Contacts of the helix formed by residues 432 - 454 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ASN* 4.1 21.7 + - + +
79D GLY 2.9 20.6 + - - +
214D GLN* 5.7 0.7 + - - -
431D SER* 1.3 70.9 - - - +
433D PRO* 1.4 65.6 - - - +
434D GLN* 2.8 27.9 + - - +
435D LYS* 2.9 46.3 + - + +
436D MET* 3.0 12.2 + - - +
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Residues in contact with PRO 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422D PRO 4.8 1.7 - - - +
423D THR* 3.0 47.2 - - - +
425D VAL* 3.8 17.3 - - + +
426D GLN* 5.5 0.7 - - - -
427D TRP* 4.0 22.0 - - + +
431D SER 3.4 10.0 - - - +
432D ASP* 1.4 88.1 - - - +
434D GLN* 1.3 62.2 + - + +
435D LYS 3.3 0.5 + - - -
436D MET* 3.9 0.9 - - - +
437D HIS* 3.3 17.8 + - - -
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Residues in contact with GLN 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D TRP* 3.5 34.0 - - - -
213D PRO 4.5 0.2 - - - +
214D GLN* 3.2 30.9 - - + +
215D CYS* 6.0 0.5 - - - +
233D GLU* 6.2 0.4 - - - +
423D THR* 3.3 34.1 + - - +
432D ASP* 2.8 21.6 + - - +
433D PRO* 1.3 76.6 - - + +
435D LYS* 1.3 59.7 + - - +
437D HIS* 4.2 1.6 - - - +
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Residues in contact with LYS 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASN* 4.6 8.4 - - - +
78D ASN 2.8 30.9 + - - +
79D GLY 4.0 2.7 - - - +
80D PRO* 3.5 28.0 - - + +
81D HIS* 3.7 17.8 + - - -
212D HIS* 6.1 0.4 + - - -
213D PRO* 3.9 19.4 - - + +
214D GLN* 3.7 43.0 + - + +
236D TYR* 4.3 12.9 + - - -
432D ASP* 2.9 25.8 + - + +
434D GLN* 1.3 76.7 - - - +
436D MET* 1.3 66.0 + - - +
437D HIS 3.2 2.4 + - - -
438D ASN 3.8 1.9 + - - -
439D HIS* 3.4 22.0 + - - +
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Residues in contact with MET 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D PRO* 3.7 23.3 - - + -
389D PHE* 6.2 0.9 - - + -
390D THR* 3.7 26.9 - - + -
421D ILE* 4.8 1.8 - - - -
427D TRP* 3.5 45.5 - - + +
431D SER* 3.5 29.2 - - - -
432D ASP 3.0 9.9 + - - +
433D PRO 3.3 2.9 + - - +
435D LYS* 1.3 76.5 - - - +
437D HIS* 1.3 65.4 + - - +
439D HIS* 4.4 6.1 - - - -
440D TYR* 2.9 43.2 + - + +
443D ILE* 4.9 9.2 - - + -
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Residues in contact with HIS 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D TRP* 3.5 57.3 - + + -
183D ASN* 2.7 31.8 + - + -
184D ARG* 5.8 0.2 - - + -
418D GLY 4.7 1.2 - - - +
419D GLU 3.2 21.1 + - - +
420D ARG* 4.6 2.7 - - - -
421D ILE* 2.7 53.6 + - - +
423D THR* 4.6 1.3 - - + -
433D PRO 3.3 11.3 + - - +
434D GLN 4.2 0.9 - - - +
435D LYS 3.2 1.0 - - - -
436D MET* 1.3 78.4 - - - +
438D ASN* 1.3 78.5 + - - +
440D TYR* 3.8 2.3 - - - +
441D ALA 4.7 0.7 + - - -
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Residues in contact with ASN 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D TYR* 5.3 3.3 + - - +
181D THR* 2.8 28.4 + - - -
182D TRP* 4.0 6.0 - - - +
183D ASN* 2.8 43.8 + - - +
196D ASN* 5.2 5.3 - - - +
213D PRO* 3.0 27.2 + - + +
214D GLN 3.8 2.4 + - - -
435D LYS 3.8 2.2 + - - -
436D MET 3.4 0.4 - - - -
437D HIS* 1.3 84.5 - - - +
439D HIS* 1.3 67.4 + - - +
440D TYR 3.1 2.9 + - - -
441D ALA* 3.3 15.6 + - - +
469D SER* 3.3 25.3 - - - +
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Residues in contact with HIS 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D PRO* 3.5 34.0 - - + +
81D HIS 4.1 18.1 + - - -
82D TYR* 4.5 13.5 - - - -
83D PRO* 4.4 9.6 - - + -
213D PRO* 5.0 6.2 + - + +
435D LYS 3.4 18.5 + - - +
436D MET* 4.3 4.7 - - - +
438D ASN* 1.3 76.5 - - - +
440D TYR* 1.3 65.1 + - - +
441D ALA 3.2 0.4 - - - -
442D TYR* 2.9 41.2 + + - +
443D ILE* 3.1 40.8 + - + +
469D SER* 3.9 7.9 + - - -
470D VAL 5.3 0.2 + - - -
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Residues in contact with TYR 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D PRO* 3.4 31.8 + - + +
386D ILE* 3.6 13.2 - - + +
387D TYR 3.0 27.2 + - - -
389D PHE* 3.2 35.4 - + + -
418D GLY* 3.9 7.2 - - - -
421D ILE* 3.5 33.0 - - + -
427D TRP* 3.5 33.4 - + - -
436D MET* 2.9 28.6 + - + +
437D HIS 3.8 1.8 - - - +
438D ASN 3.1 0.2 - - - -
439D HIS* 1.3 75.8 - - - +
441D ALA* 1.3 55.7 + - - +
443D ILE* 3.1 5.8 + - + +
444D TYR* 2.8 42.9 + + + +
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Residues in contact with ALA 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D ASN* 4.0 7.0 - - - +
418D GLY 4.4 7.4 + - - +
437D HIS 4.7 0.2 + - - -
438D ASN 3.3 13.2 + - - +
439D HIS 3.2 0.2 - - - -
440D TYR* 1.3 79.5 - - - +
442D TYR* 1.3 61.6 + - - +
444D TYR* 4.2 6.1 - - - -
445D ASN* 3.0 32.2 + - - +
467D SER* 3.4 26.0 - - - +
468D ALA* 3.8 26.7 - - - +
472D ALA* 5.6 0.2 - - - -
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Residues in contact with TYR 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PRO* 3.8 21.2 - - + +
438D ASN 4.2 0.6 + - - -
439D HIS* 2.9 44.2 + + - +
441D ALA* 1.3 77.0 - - - +
443D ILE* 1.3 61.0 + - + +
445D ASN* 3.9 1.1 - - - +
446D GLU* 2.8 67.3 + - - +
469D SER* 4.2 13.1 - - - -
470D VAL 3.9 6.5 - - - +
471D GLY 3.4 37.0 - - - -
472D ALA* 3.7 9.2 - - - -
474D LYS* 2.8 24.5 + - - -
475D PHE* 3.6 20.6 - + - -
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Residues in contact with ILE 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D PHE* 3.7 35.9 - - + +
390D THR* 5.9 2.0 - - + -
395D CYS* 5.4 2.7 - - - -
436D MET* 4.9 10.3 - - + -
439D HIS* 3.1 40.7 + - + +
440D TYR* 3.6 8.5 - - + +
442D TYR* 1.3 82.7 - - + +
444D TYR* 1.3 64.8 + - - +
446D GLU* 3.7 14.1 - - - +
447D LEU* 3.0 25.7 + - + +
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Residues in contact with TYR 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ILE* 3.9 0.9 - - + +
347D ASN* 3.1 17.7 + - - -
348D PRO* 3.6 23.1 - - + -
389D PHE* 3.9 31.1 - + + -
398D TYR* 3.9 18.2 - - - -
415D THR* 3.4 37.3 - - + +
416D ASP 3.0 28.1 + - - -
417D PHE 3.7 12.3 - - - -
418D GLY* 4.4 6.1 - - - -
440D TYR* 2.8 25.3 + + + +
441D ALA* 3.6 4.0 - - - +
443D ILE* 1.3 75.9 - - - +
445D ASN* 1.3 72.7 - - - +
447D LEU* 3.3 3.9 + - - +
448D VAL* 3.3 23.5 + - + +
467D SER* 4.8 2.2 - - - -
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Residues in contact with ASN 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D THR* 2.6 33.3 + - - -
441D ALA 3.0 24.1 + - - +
442D TYR* 4.1 0.9 - - - +
444D TYR* 1.3 87.0 - - - +
446D GLU* 1.3 61.3 + - - +
448D VAL* 3.4 5.6 + - - +
449D TRP* 2.8 31.5 + - - +
463D LEU* 3.5 16.4 - - + +
465D ALA* 3.6 9.5 - - - +
467D SER* 3.6 23.6 + - - -
468D ALA* 5.3 0.4 - - - +
472D ALA* 5.6 3.5 - - + +
475D PHE* 4.0 19.5 - - + -
478D HIS* 5.7 1.8 + - - -
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Residues in contact with GLU 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442D TYR* 2.8 50.5 + - + +
443D ILE* 3.7 15.6 - - - +
445D ASN* 1.3 73.1 - - - +
447D LEU* 1.3 65.3 + - - +
449D TRP* 3.4 1.2 + - - +
450D ASN* 3.0 42.0 + - - +
475D PHE* 3.6 26.8 - - + -
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Residues in contact with LEU 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D PHE* 3.8 22.4 - - + -
395D CYS* 3.7 46.0 - - + +
398D TYR* 3.7 26.7 - - + -
399D ALA* 4.5 12.8 - - + -
402D LEU* 4.0 7.2 - - + -
443D ILE* 3.0 17.1 + - + +
444D TYR* 3.6 4.5 - - - +
445D ASN 3.3 0.2 - - - -
446D GLU* 1.3 80.5 - - - +
448D VAL* 1.3 72.3 + - + +
450D ASN* 3.3 6.8 + - - +
451D VAL* 3.3 18.5 + - - +
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Residues in contact with VAL 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ILE* 4.1 9.9 - - + -
398D TYR* 4.5 1.6 - - + -
402D LEU* 4.2 15.3 - - + -
413D PHE* 3.9 22.4 - - + -
415D THR* 3.6 25.8 - - + -
444D TYR* 3.3 25.7 + - + +
445D ASN 3.7 4.9 - - - +
447D LEU* 1.3 79.7 - - + +
449D TRP* 1.3 67.7 + - - +
451D VAL* 2.8 14.9 + - - +
452D LEU* 3.0 15.3 - - + +
463D LEU* 3.7 24.7 - - + -
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Residues in contact with TRP 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262D ALA* 3.8 19.3 - - + -
263D LEU 6.0 0.2 - - - -
445D ASN 2.8 20.8 + - - +
446D GLU 3.7 3.4 - - - +
448D VAL* 1.3 74.4 - - - +
450D ASN* 1.3 62.6 + - - +
452D LEU* 3.1 12.2 + - + +
453D LYS* 3.0 49.0 + - + +
458D GLU* 4.6 10.7 - - + +
461D ALA* 3.6 32.3 - - + -
462D VAL* 3.7 22.2 - - - -
463D LEU* 3.9 16.1 - - + +
474D LYS 3.9 5.2 + - - -
475D PHE* 3.3 43.2 - + + -
476D PRO* 3.2 34.5 - - + -
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Residues in contact with ASN 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D GLU* 3.0 40.7 + - - +
447D LEU* 3.8 7.0 - - - +
448D VAL 3.2 0.2 - - - -
449D TRP* 1.3 77.3 - - - +
451D VAL* 1.3 63.8 + - - +
452D LEU 3.3 0.2 - - - -
453D LYS* 3.6 31.7 + - + +
454D ASP* 2.9 38.4 + - - +
475D PHE* 5.7 0.7 - - - -
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Residues in contact with VAL 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D ALA* 4.0 33.7 - - + +
402D LEU* 3.9 31.0 - - + -
403D LYS* 3.9 27.6 - - + +
406D VAL* 4.4 7.6 - - + -
447D LEU 3.3 14.9 + - - +
448D VAL* 2.8 10.5 + - - +
450D ASN* 1.3 77.1 - - - +
452D LEU* 1.3 61.4 + - + +
454D ASP* 3.3 4.4 + - - +
455D THR* 2.6 37.5 + - - +
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Residues in contact with LEU 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D VAL* 5.4 2.7 - - + -
411D ASP 4.1 19.5 - - - +
412D CYS* 4.4 3.1 - - - -
413D PHE* 3.8 29.4 - - + -
448D VAL* 3.0 23.6 - - + +
449D TRP* 3.1 7.6 + - - +
451D VAL* 1.3 77.2 - - + +
453D LYS* 1.3 66.8 + - - +
455D THR* 2.9 17.3 + - - +
456D VAL* 2.9 25.2 + - + +
457D GLY 3.0 6.9 + - - -
461D ALA* 3.9 10.8 - - + -
462D VAL 3.4 39.0 - - - +
463D LEU* 4.0 9.9 - - + -
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Residues in contact with LYS 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D TRP* 3.0 31.5 + - + +
450D ASN* 3.6 29.9 + - - +
451D VAL 3.4 0.2 - - - -
452D LEU* 1.3 77.1 - - - +
454D ASP* 1.3 65.2 + - - +
455D THR 3.5 0.3 + - - -
457D GLY* 3.5 15.3 - - - -
458D GLU* 3.5 53.5 + - + +
461D ALA* 4.6 0.8 - - + +
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Residues in contact with ASP 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D LYS* 5.3 12.1 + - - +
450D ASN* 2.9 29.4 + - - +
451D VAL* 3.8 4.7 - - - +
452D LEU 3.1 0.4 - - - -
453D LYS* 1.3 82.4 - - - +
455D THR* 1.3 63.3 + - + +
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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