Contacts of the helix formed by residues 229 - 248 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228C ILE 5.6 1.0 - - - +
188D LEU* 4.3 9.5 - - + +
191D GLN* 2.8 24.4 + - - +
227D SER 3.9 0.2 + - - -
228D ILE* 1.3 70.6 - - - +
230D GLY* 1.3 69.1 + - - +
231D TYR* 3.3 18.4 - - - +
232D TYR* 2.9 49.4 + - + +
233D ASP* 2.8 22.7 + - - +
298D TYR* 2.8 32.1 + - - -
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Residues in contact with GLY 230 (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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229C ASN* 4.9 1.6 - - - +
230C GLY* 4.0 22.7 - - - +
231C TYR* 3.7 31.1 - - - -
234C LEU* 6.5 0.2 - - - -
228D ILE 3.4 5.3 + - - -
229D ASN* 1.3 72.0 + - - +
231D TYR* 1.3 63.5 + - - +
233D ASP* 3.0 13.3 + - - +
234D LEU* 3.1 19.0 + - - +
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Residues in contact with TYR 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ILE* 2.9 41.3 - - + +
230C GLY* 3.6 24.2 - - - -
233C ASP* 2.6 33.3 + - - +
229D ASN* 3.3 18.7 - - - +
230D GLY* 1.3 74.0 - - - +
232D TYR* 1.3 59.4 + - - +
234D LEU* 3.2 8.9 + - + +
235D GLU* 2.9 25.8 + - - +
264D PHE* 3.6 22.2 - + + -
267D ILE* 4.4 10.1 - - + -
269D LYS* 3.5 30.7 - - + -
298D TYR* 4.4 8.1 - - - -
301D ASN* 5.6 0.2 - - - -
302D TYR* 3.9 28.9 - + + -
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Residues in contact with TYR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188D LEU* 3.7 11.7 - - + -
191D GLN* 3.5 32.5 - - + +
192D THR* 2.7 50.5 + - - +
195D LYS* 3.7 24.0 + - + -
217D PHE* 5.0 0.7 - - + -
229D ASN* 2.9 31.4 + - + +
231D TYR* 1.3 73.0 - - - +
233D ASP* 1.3 58.7 + - - +
235D GLU* 4.4 3.1 - - - +
236D ILE* 2.7 49.3 + - + +
298D TYR* 3.2 31.6 - + - +
302D TYR* 3.6 27.4 - + - -
3H THR* 4.8 1.6 - - - -
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Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 2.7 37.5 + - + +
267C ILE* 3.8 23.1 - - + +
269C LYS* 4.1 4.2 - - - +
217D PHE* 3.3 19.7 - - + -
221D LYS* 2.8 29.6 + - - -
228D ILE* 4.5 0.9 - - + -
229D ASN 2.8 9.2 + - - +
230D GLY 3.3 7.9 - - - +
232D TYR* 1.3 75.7 - - - +
234D LEU* 1.3 63.2 + - - +
236D ILE* 4.3 0.2 - - - +
237D ASN* 3.1 31.7 + - - +
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Residues in contact with LEU 234 (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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230C GLY 5.9 1.1 - - - +
231C TYR* 6.1 0.2 - - + -
234C LEU* 3.8 24.7 - - + -
263C ILE* 3.5 30.5 - - + -
267C ILE* 3.8 23.3 - - + -
230D GLY 3.1 16.5 + - - +
231D TYR* 3.5 9.2 - - + +
233D ASP* 1.3 74.1 - - - +
235D GLU* 1.3 66.7 + - - +
237D ASN* 3.3 3.9 + - - +
238D TYR 3.1 17.3 + - - -
260D ILE* 3.3 21.2 - - + +
263D ILE* 4.0 10.5 - - + -
264D PHE* 3.3 35.0 - - + -
267D ILE* 5.2 3.8 - - + -
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Residues in contact with GLU 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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195D LYS* 3.2 29.8 - - + +
199D THR* 4.2 0.5 + - - -
231D TYR 2.9 15.6 + - - +
232D TYR* 3.9 5.2 - - - +
234D LEU* 1.3 76.5 - - - +
236D ILE* 1.3 62.0 + - - +
238D TYR* 2.7 45.2 + - + -
239D LEU* 3.2 5.1 + - + +
260D ILE* 5.1 1.1 - - - -
264D PHE* 4.0 13.3 - - + -
272D ILE* 5.2 0.2 - - - +
276D LEU* 4.5 10.9 - - + +
302D TYR* 2.7 32.2 + - - -
1H LEU* 3.0 35.0 + - - +
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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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191D GLN 4.5 4.0 - - - +
194D LEU* 4.8 2.7 - - + -
195D LYS* 3.7 42.0 - - + +
198D LEU* 3.8 18.0 - - + +
214D ILE* 5.5 4.3 - - + -
217D PHE* 3.4 58.6 - - + -
218D GLU* 5.6 1.3 - - - +
232D TYR* 2.7 26.4 + - + +
233D ASP 4.3 1.8 - - - +
235D GLU* 1.3 72.9 - - - +
237D ASN* 1.3 58.0 + - - +
239D LEU* 3.2 9.8 + - - +
240D LYS* 2.8 28.0 + - + +
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Residues in contact with ASN 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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266C ILE* 3.0 32.5 + - - +
267C ILE* 3.0 35.2 - - + +
217D PHE* 5.3 1.6 - - - -
218D GLU* 4.5 8.1 - - - +
221D LYS* 5.6 0.3 - - - -
233D ASP* 3.1 24.0 + - - +
234D LEU 3.6 4.7 - - - +
235D GLU 3.2 0.4 - - - -
236D ILE* 1.3 74.9 - - - +
238D TYR* 1.3 61.1 + - - +
240D LYS* 3.1 22.5 + - - +
241D GLN* 2.8 36.8 + - - +
260D ILE* 5.3 3.1 - - + -
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Residues in contact with TYR 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 LEU 3.1 5.5 + - - -
235D GLU* 2.7 34.5 + - + +
237D ASN* 1.3 76.3 - - - +
239D LEU* 1.3 86.3 + - + +
241D GLN* 3.2 9.5 + - - +
242D ILE* 3.0 43.8 + - + +
257D ALA* 3.9 12.2 - - + +
260D ILE* 3.5 32.0 - - + +
261D ILE* 3.4 36.3 - - + -
276D LEU* 4.4 11.4 - - + -
279D GLU* 2.7 40.1 + - - +
280D LEU* 4.4 7.1 + - + -
283D ILE* 3.9 4.7 - - + +
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Residues in contact with LEU 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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195D LYS* 4.0 5.8 - - + +
198D LEU* 3.6 33.7 - - + -
199D THR* 3.3 33.4 - - - +
202D ILE* 4.3 22.9 - - + +
214D ILE* 5.0 0.2 - - - -
235D GLU* 3.2 12.3 + - + +
236D ILE* 3.5 11.0 - - - +
237D ASN 3.2 0.2 - - - -
238D TYR* 1.3 114.4 - - + +
240D LYS* 1.3 60.6 - - - +
242D ILE* 3.1 5.2 + - + +
243D TYR* 2.8 30.0 + - - +
279D GLU* 3.9 7.2 - - - +
283D ILE* 4.5 4.5 - - + -
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Residues in contact with LYS 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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211D GLN* 5.3 2.8 + - - -
214D ILE* 3.1 49.5 - - + +
215D ASN* 5.7 0.6 - - - +
218D GLU* 4.1 22.3 + - - +
236D ILE* 2.8 17.2 + - + +
237D ASN* 3.1 24.9 + - - +
239D LEU* 1.3 78.3 - - - +
241D GLN* 1.3 57.0 + - + +
243D TYR* 3.4 5.0 - - + +
244D GLN* 3.2 46.3 + - + +
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Residues in contact with GLN 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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266C ILE* 4.2 18.6 - - + +
237D ASN* 2.8 21.1 + - - +
238D TYR* 3.5 9.0 - - - +
239D LEU 3.1 0.2 - - - -
240D LYS* 1.3 76.1 - - + +
242D ILE* 1.3 64.1 + - - +
244D GLN* 3.5 21.7 + - - +
245D PHE* 3.1 18.7 + - - +
253D SER* 3.4 53.6 + - - +
256D ASN* 3.4 30.4 + - + +
257D ALA 4.0 7.2 - - - +
260D ILE* 5.6 1.6 - - + -
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Residues in contact with ILE 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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202D ILE* 3.9 15.9 - - + -
238D TYR* 3.0 33.0 + - + +
239D LEU* 3.1 9.2 + - - +
241D GLN* 1.3 73.0 - - - +
243D TYR* 1.3 66.2 + - - +
245D PHE* 3.3 6.9 + - + +
246D LEU* 3.0 28.4 + - + +
254D TYR* 4.1 20.6 - - + -
257D ALA* 3.4 23.8 - - + -
280D LEU* 3.7 21.5 - - + -
283D ILE* 3.8 29.6 - - + -
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Residues in contact with TYR 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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202D ILE* 3.6 19.5 - - + -
207D LEU* 3.5 39.9 + - + +
210D ALA* 4.1 5.6 - - + -
211D GLN* 3.0 47.5 + - + +
214D ILE* 3.8 21.1 - - + -
239D LEU 2.8 17.0 + - - +
240D LYS* 3.4 9.2 - - + +
242D ILE* 1.3 77.1 - - - +
244D GLN* 1.3 73.3 + - + +
246D LEU* 3.1 14.8 + - - +
247D THR* 3.2 37.2 + - + +
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Residues in contact with GLN 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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240D LYS* 3.2 39.5 + - - +
241D GLN* 3.6 30.3 + - - +
242D ILE 3.3 0.2 - - - -
243D TYR* 1.3 87.7 - - + +
245D PHE* 1.3 60.1 + - - +
247D THR* 2.9 8.7 + - - -
248D ASP* 2.8 46.3 + - + +
249D LYS 3.5 1.4 + - - -
253D SER* 3.7 13.9 + - - +
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Residues in contact with PHE 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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281A THR* 3.7 33.2 - - + -
284A SER* 4.1 9.0 - - - -
285A ALA* 4.0 19.7 - - + -
241D GLN 3.1 11.5 + - - +
242D ILE* 3.4 15.7 - - + +
244D GLN* 1.3 77.9 - - - +
246D LEU* 1.3 69.0 + - + +
249D LYS* 3.0 38.3 - - + +
250D ASN 3.3 26.5 - - - -
251D ILE* 4.0 9.9 - - + -
253D SER* 3.7 10.0 - - - -
254D TYR* 3.4 46.0 - + + +
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Residues in contact with LEU 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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285A ALA* 6.3 2.2 - - + -
202D ILE* 3.9 27.1 - - + +
205D ARG* 3.3 52.0 - - - +
207D LEU* 4.0 16.4 - - + +
242D ILE* 3.0 30.5 + - + +
243D TYR 3.1 6.9 + - - +
245D PHE* 1.3 86.8 - - + +
247D THR* 1.3 62.0 + - - +
249D LYS* 4.4 10.1 - - - +
283D ILE* 5.1 0.9 - - + -
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Residues in contact with THR 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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207D LEU* 3.7 24.2 - - + -
243D TYR* 3.5 36.0 + - + +
244D GLN* 2.9 15.1 + - - -
246D LEU* 1.3 81.1 - - - +
248D ASP* 1.3 80.7 + - - -
249D LYS* 2.8 29.2 + - - -
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Residues in contact with ASP 248 (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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244D GLN* 2.8 25.8 + - + +
247D THR* 1.3 91.2 + - - +
249D LYS* 1.3 70.0 + - - +
250D ASN* 3.2 10.6 + - + +
253D SER* 5.7 1.6 - - - +
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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