Contacts of the helix formed by residues 231 - 248 (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 231 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C ALA 3.8 0.8 + - - -
230C SER* 1.3 70.5 + - - +
232C TRP* 1.3 62.0 + - + +
234C ALA* 3.0 5.9 + - + +
235C VAL* 2.8 45.9 + - + +
360C THR* 4.4 6.3 - - + -
361C ILE* 4.6 16.4 - - + -
364C TYR* 3.4 65.3 + - + +
365C PHE* 4.2 16.8 - - + -
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Residues in contact with TRP 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C SER* 3.0 11.2 + - - +
231C LEU* 1.3 78.9 - - + +
233C GLY* 1.3 56.7 + - - +
234C ALA 3.1 0.2 - - - -
235C VAL* 4.5 16.8 - - + +
236C ILE* 2.8 68.9 + - + +
239C ILE* 5.8 4.7 - - + -
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Residues in contact with GLY 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LEU 3.6 17.9 - - - -
228C GLY* 4.1 10.1 - - - +
230C SER* 3.0 15.6 + - - -
232C TRP* 1.3 78.4 - - - +
234C ALA* 1.3 57.4 + - - +
236C ILE* 4.3 4.3 - - - -
237C ALA* 3.7 17.3 + - - +
259C MET* 4.7 5.9 - - - +
263C TRP* 4.5 5.9 + - - -
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Residues in contact with ALA 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C SER 3.1 9.4 + - - +
231C LEU* 3.0 10.2 + - + +
233C GLY* 1.3 79.5 - - - +
235C VAL* 1.3 59.8 + - - +
236C ILE 3.3 1.3 - - - -
237C ALA* 3.4 0.5 + - - +
238C VAL* 3.0 34.1 + - - +
284C ILE* 4.0 22.4 - - + -
288C PHE* 4.6 0.2 - - + -
289C PHE* 3.7 27.5 - - + -
360C THR* 4.5 11.0 - - + -
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Residues in contact with VAL 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 2.8 32.4 + - + +
232C TRP* 4.4 17.0 - - + +
234C ALA* 1.3 74.2 - - - +
236C ILE* 1.3 60.2 + - - +
238C VAL* 4.4 3.3 - - - +
239C ILE* 3.1 40.0 + - + +
357C VAL* 4.7 14.8 - - + +
360C THR* 3.6 24.9 - - + -
361C ILE* 3.7 19.1 - - + -
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Residues in contact with ILE 236 (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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232C TRP* 2.8 53.9 + - + +
233C GLY* 4.7 3.4 - - - -
235C VAL* 1.3 77.1 - - - +
237C ALA* 1.3 61.2 + - - +
239C ILE* 3.5 9.1 + - + +
240C LEU* 3.0 40.2 + - + +
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Residues in contact with ALA 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C GLY 3.7 14.1 + - - +
234C ALA 3.4 5.2 + - - +
235C VAL 3.4 0.2 - - - -
236C ILE* 1.3 81.5 - - - +
238C VAL* 1.3 56.7 + - - +
240C LEU* 3.4 6.4 + - - +
241C VAL* 2.9 35.5 + - - +
255C VAL* 4.0 8.0 - - + +
259C MET* 4.7 6.1 - - + -
263C TRP* 3.2 37.7 - - + -
289C PHE* 4.9 0.4 - - + -
294C TYR* 4.9 0.4 - - - -
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ALA 3.0 16.0 + - - +
235C VAL* 4.4 3.6 - - - +
237C ALA* 1.3 73.9 - - - +
239C ILE* 1.3 61.6 + - - +
241C VAL* 3.7 0.6 + - - -
242C HIS* 2.5 36.8 + - + -
289C PHE* 3.4 33.4 - - + -
293C ILE* 4.4 1.8 - - + -
294C TYR* 3.5 20.2 - - + +
356C PRO* 3.6 38.4 - - + -
357C VAL* 4.2 8.2 - - + +
360C THR* 3.6 15.5 - - - +
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Residues in contact with ILE 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C TRP* 5.8 4.9 - - + -
235C VAL* 3.1 33.0 + - + +
236C ILE* 3.6 10.3 - - + +
237C ALA 3.2 0.2 - - - -
238C VAL* 1.3 75.1 - - - +
240C LEU* 1.3 62.4 + - + +
242C HIS* 2.6 31.0 + - - +
243C VAL* 3.1 28.4 + - + +
353C ILE* 4.9 9.2 - - + -
357C VAL* 3.8 21.8 - - + -
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 6.1 1.6 - - + -
236C ILE* 3.0 26.6 + - + +
237C ALA* 3.7 2.0 - - - +
239C ILE* 1.3 84.0 - - + +
241C VAL* 1.3 63.4 + - - +
242C HIS 3.0 1.2 + - - -
243C VAL* 3.2 19.5 + - + +
244C LEU* 3.1 34.5 + - + +
255C VAL* 3.5 22.9 - - + -
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Residues in contact with VAL 241 (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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237C ALA 2.9 21.8 + - - +
238C VAL 3.7 1.1 - - - +
239C ILE 3.0 0.4 + - - -
240C LEU* 1.3 75.9 - - - +
242C HIS* 1.3 80.5 + - + +
245C TRP* 3.0 24.9 + - + -
251C GLY* 3.4 13.4 - - - +
252C ALA* 3.7 19.1 - - - +
255C VAL* 3.4 31.8 - - + +
263C TRP* 5.1 0.7 - - + -
294C TYR* 3.6 17.0 - - + +
2I NAG 3.8 19.7 - - + -
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Residues in contact with HIS 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C VAL* 2.5 28.4 + - + -
239C ILE 2.6 14.9 + - - +
241C VAL* 1.3 89.8 - - + +
243C VAL* 1.3 55.7 + - - +
244C LEU 3.1 5.2 - - - -
245C TRP* 3.3 7.8 + + - +
246C ALA* 2.8 25.8 + - - +
294C TYR* 3.8 18.9 - + - -
298C SER* 2.3 33.6 + - - -
352C PHE* 3.4 28.3 - + + -
353C ILE* 4.2 17.1 - - + +
356C PRO* 3.1 34.9 - - + +
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Residues in contact with VAL 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.4 17.6 - - + +
239C ILE* 3.7 23.1 - - + +
240C LEU* 3.3 36.8 - - + +
242C HIS* 1.3 74.8 - - - +
244C LEU* 1.3 66.4 + - + +
246C ALA* 3.6 12.2 - - + +
247C CYS* 3.4 22.5 - - - -
353C ILE* 4.1 20.9 - - + -
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Residues in contact with LEU 244 (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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9C VAL* 4.6 6.5 - - + -
13C ALA* 3.5 34.3 - - + +
240C LEU* 3.1 21.4 + - + +
242C HIS 3.1 0.6 - - - -
243C VAL* 1.3 87.4 - - + +
245C TRP* 1.3 62.0 + - - +
246C ALA 2.9 4.3 - - - -
247C CYS* 3.0 17.3 + - - +
249C ILE* 3.0 29.0 + - + +
251C GLY* 3.7 22.0 - - - +
254C ILE* 3.8 35.9 - - + -
255C VAL* 5.0 7.0 - - + +
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Residues in contact with TRP 245 (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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241C VAL* 3.0 20.7 + - + +
242C HIS* 3.3 8.4 + + - +
244C LEU* 1.3 77.9 - - - +
246C ALA* 1.3 63.1 + - - +
248C GLY* 3.3 6.8 + - - -
249C ILE 3.0 12.1 + - - -
250C HIS* 3.3 33.9 - + + -
251C GLY* 3.0 28.0 - - - +
252C ALA 3.4 3.7 - - - +
298C SER* 3.2 19.1 - - - -
333C ASN* 4.2 5.8 - - - -
334C GLU* 3.4 24.7 - - - -
337C THR* 3.4 34.7 - - + -
338C PHE* 4.3 17.9 - + - -
342C ILE 5.0 0.5 - - - +
343C VAL* 3.5 15.8 - - + +
352C PHE* 3.8 19.1 - + + -
2I NAG 2.9 28.1 + - - -
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Residues in contact with ALA 246 (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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6C GLU* 4.2 14.6 - - - +
242C HIS 2.8 15.6 + - - +
243C VAL* 3.6 13.9 - - - +
244C LEU 2.9 0.2 - - - -
245C TRP* 1.3 74.9 - - - +
247C CYS* 1.3 56.2 + - - +
248C GLY 2.7 14.8 + - - -
343C VAL* 2.6 29.4 - - - +
344C MET* 4.0 8.5 - - - +
349C LEU* 3.9 26.2 - - + -
353C ILE* 5.0 2.7 - - + -
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Residues in contact with CYS 247 (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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6C GLU* 4.1 10.1 - - - -
9C VAL* 3.5 22.2 - - - -
10C MET* 3.5 55.0 - - + +
13C ALA* 5.5 2.0 - - - -
243C VAL 3.4 17.7 - - - -
244C LEU* 3.0 8.7 + - - +
246C ALA* 1.3 77.7 - - - +
248C GLY* 1.3 58.8 + - - +
249C ILE* 3.4 12.5 + - + +
343C VAL* 4.3 1.1 - - - -
344C MET* 4.3 13.3 - - - +
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Residues in contact with GLY 248 (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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244C LEU 3.1 0.8 + - - -
245C TRP* 3.3 3.6 + - - -
246C ALA 2.7 11.5 + - - -
247C CYS* 1.3 74.9 - - - +
249C ILE* 1.3 63.0 + - - +
250C HIS 4.0 0.2 + - - -
338C PHE* 3.5 25.0 - - - -
343C VAL* 3.3 22.9 - - - -
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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