Contacts of the helix formed by residues 348 - 369 (chain D) 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 LEU 348 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304D LEU* 5.0 6.5 - - + -
340D MET* 3.1 48.2 - - + -
342D ILE* 4.1 14.1 - - + +
345D ASN* 3.2 24.1 + - + +
347D LEU* 1.3 80.2 - - + +
349D LEU* 1.3 60.5 + - - +
350D ILE 3.1 0.2 - - - -
351D PRO* 3.2 18.0 - - + +
352D PHE* 3.3 15.0 + - - +
415D TYR* 4.6 8.2 - - + -
418D PHE* 3.8 35.7 - - + +
419D LEU* 4.4 5.8 - - + +
422D TRP* 4.3 15.9 - - + -
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLU* 5.5 3.1 - - - +
246D ALA* 3.4 34.5 - - + -
342D ILE* 3.4 19.5 - - + +
344D MET* 3.8 23.8 - - - +
345D ASN 2.5 26.4 + - - +
346D PRO* 4.1 7.6 - - + -
347D LEU 2.9 0.2 + - - -
348D LEU* 1.3 73.3 - - - +
350D ILE* 1.3 66.1 + - + +
352D PHE* 3.2 31.9 + - + +
353D ILE* 3.2 34.5 + - + +
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Residues in contact with ILE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D PRO* 3.0 27.1 - - + +
347D LEU* 2.8 10.7 + - + +
349D LEU* 1.3 81.9 - - + +
351D PRO* 1.3 65.0 - - + +
353D ILE* 3.6 4.1 + - - +
354D VAL* 3.3 27.0 + - + +
418D PHE* 3.4 29.8 - - + -
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Residues in contact with PRO 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU 3.3 7.6 - - - +
348D LEU* 3.2 11.7 - - + +
350D ILE* 1.3 99.9 - - + +
352D PHE* 1.3 57.9 - - - -
354D VAL* 4.3 7.6 - - + -
355D VAL* 2.9 33.8 + - + +
414D ILE* 4.2 9.4 - - + +
415D TYR* 3.3 34.0 + - + -
418D PHE* 3.5 37.5 - - + -
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Residues in contact with PHE 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242D HIS* 3.2 32.2 - + + -
245D TRP* 3.5 34.1 - + + -
246D ALA 4.4 0.7 - - - -
298D SER* 2.9 44.3 - - - +
299D GLY* 3.7 4.4 - - - -
301D THR* 5.0 1.6 - - - -
337D THR* 4.3 12.8 - - + -
342D ILE* 3.7 23.6 - - + -
348D LEU 3.3 14.0 + - - +
349D LEU* 3.2 33.6 + - + +
351D PRO* 1.3 78.3 - - - +
353D ILE* 1.3 58.9 + - + +
356D PRO* 3.1 18.4 - - - +
415D TYR* 3.2 21.6 + - + +
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Residues in contact with ILE 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238D VAL* 5.4 0.7 - - - +
239D ILE* 4.9 18.2 - - + +
242D HIS* 4.4 21.2 - - + +
243D VAL* 4.2 30.5 - - + -
246D ALA* 5.3 2.9 - - + -
349D LEU* 3.2 25.9 + - + +
350D ILE* 4.2 3.4 - - - +
352D PHE* 1.3 82.6 - - + +
354D VAL* 1.3 67.9 + - + +
356D PRO* 3.1 15.9 - - - +
357D VAL* 3.8 9.1 + - + +
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Residues in contact with VAL 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350D ILE* 3.3 21.8 + - + +
351D PRO* 4.2 3.4 - - + +
353D ILE* 1.3 78.9 - - + +
355D VAL* 1.3 73.3 + - - +
356D PRO 2.9 1.7 - - - -
357D VAL* 2.9 25.6 + - + +
358D VAL* 3.0 25.9 + - + -
414D ILE* 4.3 22.4 - - + -
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Residues in contact with VAL 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D ALA* 3.6 20.0 - - + +
351D PRO* 2.9 22.8 + - + +
354D VAL* 1.3 75.9 - - - +
356D PRO* 1.3 65.8 - - + +
358D VAL* 3.4 5.5 - - - +
359D LEU* 3.0 29.5 + - + +
411D ALA* 3.4 32.1 - - + -
414D ILE* 3.6 38.1 - - + -
415D TYR* 4.4 14.6 - - + -
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Residues in contact with PRO 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D VAL* 3.2 23.8 - - + -
242D HIS* 3.1 35.2 - - + +
293D ILE* 4.1 12.0 - - + +
298D SER 4.1 3.6 - - - +
299D GLY* 4.6 6.7 - - - -
300D ALA 5.3 0.4 - - - +
352D PHE 3.1 15.0 - - - +
353D ILE 3.1 7.9 - - - +
354D VAL 2.9 0.4 - - - -
355D VAL* 1.3 93.2 - - + +
357D VAL* 1.3 53.8 + - - +
359D LEU* 2.6 30.4 + - + +
360D THR* 2.7 19.2 + - - -
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Residues in contact with VAL 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235D VAL* 4.4 14.1 - - + +
238D VAL* 4.5 8.5 - - + -
239D ILE* 3.5 35.4 - - + -
353D ILE* 3.8 13.9 - - + +
354D VAL* 2.9 21.3 + - + +
356D PRO* 1.3 73.3 - - - +
358D VAL* 1.3 71.0 + - + +
360D THR* 3.9 8.7 - - - -
361D ILE* 3.0 41.3 + - + +
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Residues in contact with VAL 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354D VAL* 3.0 31.9 + - + +
355D VAL 3.4 4.7 - - - +
356D PRO 3.0 0.2 + - - -
357D VAL* 1.3 83.1 - - + +
359D LEU* 1.3 70.5 + - - +
361D ILE* 4.8 8.1 - - + -
362D VAL* 4.0 21.3 - - + +
410D LEU* 4.7 10.9 - - + +
414D ILE* 4.3 18.4 - - + -
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Residues in contact with LEU 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D TRP 3.6 16.2 - - - +
293D ILE* 4.0 19.6 - - + +
295D MET* 4.4 5.6 - - + -
300D ALA* 4.6 9.2 - - + -
355D VAL* 3.0 21.5 - - + +
356D PRO* 2.6 17.5 + - + +
357D VAL 3.0 0.2 - - - -
358D VAL* 1.3 83.8 - - - +
360D THR* 1.3 62.4 + - - +
361D ILE 3.6 0.2 - - - -
362D VAL* 3.9 3.1 - - - +
363D SER* 2.8 36.3 + - - -
407D ASN* 3.2 50.0 - - + +
410D LEU* 4.2 15.7 - - + -
411D ALA 5.0 0.7 - - - +
414D ILE* 6.4 1.1 - - + -
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Residues in contact with THR 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LEU* 4.3 7.6 - - + -
234D ALA* 4.0 19.5 - - + +
235D VAL* 3.8 22.9 - - + -
238D VAL* 3.5 25.8 - - - +
288D PHE* 3.9 20.9 - - + -
293D ILE* 3.7 11.9 - - - +
356D PRO 2.7 14.8 + - - -
357D VAL* 3.9 3.6 - - - -
359D LEU* 1.3 74.0 - - - +
361D ILE* 1.3 59.9 + - - +
362D VAL 3.0 0.5 + - - -
363D SER 3.0 1.0 + - - -
364D TYR* 2.6 35.4 + - - +
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Residues in contact with ILE 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LEU* 4.4 17.7 - - + -
235D VAL* 4.4 16.8 - - + -
357D VAL* 3.0 23.3 + - + +
358D VAL* 4.8 6.5 - - + -
360D THR* 1.3 80.1 - - - +
362D VAL* 1.3 72.3 + - + +
364D TYR* 3.8 5.3 + - - +
365D PHE* 3.3 34.3 + - + -
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Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D VAL* 4.0 26.9 - - + +
359D LEU* 3.9 6.2 - - - +
360D THR 3.1 0.8 - - - -
361D ILE* 1.3 84.1 - - + +
363D SER* 1.3 68.8 + - - +
364D TYR 3.3 0.5 + - - -
365D PHE* 3.4 3.7 + - - +
366D ALA* 3.1 21.0 + - + +
403D LEU* 4.5 8.7 - - + -
406D VAL* 4.7 5.2 - - + -
407D ASN* 4.3 7.9 - - - +
410D LEU* 4.2 25.4 - - + -
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Residues in contact with SER 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D PHE* 4.1 16.4 - - - -
292D TRP* 4.2 6.0 + - - +
293D ILE* 4.5 4.3 - - - -
359D LEU 2.8 24.6 + - - -
360D THR 3.9 0.7 - - - -
362D VAL* 1.3 75.6 - - - +
364D TYR* 1.3 64.4 + - - +
366D ALA* 3.5 1.8 + - - +
367D MET* 3.2 25.8 + - - +
403D LEU* 3.6 24.8 - - - +
407D ASN* 3.2 27.2 + - - -
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Residues in contact with TYR 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ALA 4.2 13.1 + - - -
230D SER* 5.3 0.5 - - - -
231D LEU* 3.1 56.0 + - + +
283D THR* 3.8 9.8 - - + +
284D ILE* 3.8 21.3 - - + -
288D PHE* 3.9 12.5 - - + -
360D THR 2.6 22.5 + - - +
361D ILE 3.8 3.8 - - - +
363D SER* 1.3 74.6 - - - +
365D PHE* 1.3 90.8 + + - +
367D MET* 3.2 5.2 + - - +
368D GLU* 3.0 54.0 + - + +
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Residues in contact with PHE 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D LEU* 3.8 20.0 - - + -
361D ILE* 3.3 31.4 - - + +
362D VAL* 3.4 4.7 + - - +
363D SER 3.3 0.4 - - - -
364D TYR* 1.3 101.0 - + - +
366D ALA* 1.3 54.5 + - - +
367D MET 2.5 17.4 + - - -
368D GLU* 2.6 14.4 + - + +
369D TRP* 2.8 64.0 + + + +
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Residues in contact with ALA 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D VAL* 3.1 13.6 + - + +
363D SER 3.7 9.9 - - - +
365D PHE* 1.3 77.4 - - - +
367D MET* 1.3 52.6 + - - +
369D TRP* 4.8 1.9 - - - -
371D LEU* 3.1 24.4 + - + -
372D VAL* 2.6 54.6 + - + -
403D LEU* 4.1 13.7 - - + -
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Residues in contact with MET 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D THR* 3.5 27.8 - - + +
288D PHE* 3.9 16.8 - - + -
292D TRP* 5.3 10.3 - - + -
363D SER 3.2 14.6 - - - +
364D TYR 3.2 2.1 + - - +
365D PHE 2.5 5.5 + - - -
366D ALA* 1.3 77.3 - - - +
368D GLU* 1.3 61.8 + - - +
370D GLY* 3.5 9.8 + - - -
372D VAL* 3.3 17.9 - - + +
373D ALA 3.1 24.5 - - - +
374D ARG* 3.3 29.5 + - + -
375D PRO* 3.1 39.3 - - + -
403D LEU* 4.5 9.9 - - + -
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Residues in contact with GLU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D THR* 2.9 21.8 + - - +
364D TYR* 3.0 51.1 + - + +
365D PHE* 2.6 13.2 + - + +
367D MET* 1.3 69.1 - - - +
369D TRP* 1.3 70.3 + - + +
370D GLY* 2.7 17.1 + - - -
374D ARG* 3.3 16.1 + - - +
1L GLC 5.0 4.4 + - - -
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Residues in contact with TRP 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D PHE* 2.8 62.7 + + + +
366D ALA* 4.8 0.9 - - - -
368D GLU* 1.3 83.1 - - + +
370D GLY* 1.3 59.1 + - - +
371D LEU* 3.1 28.0 + - + +
1L GLC 3.4 60.3 + - - -
2L GLC 4.0 50.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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