Contacts of the helix formed by residues 387 - 414 (chain D) in PDB entry 2YVX
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 LEU 387 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 4.9 2.9 - - + +
282A TRP* 6.5 1.1 - - + -
375D VAL* 3.4 34.1 - - + +
378D VAL* 3.2 48.2 - - + +
379D TYR* 4.0 19.3 - - + +
383D HIS 3.9 9.6 - - - +
384D PRO 3.8 9.4 + - - +
385D LEU 2.6 6.1 + - - +
386D LEU* 1.3 71.6 - - - +
388D PRO* 1.3 63.9 - - + +
389D VAL 3.4 1.1 - - - -
390D VAL* 3.6 14.1 - - - +
391D GLY* 3.7 4.5 + - - -
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Residues in contact with PRO 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 3.4 21.3 - - + -
282A TRP* 5.9 2.0 - - + -
365B LEU* 3.7 37.0 - - + -
386D LEU* 3.1 10.8 - - - -
387D LEU* 1.3 91.1 - - + +
389D VAL* 1.3 73.6 + - + +
390D VAL 2.9 2.6 + - - -
391D GLY* 3.2 1.5 + - - +
392D VAL* 2.8 32.9 + - + +
446D LEU* 3.3 29.6 - - + -
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Residues in contact with VAL 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D LEU* 5.1 13.0 - - + -
386D LEU* 2.8 53.4 - - + +
388D PRO* 1.3 78.9 - - - +
390D VAL* 1.3 64.7 - - + +
393D SER* 2.2 37.4 + - - -
439D TYR* 4.3 13.6 - - + +
442D VAL* 3.3 27.0 - - - +
443D ALA* 3.7 21.5 - - + -
446D LEU* 4.0 8.1 - - + -
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Residues in contact with VAL 390 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D TYR* 4.9 12.8 - - + -
323D LEU* 4.2 2.5 - - + +
374D LEU* 3.3 21.5 - - + -
375D VAL* 4.0 4.9 - - + -
378D VAL* 3.0 53.2 - - + -
386D LEU 4.1 1.3 - - - +
387D LEU* 3.6 19.1 - - - +
388D PRO 2.9 0.2 + - - -
389D VAL* 1.3 88.0 - - + +
391D GLY* 1.3 61.3 + - - +
393D SER* 2.6 18.4 + - - -
394D LEU* 2.9 19.8 + - - +
439D TYR* 4.8 7.6 - - - +
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Residues in contact with GLY 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 5.0 2.5 - - - -
371D SER* 3.3 10.5 - - - -
375D VAL* 3.2 25.2 - - - +
387D LEU 3.7 3.7 + - - -
388D PRO* 3.2 4.1 + - - -
390D VAL* 1.3 78.8 - - - +
392D VAL* 1.3 62.8 + - - +
393D SER 3.1 0.9 + - - -
394D LEU* 4.8 1.1 - - - -
395D VAL* 3.2 29.7 + - - +
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Residues in contact with VAL 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B GLY 5.4 1.1 - - - +
364B LEU* 3.2 32.3 - - + -
365B LEU* 4.1 29.2 - - + +
368B LEU* 3.9 18.1 - - + +
388D PRO* 2.8 26.1 + - + +
391D GLY* 1.3 71.2 - - - -
393D SER* 1.3 48.9 + - - +
395D VAL* 4.6 0.3 - - - +
396D LEU* 2.6 40.4 + - + +
442D VAL* 3.5 26.0 - - + -
446D LEU* 5.6 6.7 - - + -
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Residues in contact with SER 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D LEU* 3.4 10.0 - - - +
389D VAL 2.2 28.3 + - - -
390D VAL 2.6 15.1 + - - -
392D VAL* 1.3 74.7 - - - +
394D LEU* 1.3 67.6 + - - +
395D VAL 2.9 1.7 + - - -
396D LEU 2.9 0.2 + - - -
397D ILE* 2.6 44.1 + - - +
438D ILE* 4.0 7.2 - - - -
439D TYR* 3.7 11.6 - - - -
442D VAL* 3.5 16.8 - - - +
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Residues in contact with LEU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C ILE* 5.7 4.0 - - + -
323D LEU* 4.0 16.7 - - + +
326D THR* 5.4 10.5 - - + -
367D GLY 3.9 8.1 - - - +
370D LEU* 3.7 22.4 - - + +
371D SER* 3.9 10.3 - - - +
374D LEU* 3.0 48.9 - - + -
390D VAL 2.9 15.1 + - - +
391D GLY* 4.1 3.1 - - - +
393D SER* 1.3 78.1 + - - +
395D VAL* 1.3 55.6 + - + +
397D ILE* 3.2 6.2 - - - +
398D VAL* 2.7 58.4 + - + +
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Residues in contact with VAL 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU* 4.9 16.4 - - + -
364D LEU* 4.8 11.2 - - + -
367D GLY* 2.7 36.6 - - - +
368D LEU* 3.5 28.5 - - + +
371D SER* 3.0 25.4 - - - +
391D GLY 3.2 11.5 + - - +
392D VAL 4.6 0.9 - - - +
393D SER 3.0 0.4 - - - -
394D LEU* 1.3 74.6 - - + +
396D LEU* 1.3 55.9 + - - +
397D ILE 2.7 14.0 + - - -
398D VAL* 4.2 0.2 - - - +
399D PHE* 3.3 21.7 + - + +
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Residues in contact with LEU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B LEU* 4.8 13.2 - - + -
368B LEU* 5.6 2.0 - - + +
392D VAL* 2.6 29.3 + - + +
393D SER* 3.7 3.4 - - - +
395D VAL* 1.3 77.2 - - - +
397D ILE* 1.3 55.4 + - - +
399D PHE* 4.3 4.8 - - + +
400D PHE* 3.4 41.9 + - + +
438D ILE* 4.2 9.6 - - + -
442D VAL* 3.4 32.5 - - + -
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Residues in contact with ILE 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323D LEU* 3.6 24.9 - - + +
324D LEU* 5.9 0.9 - - + -
327D GLY* 4.1 22.0 - - - -
393D SER* 2.6 31.4 + - - +
394D LEU* 3.2 5.4 - - - +
395D VAL 2.7 0.6 + - - -
396D LEU* 1.3 76.3 - - - +
398D VAL* 1.3 70.4 + - - +
399D PHE 2.8 1.3 - - - -
400D PHE* 2.6 15.7 + - + +
401D ALA* 2.6 15.9 + - + -
431D SER 5.6 0.4 - - - +
435D GLY* 3.5 32.5 - - - +
438D ILE* 3.2 41.5 - - + -
439D TYR 4.4 1.3 - - - +
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Residues in contact with VAL 398 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326D THR* 4.6 7.9 - - + -
327D GLY* 4.8 7.0 - - - +
330D THR* 3.5 23.3 - - + +
363D GLY* 4.2 2.2 - - - +
366D LEU* 4.0 10.1 - - + -
367D GLY* 3.8 18.6 - - - +
370D LEU* 3.2 37.2 - - + -
394D LEU* 2.7 36.4 + - + +
395D VAL 4.2 0.2 - - - +
397D ILE* 1.3 75.1 - - + +
399D PHE* 1.3 62.0 + - - +
401D ALA* 3.6 4.4 - - - +
402D ASN* 3.0 23.2 + - - +
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Residues in contact with PHE 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B VAL* 6.0 1.3 - - + -
360D MET* 2.9 67.5 - - + -
363D GLY* 3.6 16.1 + - - +
364D LEU* 3.1 39.3 - - + +
395D VAL 3.3 14.7 + - - +
396D LEU* 4.3 4.3 - - + +
397D ILE 2.6 3.8 + - - -
398D VAL* 1.3 73.9 - - - +
400D PHE* 1.3 83.7 + + - +
401D ALA 2.9 2.8 + - - -
403D LEU* 3.0 40.3 + - + +
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Residues in contact with PHE 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396D LEU* 3.4 27.7 + - + +
397D ILE* 2.6 8.5 + - - +
399D PHE* 1.3 92.0 - + - +
401D ALA* 1.3 56.3 + - - +
403D LEU* 4.0 6.5 - - + +
404D VAL* 2.8 29.1 + - + +
434D THR* 6.5 0.7 - - - -
438D ILE* 3.6 30.5 - - + -
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Residues in contact with ALA 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D GLY* 3.0 32.3 - - - +
330D THR* 4.7 0.4 - - - -
331D GLY* 4.0 9.0 - - - +
397D ILE* 2.6 23.2 + - + +
398D VAL 3.6 4.9 - - - +
399D PHE 2.9 1.0 + - - -
400D PHE* 1.3 69.3 - - - +
402D ASN* 1.3 57.8 + - - +
403D LEU 2.9 1.3 - - - -
404D VAL* 2.5 37.0 + - - +
405D GLY 3.3 5.0 + - - -
431D SER* 4.2 9.0 - - - +
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Residues in contact with ASN 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ARG* 2.7 26.5 + - - -
330D THR* 3.1 25.0 - - + +
331D GLY* 4.3 1.3 - - - -
334D SER* 3.1 20.8 + - - -
359D GLU* 2.8 40.5 + - - +
363D GLY* 3.7 10.3 - - - +
398D VAL 3.0 9.8 + - - +
399D PHE 3.8 1.3 - - - +
401D ALA* 1.3 79.7 - - - +
403D LEU* 1.3 78.3 + - - +
404D VAL 3.3 0.3 + - - -
406D ALA* 2.9 24.6 + - - +
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Residues in contact with LEU 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D PHE* 3.4 54.2 - - + +
359D GLU* 4.0 9.2 - - + -
360D MET* 4.0 6.7 - - + -
399D PHE* 3.0 54.7 + - + +
400D PHE* 4.2 9.9 - - + +
401D ALA 2.9 1.6 + - - -
402D ASN* 1.3 107.9 - - - +
404D VAL* 1.3 60.8 + - - +
406D ALA* 4.0 4.5 - - + -
407D MET* 3.5 26.5 + - + +
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Residues in contact with VAL 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400D PHE* 2.8 28.7 - - + +
401D ALA* 2.5 18.7 + - - +
403D LEU* 1.3 71.8 - - + +
405D GLY* 1.3 64.9 + - - +
406D ALA 2.9 4.3 + - - -
407D MET* 2.9 3.2 + - - +
408D LEU* 2.9 40.4 + - + +
427D VAL* 6.1 2.5 - - + -
430D LEU* 5.7 12.6 - - + +
434D THR* 5.3 9.9 - - + +
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Residues in contact with GLY 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D GLY* 3.6 21.4 + - - -
334D SER* 3.0 6.3 - - - -
335D ALA* 3.0 20.8 - - - -
401D ALA 3.3 6.7 + - - -
404D VAL* 1.3 81.1 - - - +
406D ALA* 1.3 56.0 + - - +
408D LEU* 4.5 5.6 - - - -
409D PRO* 2.9 23.0 - - - +
422D VAL* 5.7 0.2 - - - -
427D VAL* 4.6 9.6 - - - +
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Residues in contact with ALA 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D SER* 2.6 18.7 + - - +
338D ILE* 3.0 21.4 - - + +
355D VAL* 5.9 1.3 - - + -
356D PHE* 6.4 0.2 - - - -
359D GLU* 4.3 16.6 - - + -
402D ASN 2.9 16.3 + - - +
403D LEU* 4.2 6.7 - - + -
404D VAL 2.9 0.6 - - - -
405D GLY* 1.3 80.2 - - - +
407D MET* 1.3 64.5 + - + +
408D LEU 3.5 0.2 - - - -
409D PRO* 4.0 0.2 - - - +
410D PHE* 2.9 30.3 - - - -
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Residues in contact with MET 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D TRP* 3.4 50.0 - - - +
355D VAL* 3.4 20.6 - - + -
356D PHE* 3.9 29.4 - - + +
403D LEU* 3.5 18.7 + - + +
404D VAL 2.9 3.9 + - - +
406D ALA* 1.3 98.1 - - + +
408D LEU* 1.3 62.9 + - - +
409D PRO 3.7 0.2 - - - -
410D PHE* 3.7 15.6 + - + +
411D LEU* 3.5 16.8 + - - +
414D ARG* 5.9 2.7 + - - -
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Residues in contact with LEU 408 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404D VAL* 2.9 28.1 + - + +
405D GLY* 4.5 2.7 - - - +
407D MET* 1.3 75.5 - - - +
409D PRO* 1.3 75.8 - - + +
410D PHE 3.1 1.6 - - - -
411D LEU* 2.7 51.6 + - + +
412D LEU* 3.2 7.3 + - + +
422D VAL* 4.0 29.6 - - + -
426D LEU* 5.0 10.3 - - + -
427D VAL* 5.4 4.7 - - + -
430D LEU* 5.0 15.0 - - + -
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Residues in contact with PRO 409 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D ALA* 4.2 4.9 - - + +
338D ILE* 4.0 7.2 - - + -
339D ILE* 3.3 33.4 - - + -
342D LEU* 3.3 26.0 - - + -
405D GLY 2.9 29.4 - - - +
406D ALA 4.0 3.6 - - - +
407D MET 3.9 0.9 - - - -
408D LEU* 1.3 86.9 - - + +
410D PHE* 1.3 64.8 + - - +
412D LEU* 3.2 10.9 + - - +
413D ARG* 3.3 10.9 + - - +
419D PRO* 4.0 11.2 - - + +
422D VAL* 4.3 11.0 - - + -
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Residues in contact with PHE 410 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338D ILE* 3.0 32.1 - - + -
342D LEU* 4.4 12.8 - - + -
347D LEU* 4.8 7.0 - - + -
348D ASP 3.4 28.0 - - - -
349D LEU* 4.9 4.3 - - - +
351D ASP* 3.9 4.0 - - + -
352D TRP* 3.6 34.3 - - + -
355D VAL* 3.4 21.5 - - + -
406D ALA 2.9 29.6 - - - -
407D MET* 3.7 15.0 - - + +
408D LEU 3.1 0.2 - - - -
409D PRO* 1.3 75.1 - - - +
411D LEU* 1.3 66.1 + - - +
413D ARG* 2.8 20.8 + - - +
414D ARG* 2.9 23.1 + - + +
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Residues in contact with LEU 411 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407D MET 3.5 12.4 + - - +
408D LEU* 2.7 42.8 + - + +
410D PHE* 1.3 74.9 - - - +
412D LEU* 1.3 66.4 + - + +
414D ARG* 3.4 29.3 + - + +
415D LEU* 3.6 22.2 + - + +
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408D LEU* 3.2 6.9 + - + +
409D PRO 3.7 6.5 - - - +
410D PHE 3.1 0.6 - - - -
411D LEU* 1.3 82.8 - - + +
413D ARG* 1.3 58.5 + - - +
415D LEU* 2.7 28.3 + - + -
416D GLY 2.8 10.4 + - - -
417D VAL* 3.4 39.8 + - + +
418D ASP 4.0 19.5 - - - +
419D PRO* 4.0 2.5 - - + +
421D LEU* 4.3 11.0 - - + -
422D VAL* 3.3 34.3 - - + -
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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
----------------------------------------------------------
220D ARG* 5.3 8.1 - - - +
342D LEU* 2.7 67.5 + - + +
343D ALA* 4.9 1.6 - - - +
345D ARG* 5.7 3.0 - - - +
347D LEU 4.8 0.2 + - - -
348D ASP* 4.5 19.0 + - - +
349D LEU* 5.0 21.0 - - + +
409D PRO 3.3 7.9 + - - +
410D PHE* 2.8 16.6 + - - +
412D LEU* 1.3 69.8 - - - +
414D ARG* 1.3 62.2 + - - +
415D LEU 2.9 6.1 + - - -
416D GLY* 3.1 12.4 + - - +
417D VAL 4.1 9.8 + - - +
419D PRO* 5.4 10.4 - - + +
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349D LEU* 4.2 31.8 + - + +
352D TRP* 2.8 65.8 - - - +
407D MET* 5.9 2.4 + - - -
410D PHE* 2.9 19.6 + - + +
411D LEU* 3.5 25.4 - - + +
412D LEU 3.1 0.4 - - - -
413D ARG* 1.3 75.7 - - - +
415D LEU* 1.3 65.2 + - + +
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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