Contacts of the helix formed by residues 432 - 455 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASN* 4.3 13.6 - - + +
79B GLY 2.8 16.7 + - - +
214B GLN* 5.3 1.2 + - - -
431B SER* 1.3 73.4 - - - +
433B PRO* 1.3 76.6 - - - +
434B GLN* 3.2 21.6 + - - +
435B LYS* 3.0 49.4 + - + +
436B MET* 3.0 21.1 + - - +
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Residues in contact with PRO 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PRO 5.1 1.2 - - - +
423B THR* 3.1 47.9 - - - +
425B VAL* 3.9 16.2 - - + +
426B GLN* 5.5 1.1 - - - -
427B TRP* 3.9 19.7 + - + +
431B SER 3.5 8.5 - - - +
432B ASP* 1.3 90.3 - - - +
434B GLN* 1.3 62.8 + - + +
435B LYS 3.2 1.0 + - - -
436B MET* 3.2 1.7 + - - +
437B HIS 3.2 19.2 + - - -
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Residues in contact with GLN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TRP* 3.7 30.0 - - - -
213B PRO 4.4 0.3 - - - +
214B GLN* 3.1 33.2 - - + +
215B CYS* 5.9 0.5 - - - +
423B THR* 3.5 32.7 + - - +
432B ASP* 3.2 18.7 + - - +
433B PRO* 1.3 78.9 - - + +
435B LYS* 1.3 58.3 + - - +
437B HIS* 4.3 2.7 - - - +
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Residues in contact with LYS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 4.3 8.5 + - - +
78B ASN 2.8 39.4 + - - +
79B GLY 4.1 1.3 - - - +
80B PRO* 3.4 28.7 - - + +
81B HIS* 4.7 8.3 - - - +
213B PRO* 3.8 19.4 - - + +
214B GLN* 4.0 39.4 - - - +
236B TYR* 5.2 8.5 - - - -
432B ASP* 3.0 34.7 + - - +
434B GLN* 1.3 77.3 - - - +
436B MET* 1.3 65.7 + - - +
437B HIS 3.2 2.3 + - - -
438B ASN 3.8 2.4 + - - -
439B HIS* 3.4 20.4 + - - +
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Residues in contact with MET 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PRO* 4.0 18.6 - - + -
389B PHE* 6.0 1.3 - - + -
390B THR* 3.6 15.9 - - + -
421B ILE* 4.9 1.6 - - - -
427B TRP* 3.5 60.6 - - + +
431B SER* 3.5 32.1 - - - -
432B ASP 3.0 8.8 + - - +
433B PRO 3.2 2.2 + - - +
435B LYS* 1.3 76.4 - - - +
437B HIS* 1.3 66.9 + - - +
439B HIS* 4.3 9.0 - - - -
440B TYR* 2.8 44.6 + - + +
443B ILE* 5.2 8.5 - - + -
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Residues in contact with HIS 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B TRP* 3.3 61.6 + + + -
183B ASN* 2.7 27.9 + - + +
418B GLY 4.8 1.4 - - - +
419B GLU 3.1 23.5 + - - +
420B ARG* 4.5 2.5 - - - -
421B ILE* 2.7 47.2 + - + +
423B THR* 4.6 2.0 - - + -
433B PRO 3.2 12.0 + - - +
434B GLN 4.3 1.3 - - - +
435B LYS 3.2 0.6 - - - -
436B MET* 1.3 79.1 - - - +
438B ASN* 1.3 74.0 + - - +
440B TYR* 3.8 10.7 - - - +
441B ALA 4.7 0.7 + - - -
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Residues in contact with ASN 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 5.1 4.3 + - - +
181B THR* 2.8 28.6 + - - -
182B TRP* 4.1 4.2 - - - +
183B ASN* 2.8 45.5 + - - +
196B ASN* 5.2 6.0 - - - +
213B PRO* 2.9 29.0 + - + +
214B GLN* 3.8 4.6 + - - +
435B LYS 3.8 2.2 + - - -
436B MET 3.4 0.2 - - - -
437B HIS* 1.3 84.1 - - - +
439B HIS* 1.3 65.4 + - - +
440B TYR 3.1 3.5 + - - -
441B ALA 3.4 8.0 + - - -
469B SER* 3.1 28.9 + - - +
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Residues in contact with HIS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PRO* 3.3 36.6 - - + +
81B HIS 4.1 16.9 + - - -
82B TYR* 4.9 8.9 - - + -
83B PRO* 4.5 9.6 - - + +
213B PRO* 5.0 6.4 - - + +
435B LYS 3.4 17.4 + - - +
436B MET* 3.3 8.6 + - - +
438B ASN* 1.3 76.8 - - - +
440B TYR* 1.3 64.5 + - - +
441B ALA 3.3 0.2 - - - -
442B TYR* 3.1 37.7 + + - +
443B ILE* 3.1 49.7 + - + +
469B SER* 4.0 8.7 + - - -
470B VAL 5.4 0.2 + - - -
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Residues in contact with TYR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B PRO* 3.3 38.9 + - + +
386B ILE* 3.5 12.6 - - + +
387B TYR 2.8 28.0 + - - -
389B PHE* 3.4 26.0 - + + -
418B GLY* 3.7 11.2 - - - -
421B ILE* 3.5 34.1 - - + -
427B TRP* 3.6 33.0 - + - -
436B MET* 2.8 27.1 + - + +
437B HIS 3.8 2.5 - - - +
438B ASN 3.1 0.4 - - - -
439B HIS* 1.3 76.5 - - - +
441B ALA* 1.3 64.3 + - - +
442B TYR 3.1 0.3 + - - -
443B ILE* 3.1 4.4 + - + +
444B TYR* 2.8 31.2 + - + +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B ASN* 4.0 5.6 - - - +
418B GLY 4.3 7.4 + - - +
437B HIS 4.7 0.2 + - - -
438B ASN 3.4 11.9 + - - +
439B HIS 3.3 0.4 - - - -
440B TYR* 1.3 79.0 - - - +
442B TYR* 1.3 62.9 + - - +
444B TYR* 3.5 5.7 - - - +
445B ASN* 2.9 31.7 + - - -
467B SER* 3.4 28.3 - - - +
468B ALA* 3.7 27.1 - - - +
469B SER 5.2 0.7 - - - -
472B ALA* 5.6 0.2 - - - -
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Residues in contact with TYR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 3.8 21.5 - - + +
438B ASN 4.2 0.8 + - - -
439B HIS* 3.1 39.8 + + - +
440B TYR 3.1 0.6 - - - -
441B ALA* 1.3 77.2 - - - +
443B ILE* 1.3 67.4 + - + +
446B GLU* 2.9 64.0 + - - +
469B SER* 4.0 14.0 - - - +
470B VAL 3.6 15.0 - - - +
471B GLY 3.5 29.6 - - - -
472B ALA* 3.7 10.1 - - - -
474B LYS* 2.8 23.7 + - - -
475B PHE* 3.7 17.2 - + - -
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Residues in contact with ILE 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 3.9 34.5 - - + +
390B THR* 6.0 0.9 - - + -
395B CYS* 5.5 2.5 - - - -
436B MET* 5.2 10.1 - - + -
439B HIS* 3.1 46.7 + - + +
440B TYR* 3.8 7.6 - - + +
442B TYR* 1.3 86.7 - - + +
444B TYR* 1.3 64.9 + - - +
446B GLU* 3.9 13.7 - - - +
447B LEU* 3.2 22.2 + - + +
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Residues in contact with TYR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 3.5 1.0 + - + -
347B ASN* 3.1 15.8 + - - -
348B PRO* 3.5 21.5 - - + -
389B PHE* 3.8 31.1 - + + -
398B TYR* 3.9 18.6 - - - -
415B THR* 3.3 36.5 - - + +
416B ASP 2.8 28.1 + - - -
417B PHE 3.6 14.4 - - - -
418B GLY* 4.3 6.5 - - - -
440B TYR* 2.8 21.0 + + + +
441B ALA* 3.5 3.6 - - - +
443B ILE* 1.3 79.6 - - - +
445B ASN* 1.3 71.9 + - - +
447B LEU* 3.2 10.6 + - - +
448B VAL* 3.3 17.5 + - + +
467B SER* 4.5 2.9 - - - -
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Residues in contact with ASN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 2.7 35.5 + - - +
441B ALA 2.9 23.7 + - - +
442B TYR* 4.2 1.1 - - - +
444B TYR* 1.3 85.2 - - - +
446B GLU* 1.3 67.9 + - - +
448B VAL* 3.2 7.3 + - - +
449B TRP* 2.8 25.1 + - - +
463B LEU* 3.8 9.5 - - + +
465B ALA* 3.3 12.1 - - - +
467B SER* 3.4 24.9 + - - -
468B ALA* 5.2 1.0 - - - +
472B ALA* 5.5 3.5 - - + +
475B PHE* 3.9 19.7 - - + -
478B HIS* 5.5 1.9 + - - -
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Residues in contact with GLU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B TYR* 2.9 50.1 + - + +
443B ILE* 3.9 16.4 - - - +
444B TYR 3.3 0.2 - - - -
445B ASN* 1.3 76.1 - - - +
447B LEU* 1.3 55.0 + - - +
449B TRP* 3.2 0.7 + - - +
450B ASN* 2.8 56.1 + - - +
474B LYS* 5.0 0.5 + - - -
475B PHE* 3.6 26.5 - - + -
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Residues in contact with LEU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B PHE* 3.8 24.5 - - + -
395B CYS* 3.8 43.5 - - + +
398B TYR* 3.8 23.6 - - + -
399B ALA* 4.2 14.6 - - + -
402B LEU* 4.2 6.5 - - + -
443B ILE* 3.2 12.6 + - + +
444B TYR 3.4 9.0 - - - +
446B GLU* 1.3 81.3 - - - +
448B VAL* 1.3 70.7 + - + +
450B ASN* 3.3 7.5 + - - +
451B VAL* 3.3 18.4 + - - +
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 4.1 13.7 - - + -
398B TYR* 4.4 2.7 - - + -
402B LEU* 3.9 22.4 - - + -
413B PHE* 3.6 29.4 - - + -
415B THR* 3.9 20.2 - - + -
444B TYR* 3.5 22.9 - - + +
445B ASN 3.2 5.1 + - - +
447B LEU* 1.3 81.1 - - + +
449B TRP* 1.3 63.9 + - - +
451B VAL* 2.9 14.4 + - - +
452B LEU* 3.0 17.0 + - - +
463B LEU* 3.6 15.7 - - + -
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Residues in contact with TRP 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B ALA* 3.7 18.6 - - + -
263B LEU 6.0 0.4 - - - -
445B ASN 2.8 20.8 + - - +
446B GLU 3.4 3.6 - - - +
448B VAL* 1.3 72.9 - - - +
450B ASN* 1.3 71.1 + - - +
451B VAL 3.1 0.7 + - - -
452B LEU* 3.1 9.9 + - - +
453B LYS* 2.9 43.5 + - + +
458B GLU* 4.7 15.2 - - + +
461B ALA* 3.5 42.2 - - + -
462B VAL* 3.9 5.8 - - - -
463B LEU* 4.1 14.1 - - + +
474B LYS 3.9 5.6 + - - -
475B PHE* 3.5 40.2 - + + -
476B PRO* 3.3 36.6 - - + -
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Residues in contact with ASN 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B GLU* 2.8 38.6 + - - +
447B LEU* 3.6 7.8 - - - +
448B VAL 3.3 0.2 - - - -
449B TRP* 1.3 84.8 - - - +
451B VAL* 1.3 56.8 + - + +
453B LYS* 3.8 27.9 + - - +
454B ASP* 2.6 41.9 + - - +
475B PHE* 5.3 0.9 - - - -
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Residues in contact with VAL 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B ALA* 3.8 32.5 - - + +
402B LEU* 4.1 24.0 - - + -
403B LYS* 3.6 35.0 - - + +
406B VAL* 4.6 5.8 - - + -
413B PHE* 5.1 1.8 - - + -
447B LEU 3.3 15.2 + - - +
448B VAL* 2.9 10.3 + - - +
450B ASN* 1.3 76.8 - - - +
452B LEU* 1.3 64.5 + - + +
454B ASP* 3.2 4.6 + - - +
455B THR* 2.8 33.6 + - + +
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406B VAL* 4.2 11.4 - - + -
411B ASP 3.4 26.0 - - - +
412B CYS* 4.3 0.2 - - - -
413B PHE* 3.6 38.4 - - + -
448B VAL 3.0 31.1 + - - +
449B TRP* 3.1 5.2 + - - +
451B VAL* 1.3 78.3 - - - +
453B LYS* 1.3 63.9 + - - +
455B THR* 3.0 3.9 + - - -
456B VAL* 2.9 40.4 + - + +
457B GLY 3.0 1.9 + - - -
461B ALA* 3.6 24.7 - - + -
462B VAL 4.5 7.6 - - - +
463B LEU* 3.8 14.1 - - + -
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Residues in contact with LYS 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B TRP* 2.9 35.3 + - + +
450B ASN* 3.6 30.9 + - - +
452B LEU* 1.3 77.0 - - - +
454B ASP* 1.3 71.5 + - - +
457B GLY* 3.2 21.6 - - - -
458B GLU* 3.4 47.3 + - + +
461B ALA* 4.2 1.3 - - - +
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Residues in contact with ASP 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LYS* 5.6 9.6 + - - +
450B ASN* 2.6 26.9 + - - +
451B VAL* 4.0 4.7 - - - +
452B LEU 3.2 0.2 - - - -
453B LYS* 1.3 91.2 - - - +
455B THR* 1.3 65.3 + - + +
457B GLY* 5.2 0.2 - - - -
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LYS* 4.1 29.4 - - + +
406B VAL* 3.4 31.2 - - + +
451B VAL* 2.8 25.3 + - + +
452B LEU* 3.0 9.1 + - - -
454B ASP* 1.3 83.9 - - + +
456B VAL* 1.3 70.7 + - - +
457B GLY* 3.1 4.1 + - - -
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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