Contacts of the helix formed by residues 396 - 425 (chain D) in PDB entry 2YPT
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 PHE 396 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D CYS* 3.3 55.9 - - + -
362D LEU* 3.6 31.6 - - + -
363D PHE 4.0 0.4 - - - -
366D LEU* 4.4 8.5 - - + -
391D ILE* 2.9 43.5 + - + +
392D PHE* 3.6 21.5 - + - +
394D PHE 3.4 0.4 - - - -
395D ILE* 1.3 75.6 - - + +
397D SER* 1.4 54.1 + - - +
398D PRO* 3.4 2.7 - - - -
399D TYR* 2.9 17.0 + + + +
400D ASN* 2.8 51.0 + - - +
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Residues in contact with SER 397 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 5.7 1.9 - - - +
26D PHE* 3.7 17.7 - - - -
27D SER* 5.1 6.9 + - - -
393D GLN 3.0 20.4 + - - -
394D PHE* 2.9 24.7 + - - +
396D PHE* 1.4 74.2 - - - +
398D PRO* 1.4 67.1 - - - +
400D ASN* 3.4 10.9 + - - +
401D GLU* 3.0 28.7 + - - +
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Residues in contact with PRO 398 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 3.5 33.2 - - + -
394D PHE 4.4 1.8 - - - +
395D ILE 3.3 17.0 - - - +
396D PHE* 3.5 0.9 - - - -
397D SER* 1.4 92.3 - - - +
399D TYR* 1.4 61.6 + - + +
401D GLU* 3.4 2.9 + - - +
402D VAL* 3.2 28.8 + - + +
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Residues in contact with TYR 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ASN* 2.8 37.5 + - - -
358D LEU* 3.6 31.2 - - + +
359D CYS* 3.7 18.6 - - - -
362D LEU* 6.2 4.3 - - + -
396D PHE* 2.9 19.8 + + + +
398D PRO* 1.4 75.5 - - + +
400D ASN* 1.3 70.3 + - - +
402D VAL* 3.2 8.2 + - + +
403D LEU* 2.9 60.5 + - + +
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Residues in contact with ASN 400 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355D ASN* 5.0 1.2 - - - +
359D CYS* 4.6 5.5 - - - -
392D PHE 2.9 27.9 + - - -
393D GLN* 4.9 2.4 + - - +
396D PHE* 2.8 30.9 + - - +
397D SER* 3.8 8.5 - - - +
399D TYR* 1.3 90.2 - - - +
401D GLU* 1.4 54.6 + - + +
403D LEU* 4.0 7.5 - - - +
404D SER* 2.8 36.8 + - - +
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Residues in contact with GLU 401 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D PHE* 4.3 9.4 - - + -
30D VAL* 3.8 32.9 - - + +
34D GLU* 3.9 10.2 - - - +
397D SER* 3.0 20.2 + - - +
398D PRO 3.7 4.9 - - - +
400D ASN* 1.4 75.7 - - + +
402D VAL* 1.4 64.3 - - + +
404D SER* 3.6 7.5 + - - -
405D PHE* 3.2 22.3 + - - +
455D TRP* 3.7 31.5 - - + -
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Residues in contact with VAL 402 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D PRO 3.2 18.3 + - - +
399D TYR* 3.2 7.2 + - + +
401D GLU* 1.4 73.4 - - + +
403D LEU* 1.4 59.3 + - - +
405D PHE* 3.1 9.7 + - + +
406D CYS* 2.9 42.3 + - - -
455D TRP* 6.4 0.2 - - - -
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Residues in contact with LEU 403 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D ILE* 5.3 8.3 - - + -
355D ASN* 3.4 35.9 - - + +
399D TYR* 2.9 47.8 + - + +
400D ASN* 4.0 6.5 - - - +
402D VAL* 1.4 77.2 - - - +
404D SER* 1.4 57.0 + - - +
406D CYS* 3.3 8.9 + - + +
407D LEU* 2.9 52.9 + - + +
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Residues in contact with SER 404 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D ASN 2.8 23.0 + - - -
401D GLU* 3.8 10.8 - - - -
402D VAL 3.3 0.2 - - - -
403D LEU* 1.4 75.1 - - - +
405D PHE* 1.4 56.4 + - - +
407D LEU* 3.5 9.4 + - - +
408D THR* 2.7 36.4 + - - -
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Residues in contact with PHE 405 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D GLU 3.2 12.9 + - - +
402D VAL* 3.1 13.3 + - + +
404D SER* 1.4 75.0 - - - +
406D CYS* 1.3 65.6 + - - +
408D THR* 3.3 6.8 + - - -
409D VAL* 3.1 46.1 + - + +
412D ARG* 5.2 0.7 - - - -
454D MET* 3.3 30.5 - - + -
455D TRP* 3.5 52.9 - + + -
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Residues in contact with CYS 406 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402D VAL* 2.9 32.1 + - - +
403D LEU* 3.6 11.4 - - + +
405D PHE* 1.3 83.3 - - - +
407D LEU* 1.3 56.7 + - + +
409D VAL* 3.4 9.8 + - - +
410D LEU* 3.0 26.9 + - - +
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Residues in contact with LEU 407 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D ASN* 5.8 4.5 - - + +
351D ILE* 3.8 31.6 - - + -
403D LEU* 2.9 46.4 + - + +
404D SER* 3.9 7.9 - - - +
406D CYS* 1.3 73.9 - - + +
408D THR* 1.4 59.8 + - - +
410D LEU* 3.6 24.2 + - + +
411D SER* 2.9 27.5 + - - -
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Residues in contact with THR 408 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D SER* 2.7 22.5 + - - -
405D PHE* 3.3 8.6 + - - -
407D LEU* 1.4 72.7 - - - +
409D VAL* 1.4 63.9 + - - +
411D SER* 3.4 7.8 + - - -
412D ARG* 3.2 34.3 + - - +
454D MET 4.5 1.1 - - - +
455D TRP 3.9 13.5 + - - +
456D HIS 3.5 17.9 + - - +
457D TYR 3.4 23.8 - - - +
458D SER* 4.0 5.8 - - - +
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Residues in contact with VAL 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D PHE* 3.1 42.7 + - + +
406D CYS* 3.4 10.5 + - - +
408D THR* 1.4 75.3 - - - +
410D LEU* 1.4 61.2 + - - +
412D ARG* 3.4 32.7 + - - +
413D ARG* 3.3 40.7 + - + +
----------------------------------------------------------
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Residues in contact with LEU 410 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D ASN* 5.8 2.0 - - + -
351D ILE* 3.8 27.4 - - + -
406D CYS 3.0 17.7 + - - +
407D LEU* 3.6 19.3 - - + +
408D THR 3.3 0.2 - - - -
409D VAL* 1.4 74.1 - - - +
411D SER* 1.4 53.4 + - - +
413D ARG* 3.2 11.7 + - + +
414D PHE* 2.8 78.1 + - + +
----------------------------------------------------------
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Residues in contact with SER 411 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D LEU 2.9 18.8 + - - -
408D THR* 3.4 8.5 + - - -
410D LEU* 1.4 76.6 - - - +
412D ARG* 1.4 56.3 + - - +
414D PHE* 3.4 10.6 + - - +
415D GLU* 3.0 33.1 + - - +
458D SER* 2.8 32.3 + - - -
459D HIS* 4.9 3.3 + - - -
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Residues in contact with ARG 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D PHE* 5.2 0.2 - - - -
408D THR* 3.2 18.2 + - - +
409D VAL* 3.4 33.6 - - - +
411D SER* 1.4 73.7 - - - +
413D ARG* 1.3 63.9 + - + +
415D GLU* 3.3 4.0 + - - +
416D PHE* 3.2 31.7 + - + -
453D SER* 3.0 14.6 + - - -
454D MET* 2.8 39.8 + - - +
457D TYR* 2.7 36.2 + - - +
458D SER 3.2 17.7 + - - +
459D HIS 4.4 0.7 - - - -
460D PRO* 3.9 32.2 - - + +
461D PRO* 5.4 2.7 - - - -
464D GLU* 6.1 0.4 - - - -
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Residues in contact with ARG 413 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D VAL* 3.3 28.5 + - + +
410D LEU* 3.2 14.0 + - + +
412D ARG* 1.3 76.0 - - + +
414D PHE* 1.3 61.5 + - + +
416D PHE* 3.5 11.0 + - + +
417D GLN* 3.2 40.7 + - - +
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Residues in contact with PHE 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339D HIS* 3.4 12.5 - - + -
344D HIS* 3.1 81.2 - + + +
347D LYS* 4.0 20.2 - - + -
348D ASN* 4.8 6.1 - - + -
351D ILE* 5.4 0.7 - - + -
410D LEU* 2.8 58.5 + - + +
411D SER* 3.6 9.6 - - - +
412D ARG 3.3 0.2 - - - -
413D ARG* 1.3 77.7 - - + +
415D GLU* 1.3 56.8 + - - +
417D GLN* 3.9 10.1 - - - -
418D ALA 3.2 10.9 + - - -
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Residues in contact with GLU 415 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D HIS* 3.0 27.7 + - - -
339D HIS* 2.8 29.8 + - - -
411D SER* 3.0 21.6 + - - +
412D ARG 3.6 5.8 - - - +
413D ARG 3.3 0.4 - - - -
414D PHE* 1.3 74.6 - - + +
416D PHE* 1.3 58.7 + - - +
418D ALA 3.3 1.2 + - - -
419D ASP* 3.0 36.4 + - - +
458D SER 4.5 1.1 - - - +
459D HIS* 3.2 43.8 + - + +
460D PRO* 3.8 15.5 - - + -
465D ARG* 3.8 6.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE 416 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412D ARG* 3.2 27.5 + - + -
413D ARG* 3.7 12.3 - - + +
414D PHE 3.5 0.2 - - - -
415D GLU* 1.3 75.6 - - - +
417D GLN* 1.4 58.4 + - + +
419D ASP* 3.4 9.1 + - + +
420D ALA* 3.0 28.8 + - - +
460D PRO* 3.5 31.6 - - + +
464D GLU* 3.6 44.0 - - + -
465D ARG* 4.0 10.5 - - + -
468D ALA* 4.1 17.7 - - + -
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Residues in contact with GLN 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342D LEU* 3.4 27.2 - - + +
344D HIS* 2.8 37.7 + - + -
413D ARG* 3.2 30.6 + - - +
414D PHE* 3.7 9.3 - - - +
416D PHE* 1.4 75.7 - - + +
418D ALA* 1.3 57.7 + - - +
420D ALA* 3.4 8.9 + - - +
421D PHE 3.0 21.5 + - - -
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Residues in contact with ALA 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D HIS* 3.3 48.0 - - + +
338D GLY* 4.6 0.2 - - - -
339D HIS* 3.6 34.1 - - + +
342D LEU* 4.1 8.5 - - - +
344D HIS* 4.6 0.7 - - + -
414D PHE 3.2 5.3 + - - +
415D GLU 3.7 0.4 - - - +
417D GLN* 1.3 76.9 - - - +
419D ASP* 1.4 57.3 + - - +
421D PHE* 3.6 4.7 + - - +
422D ALA 3.2 19.1 + - - -
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Residues in contact with ASP 419 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D HIS* 2.8 21.6 + - - -
415D GLU 3.0 24.5 + - - +
416D PHE* 3.6 11.3 - - + +
417D GLN 3.3 0.2 - - - -
418D ALA* 1.4 73.5 - - - +
420D ALA* 1.4 60.6 + - - +
422D ALA* 3.3 5.0 + - - +
423D LYS* 3.2 21.1 + - - +
431D LEU* 3.4 19.3 - - + +
435D LEU* 4.8 0.3 - - - +
465D ARG* 2.9 47.3 + - - +
468D ALA* 6.1 2.7 - - + -
469D LEU* 3.8 21.9 - - + +
----------------------------------------------------------
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Residues in contact with ALA 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D PHE 3.0 17.5 + - - +
417D GLN* 3.4 9.6 + - - +
419D ASP* 1.4 74.7 - - - +
421D PHE* 1.4 56.4 + - - +
423D LYS* 3.4 9.0 + - - +
424D LYS* 3.0 26.4 + - - +
----------------------------------------------------------
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Residues in contact with PHE 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ILE* 5.5 10.3 - - + -
334D GLY 3.5 17.7 - - - -
337D LEU* 4.4 7.2 - - + -
338D GLY* 3.5 17.5 - - - -
341D LYS* 3.7 26.0 - - + -
342D LEU* 4.0 22.7 - - + -
417D GLN 3.0 15.8 + - - +
418D ALA* 3.6 7.4 - - - +
419D ASP 3.3 0.2 - - - -
420D ALA* 1.4 75.4 - - - +
422D ALA* 1.4 58.1 + - - +
424D LYS* 3.3 12.5 + - + +
425D LEU* 3.1 50.2 + - + +
----------------------------------------------------------
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Residues in contact with ALA 422 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D ALA 4.2 6.7 - - - +
334D GLY* 4.4 0.9 - - - -
335D HIS 4.1 15.5 - - - +
418D ALA 3.2 13.2 + - - +
419D ASP 3.3 10.7 + - - +
421D PHE* 1.4 73.7 - - - +
423D LYS* 1.4 59.5 + - - +
425D LEU* 3.3 18.8 + - - +
427D LYS* 3.2 28.1 + - + +
428D ALA 4.5 2.2 - - - -
431D LEU* 3.7 25.6 - - + -
469D LEU* 5.3 0.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419D ASP 3.2 12.6 + - - +
420D ALA* 3.6 11.7 - - - +
422D ALA* 1.4 73.5 - - - +
424D LYS* 1.4 58.8 + - - +
425D LEU 3.2 0.7 - - - -
426D GLY* 3.2 17.7 + - - -
428D ALA* 3.7 27.2 - - + +
468D ALA 6.0 1.1 - - - +
469D LEU* 4.4 11.4 - - + +
----------------------------------------------------------
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Residues in contact with LYS 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D ALA 3.0 14.8 + - - +
421D PHE* 3.3 20.2 + - + +
423D LYS* 1.4 74.6 - - - +
425D LEU* 1.4 58.5 - - + +
426D GLY 3.3 0.6 + - - -
----------------------------------------------------------
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Residues in contact with LEU 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D MET* 5.5 15.9 - - + -
244D SER* 5.7 6.1 - - - +
245D ILE* 5.4 10.1 - - + -
334D GLY* 3.7 29.4 - - - +
337D LEU* 5.7 2.0 - - + -
421D PHE* 3.1 46.2 + - + +
422D ALA* 3.5 9.6 - - - +
423D LYS 3.2 0.4 - - - -
424D LYS* 1.4 76.8 - - + +
426D GLY* 1.3 58.3 + - - +
427D LYS* 3.4 12.0 + - + +
----------------------------------------------------------
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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