Contacts of the helix formed by residues 400 - 431 (chain D) in PDB entry 3QNQ
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 GLY 400 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D TRP* 3.4 21.7 + - - -
372D VAL* 4.3 7.0 - - - -
373D ALA 5.5 0.2 - - - -
390D GLY 4.0 15.9 - - - -
394D SER* 4.1 6.0 + - - -
397D LYS 3.0 9.5 + - - -
398D ILE 2.9 1.0 - - - -
399D SER* 1.3 78.8 - - - +
401D VAL* 1.3 65.6 + - - +
402D ILE 3.0 2.1 + - - -
403D LEU 3.3 8.7 + - - -
404D GLN* 3.3 11.8 + - - +
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Residues in contact with VAL 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D LEU* 3.8 27.1 - - + +
390D GLY 4.2 0.8 - - - -
391D TYR* 3.4 38.1 - - + +
397D LYS 4.1 0.6 + - - -
398D ILE* 3.6 26.0 - - + +
400D GLY* 1.3 77.8 - - - +
402D ILE* 1.3 62.8 + - + +
404D GLN* 3.5 11.7 + - - +
405D LEU* 3.2 30.4 + - + +
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Residues in contact with ILE 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D LEU* 5.9 1.1 - - + +
372D VAL* 4.5 10.5 - - + -
398D ILE* 3.4 20.2 + - + +
399D SER* 3.7 21.1 - - - +
400D GLY 3.0 1.0 - - - -
401D VAL* 1.3 77.4 - - + +
403D LEU* 1.3 73.2 + - + +
404D GLN 3.1 1.8 - - - -
405D LEU* 3.1 13.1 + - + +
406D VAL* 2.9 34.6 + - + +
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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
----------------------------------------------------------
292D TRP* 3.5 21.3 - - + +
362D VAL* 4.5 8.1 - - + -
363D SER* 3.6 45.1 - - - +
366D ALA* 4.1 13.0 - - + -
367D MET* 4.5 6.1 - - + -
372D VAL* 3.8 34.1 - - + -
400D GLY 3.3 10.1 + - - +
402D ILE* 1.3 86.4 - - + +
404D GLN* 1.3 52.9 + - - +
406D VAL* 3.2 11.3 + - + +
407D ASN* 2.6 46.8 + - - +
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Residues in contact with GLN 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D LEU 2.8 25.1 + - - +
292D TRP* 3.7 17.0 - - + +
295D MET* 3.6 10.4 - - - +
386D ILE* 2.5 48.9 + - + +
387D LEU* 3.6 15.3 - - + +
389D SER* 3.4 3.4 + - - -
390D GLY* 3.0 30.1 + - - +
400D GLY 3.3 3.7 + - - +
401D VAL* 3.6 8.7 - - - +
402D ILE 3.1 0.8 - - - -
403D LEU* 1.3 73.5 - - - +
405D LEU* 1.3 57.4 + - - +
406D VAL 2.9 1.5 + - - -
407D ASN* 3.1 5.6 + - - +
408D PHE* 2.7 37.3 + - - +
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Residues in contact with LEU 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ILE* 5.9 0.2 - - + -
387D LEU* 3.6 32.1 - - + -
401D VAL* 3.2 22.2 + - + +
402D ILE* 3.1 16.0 + - + +
404D GLN* 1.3 76.8 - - - +
406D VAL* 1.3 61.1 + - + +
408D PHE* 3.6 17.5 - - + +
409D ALA* 3.3 22.0 + - - +
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Residues in contact with VAL 406 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D VAL* 4.7 9.0 - - + -
402D ILE* 2.9 23.8 + - + +
403D LEU* 3.3 14.6 - - + +
404D GLN 2.9 1.2 - - - -
405D LEU* 1.3 75.9 - - + +
407D ASN* 1.3 58.0 + - - +
409D ALA* 3.3 6.1 + - - +
410D LEU* 2.7 54.6 + - + +
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Residues in contact with ASN 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D TRP* 3.8 12.2 + - - -
295D MET* 3.1 17.7 - - + +
359D LEU* 3.2 33.5 - - + +
362D VAL* 4.3 7.6 - - - +
363D SER* 3.2 18.2 + - - -
403D LEU* 2.6 53.7 + - - +
404D GLN* 3.7 4.8 - - - +
406D VAL* 1.3 69.1 - - - +
408D PHE* 1.3 70.7 + - - +
410D LEU* 3.4 8.3 - - - +
411D ALA* 2.8 24.9 + - - +
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Residues in contact with PHE 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D MET* 3.0 12.3 - - + +
302D LEU* 4.1 18.4 - - + -
303D ALA* 3.7 31.8 - - + +
306D VAL* 4.2 27.1 - - + -
386D ILE* 4.3 17.3 - - + -
387D LEU* 6.4 0.2 - - + -
404D GLN 2.7 21.1 + - - +
405D LEU* 3.6 20.2 - - + +
407D ASN* 1.3 73.5 - - - +
409D ALA* 1.3 54.0 + - - +
411D ALA* 3.8 1.7 - - - +
412D PHE* 2.8 44.5 + + + +
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Residues in contact with ALA 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D LEU 3.3 13.2 + - - +
406D VAL* 3.3 5.0 + - - +
408D PHE* 1.3 80.0 - - - +
410D LEU* 1.3 64.6 + - - +
412D PHE* 3.2 12.6 + - + +
413D VAL* 3.0 32.7 + - + +
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Residues in contact with LEU 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D VAL* 4.7 13.5 - - + +
359D LEU* 4.2 11.9 - - + -
362D VAL* 4.2 27.1 - - + -
406D VAL* 2.7 44.8 + - + +
407D ASN* 3.4 9.9 - - - +
409D ALA* 1.3 72.7 - - - +
411D ALA* 1.3 61.1 + - - +
413D VAL* 3.1 17.3 - - + +
414D ILE* 3.0 27.2 - - + +
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Residues in contact with ALA 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D ALA* 3.1 35.9 - - + -
303D ALA* 4.3 4.3 - - + -
355D VAL* 3.4 25.8 - - + -
359D LEU* 5.0 2.6 - - + +
407D ASN 2.8 15.2 + - - +
408D PHE 3.8 1.6 - - - +
410D LEU* 1.3 68.3 - - - +
412D PHE* 1.3 54.0 + - - +
413D VAL 2.7 6.6 + - - -
414D ILE* 2.7 23.2 + - - +
415D TYR* 2.8 20.8 + - + +
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Residues in contact with PHE 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D ALA* 3.8 29.3 - - + +
306D VAL* 4.6 13.0 - - + -
307D GLY* 4.2 22.4 - - - -
310D LEU* 5.0 4.3 - - + -
311D PHE* 4.2 24.2 - + - -
408D PHE* 2.8 27.6 + + + +
409D ALA* 3.5 12.8 - - + +
411D ALA* 1.3 74.9 - - - +
413D VAL* 1.3 64.2 + - + +
415D TYR* 4.2 3.9 - - + +
416D LEU* 3.6 33.2 + - + +
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Residues in contact with VAL 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D ALA* 3.0 17.9 + - + +
410D LEU* 3.1 24.7 - - + +
411D ALA 2.7 4.8 + - - -
412D PHE* 1.3 85.2 - - + +
414D ILE* 1.3 63.2 + - + +
415D TYR 3.2 1.6 - - - -
416D LEU* 4.1 8.5 - - + +
417D PRO* 3.0 24.8 - - - +
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Residues in contact with ILE 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351D PRO* 4.2 7.6 - - + +
354D VAL* 4.3 19.3 - - + -
355D VAL* 3.6 29.8 - - + -
358D VAL* 4.3 25.1 - - + -
359D LEU* 6.4 1.1 - - + -
410D LEU* 3.0 24.9 - - + +
411D ALA* 2.7 8.9 + - - +
413D VAL* 1.3 78.1 - - + +
415D TYR* 1.3 57.3 - - - +
417D PRO* 3.4 4.7 - - - +
418D PHE* 3.1 28.9 - - + -
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Residues in contact with TYR 415 (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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299D GLY* 3.8 13.7 - - - -
300D ALA* 4.1 19.3 - - + -
301D THR* 4.2 5.1 + - - -
303D ALA 5.4 0.2 - - - -
304D LEU* 3.5 61.6 - - + +
342D ILE* 5.5 0.6 - - + +
348D LEU* 4.6 7.2 - - + -
351D PRO* 3.3 43.7 + - + -
352D PHE* 3.2 28.3 - - - +
355D VAL* 4.4 9.6 - - + -
411D ALA* 2.8 21.2 + - + +
412D PHE* 4.6 4.0 - - + +
414D ILE* 1.3 78.9 - - - +
416D LEU* 1.3 67.2 + - - +
418D PHE* 2.8 18.4 + - - +
419D LEU* 2.9 11.6 + - + -
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Residues in contact with LEU 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D GLY* 5.4 0.2 - - - -
311D PHE* 4.2 38.8 - - + -
412D PHE* 3.6 34.0 + - + +
413D VAL* 4.1 7.2 - - + +
415D TYR* 1.3 75.1 - - - +
417D PRO* 1.3 63.1 - - + +
419D LEU* 3.0 23.8 + - + +
420D LYS* 2.7 41.3 + - + +
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Residues in contact with PRO 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D VAL 3.0 25.8 - - - +
414D ILE* 3.4 7.2 - - - +
415D TYR 3.3 4.7 - - - -
416D LEU* 1.3 90.2 - - + +
418D PHE* 1.3 72.1 + - + +
420D LYS* 3.6 6.2 + - + +
421D ILE* 3.3 25.7 + - - +
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Residues in contact with PHE 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU* 3.9 27.3 - - + +
348D LEU* 3.8 20.6 - - + -
350D ILE* 3.4 33.2 - - + -
351D PRO* 3.5 26.7 - - + -
414D ILE* 3.1 32.8 - - + -
415D TYR 2.8 7.6 + - - +
417D PRO* 1.3 79.2 - - + +
419D LEU* 1.3 67.3 + - - +
420D LYS 3.2 0.2 - - - -
421D ILE* 3.1 11.1 + - + +
422D TRP* 2.9 24.4 + - - +
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Residues in contact with LEU 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D LEU* 4.2 19.1 - - + +
307D GLY* 3.2 41.5 - - - +
308D MET* 3.5 28.9 - - + +
311D PHE* 4.9 5.2 - - + -
312D ALA* 5.0 3.6 - - + +
317D LEU* 4.1 14.1 - - + -
340D MET* 5.9 2.0 - - - -
348D LEU* 4.4 6.6 - - + +
415D TYR* 2.9 11.2 + - + +
416D LEU* 3.5 24.9 - - + +
418D PHE* 1.3 76.5 - - - +
420D LYS* 1.3 59.1 + - - +
422D TRP* 3.6 5.2 - - + +
423D ASP* 3.0 31.1 + - + +
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Residues in contact with LYS 420 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D LEU* 2.7 25.1 + - + +
417D PRO* 3.7 7.0 - - + +
419D LEU* 1.3 76.0 - - - +
421D ILE* 1.3 62.6 + - + +
423D ASP* 3.5 6.4 + - - +
424D LYS* 3.2 35.7 + - - +
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Residues in contact with ILE 421 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU* 3.6 31.4 - - + -
417D PRO 3.3 14.1 + - - +
418D PHE* 3.1 11.9 + - + +
420D LYS* 1.3 77.3 - - + +
422D TRP* 1.3 64.2 + - - +
424D LYS* 3.1 17.4 + - - +
425D GLN* 2.9 35.4 + - - +
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Residues in contact with TRP 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D LEU* 3.3 34.9 - - + +
340D MET* 3.5 39.3 + - + +
341D PRO* 4.1 9.2 - - + -
345D ASN* 3.6 38.8 - - - -
347D LEU* 4.4 14.4 - - + -
348D LEU* 4.3 7.9 - - + -
418D PHE 2.9 15.7 + - - +
419D LEU* 3.6 8.3 - - + +
421D ILE* 1.3 73.1 - - - +
423D ASP* 1.3 54.5 + - - +
424D LYS 2.7 4.7 + - - -
425D GLN* 2.5 49.5 + - - +
426D LYS* 2.9 47.0 + - + +
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Residues in contact with ASP 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311D PHE 3.5 5.8 - - - +
312D ALA* 3.2 14.9 - - - +
313D ARG* 2.5 32.5 + - - +
314D SER* 2.9 32.1 + - - -
317D LEU* 3.5 16.8 - - + +
419D LEU* 3.0 17.3 + - + +
420D LYS* 3.7 7.0 - - - +
422D TRP* 1.3 78.4 - - - +
424D LYS* 1.3 56.9 + - - +
425D GLN 3.4 0.4 - - - -
426D LYS* 3.8 3.8 - - - -
427D ILE* 2.9 28.6 + - - +
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Residues in contact with LYS 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420D LYS* 3.2 27.7 + - - +
421D ILE* 3.1 12.1 + - - +
422D TRP 2.7 3.4 + - - -
423D ASP* 1.3 74.2 - - - +
425D GLN* 1.3 61.6 + - - +
427D ILE* 3.3 26.4 - - + +
428D ALA* 3.9 6.9 - - - +
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Residues in contact with GLN 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU* 5.1 2.6 - - - +
421D ILE* 2.9 33.6 - - - +
422D TRP* 2.5 33.7 + - + +
424D LYS* 1.3 74.3 - - - +
426D LYS* 1.3 74.2 + - - +
427D ILE 3.5 0.2 - - - -
428D ALA* 3.3 7.3 + - - +
429D GLU* 3.3 25.8 + - - +
438D ASN 6.1 2.8 - - - -
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Residues in contact with LYS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D SER* 3.6 20.4 - - - +
316D GLN* 2.9 35.3 + - - +
317D LEU* 4.4 6.7 - - + -
340D MET 5.4 0.4 + - - -
341D PRO* 5.9 0.2 - - - +
422D TRP* 2.9 66.1 + - + +
423D ASP* 4.0 1.8 - - - +
425D GLN* 1.3 83.8 - - - +
427D ILE* 1.3 58.0 + - - +
428D ALA 3.0 5.2 - - - -
429D GLU* 3.5 27.0 + - - +
430D GLU* 2.8 35.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D ARG* 3.8 14.6 - - + +
314D SER* 3.4 34.8 - - - +
423D ASP 2.9 17.9 + - - +
424D LYS* 3.3 33.7 - - + +
426D LYS* 1.3 74.6 - - - +
428D ALA* 1.3 61.8 + - + +
430D GLU* 4.0 9.6 - - - +
431D LYS* 3.3 42.7 + - + +
----------------------------------------------------------
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Residues in contact with ALA 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424D LYS 3.9 13.0 - - - +
425D GLN* 3.3 12.1 + - - +
426D LYS 3.0 0.6 - - - -
427D ILE* 1.3 81.9 - - + +
429D GLU* 1.3 61.7 + - - +
430D GLU 3.1 1.3 - - - -
431D LYS* 3.6 3.4 + - - +
432D GLY 3.0 8.7 + - - -
433D GLU* 3.0 34.1 + - + +
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Residues in contact with GLU 429 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D GLN* 3.4 21.0 + - - +
425D GLN* 3.3 12.4 + - - +
426D LYS* 3.5 33.8 + - - +
428D ALA* 1.3 79.2 - - - +
430D GLU* 1.3 61.9 - - - +
432D GLY* 3.3 12.5 + - - +
433D GLU* 4.3 10.0 - - - +
434D ALA 6.0 1.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 430 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D SER* 3.5 10.2 - - - -
315D GLN* 2.8 32.0 + - - +
316D GLN* 2.7 53.2 + - + +
426D LYS 2.8 24.1 + - - +
427D ILE* 4.0 8.2 - - - +
429D GLU* 1.3 75.7 - - - +
431D LYS* 1.3 63.2 + - + +
432D GLY* 2.9 6.0 + - - -
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Residues in contact with LYS 431 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427D ILE* 3.3 32.2 + - + +
428D ALA* 4.2 3.1 - - - +
430D GLU* 1.3 78.8 - - + +
432D GLY* 1.3 59.9 + - - +
433D GLU 3.8 0.9 - - - -
----------------------------------------------------------
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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).
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