Contacts of the helix formed by residues 393 - 416 (chain B) in PDB entry 1KKQ
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 393 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B LEU* 5.8 2.5 - - + -
301B ASP* 4.3 10.9 - - - +
304B ASP* 3.4 14.3 + - - +
392B LEU* 1.3 100.0 - - - +
394B VAL* 1.3 59.5 + - - +
395B GLY 3.0 7.2 + - - -
396B HIS* 3.0 18.4 + - + +
397B ILE* 3.2 20.2 + - + +
204D LYS* 5.5 4.6 - - - +
411D HIS* 3.1 19.0 - - - +
414D SER* 4.2 4.8 + - - -
415D ASN* 2.9 31.8 + - - +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY* 3.1 29.2 - - - +
388B ARG 4.5 2.9 - - - +
391B LEU* 3.7 33.5 - - + +
392B LEU 3.6 4.2 + - - -
393B ASN* 1.3 73.9 - - - +
395B GLY* 1.3 62.8 + - - +
397B ILE* 4.1 3.6 - - - +
398B GLU* 3.3 33.9 + - - +
371D ASP* 3.9 23.2 + - + +
415D ASN* 3.6 0.8 + - - -
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Residues in contact with GLY 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ASN 3.0 1.6 + - - -
394B VAL* 1.3 81.2 - - - +
396B HIS* 1.3 66.7 + - - +
398B GLU* 3.2 16.7 + - - +
399B LYS* 3.2 15.1 + - - +
371D ASP* 4.4 4.2 + - - -
415D ASN* 3.2 31.9 + - - +
416D HIS* 5.8 0.7 - - - -
417D PRO* 5.7 0.2 - - - +
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Residues in contact with HIS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLY 4.6 11.4 - - - -
299B ASN* 5.2 7.6 + - + -
300B LEU* 3.8 26.5 - - + +
393B ASN* 3.0 13.7 + - + +
395B GLY* 1.3 78.1 - - - +
397B ILE* 1.3 61.8 + - + +
399B LYS* 3.2 13.9 + - + +
400B MET* 3.1 24.9 + - + +
414D SER* 3.0 34.9 + - - +
415D ASN* 3.5 13.4 + - - +
417D PRO* 6.2 0.9 - - + -
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Residues in contact with ILE 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU* 4.0 18.4 - - + -
304B ASP* 4.3 13.5 - - + +
308B LEU* 3.8 23.8 - - + -
384B CYS* 4.1 11.7 - - + -
385B CYS 3.9 25.6 - - - +
386B GLY* 4.6 2.9 - - - -
391B LEU* 3.5 38.1 - - + -
393B ASN* 3.2 14.7 + - + +
394B VAL 4.4 4.0 - - - +
396B HIS* 1.3 76.5 - - + +
398B GLU* 1.3 58.5 + - - +
400B MET* 3.0 12.5 + - + +
401B GLN* 2.9 28.1 + - - +
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B GLY* 4.7 19.8 - - - +
394B VAL* 3.3 27.8 + - - +
395B GLY* 3.2 10.0 + - - +
396B HIS 3.1 0.8 - - - -
397B ILE* 1.3 80.7 - - - +
399B LYS* 1.3 55.7 + - - +
401B GLN* 4.0 12.5 - - - +
402B GLU* 3.0 28.3 + - - +
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Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B GLY 3.2 8.2 + - - +
396B HIS* 3.2 17.1 + - + +
398B GLU* 1.3 76.5 - - - +
400B MET* 1.3 63.9 + - - +
401B GLN 3.4 0.2 - - - -
402B GLU* 3.7 26.2 - - - +
403B GLY* 3.4 14.6 + - - -
417D PRO* 4.3 28.2 - - + +
418D ASP* 4.3 20.9 - - - +
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Residues in contact with MET 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 5.7 0.2 - - - +
294B ILE* 4.4 3.6 - - + -
295B PRO 3.6 12.6 - - - +
296B GLY* 3.4 17.9 - - - +
297B PHE* 3.4 39.9 - - + +
300B LEU* 4.4 17.5 - - + -
308B LEU* 5.8 0.2 - - + -
384B CYS* 3.6 27.8 - - + -
396B HIS* 3.1 21.6 + - - +
397B ILE* 3.1 14.4 - - + +
399B LYS* 1.3 77.6 - - - +
401B GLN* 1.3 62.5 + - - +
403B GLY* 3.3 9.2 + - - -
404B ILE* 3.3 17.6 + - + +
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Residues in contact with GLN 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ALA* 3.2 19.0 + - - +
384B CYS 2.7 24.0 - - - +
385B CYS* 3.1 31.7 - - - +
386B GLY 4.3 3.6 + - - -
387B ASP* 5.3 2.7 + - - +
397B ILE 2.9 11.5 + - - +
398B GLU* 4.2 10.8 - - - +
400B MET* 1.3 72.1 - - - +
402B GLU* 1.3 65.0 + - - +
403B GLY 2.8 6.1 - - - -
404B ILE* 4.1 8.5 - - - +
405B VAL* 2.8 42.1 + - + +
430B MET* 5.7 4.8 - - - +
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU 3.0 22.0 + - - +
399B LYS* 3.7 26.8 - - - +
400B MET 3.3 0.2 - - - -
401B GLN* 1.3 78.7 + - - +
403B GLY* 1.3 57.4 + - - +
405B VAL* 4.2 6.0 - - - +
406B HIS* 3.5 22.9 + - - +
409B ARG* 5.5 1.0 + - - -
418D ASP* 5.1 5.4 - - - +
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Residues in contact with GLY 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 4.2 16.7 - - - +
206B LEU* 3.4 18.0 - - - +
399B LYS 3.4 7.4 + - - -
400B MET 3.3 8.5 + - - -
401B GLN 2.8 0.8 - - - -
402B GLU* 1.3 80.0 - - - +
404B ILE* 1.3 65.4 + - - +
405B VAL 3.3 0.4 - - - -
406B HIS* 3.8 6.1 - - - +
407B VAL* 3.4 15.4 + - - +
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Residues in contact with ILE 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 4.0 12.3 - - + -
210B ILE* 4.4 15.5 - - + -
294B ILE* 4.4 9.6 - - + -
377B LEU* 3.8 25.9 - - + +
380B ALA* 3.8 31.0 - - + +
381B ALA* 3.8 13.7 - - + +
384B CYS* 3.8 25.8 - - + -
400B MET* 3.3 18.1 + - + +
401B GLN* 2.9 8.4 + - - +
403B GLY* 1.3 76.5 - - - +
405B VAL* 1.3 59.1 + - - +
407B VAL* 3.2 8.2 + - - +
408B LEU* 3.0 24.5 + - + +
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Residues in contact with VAL 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ALA* 3.8 26.0 - - + -
401B GLN* 2.8 28.4 + - + +
402B GLU* 4.4 5.4 - - - +
404B ILE* 1.3 76.4 - - - +
406B HIS* 1.3 59.0 + - - +
408B LEU* 3.5 13.7 - - + +
409B ARG* 3.1 36.7 + - - +
423B PHE* 3.8 23.2 - - + -
427B LEU* 5.5 0.7 - - + -
430B MET* 5.2 10.3 - - + -
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Residues in contact with HIS 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B THR* 6.4 1.1 - - - -
203B LEU* 3.9 25.7 - - + +
402B GLU 3.5 18.5 + - - +
403B GLY* 4.0 6.7 - - - +
404B ILE 3.2 0.8 - - - -
405B VAL* 1.3 73.8 - - - +
407B VAL* 1.3 68.1 + - + +
408B LEU 2.9 5.5 + - - -
409B ARG* 3.3 34.0 + - - +
410B LEU* 3.2 52.3 + - + +
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Residues in contact with VAL 407 (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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203B LEU* 3.2 35.4 - - + +
204B LYS 5.6 0.4 - - - +
206B LEU* 3.9 15.5 - - + -
207B ALA* 3.5 32.8 - - + +
210B ILE* 5.8 0.4 - - + -
377B LEU* 4.0 11.7 - - + -
403B GLY 3.4 7.5 + - - +
404B ILE* 3.2 10.2 + - - +
406B HIS* 1.3 83.1 + - + +
408B LEU* 1.3 55.7 - - - +
410B LEU* 4.0 5.1 - - + +
411B HIS* 3.1 26.7 + - - +
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Residues in contact with LEU 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B ASP* 4.6 6.7 - - - +
377B LEU* 3.8 37.0 - - + +
378B PHE* 4.6 17.7 - - + +
381B ALA* 4.9 2.7 - - + -
404B ILE 3.0 12.7 + - - +
405B VAL* 3.5 20.2 - - + +
406B HIS 2.9 0.6 - - - -
407B VAL* 1.3 77.0 - - - +
409B ARG* 1.3 66.8 + - - +
410B LEU 3.0 1.5 + - - -
411B HIS* 3.2 1.3 + - + -
412B LEU* 2.9 50.6 + - + +
423B PHE* 4.1 23.1 - - + -
426B LEU* 4.7 13.0 - - + -
427B LEU* 5.8 1.6 - - + -
430B MET* 5.9 1.6 - - - -
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Residues in contact with ARG 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B GLU 5.5 1.4 + - - -
405B VAL* 3.1 29.6 + - - +
406B HIS* 3.4 39.1 - - - +
408B LEU* 1.3 78.6 - - - +
410B LEU* 1.3 64.2 + - + +
412B LEU* 3.4 3.5 + - - +
413B GLN* 2.8 38.6 + - + +
423B PHE* 3.8 47.1 - - + +
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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
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406B HIS* 3.2 43.0 + - + +
407B VAL* 4.0 5.8 - - + +
408B LEU 3.1 0.8 - - - -
409B ARG* 1.3 83.8 - - + +
411B HIS* 1.3 58.5 + - - +
412B LEU 2.8 10.9 + - - -
413B GLN* 2.9 32.2 + - - +
414B SER* 3.1 17.9 + - - -
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Residues in contact with HIS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA* 4.9 11.0 - - + -
373B SER* 2.8 40.8 + - - -
374B ASP* 2.9 23.9 + - - +
377B LEU* 3.9 20.7 - - + +
407B VAL 3.1 17.9 + - - +
408B LEU 3.2 2.4 + - - +
410B LEU* 1.3 77.6 - - - +
412B LEU* 1.3 57.5 + - - +
414B SER* 4.1 4.9 - - - -
415B ASN* 3.1 45.7 + - - +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 4.7 0.4 - - + -
374B ASP* 3.5 34.1 - - + +
408B LEU* 2.9 33.6 + - + +
409B ARG 3.6 3.8 - - - +
410B LEU 2.8 0.8 + - - -
411B HIS* 1.3 78.4 - - - +
413B GLN* 1.3 68.6 + - - +
414B SER 3.3 0.9 - - - -
415B ASN* 4.5 0.9 - - - +
416B HIS* 3.2 26.5 + - + +
419B ASP 5.3 0.5 - - - +
422B LEU* 3.7 39.4 - - + +
423B PHE* 4.1 19.7 - - + +
426B LEU* 3.3 29.4 - - + -
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Residues in contact with GLN 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B ARG* 2.8 24.7 + - + +
410B LEU* 2.9 26.1 + - - +
412B LEU* 1.3 80.4 - - - +
414B SER* 1.3 64.8 + - - +
416B HIS 3.5 1.1 - - - +
417B PRO* 3.3 22.9 - - - +
419B ASP 6.1 0.2 - - - -
420B ILE 6.0 2.2 - - - +
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Residues in contact with SER 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B LEU 3.1 13.1 + - - -
411B HIS* 3.8 4.2 + - - -
413B GLN* 1.3 82.5 - - - +
415B ASN* 1.3 67.1 + - - +
417B PRO* 3.2 21.9 - - - +
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Residues in contact with ASN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ASP* 5.4 4.9 + - - -
373B SER* 5.2 2.0 + - - -
411B HIS* 3.1 44.5 + - + +
414B SER* 1.3 82.8 + - - +
416B HIS* 1.3 76.7 + - + +
417B PRO* 3.2 10.6 - - - +
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Residues in contact with HIS 416 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B LEU 4.1 4.4 + - - -
369B GLU* 3.2 27.6 + - - +
370B LEU* 3.8 9.4 - - + -
371B ASP* 4.0 7.6 + - + -
374B ASP* 2.8 30.8 + - - -
412B LEU* 3.2 10.3 + - - +
413B GLN 3.5 5.2 - - - +
415B ASN* 1.3 99.1 + - + +
417B PRO* 1.3 61.3 - - - +
418B ASP* 3.1 5.6 - - - +
419B ASP* 3.1 28.1 + - + +
420B ILE* 4.9 0.2 - - - -
422B LEU* 3.5 28.7 - - + +
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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