Contacts of the helix formed by residues 432 - 455 (chain F) in PDB entry 1XSK
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 432 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F ASN* 4.2 21.9 + - + +
79F GLY 2.9 18.5 + - - +
80F PRO* 4.2 0.2 - - - +
214F GLN* 4.9 1.4 - - - +
430F GLY 3.8 1.6 + - - -
431F SER* 1.3 69.4 - - - +
433F PRO* 1.3 73.2 - - - +
434F GLN* 2.7 29.9 + - - +
435F LYS* 3.1 27.2 + - + +
436F MET* 3.1 20.8 + - - +
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Residues in contact with PRO 433 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421F ILE* 6.0 0.2 - - - +
422F PRO 4.9 1.4 - - - +
423F THR* 3.1 41.1 - - - +
425F VAL 3.6 22.2 - - - +
426F GLN* 5.4 0.7 - - - -
427F TRP* 4.0 21.2 + - + +
431F SER 3.2 10.3 - - - +
432F ASP* 1.3 90.6 - - - +
434F GLN* 1.3 62.6 + - + +
436F MET* 3.4 1.0 + - - +
437F HIS* 3.3 17.7 + - - -
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Residues in contact with GLN 434 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F TRP* 3.5 33.3 - - - -
213F PRO 4.2 0.3 - - - +
214F GLN* 3.5 29.5 - - + +
215F CYS* 5.7 0.9 + - - +
423F THR* 3.3 31.4 + - - +
432F ASP* 2.7 24.0 + - - +
433F PRO* 1.3 75.7 - - + +
435F LYS* 1.3 59.2 + - - +
437F HIS* 3.9 2.6 - - - +
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Residues in contact with LYS 435 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ASN* 4.6 9.3 - - - +
78F ASN 2.6 36.3 + - - +
79F GLY 4.1 2.2 - - - +
80F PRO* 3.5 28.5 - - + +
81F HIS* 4.2 13.1 + - - -
212F HIS* 6.1 0.4 - - - -
213F PRO* 3.9 19.9 - - + +
214F GLN* 3.4 45.3 - - + +
236F TYR* 4.6 11.5 + - - -
432F ASP* 3.1 19.5 + - - +
434F GLN* 1.3 74.2 - - - +
436F MET* 1.3 64.2 + - - +
437F HIS 3.1 3.1 + - - -
438F ASN 3.7 2.1 + - - -
439F HIS* 3.3 21.3 + - - +
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Residues in contact with MET 436 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F PRO* 3.8 20.2 - - + -
389F PHE* 6.3 0.9 - - + -
390F THR* 3.9 28.0 - - + -
421F ILE* 4.3 1.9 - - - +
427F TRP* 3.6 42.2 - - + +
429F ASP* 5.5 0.2 - - - +
431F SER* 3.5 26.5 - - - -
432F ASP 3.1 11.0 + - - +
433F PRO 3.4 2.2 + - - +
435F LYS* 1.3 74.6 - - - +
437F HIS* 1.3 67.4 + - - +
438F ASN 3.4 0.2 - - - -
439F HIS* 3.8 11.0 - - - -
440F TYR* 2.9 45.5 + - + +
443F ILE* 4.9 7.4 - - + -
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Residues in contact with HIS 437 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F TRP* 3.2 63.2 - + + -
183F ASN* 2.7 27.4 + - + -
418F GLY 4.7 2.1 - - - +
419F GLU 3.0 24.5 + - - +
420F ARG* 4.5 2.5 - - - -
421F ILE* 2.7 56.2 + - - +
423F THR* 4.8 0.2 - - + -
433F PRO 3.3 8.8 + - - +
434F GLN 3.9 3.4 - - - +
435F LYS 3.1 1.2 - - - -
436F MET* 1.3 80.6 - - - +
438F ASN* 1.3 80.8 + - - +
440F TYR* 3.7 2.9 - - - +
441F ALA 4.7 0.2 + - - -
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Residues in contact with ASN 438 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F TYR* 5.3 4.5 + - - +
181F THR* 2.9 28.4 + - - -
182F TRP* 4.0 3.8 - - - +
183F ASN* 2.8 44.4 + - - +
196F ASN* 5.1 5.5 - - - +
213F PRO* 3.0 27.9 + - + +
214F GLN 4.2 3.4 + - - -
435F LYS 3.7 2.0 + - - -
437F HIS* 1.3 82.3 - - - +
439F HIS* 1.3 63.5 + - - +
440F TYR 3.0 6.5 + - - -
441F ALA* 3.2 15.1 + - - +
469F SER* 3.2 25.6 - - - +
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Residues in contact with HIS 439 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F PRO* 3.3 35.9 - - + +
81F HIS 4.0 18.8 + - - -
82F TYR* 4.9 9.3 - - - -
83F PRO* 4.4 9.6 - - + +
213F PRO* 4.9 6.0 - - + +
435F LYS 3.3 18.4 + - - +
436F MET* 4.2 7.2 - - - -
438F ASN* 1.3 78.7 - - - +
440F TYR* 1.3 62.7 + - - +
441F ALA 3.2 0.4 - - - -
442F TYR* 3.3 33.5 + + - +
443F ILE* 3.2 46.3 + - + +
469F SER* 4.1 11.3 + - - +
470F VAL 5.5 0.2 + - - -
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Residues in contact with TYR 440 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348F PRO* 3.3 32.1 + - + +
386F ILE* 3.5 11.0 - - + +
387F TYR 2.9 28.0 + - - -
389F PHE* 3.2 35.2 - + + -
418F GLY* 3.9 9.0 - - - -
421F ILE* 3.3 27.4 - - + -
427F TRP* 3.7 29.8 - + - -
436F MET* 2.9 29.2 + - + +
437F HIS 3.7 9.0 - - - +
438F ASN 3.0 0.6 + - - -
439F HIS* 1.3 78.9 - - - +
441F ALA* 1.3 62.7 + - - +
443F ILE* 3.4 4.3 + - + +
444F TYR* 3.0 30.2 + - + +
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Residues in contact with ALA 441 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183F ASN* 4.1 5.2 - - - +
418F GLY 4.4 7.5 + - - +
437F HIS 4.7 0.4 + - - -
438F ASN 3.2 12.9 + - - +
440F TYR* 1.3 80.3 - - - +
442F TYR* 1.3 60.6 + - - +
444F TYR* 3.5 5.1 - - - +
445F ASN* 2.9 32.9 + - - -
467F SER* 3.4 27.6 - - - +
468F ALA* 3.7 27.1 - - - +
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Residues in contact with TYR 442 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F PRO* 3.7 21.7 - - + +
438F ASN 4.2 0.8 + - - -
439F HIS* 3.3 38.6 + + - +
440F TYR 3.2 0.4 - - - -
441F ALA* 1.3 77.2 - - - +
443F ILE* 1.3 68.5 + - + +
445F ASN* 3.9 1.9 - - - +
446F GLU* 2.8 62.9 + - - +
469F SER* 4.4 12.6 - - - +
470F VAL 3.8 6.5 - - - +
471F GLY 3.4 36.3 - - - -
472F ALA* 3.8 10.5 - - + -
474F LYS* 3.0 23.3 + - - -
475F PHE* 3.5 19.5 - + - -
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Residues in contact with ILE 443 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F PHE* 3.9 34.5 - - + +
390F THR* 5.9 2.2 - - + -
395F CYS* 5.5 2.7 - - - -
436F MET* 4.9 8.7 - - + -
439F HIS* 3.2 46.4 + - + +
440F TYR* 3.8 8.5 - - + +
442F TYR* 1.3 83.7 - - + +
444F TYR* 1.3 63.9 + - - +
446F GLU* 3.7 14.6 - - - +
447F LEU* 3.1 24.4 + - + +
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Residues in contact with TYR 444 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F ILE* 3.6 1.2 + - + -
347F ASN* 3.1 15.6 + - - -
348F PRO* 3.6 21.3 - - + -
389F PHE* 3.8 32.7 - + + -
398F TYR* 3.8 19.3 - - - -
415F THR* 3.2 37.1 - - + -
416F ASP 2.9 28.4 + - - -
417F PHE 3.6 13.0 - - - -
418F GLY* 4.4 6.1 - - - -
440F TYR* 3.0 20.8 + + + +
441F ALA* 3.5 3.4 - - - +
443F ILE* 1.3 76.3 - - - +
445F ASN* 1.3 73.8 + - - +
447F LEU* 3.1 14.4 + - - +
448F VAL* 3.2 22.5 + - + +
467F SER* 4.6 2.9 - - - -
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Residues in contact with ASN 445 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415F THR* 2.6 34.2 + - - +
441F ALA 2.9 23.7 + - - +
442F TYR* 4.0 2.7 - - - +
444F TYR* 1.3 88.4 - - - +
446F GLU* 1.3 58.1 + - - +
448F VAL* 3.1 7.3 + - - +
449F TRP* 2.8 31.0 + - - +
463F LEU* 3.7 10.9 - - + +
465F ALA* 3.4 12.4 - - - +
467F SER* 3.3 25.5 + - - +
468F ALA* 5.1 1.0 - - - +
472F ALA* 5.5 3.0 - - + +
475F PHE* 4.1 17.3 - - + -
478F HIS* 5.4 2.6 + - - +
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Residues in contact with GLU 446 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442F TYR* 2.8 52.7 + - + +
443F ILE* 3.7 15.8 - - - +
445F ASN* 1.3 72.0 - - - +
447F LEU* 1.3 57.8 + - - +
449F TRP* 3.6 0.3 - - - +
450F ASN* 2.9 47.1 + - - +
474F LYS* 5.4 0.3 + - - -
475F PHE* 3.5 29.6 - - + -
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Residues in contact with LEU 447 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F PHE* 3.6 38.8 - - + -
395F CYS* 3.8 33.0 - - + +
398F TYR* 3.7 22.7 - - + -
399F ALA* 4.2 15.7 - - + -
402F LEU* 3.9 12.3 - - + -
443F ILE* 3.1 13.7 + - + +
444F TYR 3.3 9.6 - - - +
445F ASN 3.1 0.2 - - - -
446F GLU* 1.3 75.6 - - - +
448F VAL* 1.3 68.3 + - - +
450F ASN* 3.3 7.4 + - - +
451F VAL* 3.2 18.5 + - - +
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Residues in contact with VAL 448 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346F ILE* 4.1 7.6 - - + -
398F TYR* 4.4 1.6 - - + -
402F LEU* 4.0 19.7 - - + -
413F PHE* 3.5 32.3 - - + -
415F THR* 3.7 26.7 - - + -
444F TYR* 3.4 22.7 - - + +
445F ASN 3.1 5.5 + - - +
447F LEU* 1.3 81.1 - - + +
449F TRP* 1.3 63.6 + - - +
451F VAL* 3.1 12.8 + - - +
452F LEU* 3.2 13.2 + - - +
463F LEU* 3.7 15.7 - - + -
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Residues in contact with TRP 449 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F ALA* 3.8 18.8 - - + -
263F LEU 5.9 1.1 - - - -
445F ASN 2.8 21.2 + - - +
446F GLU 3.6 2.2 - - - +
448F VAL* 1.3 72.7 - - - +
450F ASN* 1.3 70.5 + - - +
452F LEU* 3.2 7.1 + - - +
453F LYS* 2.9 40.6 + - + +
458F GLU* 4.6 17.1 - - + +
461F ALA* 3.3 45.7 - - + +
462F VAL* 4.1 5.8 - - - -
463F LEU* 4.1 16.1 - - + +
474F LYS 3.9 2.0 + - - -
475F PHE* 3.2 45.3 - + + -
476F PRO* 3.5 33.7 - - + -
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Residues in contact with ASN 450 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446F GLU* 2.9 39.7 + - - +
447F LEU* 3.8 6.8 - - - +
448F VAL 3.3 0.2 - - - -
449F TRP* 1.3 88.9 - - - +
451F VAL* 1.3 56.3 + - - +
453F LYS* 3.4 23.7 + - - +
454F ASP* 2.6 43.8 + - - +
475F PHE* 5.1 1.0 - - - -
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Residues in contact with VAL 451 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F ALA* 3.6 39.3 - - + +
402F LEU* 3.8 27.8 - - + -
403F LYS* 4.1 25.4 - - + +
406F VAL* 4.4 11.7 - - + -
413F PHE* 4.6 4.3 - - + -
447F LEU 3.2 12.5 + - - +
448F VAL 3.1 10.4 + - - +
450F ASN* 1.3 74.1 - - - +
452F LEU* 1.3 66.1 + - - +
454F ASP* 3.2 4.7 + - - +
455F THR* 2.8 28.5 + - - +
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Residues in contact with LEU 452 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F VAL* 4.2 12.8 - - + -
411F ASP 3.6 22.9 - - - +
412F CYS* 4.4 2.7 - - - -
413F PHE* 3.6 29.8 - - + -
448F VAL 3.2 5.3 + - - +
449F TRP* 3.5 9.0 - - + +
451F VAL* 1.3 78.2 - - - +
453F LYS* 1.3 63.9 + - - +
455F THR* 3.0 3.3 + - - -
456F VAL* 3.0 36.2 + - + +
457F GLY 3.1 5.7 + - - -
461F ALA* 3.7 13.9 - - + -
462F VAL 3.3 35.4 - - - +
463F LEU* 3.6 19.7 - - + -
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Residues in contact with LYS 453 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449F TRP* 2.9 29.4 + - + +
450F ASN* 3.4 26.7 + - - +
452F LEU* 1.3 77.7 - - - +
454F ASP* 1.3 76.0 + - - +
457F GLY* 3.3 20.2 - - - -
458F GLU* 3.6 42.8 + - + +
461F ALA* 4.4 1.7 - - + +
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Residues in contact with ASP 454 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F LYS* 4.9 16.1 - - - +
450F ASN* 2.6 30.7 + - - +
451F VAL* 3.9 5.3 - - - +
453F LYS* 1.3 91.5 - - - +
455F THR* 1.3 62.5 + - - +
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Residues in contact with THR 455 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F LYS* 4.1 31.2 - - + +
406F VAL* 3.6 32.9 - - + +
451F VAL* 2.8 23.0 + - + +
452F LEU* 3.0 10.7 + - - -
454F ASP* 1.3 83.5 - - - +
456F VAL* 1.3 71.8 + - - +
457F GLY* 3.1 1.8 + - - -
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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