Contacts of the helix formed by residues 352 - 374 (chain B) in PDB entry 2QFZ
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 PRO 352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B TYR* 6.0 2.2 - - + +
350B GLY 3.7 7.8 - - - +
351B VAL* 1.4 90.4 - - + +
353B ALA* 1.3 60.5 + - - +
354B GLU* 3.3 5.6 - - + +
355B VAL* 3.2 23.5 + - + +
356B LEU* 3.0 24.3 + - - +
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Residues in contact with ALA 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL 3.7 1.7 + - - -
352B PRO* 1.3 71.2 - - - +
354B GLU* 1.3 60.5 + - - +
356B LEU* 3.3 11.1 + - - +
357B CYS* 3.0 37.1 + - - -
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PRO* 5.0 4.3 - - + -
353B ALA* 1.3 78.7 - - - +
355B VAL* 1.3 64.0 + - + +
357B CYS* 3.4 8.9 + - - +
358B ASN* 3.3 32.5 + - - +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B TYR* 3.6 43.3 - - + +
351B VAL* 4.1 9.9 - - + -
352B PRO* 3.2 25.8 + - + +
354B GLU* 1.3 77.9 - - + +
356B LEU* 1.3 63.6 + - - +
358B ASN* 3.3 11.5 + - + +
359B ILE* 3.1 36.5 + - + +
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Residues in contact with LEU 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LYS* 5.1 11.7 - - + -
301B ILE* 3.9 27.3 - - + +
330B PHE* 4.5 4.0 - - + -
334B ILE* 3.4 33.9 - - + -
348B VAL* 4.0 23.6 - - + +
351B VAL* 3.9 24.9 - - + +
352B PRO 3.0 7.7 + - - +
353B ALA* 3.5 14.1 - - - +
355B VAL* 1.3 77.9 - - - +
357B CYS* 1.3 57.2 + - - +
359B ILE* 3.5 5.5 + - + +
360B GLU* 3.0 27.3 + - - +
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Residues in contact with CYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PHE* 3.3 30.7 - - + -
261B ILE* 6.2 4.0 - - + -
304B ARG* 5.9 2.7 - - - -
353B ALA* 3.0 22.1 + - - -
354B GLU* 3.7 10.1 - - - +
355B VAL 3.3 0.2 - - - -
356B LEU* 1.3 73.9 - - - +
358B ASN* 1.3 62.3 + - - +
360B GLU* 3.3 14.5 + - - +
361B ALA 3.1 22.3 + - - -
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Residues in contact with ASN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLN* 3.6 29.9 + - - +
258B PHE* 3.5 21.7 - - - -
337B TYR* 6.2 0.4 - - - +
354B GLU* 3.3 20.3 + - - +
355B VAL* 3.3 13.9 + - + +
357B CYS* 1.3 74.7 - - - +
359B ILE* 1.3 59.6 + - + +
361B ALA* 3.3 3.0 + - - +
362B ASP* 2.9 37.1 + - - +
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Residues in contact with ILE 359 (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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330B PHE* 4.0 28.7 - - + -
333B PHE* 3.9 27.3 - - + +
334B ILE* 3.8 32.3 - - + +
337B TYR* 3.7 34.1 - - + -
351B VAL* 4.8 0.9 - - + -
355B VAL* 3.1 25.8 + - + +
356B LEU* 3.7 6.1 - - + +
358B ASN* 1.3 76.0 - - + +
360B GLU* 1.3 54.0 + - - +
362B ASP* 3.9 8.3 - - - +
363B THR* 2.6 38.4 + - - +
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Residues in contact with GLU 360 (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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257B TYR* 2.5 36.1 + - + +
261B ILE* 4.7 2.9 - - - +
301B ILE* 3.8 22.5 - - + +
304B ARG* 2.9 49.1 + - - +
305B ILE* 3.7 16.6 - - + +
330B PHE* 5.5 0.7 - - - -
356B LEU 3.0 13.6 + - - +
357B CYS* 3.5 15.2 - - - +
358B ASN 3.2 0.2 - - - -
359B ILE* 1.3 79.2 - - - +
361B ALA* 1.3 57.3 + - - +
363B THR* 3.4 8.0 + - - -
364B TYR* 2.9 27.2 + - - +
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Residues in contact with ALA 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B GLN* 3.9 31.9 - - + -
257B TYR* 3.7 27.1 - - + -
258B PHE* 4.1 3.8 - - + -
357B CYS 3.1 14.0 + - - +
358B ASN 3.4 8.3 - - - +
360B GLU* 1.3 73.8 - - - +
362B ASP* 1.3 66.0 + - - +
364B TYR* 3.2 3.5 + - - +
365B TRP* 3.1 30.9 + - + -
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Residues in contact with ASP 362 (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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233B LYS* 2.7 33.3 + - - +
238B TYR* 2.7 38.2 + - + -
250B LEU* 3.5 4.4 - - - +
254B GLN* 3.1 24.0 + - - +
333B PHE* 3.7 13.0 - - + +
358B ASN* 2.9 24.4 + - - +
359B ILE* 3.9 5.2 - - - +
361B ALA* 1.3 68.1 - - - +
363B THR* 1.3 66.0 + - - +
365B TRP* 3.4 1.0 + - - +
366B CYS* 3.0 29.8 + - - +
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Residues in contact with THR 363 (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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305B ILE* 3.8 22.0 - - + -
326B VAL* 3.9 22.7 - - + +
329B PHE* 3.8 18.7 - - + +
330B PHE* 3.7 17.1 - - + +
333B PHE* 3.7 18.1 - - - -
359B ILE* 2.6 25.1 + - - +
360B GLU* 3.5 5.6 - - - -
362B ASP* 1.3 76.7 - - - +
364B TYR* 1.3 63.1 + - - +
366B CYS* 4.1 0.2 - - - +
367B MET* 3.0 25.8 + - + +
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Residues in contact with TYR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B TYR* 3.6 30.3 - + + -
260B PHE* 3.9 10.1 - + - -
305B ILE* 3.8 27.1 - - + +
308B ILE* 3.8 10.8 - - + -
309B TRP* 3.7 33.9 - + + -
312B ARG* 3.8 21.8 + - - -
313B HIS* 4.0 17.0 - - - -
360B GLU 2.9 14.8 + - - +
361B ALA 3.2 8.0 + - - +
363B THR* 1.3 76.1 - - - +
365B TRP* 1.3 86.5 + + - +
367B MET* 3.9 3.1 - - + +
368B SER* 2.5 51.5 + - - -
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Residues in contact with TRP 365 (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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238B TYR* 3.4 43.5 - + + -
253B LYS* 2.8 33.1 + - + -
256B GLU* 3.5 38.6 - - + -
257B TYR* 3.8 9.2 - - + +
260B PHE* 3.6 30.7 - + - -
361B ALA 3.1 25.3 + - - +
362B ASP 4.1 0.2 - - - +
364B TYR* 1.3 97.3 - + - +
366B CYS* 1.3 61.5 + - - +
368B SER* 3.4 10.5 + - - -
369B LYS* 3.1 34.4 + - + +
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Residues in contact with CYS 366 (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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232B TRP 4.9 1.3 - - - -
233B LYS* 4.0 6.5 - - - -
236B SER* 4.0 13.6 - - - +
238B TYR* 3.7 35.0 - - - -
329B PHE* 3.5 36.5 - - + -
333B PHE* 3.8 17.7 - - + -
362B ASP 3.0 20.0 + - - +
363B THR 4.1 0.4 - - - +
365B TRP* 1.3 75.2 - - - +
367B MET* 1.3 63.7 + - - +
369B LYS* 3.3 13.9 + - - +
370B LEU* 3.3 9.5 + - - +
443B GLN* 5.4 0.2 + - - -
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Residues in contact with MET 367 (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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305B ILE* 3.9 20.4 - - + -
306B LEU* 4.3 7.6 - - + -
309B TRP* 3.9 35.9 - - + -
322B ILE 4.3 7.0 - - - +
325B LEU* 4.1 18.2 - - + +
326B VAL* 3.5 36.3 - - - -
329B PHE* 3.6 19.8 - - + -
363B THR* 3.0 18.6 + - + +
364B TYR* 4.0 4.7 - - + +
366B CYS* 1.3 76.0 - - - +
368B SER* 1.3 61.2 + - - +
370B LEU* 3.3 4.2 + - + +
371B LEU* 3.0 39.3 + - + +
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 3.6 31.2 + - - +
313B HIS* 4.8 5.0 + - - -
364B TYR* 2.5 35.0 + - - -
365B TRP* 3.5 17.0 - - - -
366B CYS 3.2 0.4 - - - -
367B MET* 1.3 78.8 - - - +
369B LYS* 1.3 57.2 + - - +
371B LEU* 3.8 1.8 - - - +
372B ASP* 3.0 35.7 + - - +
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Residues in contact with LYS 369 (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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236B SER* 3.2 27.5 + - - +
237B GLY* 3.5 31.9 + - - -
238B TYR* 3.8 11.2 - - + +
253B LYS* 4.6 8.8 - - - +
365B TRP* 3.1 21.5 + - + +
366B CYS* 3.8 8.7 - - - +
367B MET 3.3 0.6 - - - -
368B SER* 1.3 73.9 - - - +
370B LEU* 1.3 65.1 + - - +
372B ASP* 3.5 26.8 + - + +
373B GLY* 3.5 5.4 + - - -
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Residues in contact with LEU 370 (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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236B SER* 6.0 0.2 - - - -
325B LEU* 4.2 13.7 - - + -
329B PHE* 3.7 13.0 - - + -
366B CYS 3.3 9.2 + - - +
367B MET* 3.3 8.7 + - + +
369B LYS* 1.3 77.4 - - - +
371B LEU* 1.3 66.1 + - + +
373B GLY* 3.3 10.9 + - - -
374B ILE* 3.4 33.2 + - + +
425B LEU* 4.1 10.3 - - + -
439B TRP* 3.6 30.3 - - + -
443B GLN* 5.8 1.1 - - - +
449B PHE* 3.6 49.4 - - + +
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Residues in contact with LEU 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 3.6 44.1 - - + +
322B ILE* 3.9 23.1 - - + -
325B LEU* 3.7 27.4 - - + -
367B MET* 3.0 34.2 + - + +
368B SER 4.0 4.0 - - - +
369B LYS 3.3 0.2 - - - -
370B LEU* 1.3 77.4 - - + +
372B ASP* 1.3 63.6 + - - +
374B ILE* 3.2 16.6 + - + -
375B GLN* 3.4 17.2 + - - +
378B TYR* 3.8 27.5 - - + -
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B TRP* 6.0 0.2 + - - -
313B HIS* 4.8 13.7 + - - -
368B SER* 3.0 23.0 + - - +
369B LYS* 3.5 24.3 + - + +
370B LEU 3.3 0.6 - - - -
371B LEU* 1.3 75.4 - - - +
373B GLY* 1.3 59.5 + - - +
375B GLN* 3.4 28.7 - - - +
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Residues in contact with GLY 373 (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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369B LYS 3.5 5.1 + - - -
370B LEU 3.3 7.3 + - - -
371B LEU 3.1 0.6 - - - -
372B ASP* 1.3 80.4 - - - +
374B ILE* 1.3 61.1 + - - +
375B GLN 3.7 1.5 + - - -
450B SER* 3.5 20.6 + - - -
1005B UNX 4.4 11.7 - - - -
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Residues in contact with ILE 374 (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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325B LEU* 4.6 0.4 - - + -
370B LEU* 3.4 33.2 - - + +
371B LEU* 3.2 12.0 + - + -
373B GLY* 1.3 82.2 - - - +
375B GLN* 1.3 62.6 + - - +
376B ASP* 3.4 4.0 - - - -
377B ASN* 3.1 40.7 + - - +
378B TYR* 3.9 28.8 - - + +
388B LYS* 4.8 5.8 - - - +
425B LEU* 4.4 15.3 - - + -
449B PHE* 3.8 30.3 - - + +
450B SER* 3.9 13.7 - - - +
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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) + - + + + + + -
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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