Contacts of the helix formed by residues 229 - 248 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 4.5 8.3 - - + +
191C GLN* 3.1 27.1 + - - +
217C PHE* 5.0 0.5 - - - -
227C SER 3.8 0.4 + - - -
228C ILE* 1.3 70.5 - - - +
230C GLY* 1.3 70.1 + - - +
231C TYR* 3.0 27.5 - - - +
232C TYR* 3.0 41.0 + - + +
233C ASP* 2.8 22.7 + - - +
228D ILE 5.6 1.0 + - - -
230D GLY 4.9 3.4 - - - +
231D TYR* 4.4 0.7 - - - -
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Residues in contact with GLY 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C ILE 3.4 5.5 + - - -
229C ASN* 1.3 75.8 - - - +
231C TYR* 1.3 61.3 + - - -
233C ASP* 3.0 13.0 + - - +
234C LEU* 3.0 17.8 + - - +
229D ASN* 5.7 0.6 + - - -
230D GLY* 4.0 17.3 - - - +
231D TYR* 3.6 34.7 - - - -
234D LEU* 5.9 1.3 - - - +
267D ILE* 5.6 0.2 - - - +
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Residues in contact with TYR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C ASN* 3.0 18.1 - - - +
230C GLY* 1.3 73.3 - - - +
232C TYR* 1.3 65.6 + - + +
234C LEU* 3.2 12.2 + - + +
235C GLU* 3.0 29.5 + - - +
264C PHE* 3.8 22.1 - + + -
267C ILE* 4.3 8.3 - - + -
269C LYS* 4.1 35.6 + - + +
221D LYS* 4.5 1.9 + - - -
228D ILE* 3.9 26.8 - - + +
230D GLY* 3.7 23.4 - - - -
233D ASP* 2.7 38.5 + - + +
234D LEU* 6.1 0.2 - - + -
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Residues in contact with TYR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C LEU* 3.7 22.2 - - + +
191C GLN* 3.8 22.7 - - + +
192C THR* 3.4 29.3 + - - +
195C LYS* 3.5 32.6 - - + -
217C PHE* 4.6 2.5 - - + -
229C ASN* 3.0 38.3 + - + +
231C TYR* 1.3 79.3 - - + +
233C ASP* 1.3 59.6 + - - +
235C GLU* 4.3 8.3 - - - -
236C ILE* 2.7 51.2 + - + +
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Residues in contact with ASP 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C PHE* 4.2 12.7 - - + -
221C LYS* 3.4 32.6 + - - -
228C ILE* 4.1 1.2 - - + +
229C ASN 2.8 9.6 + - - +
230C GLY* 3.2 10.5 - - - +
232C TYR* 1.3 74.5 - - - +
234C LEU* 1.3 57.5 + - - +
236C ILE* 4.3 0.3 - - - +
237C ASN* 3.1 38.8 + - - +
231D TYR* 2.6 36.2 + - + +
267D ILE* 3.8 21.3 - - + +
269D LYS* 4.3 3.1 + - - +
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLY 3.0 13.9 + - - +
231C TYR* 3.5 9.6 - - + +
233C ASP* 1.3 75.1 - - - +
235C GLU* 1.3 65.2 + - - +
237C ASN* 3.3 5.0 + - - +
238C TYR 3.1 18.2 + - - -
260C ILE* 3.3 30.5 - - + +
263C ILE* 4.4 9.0 - - + -
264C PHE* 3.4 31.4 - - + -
267C ILE* 4.8 4.0 - - + -
230D GLY 6.5 0.2 - - - -
234D LEU* 3.8 32.8 - - + -
263D ILE* 3.8 33.4 - - + -
267D ILE* 4.4 11.4 - - + -
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Residues in contact with GLU 235 (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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195C LYS* 3.9 36.3 + - + +
199C THR* 5.4 2.3 + - - -
231C TYR* 3.0 17.4 + - - +
232C TYR* 3.8 9.7 - - - +
234C LEU* 1.3 76.5 - - - +
236C ILE* 1.3 62.8 + - - +
238C TYR* 3.2 23.4 + - + -
239C LEU* 3.2 18.9 + - + +
264C PHE* 3.8 11.5 - - + -
272C ILE* 4.0 18.5 - - - +
276C LEU* 4.2 24.1 - - + +
279C GLU* 5.0 7.1 - - - +
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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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191C GLN 4.5 1.1 - - - +
194C LEU 5.1 0.9 - - - -
195C LYS* 4.0 39.3 - - + +
198C LEU* 3.6 19.6 - - + +
214C ILE* 4.6 5.8 - - + -
217C PHE* 3.3 62.6 - - + -
218C GLU* 5.5 2.9 - - - +
232C TYR* 2.7 27.1 + - + +
233C ASP 4.3 1.8 - - - +
235C GLU* 1.3 72.5 - - - +
237C ASN* 1.3 57.8 + - - +
239C LEU* 3.2 9.3 + - - +
240C LYS* 2.8 26.5 + - + +
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Residues in contact with ASN 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C PHE* 6.1 0.5 - - - -
218C GLU* 4.9 6.9 - - - +
221C LYS* 5.1 0.5 + - - -
233C ASP* 3.1 31.6 + - - +
234C LEU 3.6 4.0 - - - +
235C GLU 3.2 0.2 - - - -
236C ILE* 1.3 75.8 - - - +
238C TYR* 1.3 61.0 + - - +
240C LYS* 3.1 24.7 + - - +
241C GLN* 2.8 41.2 + - - +
260C ILE* 3.8 5.3 - - + +
266D ILE* 3.1 27.7 + - - +
267D ILE* 3.4 28.6 - - + +
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C LEU 3.1 12.2 + - - +
235C GLU* 3.2 15.9 + - + +
237C ASN* 1.3 77.1 - - - +
239C LEU* 1.3 95.4 + - + +
241C GLN* 3.2 6.1 + - - +
242C ILE* 3.0 49.4 + - + +
257C ALA* 3.5 10.4 - - + +
260C ILE* 3.6 25.9 - - + +
261C ILE* 3.4 28.3 - - + -
264C PHE* 5.8 0.2 - - + -
276C LEU* 3.3 41.9 - - + +
279C GLU* 4.0 14.6 - - - +
280C LEU* 3.7 21.2 + - + -
283C ILE* 6.1 0.5 - - - +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195C LYS* 4.1 10.1 - - + +
198C LEU* 3.8 24.5 - - + -
199C THR* 3.6 34.1 - - + +
202C ILE* 2.9 32.8 - - + +
214C ILE* 4.7 0.2 - - - -
235C GLU* 3.2 23.3 + - + +
236C ILE* 3.4 10.1 - - - +
238C TYR* 1.3 98.0 - - + +
240C LYS* 1.3 61.3 + - - +
242C ILE* 3.1 5.9 + - + +
243C TYR 2.8 25.6 + - - -
279C GLU* 4.3 7.2 - - + +
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Residues in contact with LYS 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ILE* 3.7 38.1 - - + +
218C GLU* 3.8 25.8 + - - +
236C ILE* 2.8 15.3 + - + +
237C ASN* 3.3 29.3 + - - +
239C LEU* 1.3 78.6 - - - +
241C GLN* 1.3 58.8 + - + +
243C TYR* 3.4 7.0 - - + +
244C GLN* 3.1 52.5 + - + +
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Residues in contact with GLN 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ASN* 2.8 29.8 + - - +
238C TYR 3.5 7.9 - - - +
240C LYS* 1.3 77.3 - - - +
242C ILE* 1.3 64.3 + - - +
244C GLN* 3.1 26.1 + - - +
245C PHE* 3.1 18.9 + - - +
253C SER* 3.4 42.3 - - - +
256C ASN* 3.7 23.5 + - + +
257C ALA* 4.0 7.2 - - + +
260C ILE* 4.1 10.3 - - + -
266D ILE* 3.7 24.1 - - - +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 3.7 19.3 - - + -
238C TYR* 3.0 46.8 + - + +
239C LEU* 3.1 12.3 + - + +
241C GLN* 1.3 72.6 - - - +
243C TYR* 1.3 65.6 + - - +
245C PHE* 3.3 9.6 + - + +
246C LEU* 3.0 28.5 + - + +
254C TYR* 5.0 9.2 - - + -
257C ALA* 3.3 23.8 - - + -
280C LEU* 4.2 18.8 - - + -
283C ILE* 3.7 25.6 - - + -
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Residues in contact with TYR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 3.9 13.4 - - + +
207C LEU* 3.4 47.5 + - + +
210C ALA* 4.1 12.6 - - + -
211C GLN* 3.3 48.3 + - + +
214C ILE* 4.8 11.0 - - + -
239C LEU 2.8 13.2 + - - +
240C LYS* 3.4 16.8 - - + +
242C ILE* 1.3 77.0 - - - +
244C GLN* 1.3 72.4 + - + +
246C LEU* 3.1 16.9 + - - +
247C THR* 3.3 28.1 + - + +
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Residues in contact with GLN 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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240C LYS* 3.1 37.4 + - + +
241C GLN* 3.1 31.6 + - - +
243C TYR* 1.3 85.8 - - + +
245C PHE* 1.3 59.4 + - - +
247C THR* 2.9 9.3 + - - -
248C ASP* 2.8 40.8 + - + +
249C LYS 3.5 1.6 + - - -
253C SER* 3.6 13.9 + - - +
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Residues in contact with PHE 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 GLN 3.1 14.9 + - - +
242C ILE* 3.4 15.5 - - + +
243C TYR 3.2 0.2 - - - -
244C GLN* 1.3 74.9 - - - +
246C LEU* 1.3 77.0 + - + +
249C LYS* 3.0 46.0 - - + +
250C ASN 3.7 19.7 - - - +
251C ILE* 4.6 12.6 - - + -
253C SER* 3.7 11.6 - - - -
254C TYR* 3.5 49.4 - + + +
283C ILE* 5.7 8.5 - - + -
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 4.2 21.3 - - + -
205C ARG* 3.3 51.8 - - - +
207C LEU* 4.3 18.6 - - + +
242C ILE* 3.0 24.4 + - + +
243C TYR* 3.1 7.4 + - - +
245C PHE* 1.3 94.7 - - + +
247C THR* 1.3 60.0 + - - +
249C LYS* 3.2 24.8 + - - +
283C ILE* 5.2 4.9 - - + -
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Residues in contact with THR 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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207C LEU* 3.9 22.9 - - + -
243C TYR* 3.5 28.4 + - + +
244C GLN* 2.9 19.2 + - - -
246C LEU* 1.3 81.3 - - - +
248C ASP* 1.3 76.6 + - - -
249C LYS* 2.9 20.0 + - - +
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Residues in contact with ASP 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 GLN* 2.8 17.7 + - + +
247C THR* 1.3 87.5 + - - +
249C LYS* 1.3 68.9 + - - +
250C ASN* 3.2 10.8 + - + +
253C SER* 5.8 1.3 - - - +
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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