Contacts of the helix formed by residues 229 - 248 (chain B) in PDB entry 2AXZ
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 ASN 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY 5.9 0.2 + - - -
231A TYR* 4.4 0.4 - - - -
188B LEU* 4.4 8.0 - - + +
191B GLN* 2.9 22.6 + - - +
217B PHE* 5.2 0.2 - - - -
227B SER 3.8 0.2 + - - -
228B ILE* 1.3 68.9 - - - +
230B GLY* 1.3 67.7 + - - +
231B TYR* 3.4 18.5 - - - +
232B TYR* 3.0 51.7 - - + +
233B ASP* 2.8 22.4 + - - +
298B TYR* 3.0 27.5 + - - -
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Residues in contact with GLY 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLY* 4.1 9.2 - - - +
231A TYR* 3.4 45.3 - - - -
234A LEU* 5.7 2.3 - - - +
267A ILE* 5.5 0.3 - - - +
228B ILE 3.4 5.5 + - - -
229B ASN* 1.3 71.5 - - - +
231B TYR* 1.3 62.2 + - - +
233B ASP* 3.0 13.0 + - - +
234B LEU* 3.1 16.2 + - - +
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Residues in contact with TYR 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 2.8 33.3 - - + +
230A GLY* 3.4 29.1 - - - -
233A ASP* 2.4 32.6 + - + +
229B ASN* 3.3 10.2 - - - +
230B GLY* 1.3 73.1 - - - +
232B TYR* 1.3 59.1 + - - +
234B LEU* 3.2 11.0 + - + +
235B GLU* 3.0 28.6 + - - +
264B PHE* 3.8 16.5 - + + -
267B ILE* 4.4 9.2 - - + -
269B LYS* 3.7 38.2 - - + +
298B TYR* 4.1 18.4 - - - -
301B ASN* 4.9 2.9 - - - -
302B TYR* 4.2 20.6 - + + -
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Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LEU* 3.6 18.9 - - + +
191B GLN* 3.6 28.7 - - + +
192B THR* 2.8 38.2 + - - +
195B LYS* 3.4 33.5 - - + -
217B PHE* 5.0 0.2 - - + -
229B ASN* 3.0 29.8 + - + +
231B TYR* 1.3 75.0 - - - +
233B ASP* 1.3 59.4 + - - +
235B GLU* 4.4 2.9 - - - +
236B ILE* 2.7 49.0 + - + +
298B TYR* 3.3 41.1 - + - +
302B TYR* 4.3 12.3 - + - -
3F THR* 4.4 1.9 - - - +
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A TYR* 2.5 32.6 + - + +
267A ILE* 3.5 22.4 - - + +
269A LYS* 4.6 3.5 - - - +
217B PHE* 3.9 13.2 - - + -
221B LYS* 3.4 27.8 + - - -
228B ILE* 3.5 2.9 - - + +
229B ASN 2.8 10.4 + - - +
230B GLY 3.3 8.7 - - - +
232B TYR* 1.3 76.6 - - - +
234B LEU* 1.3 57.0 + - - +
236B ILE* 4.2 0.2 - - - +
237B ASN* 2.7 53.9 + - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.7 29.6 - - + -
263A ILE* 3.3 28.0 - - + -
267A ILE* 3.6 20.9 - - + -
230B GLY 3.1 11.8 + - - +
231B TYR* 3.5 12.6 - - + +
233B ASP* 1.3 74.4 - - - +
235B GLU* 1.3 66.5 + - - +
237B ASN* 3.3 2.6 + - - +
238B TYR 3.1 17.5 + - - -
260B ILE* 3.3 28.1 - - + +
263B ILE* 3.8 21.5 - - + -
264B PHE* 4.0 19.7 - - + -
267B ILE* 5.2 5.6 - - + -
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LYS* 3.1 28.8 + - + +
231B TYR 3.0 15.2 + - - +
232B TYR* 3.9 2.4 - - - +
234B LEU* 1.3 76.4 - - - +
236B ILE* 1.3 62.1 + - - +
238B TYR* 2.9 43.0 + - + -
239B LEU* 3.2 4.7 + - + +
264B PHE* 4.2 14.0 - - + -
276B LEU* 4.3 12.3 - - + +
302B TYR* 2.5 36.6 + - - -
1F LEU* 2.8 35.2 + - - +
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B GLN 4.6 4.3 - - - +
194B LEU* 5.0 2.0 - - + -
195B LYS* 4.0 40.2 - - + +
198B LEU* 3.8 20.1 - - + +
213B TYR 5.9 0.2 - - - +
214B ILE* 5.5 6.1 - - + -
217B PHE* 3.4 63.3 - - + -
232B TYR* 2.7 25.7 + - + +
235B GLU* 1.3 71.8 - - - +
237B ASN* 1.3 57.5 + - - +
239B LEU* 3.2 6.3 + - + +
240B LYS* 2.9 27.7 + - + +
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Residues in contact with ASN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A ILE 3.3 9.7 + - - -
267A ILE* 3.1 45.8 + - + +
217B PHE* 4.8 3.3 - - - -
221B LYS* 4.1 6.8 + - - +
233B ASP* 2.7 40.3 + - - +
234B LEU 3.6 2.0 - - - +
236B ILE* 1.3 76.0 - - - +
238B TYR* 1.3 61.2 + - - +
240B LYS* 3.1 25.3 + - - +
241B GLN* 2.8 35.1 + - - +
260B ILE* 3.9 6.5 - - + -
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234B LEU 3.1 13.1 + - - +
235B GLU* 2.9 30.9 + - + +
237B ASN* 1.3 76.2 - - - +
239B LEU* 1.3 86.4 + - + +
241B GLN* 3.2 5.8 + - - +
242B ILE* 3.0 39.4 + - + +
257B ALA* 3.9 10.2 - - + +
260B ILE* 3.5 28.9 - - + +
261B ILE* 3.5 36.1 - - + -
264B PHE* 6.4 0.2 - - + -
276B LEU* 4.3 15.5 - - + -
279B GLU* 2.5 40.5 + - - +
280B LEU* 4.3 7.6 + - + -
283B ILE* 4.0 5.5 - - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LYS* 4.0 6.1 - - + +
198B LEU* 3.5 34.1 - - + -
199B THR* 3.4 32.8 - - - +
202B ILE* 4.3 13.4 - - + +
235B GLU* 3.2 11.5 + - + +
236B ILE* 3.5 10.3 - - - +
238B TYR* 1.3 109.8 - - + +
240B LYS* 1.3 61.0 + - - +
242B ILE* 3.1 5.4 + - + +
243B TYR* 2.8 29.9 + - - +
279B GLU* 3.7 9.2 - - - +
283B ILE* 4.6 13.0 - - + -
1F LEU 4.7 2.2 - - - +
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Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B ILE* 3.9 44.2 - - + +
218B GLU* 4.5 19.1 - - + +
236B ILE* 2.9 16.2 + - + +
237B ASN* 3.2 30.4 - - - +
239B LEU* 1.3 77.6 - - - +
241B GLN* 1.3 61.2 + - + +
243B TYR* 3.4 3.8 - - + +
244B GLN* 3.1 55.0 + - + +
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A ILE* 3.9 16.9 - - + +
237B ASN* 2.8 20.0 + - + +
238B TYR 3.5 8.7 - - - +
239B LEU 3.1 0.2 - - - -
240B LYS* 1.3 79.3 + - + +
242B ILE* 1.3 63.5 + - - +
244B GLN* 3.3 24.4 + - - +
245B PHE* 3.1 18.9 + - - +
253B SER* 3.3 47.1 + - - +
256B ASN* 3.6 27.8 + - + +
257B ALA* 4.0 7.4 - - + +
260B ILE* 4.0 10.8 - - + -
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 3.7 24.9 - - + -
238B TYR* 3.0 32.1 + - + +
239B LEU* 3.1 9.2 + - - +
241B GLN* 1.3 73.7 - - - +
243B TYR* 1.3 68.0 + - - +
245B PHE* 3.3 10.1 + - + +
246B LEU* 3.0 29.0 + - + +
254B TYR* 4.5 15.9 - - + -
257B ALA* 3.7 19.1 - - + -
280B LEU* 3.7 25.6 - - + -
283B ILE* 3.9 20.6 - - + -
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Residues in contact with TYR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 3.6 20.2 - - + +
207B LEU* 3.5 47.2 + - + +
210B ALA* 4.2 5.4 - - + -
211B GLN* 3.1 41.4 + - + +
214B ILE* 3.9 22.0 - - + -
239B LEU 2.8 13.4 + - - +
240B LYS* 3.4 11.4 - - + +
242B ILE* 1.3 76.4 - - - +
244B GLN* 1.3 72.1 + - + +
246B LEU* 3.0 16.2 + - - +
247B THR* 3.3 31.2 + - + +
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Residues in contact with GLN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B LYS* 3.1 40.5 + - + +
241B GLN* 3.3 20.1 + - - +
242B ILE 3.3 0.2 - - - -
243B TYR* 1.3 88.3 - - + +
245B PHE* 1.3 59.9 + - - +
247B THR* 2.9 9.6 + - - -
248B ASP* 2.8 44.9 + - + +
249B LYS 3.5 1.4 + - - -
250B ASN 5.5 0.2 - - - -
253B SER* 3.1 22.3 + - - +
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Residues in contact with PHE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B GLN 3.1 12.1 + - - +
242B ILE* 3.4 18.2 - - + +
243B TYR 3.2 0.2 - - - -
244B GLN* 1.3 79.5 - - - +
246B LEU* 1.3 69.9 + - + +
249B LYS* 3.0 31.3 - - + +
250B ASN 3.3 27.6 - - - +
251B ILE* 4.0 14.1 - - + -
253B SER* 3.7 9.8 - - - -
254B TYR* 3.5 44.4 - + + +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ILE* 4.1 20.0 - - + -
205B ARG* 3.4 51.6 - - - +
207B LEU* 3.9 28.3 - - + +
242B ILE* 3.0 26.2 + - + +
243B TYR* 3.0 7.6 + - - +
245B PHE* 1.3 86.2 - - + +
247B THR* 1.3 62.9 + - - +
249B LYS* 4.3 7.1 - - - +
283B ILE* 5.1 1.3 - - + -
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B LEU* 3.5 28.7 - - + -
243B TYR* 3.3 32.9 + - + +
244B GLN* 2.9 13.9 + - - -
246B LEU* 1.3 77.1 - - - +
248B ASP* 1.3 74.4 + - - -
249B LYS* 2.9 30.6 + - - +
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLN* 2.8 22.3 + - + +
247B THR* 1.3 86.9 + - - +
249B LYS* 1.3 71.7 + - - +
250B ASN* 3.2 11.2 + - + +
253B SER* 5.9 0.4 - - - +
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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
------------------------------------------------------------
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