Contacts of the helix formed by residues 345 - 369 (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 ASN 345 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG* 5.0 3.4 - - - +
341B PRO* 2.9 19.5 + - + +
342B ILE* 3.0 16.4 + - - +
343B VAL 4.0 2.9 - - - +
344B MET* 1.3 75.7 - - - +
346B PRO* 1.3 62.5 - - - +
347B LEU* 3.4 9.9 + - - +
348B LEU* 2.8 41.2 + - - +
349B LEU* 2.7 40.3 + - - +
422B TRP* 3.6 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG* 4.5 26.4 - - + +
4B PHE* 5.6 10.3 - - + -
344B MET 3.2 11.6 - - - +
345B ASN* 1.3 88.8 - - - +
347B LEU* 1.3 66.2 + - - +
349B LEU* 3.4 11.6 + - + +
350B ILE* 3.7 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ASN* 3.4 7.2 + - - +
346B PRO* 1.3 82.6 - - - +
348B LEU* 1.3 65.0 + - + +
350B ILE* 3.3 16.7 + - + +
351B PRO* 3.5 8.5 - - - +
418B PHE* 3.7 39.8 - - + +
421B ILE* 3.4 38.1 - - + +
422B TRP* 4.4 22.4 - - + +
425B GLN* 4.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU* 5.1 8.3 - - + -
340B MET* 3.3 35.9 - - + -
341B PRO 3.6 4.3 - - - +
342B ILE* 4.1 14.8 - - + +
345B ASN* 2.8 31.9 + - - +
347B LEU* 1.3 77.2 - - + +
349B LEU* 1.3 64.5 + - - +
350B ILE 3.1 2.5 - - - -
351B PRO* 3.1 21.6 - - + +
352B PHE* 3.3 12.3 + - - +
415B TYR* 4.9 2.4 - - + -
418B PHE* 4.6 25.1 - - + +
419B LEU* 4.8 4.5 - - + -
422B TRP* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG 5.6 4.3 - - - +
246B ALA* 3.7 33.2 - - + +
342B ILE* 3.3 21.1 - - + +
344B MET* 4.0 9.9 - - - +
345B ASN 2.7 35.6 + - - +
346B PRO* 3.7 7.4 - - + +
347B LEU 3.2 0.4 - - - -
348B LEU* 1.3 72.6 - - - +
350B ILE* 1.3 66.7 + - + +
352B PHE* 3.4 29.2 + - + +
353B ILE* 3.2 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B PRO 3.7 11.4 - - - +
347B LEU* 3.5 13.5 - - + +
348B LEU 3.1 0.6 - - - -
349B LEU* 1.3 83.6 - - + +
351B PRO* 1.3 65.3 - - + +
353B ILE* 3.3 5.3 + - + +
354B VAL* 3.0 37.1 + - + +
418B PHE* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B LEU 3.5 8.1 - - - +
348B LEU* 3.1 21.8 - - + +
350B ILE* 1.3 94.6 - - + +
352B PHE* 1.3 55.2 - - - +
353B ILE 3.3 0.2 - - - -
354B VAL* 3.9 9.0 - - + -
355B VAL* 2.9 41.6 + - + +
414B ILE* 4.3 3.8 - - + +
415B TYR* 3.4 31.2 + - + -
418B PHE* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B HIS* 3.4 42.3 - - + -
245B TRP* 3.7 20.4 - + + -
246B ALA 4.6 0.7 - - - -
298B SER* 3.4 32.3 - - - -
299B GLY* 3.6 13.8 - - - -
301B THR* 5.0 0.4 - - - -
333B ASN* 4.8 0.2 - - - -
337B THR* 3.9 17.3 - - + -
342B ILE* 3.5 24.7 - - + -
348B LEU 3.3 16.7 + - - +
349B LEU* 3.5 24.7 - - + +
350B ILE 3.1 0.6 - - - -
351B PRO* 1.3 80.7 - - - +
353B ILE* 1.3 60.0 + - + +
356B PRO* 3.3 15.8 - - - +
415B TYR* 3.5 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 5.4 0.2 - - - +
239B ILE* 4.9 14.4 - - + +
242B HIS* 4.5 18.2 - - + +
243B VAL* 3.5 34.3 - - + -
246B ALA* 5.3 2.0 - - + -
349B LEU* 3.2 27.1 + - + +
350B ILE* 4.0 4.0 - - + +
352B PHE* 1.3 83.2 - - + +
354B VAL* 1.3 68.5 + - + +
355B VAL 3.4 0.2 - - - -
356B PRO* 3.0 12.9 - - - +
357B VAL* 3.5 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B ILE* 3.0 27.2 + - + +
351B PRO* 4.3 2.7 - - + +
353B ILE* 1.3 79.8 - - + +
355B VAL* 1.3 69.4 + - - +
357B VAL* 3.1 14.6 + - + +
358B VAL* 3.0 29.1 + - + -
414B ILE* 4.2 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ALA* 3.4 35.2 - - + +
351B PRO* 2.9 28.1 + - + +
354B VAL* 1.3 79.7 - - - +
356B PRO* 1.3 60.6 - - + +
358B VAL* 3.5 2.0 + - - +
359B LEU* 2.9 32.8 + - + +
411B ALA* 3.6 14.4 - - + -
414B ILE* 3.6 41.7 - - + -
415B TYR* 4.4 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 3.4 21.8 - - + -
242B HIS* 3.1 33.2 - - + +
293B ILE* 4.0 12.8 - - + +
298B SER 4.2 2.9 - - - +
299B GLY* 4.4 9.9 - - - -
352B PHE 3.3 11.4 - - - +
353B ILE 3.0 13.0 - - - +
355B VAL* 1.3 93.4 - - + +
357B VAL* 1.3 54.6 + - - +
359B LEU* 3.5 7.8 - - + +
360B THR* 2.7 40.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B VAL* 5.1 11.2 - - + -
238B VAL* 4.6 5.8 - - + -
239B ILE* 3.4 41.7 - - + -
353B ILE* 3.5 17.0 - - + +
354B VAL* 3.1 18.5 + - + +
356B PRO* 1.3 75.2 - - - +
358B VAL* 1.3 70.0 + - + +
360B THR* 2.9 6.7 + - - -
361B ILE* 2.9 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B VAL* 3.0 22.1 + - + +
355B VAL 3.9 3.1 - - - +
357B VAL* 1.3 90.5 - - + +
359B LEU* 1.3 60.6 + - + +
361B ILE* 4.4 7.7 - - + +
362B VAL* 3.2 28.3 + - + +
410B LEU* 4.4 18.8 - - + -
414B ILE* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TRP 4.4 7.2 - - - +
293B ILE* 4.0 17.2 - - + +
295B MET* 4.0 15.0 - - + -
300B ALA* 3.7 29.4 - - + -
355B VAL* 2.9 30.2 + - + +
356B PRO* 3.1 6.3 + - + +
358B VAL* 1.3 77.4 - - + +
360B THR* 1.3 60.7 + - - +
362B VAL* 4.6 1.1 - - - -
363B SER* 2.5 35.1 + - - -
407B ASN* 3.1 45.5 - - + +
410B LEU* 4.2 16.8 - - + -
411B ALA 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 4.6 5.8 - - + -
234B ALA* 4.0 29.4 - - + +
235B VAL* 4.2 17.3 - - + -
238B VAL* 3.5 17.6 - - + +
288B PHE* 4.1 9.7 - - + -
293B ILE* 3.4 19.8 - - - +
356B PRO 2.7 23.7 + - - -
357B VAL* 2.9 7.6 + - - -
359B LEU* 1.3 73.1 - - - +
361B ILE* 1.3 59.3 + - - +
363B SER* 3.3 0.5 + - - -
364B TYR* 2.7 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 361 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 4.9 11.7 - - + -
235B VAL* 4.3 19.1 - - + -
357B VAL* 2.9 26.1 + - + +
358B VAL* 4.4 8.3 - - + +
360B THR* 1.3 78.6 - - - +
362B VAL* 1.3 68.8 + - + +
364B TYR* 3.3 6.4 + - - +
365B PHE* 3.1 43.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 362 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 3.2 23.6 + - + +
359B LEU 4.3 1.8 - - - +
360B THR 3.3 0.2 - - - -
361B ILE* 1.3 83.5 - - + +
363B SER* 1.3 67.1 + - - +
365B PHE* 3.2 4.3 + - - +
366B ALA* 3.0 21.6 + - + +
403B LEU* 4.2 8.5 - - + -
406B VAL* 4.5 7.4 - - + -
407B ASN* 3.7 20.0 - - - +
410B LEU* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 363 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B PHE* 3.9 18.8 - - - -
292B TRP* 3.4 10.2 + - - -
293B ILE* 4.3 1.1 - - - -
359B LEU 2.5 25.1 + - - -
360B THR 3.8 1.6 - - - -
362B VAL* 1.3 77.8 - - - +
364B TYR* 1.3 65.8 + - - +
366B ALA* 3.4 2.1 + - - +
367B MET* 3.2 25.1 + - - +
403B LEU* 3.9 22.2 - - - -
407B ASN* 3.1 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ALA 4.3 9.2 + - - -
231B LEU* 3.4 49.3 + - + +
283B THR* 3.9 13.4 - - + +
284B ILE* 3.5 32.8 - - + -
288B PHE* 3.8 11.1 - + + -
360B THR 2.7 22.6 + - - +
361B ILE 3.3 4.0 - - - +
363B SER* 1.3 75.2 - - - +
365B PHE* 1.3 102.0 + + - +
367B MET* 3.2 11.6 + - - +
368B GLU* 3.3 35.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 3.9 17.3 - - + -
361B ILE* 3.1 34.0 + - + +
362B VAL* 3.9 3.6 - - - +
364B TYR* 1.3 104.0 - + - +
366B ALA* 1.3 69.5 + - - +
367B MET 2.9 2.0 - - - -
368B GLU* 2.7 17.9 + - + +
369B TRP* 2.9 63.8 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B VAL* 3.0 14.2 + - + +
363B SER 3.6 9.0 - - - +
365B PHE* 1.3 76.2 - - - +
367B MET* 1.3 57.9 + - - +
369B TRP* 4.0 0.8 - - - -
370B GLY 3.2 0.9 + - - -
371B LEU* 3.0 29.9 + - + +
372B VAL* 3.0 47.2 + - + -
403B LEU* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B THR* 3.3 28.3 - - + +
288B PHE* 3.6 17.3 - - + -
292B TRP* 5.1 9.0 - - + -
363B SER 3.2 15.7 - - - +
364B TYR 3.2 5.3 + - - +
365B PHE 2.7 4.2 + - - -
366B ALA* 1.3 73.8 - - - +
368B GLU* 1.3 62.4 + - - +
370B GLY* 3.4 10.2 + - - -
372B VAL* 3.1 19.9 - - + +
373B ALA 3.4 11.9 - - - +
374B ARG* 3.3 36.3 + - + -
375B PRO* 3.1 42.0 - - + -
403B LEU* 4.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B THR* 3.1 14.1 + - - +
364B TYR* 3.7 44.5 + - + +
365B PHE* 2.7 12.0 + - - +
367B MET* 1.3 69.2 - - - +
369B TRP* 1.3 71.9 + - + +
370B GLY* 2.6 16.0 + - - -
374B ARG* 2.9 29.2 + - - -
1H GLC 4.8 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B PHE* 2.9 62.0 + + + +
366B ALA 4.8 0.4 - - - -
368B GLU* 1.3 82.7 - - + +
370B GLY* 1.3 59.4 + - - +
371B LEU* 3.2 38.2 + - + +
1H GLC 3.7 58.0 + - - -
2H GLC 4.1 45.4 + - - +
----------------------------------------------------------
Back to top of page
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