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