Contacts of the helix formed by residues 230 - 247 (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 SER 230 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ILE 3.5 8.1 + - - -
227D LEU* 3.0 28.8 + - - +
228D GLY 3.2 1.0 - - - +
229D ALA* 1.3 85.0 - - - +
231D LEU* 1.3 71.4 + - - +
232D TRP* 2.8 21.1 + - - +
233D GLY 3.2 5.0 + - - -
234D ALA* 3.4 20.3 + - - +
284D ILE* 4.1 1.2 - - - +
364D TYR* 4.3 3.0 - - - -
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Residues in contact with LEU 231 (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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230D SER* 1.3 74.0 + - - +
232D TRP* 1.3 58.9 + - + +
233D GLY 3.0 4.7 - - - -
234D ALA* 3.3 1.4 + - + +
235D VAL* 2.8 36.8 + - + +
360D THR* 4.3 15.7 - - + -
361D ILE* 4.4 17.5 - - + -
364D TYR* 3.1 52.2 + - + +
365D PHE* 3.8 31.9 - - + -
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Residues in contact with TRP 232 (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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230D SER* 2.8 9.2 + - - +
231D LEU* 1.3 80.2 - - + +
233D GLY* 1.3 55.2 + - - +
235D VAL* 3.9 20.0 - - + -
236D ILE* 3.0 63.0 + - + +
239D ILE* 6.0 3.8 - - + -
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Residues in contact with GLY 233 (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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227D LEU 3.6 21.1 - - - -
228D GLY* 4.6 8.3 - - - -
230D SER* 3.2 9.5 + - - -
231D LEU 3.0 1.2 - - - -
232D TRP* 1.3 76.4 - - - +
234D ALA* 1.3 62.6 + - - +
235D VAL 3.2 1.3 - - - -
236D ILE* 4.2 1.6 - - - +
237D ALA* 3.2 24.6 + - - +
259D MET* 4.9 4.6 - - - +
263D TRP* 4.8 1.8 - - - -
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D GLY 4.4 1.9 + - - -
230D SER 3.4 8.2 + - - +
231D LEU* 3.3 4.8 + - + +
233D GLY* 1.3 75.9 - - - +
235D VAL* 1.3 58.4 + - - +
236D ILE 3.5 0.2 - - - -
238D VAL* 3.1 33.8 + - - +
263D TRP* 5.2 0.2 - - - -
284D ILE* 3.4 36.8 - - + -
289D PHE* 3.5 23.6 - - + -
360D THR* 4.0 13.9 - - + -
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Residues in contact with VAL 235 (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* 2.8 18.2 + - + +
232D TRP* 3.9 30.5 - - + -
234D ALA* 1.3 77.6 - - - +
236D ILE* 1.3 62.4 + - - +
237D ALA 3.2 0.2 - - - -
238D VAL* 4.3 2.2 - - - +
239D ILE* 3.2 36.1 + - + +
357D VAL* 4.4 16.8 - - + +
360D THR* 3.8 27.1 - - + +
361D ILE* 4.4 22.2 - - + -
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Residues in contact with ILE 236 (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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232D TRP* 3.0 54.5 + - + +
233D GLY* 4.5 2.7 - - - +
235D VAL* 1.3 75.5 - - + +
237D ALA* 1.3 60.1 + - - +
239D ILE* 3.9 9.7 - - + +
240D LEU* 3.0 40.1 + - + +
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Residues in contact with ALA 237 (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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233D GLY 3.2 16.1 + - - +
234D ALA 3.9 3.6 - - - +
235D VAL 3.2 0.2 - - - -
236D ILE* 1.3 77.1 - - - +
238D VAL* 1.3 60.8 + - - +
240D LEU* 3.1 4.2 + - - +
241D VAL* 2.9 35.4 + - - +
255D VAL* 3.9 10.5 - - + +
259D MET* 4.9 4.5 - - + -
263D TRP* 3.3 39.7 - - + -
289D PHE* 4.8 0.7 - - + -
294D TYR* 4.9 0.2 - - - -
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Residues in contact with VAL 238 (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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234D ALA 3.1 19.7 + - - +
235D VAL* 3.8 3.6 + - - +
237D ALA* 1.3 80.5 - - - +
239D ILE* 1.3 61.3 + - - +
241D VAL* 4.5 0.4 - - - -
242D HIS* 3.3 27.3 + - + -
289D PHE* 3.4 29.2 - - + -
293D ILE* 4.1 9.2 - - + -
294D TYR* 4.0 11.9 - - - +
353D ILE 5.6 0.5 - - - +
356D PRO* 3.2 33.2 - - + -
357D VAL* 4.0 9.4 - - + +
360D THR* 3.5 18.8 - - - +
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Residues in contact with ILE 239 (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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232D TRP* 6.0 3.1 - - + -
235D VAL* 3.2 29.7 + - + +
236D ILE* 3.9 10.5 - - + +
238D VAL* 1.3 75.7 - - - +
240D LEU* 1.3 71.8 + - + +
242D HIS* 3.4 2.4 + - - +
243D VAL* 3.1 36.7 + - + +
353D ILE* 4.9 13.8 - - + +
357D VAL* 3.5 25.1 - - + -
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Residues in contact with LEU 240 (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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236D ILE* 3.0 32.0 + - + +
237D ALA* 3.1 4.2 + - - +
239D ILE* 1.3 83.9 - - + +
241D VAL* 1.3 64.4 + - - +
242D HIS 3.2 0.5 + - - -
243D VAL* 4.9 10.5 - - + -
244D LEU* 3.3 32.4 + - + +
255D VAL* 3.5 24.0 - - + -
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Residues in contact with VAL 241 (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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237D ALA 2.9 19.7 + - - +
238D VAL 4.0 1.1 - - - +
239D ILE 3.3 0.4 - - - -
240D LEU* 1.3 77.1 - - - +
242D HIS* 1.3 82.0 + - + +
244D LEU 4.0 0.2 - - - -
245D TRP* 3.0 29.3 + - + -
251D GLY* 3.5 15.7 - - - +
252D ALA* 3.6 23.8 - - - +
255D VAL* 3.7 24.5 - - + -
256D GLY 4.9 0.9 - - - +
263D TRP* 5.4 1.1 - - + -
294D TYR* 3.3 21.3 - - + +
2K NAG 4.2 6.7 - - + -
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Residues in contact with HIS 242 (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* 3.3 18.1 + - + +
239D ILE 3.4 2.7 + - - +
240D LEU 3.1 0.4 - - - -
241D VAL* 1.3 99.8 - - + +
243D VAL* 1.3 58.8 + - - +
244D LEU 2.9 5.2 - - - -
245D TRP* 3.7 6.1 - - - +
246D ALA* 2.9 30.1 + - - +
294D TYR* 3.8 20.4 - + - -
298D SER* 2.5 32.8 + - - -
352D PHE* 3.2 28.1 - + + +
353D ILE* 4.4 15.8 - - + +
356D PRO* 3.1 34.5 - - + +
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Residues in contact with VAL 243 (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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6D GLU* 5.3 2.3 - - - +
9D VAL* 3.9 30.1 - - + +
239D ILE* 3.1 30.5 + - + +
240D LEU* 4.3 13.2 - - + +
242D HIS* 1.3 75.6 - - - +
244D LEU* 1.3 61.4 + - + +
246D ALA* 3.7 8.8 - - + +
247D CYS* 3.5 20.1 + - - +
353D ILE* 4.2 20.6 - - + -
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Residues in contact with LEU 244 (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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9D VAL* 5.7 1.8 - - + -
13D ALA* 3.3 36.3 - - + +
16D VAL* 6.0 1.1 - - + -
240D LEU* 3.3 24.2 + - + +
241D VAL 3.8 0.2 - - - +
242D HIS 2.9 1.8 - - - -
243D VAL* 1.3 76.9 - - + +
245D TRP* 1.3 58.4 + - - +
246D ALA 3.1 1.3 - - - -
247D CYS* 2.9 21.1 + - - +
248D GLY 3.1 0.2 + - - -
249D ILE* 3.1 34.8 + - + +
251D GLY* 3.8 24.9 - - - +
254D ILE* 4.2 18.8 - - + -
255D VAL* 3.8 21.5 - - + -
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Residues in contact with TRP 245 (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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241D VAL* 3.0 28.9 + - + -
242D HIS* 3.1 3.2 + - - +
244D LEU* 1.3 74.6 - - - +
246D ALA* 1.3 66.1 + - - +
248D GLY* 3.0 9.4 + - - -
249D ILE 3.2 22.2 - - - -
250D HIS* 3.2 39.7 - + + -
251D GLY 3.5 11.0 - - - +
252D ALA 3.7 2.2 - - - +
298D SER* 4.0 12.6 - - - -
333D ASN* 4.9 1.1 - - - -
334D GLU* 3.7 16.2 - - + -
337D THR* 3.9 22.0 - - + -
338D PHE* 3.8 28.7 - + - -
343D VAL* 3.4 22.4 - - + +
352D PHE* 3.5 27.1 - + + -
2K NAG 2.8 37.3 + - - -
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Residues in contact with ALA 246 (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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6D GLU* 4.5 10.3 - - - +
242D HIS 2.9 15.7 + - - +
243D VAL* 3.7 11.4 - - + +
245D TRP* 1.3 78.5 - - - +
247D CYS* 1.3 58.7 + - - +
248D GLY 2.9 5.5 + - - -
343D VAL* 3.4 3.5 - - - +
344D MET* 3.2 28.5 + - - +
349D LEU* 3.4 39.5 - - + -
352D PHE* 4.4 0.8 - - - -
353D ILE* 5.3 4.5 - - + -
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Residues in contact with CYS 247 (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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6D GLU* 3.8 16.6 - - - -
9D VAL* 3.4 32.3 - - + -
10D MET* 3.6 51.7 - - - +
13D ALA* 5.1 1.1 - - + -
243D VAL 3.5 5.1 + - - +
244D LEU* 2.9 12.1 + - - +
246D ALA* 1.3 77.8 - - - +
248D GLY* 1.3 58.3 + - - +
249D ILE* 3.4 15.8 + - + +
343D VAL* 4.5 1.5 - - - +
344D MET* 4.7 3.4 - - - -
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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