Contacts of the helix formed by residues 400 - 430 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TRP* 3.1 24.2 + - - -
372B VAL* 4.0 9.4 - - - -
390B GLY 4.1 7.9 - - - -
394B SER* 3.7 16.1 + - - -
397B LYS 3.0 10.5 + - - -
398B ILE 2.8 1.2 - - - -
399B SER* 1.3 79.0 + - - +
401B VAL* 1.3 64.0 + - - +
402B ILE 3.3 1.3 - - - -
403B LEU 3.4 7.1 + - - -
404B GLN* 3.4 7.3 + - - +
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.6 31.9 - - + +
391B TYR* 3.6 37.7 - - + +
398B ILE* 3.0 24.0 + - + +
400B GLY* 1.3 77.4 - - - +
402B ILE* 1.3 57.8 + - + +
404B GLN* 3.3 11.9 + - - +
405B LEU* 3.1 36.0 + - + +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LEU* 4.9 7.0 - - + +
372B VAL* 4.6 10.3 - - + -
398B ILE* 3.7 20.4 - - + +
399B SER* 3.4 21.3 - - - +
401B VAL* 1.3 74.8 - - + +
403B LEU* 1.3 70.1 + - - +
405B LEU* 4.0 13.9 - - + +
406B VAL* 3.0 33.6 + - + +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TRP* 3.4 22.0 - - + +
362B VAL* 4.2 7.4 - - + -
363B SER* 3.9 37.5 - - - +
366B ALA* 4.0 13.0 - - + -
367B MET* 4.5 5.4 - - + -
372B VAL* 3.6 33.4 - - + -
400B GLY 3.4 10.4 + - - +
401B VAL 3.3 0.4 - - - -
402B ILE* 1.3 83.0 - - - +
404B GLN* 1.3 57.5 + - - +
406B VAL* 3.3 9.7 - - + +
407B ASN* 2.8 53.3 + - - +
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Residues in contact with GLN 404 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU 2.7 27.1 + - - +
292B TRP* 3.6 16.9 - - + +
295B MET* 4.1 14.2 - - - +
386B ILE* 2.5 32.0 + - + +
387B LEU* 3.9 8.6 - - + +
389B SER* 2.8 22.8 + - - -
390B GLY* 3.1 26.5 + - - +
400B GLY 3.4 3.4 + - - +
401B VAL* 3.3 9.1 + - - +
402B ILE 3.2 0.4 - - - -
403B LEU* 1.3 73.3 - - - +
405B LEU* 1.3 58.0 + - - +
406B VAL 2.9 1.1 - - - -
407B ASN* 2.8 6.4 + - - +
408B PHE* 2.6 37.0 + - - +
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Residues in contact with LEU 405 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 3.8 28.9 - - + -
401B VAL* 3.1 28.0 + - + +
402B ILE* 4.0 14.4 - - + +
404B GLN* 1.3 76.0 - - - +
406B VAL* 1.3 60.7 - - + +
408B PHE* 3.7 17.4 - - + +
409B ALA* 3.2 23.0 + - - +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B VAL* 4.5 13.7 - - + -
402B ILE* 3.0 29.3 + - + +
403B LEU* 3.3 12.1 - - + +
404B GLN 2.9 0.6 - - - -
405B LEU* 1.3 75.6 - - + +
407B ASN* 1.3 68.7 + - - +
409B ALA* 3.3 7.2 + - - +
410B LEU* 2.9 36.3 + - + +
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Residues in contact with ASN 407 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TRP* 3.3 15.5 + - - +
295B MET* 3.3 17.7 - - + -
359B LEU* 3.1 30.2 - - + +
362B VAL* 3.7 19.1 - - - +
363B SER* 3.1 24.8 + - - -
403B LEU* 2.8 34.9 + - - +
404B GLN* 2.8 10.0 + - - +
406B VAL* 1.3 70.2 - - - +
408B PHE* 1.3 65.1 + - - +
410B LEU* 3.0 3.9 + - - +
411B ALA* 2.8 25.5 + - - +
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Residues in contact with PHE 408 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 3.4 9.6 - - + +
302B LEU* 4.5 13.7 - - + -
303B ALA* 3.5 35.0 - - + -
306B VAL* 4.1 26.2 - - + -
386B ILE* 4.5 22.0 - - + -
404B GLN 2.6 20.8 + - - +
405B LEU* 3.7 20.0 - - + +
407B ASN* 1.3 72.3 - - - +
409B ALA* 1.3 57.4 + - - +
411B ALA* 3.8 2.4 - - - +
412B PHE* 2.8 34.6 + + + +
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B LEU 3.2 15.9 + - - +
406B VAL* 3.5 7.0 - - - +
407B ASN 3.2 0.4 - - - -
408B PHE* 1.3 76.6 - - - +
410B LEU* 1.3 67.7 + - + +
412B PHE* 3.4 8.9 + - - +
413B VAL* 3.1 30.8 + - + +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 4.4 15.0 - - + -
359B LEU* 4.2 15.9 - - + -
362B VAL* 3.7 34.5 - - + -
406B VAL* 2.9 23.9 + - + +
407B ASN 3.0 8.0 + - - +
409B ALA* 1.3 77.0 - - + +
411B ALA* 1.3 58.0 + - - +
413B VAL* 3.0 19.0 - - + +
414B ILE* 2.9 28.3 - - + +
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Residues in contact with ALA 411 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA* 3.2 36.1 - - + -
303B ALA* 3.9 8.5 - - + -
355B VAL* 3.6 17.7 - - + -
359B LEU* 4.4 1.5 - - + +
407B ASN 2.8 17.8 + - - +
408B PHE* 3.8 3.8 - - - +
410B LEU* 1.3 68.8 - - - +
412B PHE* 1.3 60.2 + - - +
413B VAL 2.8 11.4 + - - -
414B ILE* 2.9 13.3 + - - +
415B TYR* 3.0 19.3 + - + +
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Residues in contact with PHE 412 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ALA* 3.5 27.5 - - + +
304B LEU* 5.8 0.2 - - - -
306B VAL* 4.4 8.5 - - + -
307B GLY* 3.7 28.0 - - - -
310B LEU* 4.2 22.7 - - + -
311B PHE* 4.2 14.8 - + - -
408B PHE* 2.8 26.9 + + + +
409B ALA* 3.4 8.3 + - - +
411B ALA* 1.3 75.6 - - - +
413B VAL* 1.3 63.5 + - + +
415B TYR* 5.0 1.6 - - + -
416B LEU* 3.3 36.7 + - + +
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Residues in contact with VAL 413 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ALA* 3.1 15.7 - - + +
410B LEU* 3.0 28.9 - - + +
411B ALA 2.9 0.4 - - - -
412B PHE* 1.3 88.8 - - + +
414B ILE* 1.3 64.1 + - + +
415B TYR 3.3 1.3 - - - -
416B LEU* 4.2 5.8 - - + +
417B PRO* 3.0 23.7 - - - +
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Residues in contact with ILE 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B PRO* 4.6 6.5 - - + -
354B VAL* 4.2 20.0 - - + -
355B VAL* 3.6 29.6 - - + -
358B VAL* 4.1 27.8 - - + -
410B LEU* 2.9 22.7 - - + +
411B ALA* 2.9 1.6 + - - +
413B VAL* 1.3 80.3 - - + +
415B TYR* 1.3 61.9 + - - +
417B PRO* 3.4 7.8 - - - +
418B PHE* 3.0 33.2 - - + -
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Residues in contact with TYR 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B GLY* 3.3 25.1 - - - -
300B ALA* 3.7 26.0 + - + -
301B THR* 4.1 2.2 + - - -
303B ALA* 4.6 1.1 - - + -
304B LEU* 3.6 61.5 - - + +
342B ILE* 5.8 1.1 - - + -
348B LEU* 4.9 3.8 - - + -
351B PRO* 3.4 43.8 + - + -
352B PHE* 3.5 19.3 - - + -
355B VAL* 4.4 5.8 - - + -
411B ALA 3.0 22.1 + - - +
412B PHE* 4.8 2.7 - - + +
414B ILE* 1.3 77.3 - - - +
416B LEU* 1.3 55.3 + - - +
418B PHE* 2.6 31.9 + - + +
419B LEU* 3.1 11.1 + - + -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY 4.5 0.4 - - - +
311B PHE* 4.1 42.4 - - + -
412B PHE* 3.3 41.9 + - + +
413B VAL* 4.2 6.1 - - + +
415B TYR* 1.3 76.2 - - - +
417B PRO* 1.3 63.7 - - + +
419B LEU* 3.2 23.7 + - + +
420B LYS* 3.0 50.7 + - + +
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Residues in contact with PRO 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B VAL 3.0 24.0 - - - +
414B ILE* 3.4 9.6 - - - +
415B TYR 3.2 3.6 - - - +
416B LEU* 1.3 90.3 - - + +
418B PHE* 1.3 67.5 + - + +
420B LYS* 3.6 16.9 + - + +
421B ILE* 3.1 31.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.7 36.8 - - + +
348B LEU* 4.6 9.0 - - + +
350B ILE* 3.5 29.8 - - + -
351B PRO* 3.6 40.4 - - + -
414B ILE* 3.0 32.8 - - + -
415B TYR* 2.6 14.0 + - + +
417B PRO* 1.3 79.7 - - + +
419B LEU* 1.3 59.1 + - - +
421B ILE* 3.3 14.3 + - + +
422B TRP* 3.3 16.8 + - - +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 3.9 30.1 - - + -
307B GLY* 3.2 43.3 - - - +
308B MET* 4.4 9.0 - - + -
311B PHE* 5.2 2.7 - - + +
312B ALA* 4.8 4.0 - - + +
317B LEU* 4.4 18.2 - - + -
340B MET* 5.8 1.6 - - + -
348B LEU* 4.8 5.3 - - + +
415B TYR* 3.1 6.8 + - + +
416B LEU* 3.7 25.1 - - + +
418B PHE* 1.3 74.0 - - - +
420B LYS* 1.3 65.2 + - + +
422B TRP* 3.1 8.0 + - + +
423B ASP* 2.8 36.1 + - + +
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Residues in contact with LYS 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PHE* 4.4 23.6 - - + +
416B LEU* 3.0 47.9 + - + +
417B PRO* 3.6 17.2 - - + +
419B LEU* 1.3 80.3 - - + +
421B ILE* 1.3 57.6 + - + +
423B ASP* 3.4 6.1 + - - +
424B LYS* 3.0 52.3 + - - +
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Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 3.4 28.3 - - + -
417B PRO* 3.1 23.1 - - + +
418B PHE* 3.3 15.9 + - + +
419B LEU 3.2 0.4 - - - -
420B LYS* 1.3 76.4 - - + +
422B TRP* 1.3 60.2 + - - +
424B LYS* 4.1 7.6 - - - +
425B GLN* 3.4 30.8 + - + +
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Residues in contact with TRP 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B LEU* 3.7 31.9 - - + +
340B MET* 3.5 27.1 + - + +
341B PRO* 4.2 7.6 - - + -
345B ASN* 3.6 31.0 - - - -
347B LEU* 4.4 13.5 - - + -
348B LEU* 3.5 26.6 - - + +
418B PHE 3.3 10.8 + - - +
419B LEU* 3.1 12.5 + - - +
421B ILE* 1.3 74.9 - - - +
423B ASP* 1.3 58.5 + - - +
424B LYS 3.0 1.1 - - - -
425B GLN* 2.7 51.7 + - - +
426B LYS* 2.7 49.6 + - + +
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Residues in contact with ASP 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PHE 4.2 2.9 - - - +
312B ALA* 3.1 28.1 - - - +
313B ARG* 2.6 33.0 + - - +
314B SER* 3.1 21.7 + - - -
317B LEU* 3.3 15.0 - - + +
419B LEU* 2.8 23.4 + - + +
420B LYS* 3.7 7.2 - - - +
422B TRP* 1.3 72.3 - - - +
424B LYS* 1.3 58.9 + - + +
426B LYS* 3.2 4.5 + - - +
427B ILE* 2.8 30.8 + - - +
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Residues in contact with LYS 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B LYS* 3.0 36.7 + - - +
421B ILE* 4.2 7.9 - - - +
422B TRP 3.0 1.0 - - - -
423B ASP* 1.3 75.7 - - + +
425B GLN* 1.3 63.9 + - - +
427B ILE* 3.3 13.2 - - + +
428B ALA* 3.3 21.1 + - - +
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Residues in contact with GLN 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU* 4.9 6.5 - - - +
421B ILE* 3.4 25.0 + - + +
422B TRP* 2.7 40.6 + - + +
424B LYS* 1.3 75.1 - - - +
426B LYS* 1.3 64.0 + - + +
428B ALA* 3.3 18.7 - - - +
429B GLU* 3.4 13.2 + - - +
----------------------------------------------------------
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Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B SER* 3.8 15.5 - - - +
316B GLN* 3.2 34.4 + - - +
317B LEU* 4.7 3.8 - - + -
340B MET 4.5 2.0 + - - -
341B PRO* 5.6 1.6 - - - +
422B TRP* 2.7 67.6 + - + +
423B ASP* 3.5 9.2 - - - +
425B GLN* 1.3 78.0 - - - +
427B ILE* 1.3 66.0 + - - +
428B ALA 3.0 1.6 - - - -
429B GLU* 3.4 26.4 + - - +
430B GLU* 3.0 33.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ARG* 5.0 16.2 - - + +
314B SER* 3.9 17.2 - - - +
423B ASP* 2.8 22.8 + - - +
424B LYS* 3.3 24.2 - - + +
426B LYS* 1.3 72.7 - - - +
428B ALA* 1.3 61.3 + - - +
430B GLU* 3.4 9.8 + - + +
431B LYS* 3.2 35.1 + - + +
----------------------------------------------------------
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B LYS 3.3 14.2 + - - +
425B GLN* 3.3 14.4 - - - +
426B LYS 3.0 0.2 - - - -
427B ILE* 1.3 78.7 - - - +
429B GLU* 1.3 58.3 + - - +
431B LYS* 3.1 23.3 + - - +
433B GLU* 3.4 38.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B GLN* 3.8 16.8 + - - +
425B GLN 3.6 10.7 - - - +
426B LYS* 3.5 37.6 + - - +
428B ALA* 1.3 78.4 - - - +
430B GLU* 1.3 57.1 + - + +
431B LYS 3.1 1.8 - - - -
432B GLY* 2.9 17.9 + - - -
433B GLU* 4.2 10.1 - - - +
434B ALA 5.4 2.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B SER* 3.5 12.4 - - - -
315B GLN* 3.0 44.2 + - - +
316B GLN* 2.7 49.6 + - - +
426B LYS* 3.0 21.9 + - - +
427B ILE* 3.7 11.3 - - + +
428B ALA 3.1 0.4 - - - -
429B GLU* 1.3 77.5 - - + +
431B LYS* 1.3 60.4 + - + +
432B GLY 3.3 1.5 + - - -
----------------------------------------------------------
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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