Contacts of the helix formed by residues 402 - 425 (chain B) in PDB entry 1KNU
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 ASN 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B LEU* 5.2 0.2 - - - +
310B ASP* 5.4 6.1 - - + +
313B ASP* 3.0 13.7 + - - +
401B LEU* 1.3 81.5 - - + +
403B VAL* 1.3 60.9 + - - +
404B LYS* 3.6 6.6 + - - +
405B PRO* 2.9 44.5 - - + +
406B ILE* 3.6 13.5 - - - +
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Residues in contact with VAL 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLY* 3.7 27.8 - - - +
400B LEU* 4.0 24.7 - - + +
401B LEU 4.0 1.3 - - - -
402B ASN* 1.3 72.2 + - - +
404B LYS* 1.3 66.4 + - - +
405B PRO 3.5 0.2 - - - -
406B ILE* 3.2 8.8 + - - +
407B GLU* 3.1 43.3 + - + +
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Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ASN* 3.4 6.0 + - - +
403B VAL* 1.3 78.4 - - - +
405B PRO* 1.3 66.5 - - + +
407B GLU* 3.3 4.9 + - - +
408B ASP* 2.9 54.4 + - - +
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Residues in contact with PRO 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 3.7 22.4 - - + -
402B ASN* 2.9 50.0 - - + +
404B LYS* 1.3 86.6 - - + +
406B ILE* 1.3 61.9 + - - +
408B ASP* 3.5 11.9 - - + +
409B ILE* 3.0 32.3 + - + +
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Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 4.1 19.3 - - + -
313B ASP* 4.4 8.7 - - + +
317B LEU* 3.9 13.2 - - + -
393B LEU* 3.8 40.0 - - + +
394B SER 3.9 13.9 - - - +
395B GLY* 4.0 3.4 - - - +
400B LEU* 3.6 36.3 - - + -
402B ASN 3.6 19.3 - - - +
403B VAL* 3.2 9.6 + - - +
404B LYS 3.2 0.8 - - - -
405B PRO* 1.3 76.6 - - - +
407B GLU* 1.3 58.2 + - - +
409B ILE* 3.0 6.8 + - - +
410B GLN* 2.9 24.8 + - - +
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LYS* 3.8 27.9 - - - +
395B GLY* 4.0 22.4 + - - +
403B VAL* 3.1 35.1 + - + +
404B LYS* 4.0 4.0 - - - +
406B ILE* 1.3 72.4 - - - +
408B ASP* 1.3 61.5 + - - +
410B GLN* 3.7 14.3 + - - +
411B ASP* 2.8 30.7 + - - +
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Residues in contact with ASP 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LYS* 2.9 56.3 + - - +
405B PRO* 3.5 10.0 - - + +
406B ILE 3.2 0.2 - - - -
407B GLU* 1.3 75.4 - - - +
409B ILE* 1.3 61.2 + - + +
411B ASP* 2.9 26.6 + - - +
412B ASN* 3.2 8.3 + - - +
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Residues in contact with ILE 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B ILE* 4.6 2.9 - - + -
304B PRO 3.8 14.8 - - - +
305B GLY* 3.6 37.2 - - - +
306B PHE 4.2 1.3 - - - +
309B LEU* 4.4 12.8 - - + -
393B LEU* 3.6 27.1 - - + -
405B PRO* 3.0 17.6 + - + +
406B ILE 3.3 6.5 - - - +
408B ASP* 1.3 74.5 - - + +
410B GLN* 1.3 67.0 + - - +
412B ASN* 2.9 10.2 + - + +
413B LEU* 2.9 32.1 + - + +
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Residues in contact with GLN 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LYS* 5.4 8.9 - - - +
437A GLN* 4.3 18.3 + - - -
390B VAL* 3.2 40.0 - - + +
393B LEU* 3.0 30.3 + - + +
394B SER* 3.9 10.0 + - - -
395B GLY 4.8 6.9 - - - +
406B ILE 2.9 11.1 + - - +
407B GLU* 3.9 14.3 + - - +
409B ILE* 1.3 76.6 - - - +
411B ASP* 1.3 53.9 + - - +
413B LEU* 3.1 9.4 + - - +
414B LEU* 2.8 52.7 + - + +
439B MET* 4.9 0.2 - - - +
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Residues in contact with ASP 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER* 3.1 27.4 + - - +
430A GLN* 3.5 24.6 - - + +
407B GLU 2.8 14.2 + - - +
408B ASP* 2.9 18.2 - - - +
410B GLN* 1.3 78.6 - - - +
412B ASN* 1.3 62.4 + - - +
414B LEU* 3.3 4.9 + - - +
415B GLN* 3.1 39.0 + - - +
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Residues in contact with ASN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.3 24.2 - - - +
214B LEU* 3.8 17.1 - - + +
408B ASP 3.2 6.0 + - - +
409B ILE* 2.9 11.9 + - + +
411B ASP* 1.3 78.8 - - - +
413B LEU* 1.3 64.6 + - + +
415B GLN* 3.3 14.6 + - - +
416B ALA* 3.0 18.5 + - - +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.8 16.2 - - + -
218B LEU* 3.7 29.2 - - + -
303B ILE* 4.1 9.4 - - + -
304B PRO* 5.6 0.2 - - + -
386B ILE* 3.5 5.0 - - + +
389B ALA* 3.6 36.3 - - + +
390B VAL* 3.9 15.7 - - + +
393B LEU* 3.9 18.4 - - + -
409B ILE* 2.9 27.6 + - + +
410B GLN* 3.1 10.1 + - - +
412B ASN* 1.3 77.3 - - + +
414B LEU* 1.3 50.9 + - - +
416B ALA* 3.1 5.2 + - - +
417B LEU* 2.7 35.5 + - - +
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLN* 3.2 38.6 - - + +
433A ALA* 3.8 12.3 - - + -
434A LYS* 6.0 1.8 - - - +
437A GLN* 5.4 3.6 - - - +
390B VAL* 3.8 28.5 - - + -
410B GLN* 2.8 43.8 + - + +
411B ASP* 3.6 1.6 - - - +
413B LEU* 1.3 72.1 - - - +
415B GLN* 1.3 57.2 + - - +
417B LEU* 3.6 5.4 - - + +
418B GLU* 2.8 31.9 + - - +
432B PHE* 3.9 15.8 - - + -
436B LEU* 3.9 24.7 - - + -
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER* 4.7 9.5 - - - -
430A GLN* 3.8 16.8 - - - +
207B GLU* 5.1 10.8 + - - +
211B LEU* 3.9 20.6 - - + +
411B ASP* 3.1 31.0 + - - +
412B ASN* 3.5 31.3 - - - +
413B LEU 3.2 0.2 - - - -
414B LEU* 1.3 74.8 - - - +
416B ALA* 1.3 64.6 + - - +
418B GLU* 3.4 8.4 + - - +
419B LEU* 3.2 23.7 + - - +
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Residues in contact with ALA 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.7 29.7 - - + +
212B ARG* 4.8 2.1 + - - -
214B LEU* 3.8 23.1 - - + -
215B ALA* 5.0 0.8 - - - +
386B ILE* 3.9 14.0 - - + +
412B ASN 3.0 13.8 + - - +
413B LEU 3.5 7.4 - - - +
415B GLN* 1.3 77.2 - - - +
417B LEU* 1.3 62.3 + - - +
419B LEU* 3.4 2.3 + - - +
420B GLN* 3.0 24.9 + - - +
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Residues in contact with LEU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B ASP* 4.1 11.4 - - - +
386B ILE* 3.6 28.2 - - + +
387B PHE* 4.3 12.1 - - + +
390B VAL* 4.3 17.9 - - + -
413B LEU 2.7 20.9 + - - +
414B LEU* 3.6 9.4 - - + +
416B ALA* 1.3 74.5 - - - +
418B GLU* 1.3 61.5 + - - +
420B GLN* 3.3 2.2 + - + +
421B LEU* 3.0 45.7 + - + +
432B PHE* 3.9 22.9 - - + -
435B LEU* 4.0 26.0 - - + -
436B LEU* 5.4 3.6 - - + -
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 3.2 23.6 - - - +
422A LYS* 4.0 14.8 + - - -
430A GLN* 3.7 17.1 + - - -
414B LEU 2.8 20.2 + - - +
415B GLN* 3.7 8.5 - - - +
417B LEU* 1.3 74.5 - - - +
419B LEU* 1.3 61.3 + - - +
421B LEU* 3.6 3.1 + - - +
422B LYS* 3.2 48.3 + - - +
432B PHE* 3.4 41.3 - - + +
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B SER* 3.8 28.7 - - - +
211B LEU* 3.9 20.2 - - + -
212B ARG* 3.8 23.3 - - + -
415B GLN 3.2 16.4 + - - +
416B ALA 3.9 3.6 - - - +
418B GLU* 1.3 74.5 - - - +
420B GLN* 1.3 65.2 + - - +
422B LYS* 3.3 11.1 + - + +
423B LEU* 3.0 45.4 + - + +
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Residues in contact with GLN 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ARG* 2.7 47.3 + - - +
215B ALA* 4.2 5.4 - - - +
382B SER* 3.2 27.5 + - - +
383B ASP* 3.2 28.5 + - - +
386B ILE* 3.6 22.2 - - + -
416B ALA 3.0 18.4 + - - +
417B LEU* 3.5 5.6 - - + +
419B LEU* 1.3 77.4 - - - +
421B LEU* 1.3 58.2 + - + +
423B LEU* 3.4 1.5 + - - +
424B ASN* 2.7 54.4 + - - +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B LEU* 4.1 7.6 - - + -
383B ASP* 3.8 25.8 - - + +
417B LEU* 3.0 32.5 + - + +
418B GLU 3.9 3.6 - - - +
419B LEU 3.3 0.2 - - - -
420B GLN* 1.3 73.7 - - - +
422B LYS* 1.3 59.7 + - + +
425B HIS* 2.7 41.6 + - - +
428B SER 6.0 0.9 - - - -
431B LEU* 3.9 29.2 - - + -
432B PHE* 3.4 46.2 - - + +
435B LEU* 4.2 14.1 - - + -
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Residues in contact with LYS 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 5.3 8.4 + - - -
422A LYS* 6.0 3.6 - - - +
418B GLU* 3.2 38.4 + - + +
419B LEU* 3.3 12.8 + - + +
421B LEU* 1.3 77.5 - - + +
423B LEU* 1.3 59.8 + - + +
425B HIS 4.7 3.4 - - - -
426B PRO* 3.3 27.4 - - - +
429B SER* 5.1 25.8 - - - +
432B PHE* 6.4 2.5 - - + -
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ARG* 3.8 33.9 - - + +
419B LEU* 3.0 40.2 + - + +
420B GLN* 3.9 3.1 - - - +
422B LYS* 1.3 80.3 - - + +
424B ASN* 1.3 58.6 + - - +
425B HIS 3.3 0.4 - - - -
426B PRO* 3.2 17.4 - - - +
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Residues in contact with ASN 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ASP* 2.7 31.3 + - - +
382B SER* 4.8 0.9 - - - -
383B ASP* 3.1 19.5 + - - +
420B GLN* 2.7 36.7 + - - +
423B LEU* 1.3 74.3 - - + +
425B HIS* 1.3 81.1 + - - +
426B PRO* 3.6 3.5 - - - +
427B GLU* 5.0 0.3 - - - +
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Residues in contact with HIS 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU 4.7 4.5 - - - -
378B GLU* 3.3 25.9 + - + -
379B LEU* 4.4 2.0 - - + -
380B ASP* 5.0 1.4 + - - -
383B ASP* 3.0 32.1 + - - -
421B LEU* 2.7 23.9 + - - +
422B LYS* 3.9 2.0 - - - +
424B ASN* 1.3 102.6 + - - +
426B PRO* 1.3 67.9 - - - +
427B GLU* 3.0 18.5 + - - +
428B SER* 3.1 29.0 + - - +
429B SER* 5.0 0.7 - - - -
431B LEU* 3.6 28.3 - - + +
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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) + - + + + + + -
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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