Contacts of the helix formed by residues 348 - 369 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LEU* 5.7 3.6 - - + -
340C MET* 3.3 48.2 - - + -
341C PRO 4.4 0.9 - - - +
342C ILE* 3.7 19.0 - - + +
345C ASN* 2.8 25.1 - - - +
347C LEU* 1.3 79.4 - - + +
349C LEU* 1.3 61.4 + - - +
350C ILE 3.0 2.3 + - - -
351C PRO* 3.1 17.8 - - + +
352C PHE* 3.3 12.5 + - - +
415C TYR* 4.5 3.6 - - + -
418C PHE* 3.6 37.5 - - + +
419C LEU* 4.5 2.0 - - - +
422C TRP* 3.9 24.7 - - + -
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Residues in contact with LEU 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ARG* 5.3 9.6 - - + +
6C GLU* 5.2 5.4 - - - +
246C ALA* 3.9 25.6 - - + -
342C ILE* 3.5 15.1 - - - +
343C VAL 3.4 25.8 - - - +
344C MET* 5.6 2.2 - - - +
345C ASN 2.9 22.5 + - - +
346C PRO* 4.1 11.7 - - + +
347C LEU 2.9 0.4 + - - -
348C LEU* 1.3 78.1 - - - +
350C ILE* 1.3 60.2 + - + +
352C PHE* 3.1 28.8 - - + +
353C ILE* 3.2 30.9 + - + +
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Residues in contact with ILE 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C PRO 3.5 22.2 - - - +
347C LEU* 2.9 15.2 + - + +
348C LEU 3.0 0.8 - - - -
349C LEU* 1.3 74.4 - - + +
351C PRO* 1.3 64.7 - - + +
352C PHE 2.8 8.4 + - - -
353C ILE* 3.1 4.7 + - - +
354C VAL* 2.9 37.1 + - + +
418C PHE* 3.7 26.9 - - + -
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Residues in contact with PRO 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347C LEU 3.5 1.6 - - - +
348C LEU* 3.1 15.3 - - + +
350C ILE* 1.3 89.8 - - + +
352C PHE* 1.3 58.0 + - - -
354C VAL* 4.0 11.7 - - + -
355C VAL* 3.2 26.0 + - + +
356C PRO* 4.1 0.2 - - - +
414C ILE* 3.9 18.2 - - + +
415C TYR* 3.1 42.4 + - + -
418C PHE* 3.4 35.7 - - + -
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Residues in contact with PHE 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C HIS* 3.4 36.5 - + + -
245C TRP* 3.8 20.6 - + + -
298C SER* 3.2 37.9 - - - -
299C GLY* 3.6 13.7 - - - -
301C THR* 4.9 2.0 - - - -
333C ASN* 4.8 0.4 - - - -
337C THR* 3.9 14.8 - - + -
342C ILE* 3.6 24.7 - - + -
348C LEU 3.3 13.4 + - - +
349C LEU* 3.1 25.1 - - + +
350C ILE 2.8 0.6 - - - -
351C PRO* 1.3 79.3 - - - +
353C ILE* 1.3 69.0 + - + +
356C PRO* 2.9 26.0 - - - +
415C TYR* 3.6 12.3 - - - +
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Residues in contact with ILE 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ILE* 4.8 13.7 - - + +
242C HIS* 4.2 22.4 - - + +
243C VAL* 4.1 28.3 - - + -
246C ALA* 5.0 1.6 - - + -
349C LEU* 3.2 35.0 - - + +
350C ILE* 3.1 4.0 + - - +
352C PHE* 1.3 88.1 - - + +
354C VAL* 1.3 60.7 + - + +
356C PRO* 4.0 4.4 - - - +
357C VAL* 3.3 23.8 - - + +
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C ILE* 2.9 25.7 + - + +
351C PRO* 4.6 1.6 - - + -
353C ILE* 1.3 80.4 - - - +
355C VAL* 1.3 72.7 + - - +
356C PRO 3.2 1.3 - - - -
357C VAL* 3.0 13.2 + - + +
358C VAL* 3.0 34.7 + - + +
414C ILE* 3.8 28.0 - - + -
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Residues in contact with VAL 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C ALA* 3.3 34.3 - - + +
351C PRO* 3.2 18.7 + - + +
354C VAL* 1.3 77.8 - - - +
356C PRO* 1.3 61.1 - - + +
358C VAL* 3.3 7.0 - - + +
359C LEU* 2.6 49.7 + - + +
411C ALA* 3.8 17.0 - - + -
414C ILE* 3.9 29.8 - - + -
415C TYR* 4.4 13.5 - - + -
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Residues in contact with PRO 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C VAL* 3.6 17.0 - - + +
242C HIS* 3.1 31.6 - - + +
293C ILE* 4.0 13.4 - - + +
294C TYR* 6.2 0.2 - - + -
298C SER 4.0 3.6 - - - +
299C GLY* 4.0 9.4 - - - -
300C ALA 5.6 0.7 - - - +
351C PRO 4.1 0.4 - - - +
352C PHE 2.9 30.5 - - - +
353C ILE* 4.4 3.4 - - + +
354C VAL 3.4 2.7 - - - +
355C VAL* 1.3 95.5 - - + +
357C VAL* 1.3 57.2 + - + +
359C LEU* 3.3 4.1 + - + +
360C THR* 2.8 32.1 + - - -
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Residues in contact with VAL 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C VAL* 4.7 12.1 - - + -
238C VAL* 4.4 10.8 - - + +
239C ILE* 3.8 31.9 - - + -
353C ILE 3.3 20.2 - - - +
354C VAL* 3.0 21.6 + - + +
356C PRO* 1.3 74.6 - - + +
358C VAL* 1.3 71.7 + - + +
360C THR* 3.1 6.5 + - - -
361C ILE* 2.9 35.5 + - + +
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Residues in contact with VAL 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C VAL* 3.0 28.1 + - + +
355C VAL 3.3 9.2 - - - +
357C VAL* 1.3 81.3 - - + +
359C LEU* 1.3 73.2 + - + +
361C ILE* 3.3 15.8 - - + +
362C VAL* 2.9 35.6 + - + +
410C LEU* 4.4 11.2 - - + -
414C ILE* 3.8 25.4 - - + -
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Residues in contact with LEU 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C TRP 3.9 10.8 - - - +
293C ILE* 3.8 17.5 - - + +
295C MET* 4.5 3.8 - - - -
300C ALA* 4.0 24.0 - - + -
355C VAL* 2.6 28.8 + - + +
356C PRO* 3.6 6.3 - - + +
358C VAL* 1.3 80.6 - - + +
360C THR* 1.3 56.9 + - - +
362C VAL* 4.2 1.3 - - - +
363C SER* 2.7 34.8 + - - -
407C ASN* 3.2 49.1 - - + +
410C LEU* 3.9 27.6 - - + -
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Residues in contact with THR 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LEU* 4.4 7.4 - - + -
234C ALA* 4.5 9.6 - - + -
235C VAL* 3.6 33.0 - - + +
238C VAL* 3.6 18.0 - - + +
288C PHE* 4.1 8.3 - - + -
289C PHE* 4.7 0.9 - - - -
293C ILE* 3.0 26.8 - - - +
356C PRO 2.8 16.1 + - - -
357C VAL* 3.1 7.4 + - - -
359C LEU* 1.3 74.5 - - - +
361C ILE* 1.3 61.8 + - - +
362C VAL 3.1 1.3 - - - -
363C SER* 3.3 1.0 + - - -
364C TYR* 2.8 33.6 + - - +
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Residues in contact with ILE 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LEU* 4.6 12.6 - - + -
235C VAL* 3.7 26.7 - - + -
357C VAL* 2.9 28.0 + - + +
358C VAL* 3.3 17.9 - - + +
360C THR* 1.3 71.5 - - - +
362C VAL* 1.3 75.3 + - + +
364C TYR* 3.9 5.7 - - - +
365C PHE* 3.5 34.7 + - + -
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Residues in contact with VAL 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C VAL* 2.9 23.6 + - + +
359C LEU* 4.2 2.7 - - - +
361C ILE* 1.3 85.1 - - + +
363C SER* 1.3 70.6 + - - +
364C TYR 3.0 2.3 + - - -
365C PHE* 3.3 5.3 + - - +
366C ALA* 3.1 21.5 + - + +
403C LEU* 4.7 7.9 - - + -
406C VAL* 5.3 7.2 - - + -
407C ASN* 4.3 13.5 - - - +
410C LEU* 4.2 22.9 - - + -
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Residues in contact with SER 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C PHE* 3.7 20.0 - - - -
292C TRP* 4.1 1.0 + - - +
293C ILE* 3.9 8.8 - - - +
359C LEU 2.7 21.7 + - - -
360C THR 4.0 0.7 - - - -
362C VAL* 1.3 79.3 - - - +
364C TYR* 1.3 64.0 + - - +
366C ALA* 3.5 3.5 + - - +
367C MET* 3.4 24.4 + - - +
403C LEU* 3.8 22.2 - - - +
407C ASN* 3.0 27.5 + - - -
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Residues in contact with TYR 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C ALA 4.7 4.0 + - - -
230C SER* 5.4 0.7 - - - -
231C LEU* 3.4 51.0 + - + +
283C THR* 3.7 20.5 - - + +
284C ILE* 3.5 34.5 - - + -
288C PHE* 4.1 11.0 - - + -
360C THR 2.8 18.7 + - - +
361C ILE 3.9 2.9 - - - +
362C VAL 3.0 0.4 + - - -
363C SER* 1.3 79.1 - - - +
365C PHE* 1.3 92.3 + + - +
367C MET 3.4 4.0 + - - -
368C GLU* 3.2 37.0 + - + +
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Residues in contact with PHE 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C LEU* 4.2 14.8 - - + -
361C ILE* 3.5 20.1 + - + -
362C VAL* 3.3 6.7 + - - +
364C TYR* 1.3 102.0 - + - +
366C ALA* 1.3 52.3 + - - +
367C MET 2.6 13.0 + - - -
368C GLU* 2.6 7.1 + - + +
369C TRP* 2.6 80.2 + + + +
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Residues in contact with ALA 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C VAL* 3.1 13.2 + - + +
363C SER* 3.5 14.1 - - - +
364C TYR 3.4 0.2 - - - -
365C PHE* 1.3 76.3 - - - +
367C MET* 1.3 52.1 + - - +
369C TRP* 4.2 8.4 - - - +
371C LEU* 3.0 20.9 + - + -
372C VAL* 2.7 49.7 + - + -
403C LEU* 4.4 8.5 - - + -
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Residues in contact with MET 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C THR* 3.2 38.1 - - + +
288C PHE* 4.1 15.7 - - + -
292C TRP* 5.3 7.0 - - - -
363C SER 3.4 12.8 + - - +
364C TYR 3.9 0.9 - - - +
365C PHE 2.6 5.7 + - - -
366C ALA* 1.3 75.4 - - - +
368C GLU* 1.3 60.9 + - - +
370C GLY* 3.6 7.8 + - - -
372C VAL* 3.2 38.9 - - + +
373C ALA 3.8 6.5 - - - +
374C ARG* 3.3 30.7 + - + -
375C PRO* 3.3 35.4 - - + -
403C LEU* 4.8 7.4 - - + -
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Residues in contact with GLU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C THR* 2.7 24.4 + - - +
364C TYR* 3.2 46.1 + - + +
365C PHE* 2.6 12.4 + - + +
367C MET* 1.3 69.3 - - - +
369C TRP* 1.3 71.4 + - + +
370C GLY* 2.7 17.2 + - - -
374C ARG* 3.3 20.2 + - - +
1J GLC 4.4 9.5 + - - +
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Residues in contact with TRP 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C PHE* 2.6 63.8 + + + +
366C ALA* 4.3 1.3 - - - -
368C GLU* 1.3 82.0 - - + +
370C GLY* 1.3 54.6 + - - +
371C LEU* 2.9 38.0 + - + +
1J GLC 3.5 57.0 + - - -
2J GLC 3.9 48.0 + - - +
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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