Contacts of the helix formed by residues 348 - 369 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A LEU* 5.1 6.1 - - + -
340A MET* 3.5 50.3 - - + +
341A PRO 4.1 4.9 - - - +
342A ILE* 3.7 19.5 - - + +
345A ASN* 2.8 22.3 - - - +
347A LEU* 1.3 75.1 - - + +
349A LEU* 1.3 60.7 + - - +
350A ILE 3.2 0.4 - - - -
351A PRO* 3.2 11.7 - - + +
352A PHE* 3.1 23.0 + - - +
415A TYR* 4.5 2.4 - - + -
418A PHE* 4.7 12.1 - - + +
419A LEU* 5.0 2.5 - - - +
422A TRP* 3.9 37.2 - - + -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG 5.6 5.8 - - - +
6A GLU* 5.2 3.6 - - - +
246A ALA* 3.4 35.2 - - + +
342A ILE* 3.0 36.8 - - + +
343A VAL* 4.2 10.3 - - - +
344A MET* 4.7 4.7 - - - +
345A ASN 2.9 21.2 + - - +
346A PRO* 4.1 7.9 - - + -
347A LEU 2.8 2.0 + - - -
348A LEU* 1.3 78.0 - - - +
350A ILE* 1.3 66.9 + - + +
352A PHE* 3.8 15.9 - - + -
353A ILE* 3.1 32.4 + - + +
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PRO* 3.0 31.9 - - + +
347A LEU* 2.9 8.5 + - - +
349A LEU* 1.3 81.2 - - + +
351A PRO* 1.3 63.4 - - + +
353A ILE* 4.1 1.8 - - - +
354A VAL* 3.1 33.3 + - + +
418A PHE* 3.3 27.1 - - + -
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Residues in contact with PRO 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU 3.2 10.8 - - - +
348A LEU* 3.2 12.8 - - - +
350A ILE* 1.3 95.3 - - + +
352A PHE* 1.3 64.7 + - - +
354A VAL* 4.3 6.3 - - + +
355A VAL* 2.9 33.1 + - + +
414A ILE* 3.7 18.6 - - + +
415A TYR* 3.1 37.6 + - + -
418A PHE* 3.6 23.1 - - + -
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Residues in contact with PHE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A HIS* 3.6 36.9 - + + -
245A TRP* 3.8 19.7 - + + -
246A ALA 4.8 0.9 - - - -
298A SER* 3.2 42.2 - - - -
299A GLY* 4.1 3.2 - - - -
301A THR* 4.8 2.5 - - - -
337A THR* 4.2 12.6 - - + -
342A ILE* 3.7 26.9 - - + -
343A VAL* 6.6 0.2 - - - -
348A LEU 3.1 20.8 + - - +
349A LEU* 3.6 22.4 - - + +
350A ILE 3.3 0.2 - - - -
351A PRO* 1.3 77.7 - - - +
353A ILE* 1.3 61.9 + - + +
356A PRO* 3.1 24.9 - - - +
415A TYR* 3.1 21.1 + - - +
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Residues in contact with ILE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ILE* 5.2 13.1 - - + +
242A HIS* 4.2 23.6 - - + +
243A VAL* 3.5 36.6 - - + -
246A ALA* 4.9 6.5 - - + -
349A LEU* 3.1 25.1 + - + +
350A ILE* 4.2 2.0 - - - +
352A PHE* 1.3 81.8 - - + +
354A VAL* 1.3 70.9 + - + +
356A PRO* 3.6 8.3 - - - +
357A VAL* 3.5 16.0 + - + +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ILE* 3.1 23.9 + - + +
351A PRO* 4.3 1.8 - - + +
353A ILE* 1.3 76.2 - - + +
355A VAL* 1.3 74.9 + - + +
357A VAL* 2.8 26.7 + - + +
358A VAL* 2.8 27.8 + - + -
414A ILE* 4.1 21.8 - - + -
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A GLY 4.6 0.2 - - - +
300A ALA* 3.7 17.0 - - + -
351A PRO* 2.9 24.3 + - + +
354A VAL* 1.3 78.0 - - - +
356A PRO* 1.3 57.7 - - + +
358A VAL* 3.2 6.0 + - - +
359A LEU* 2.7 42.9 + - + +
411A ALA* 3.6 35.2 - - + +
414A ILE* 3.5 37.0 - - + -
415A TYR* 4.6 9.2 - - + -
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Residues in contact with PRO 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A VAL* 4.2 8.3 - - + +
242A HIS* 3.2 38.6 - - + +
293A ILE* 4.1 15.0 - - + +
299A GLY* 3.7 15.0 - - - -
300A ALA 4.9 0.7 - - - +
352A PHE 3.1 23.1 - - - +
353A ILE 3.6 4.5 - - - +
354A VAL 2.9 2.7 - - - -
355A VAL* 1.3 94.7 - - + +
357A VAL* 1.3 54.4 + - - +
359A LEU* 2.8 7.1 + - + +
360A THR* 2.7 38.0 + - - -
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A VAL* 4.0 31.6 - - + -
238A VAL* 4.5 6.6 - - + +
239A ILE* 4.4 22.2 - - + -
353A ILE* 3.5 15.4 + - + +
354A VAL* 2.8 36.1 + - + +
356A PRO* 1.3 75.0 - - - +
358A VAL* 1.3 57.9 + - + +
360A THR* 3.9 8.4 - - - -
361A ILE* 3.1 30.7 + - + +
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A VAL* 2.8 30.8 + - + +
355A VAL* 3.3 10.1 - - - +
356A PRO 2.9 0.4 + - - -
357A VAL* 1.3 74.4 - - + +
359A LEU* 1.3 65.4 + - + +
360A THR 2.8 15.0 + - - -
361A ILE* 2.8 18.3 + - - +
362A VAL* 3.0 27.7 + - + +
410A LEU* 4.6 9.2 - - + -
414A ILE* 4.4 17.7 - - + -
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A TRP 4.1 2.7 - - - +
293A ILE* 3.3 18.1 - - + +
295A MET* 3.4 32.8 - - + -
300A ALA* 4.2 17.5 - - + -
355A VAL* 2.7 30.4 + - + +
356A PRO* 2.8 5.6 + - + +
358A VAL* 1.3 75.8 - - + +
360A THR* 1.3 59.6 + - - +
362A VAL* 3.6 3.6 + - - -
363A SER* 2.8 30.5 + - - -
407A ASN* 3.0 40.2 - - + +
410A LEU* 4.0 20.0 - - + -
414A ILE* 6.1 0.2 - - + -
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Residues in contact with THR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 4.4 8.3 - - + -
234A ALA* 3.5 23.1 + - + +
235A VAL* 3.6 16.4 - - + -
238A VAL* 3.9 13.2 - - - +
288A PHE* 3.7 17.0 - - + -
289A PHE* 5.0 1.4 - - - -
293A ILE* 3.7 25.4 - - - +
356A PRO 2.7 20.2 + - - -
357A VAL* 3.9 9.4 - - - -
358A VAL 2.8 3.2 + - - -
359A LEU* 1.3 71.4 - - - +
361A ILE* 1.3 56.9 + - - +
363A SER 3.3 0.9 + - - -
364A TYR* 2.8 27.4 + - - +
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Residues in contact with ILE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 4.7 12.8 - - + -
235A VAL* 4.6 13.5 - - + -
357A VAL* 3.1 26.5 - - + +
358A VAL* 2.8 10.0 + - - +
360A THR* 1.3 67.9 - - - +
362A VAL* 1.3 55.2 + - + +
363A SER 2.7 15.6 + - - -
364A TYR* 4.3 5.2 - - - +
365A PHE* 3.1 55.2 + - + +
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A VAL* 3.0 31.0 + - + +
359A LEU* 4.1 4.5 - - - +
361A ILE* 1.3 75.8 - - + +
363A SER* 1.3 63.1 + - - +
365A PHE* 5.5 1.3 - - - -
366A ALA* 3.7 10.2 - - + +
403A LEU* 3.4 13.5 - - + +
406A VAL* 4.9 9.2 - - + -
407A ASN* 4.1 7.1 - - - +
410A LEU* 3.7 26.0 - - + -
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PHE* 3.7 17.9 - - - -
292A TRP* 5.1 0.4 - - - -
293A ILE* 4.1 5.0 - - - +
359A LEU 2.8 20.7 + - - -
360A THR 3.3 2.9 + - - -
361A ILE 2.7 1.2 + - - -
362A VAL* 1.3 79.3 + - - +
364A TYR* 1.3 61.2 + - - +
365A PHE 3.0 1.8 - - - -
366A ALA* 3.7 7.9 - - - -
367A MET* 2.9 35.7 + - - +
403A LEU* 3.2 15.1 - - - +
407A ASN* 3.0 24.9 + - - -
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Residues in contact with TYR 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ALA 3.9 13.2 + - - -
230A SER* 4.5 1.2 - - - -
231A LEU* 3.4 57.2 + - + +
283A THR* 3.9 19.1 - - + +
284A ILE* 3.4 37.5 - - + -
288A PHE* 3.9 8.5 - - + -
360A THR 2.8 17.6 + - - +
361A ILE* 3.2 3.1 + - - +
363A SER* 1.3 76.6 - - - +
365A PHE* 1.3 70.7 + + - +
367A MET* 4.1 0.7 - - - -
368A GLU* 3.0 40.5 + - + +
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Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 4.4 17.0 - - + -
361A ILE* 3.1 44.3 + - + +
362A VAL* 5.5 1.1 - - - -
364A TYR* 1.3 91.5 - + - +
366A ALA* 1.3 58.3 + - - +
367A MET 2.7 5.0 + - - -
368A GLU* 4.1 3.6 - - + +
369A TRP* 2.7 89.0 + + + +
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Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A VAL* 3.7 21.0 - - + +
363A SER* 3.5 6.9 + - - +
365A PHE* 1.3 77.7 - - - +
367A MET* 1.3 51.0 + - - +
369A TRP* 4.2 1.3 - - - -
371A LEU* 3.1 25.3 + - + +
372A VAL* 2.7 50.5 + - + -
403A LEU* 3.9 9.4 - - + -
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Residues in contact with MET 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A THR* 3.2 39.0 - - + +
288A PHE* 4.1 16.6 - - + -
292A TRP* 5.0 6.7 - - - -
363A SER 2.9 18.7 + - - +
365A PHE 2.7 1.6 + - - -
366A ALA* 1.3 77.2 - - - +
368A GLU* 1.3 65.0 + - - +
369A TRP 3.4 0.2 - - - -
370A GLY* 3.4 11.2 + - - -
372A VAL* 3.6 35.8 - - + +
373A ALA 4.0 8.1 - - - +
374A ARG* 3.5 26.6 + - + -
375A PRO* 3.3 36.6 - - + -
403A LEU* 4.7 7.9 - - + -
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Residues in contact with GLU 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A THR* 2.6 27.4 + - - +
364A TYR* 3.0 45.8 + - + +
365A PHE* 2.9 6.3 + - + +
367A MET* 1.3 73.0 - - - +
369A TRP* 1.3 74.6 + - + +
370A GLY* 2.8 14.9 + - - -
374A ARG* 3.1 20.2 + - - +
1F GLC 4.7 6.1 + - - -
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Residues in contact with TRP 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A PHE* 2.7 66.4 + + + +
366A ALA* 4.7 0.4 - - - -
368A GLU* 1.3 80.5 - - + +
370A GLY* 1.3 50.5 + - - +
371A LEU* 2.6 50.9 + - + +
1F GLC 3.5 60.4 + - - -
2F GLC 3.8 47.8 + - - +
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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
------------------------------------------------------------
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