Contacts of the helix formed by residues 229 - 250 (chain B) in PDB entry 4U1D
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 ASP 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ASP* 3.1 28.1 + - + +
228B SER* 1.3 78.4 - - - +
230B ALA* 1.3 66.5 + - - +
231B ASP* 3.1 14.7 + - - +
232B THR* 2.9 35.9 + - - +
233B LEU* 3.2 25.1 + - - +
235B ARG* 4.8 0.5 + - - -
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Residues in contact with ALA 230 (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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228B SER 3.7 3.1 + - - -
229B ASP* 1.3 73.6 + - - +
231B ASP* 1.3 60.9 + - - +
233B LEU* 3.3 7.7 + - - +
234B GLN* 2.8 31.2 + - - +
271B LYS* 4.8 11.2 - - + +
272B ARG* 3.7 41.9 - - + +
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Residues in contact with ASP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 3.1 12.9 + - - +
230B ALA* 1.3 78.2 - - - +
232B THR* 1.3 64.2 + - - +
234B GLN* 3.2 5.4 + - - +
235B ARG* 3.1 47.5 + - - +
272B ARG* 2.5 37.5 + - - -
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 2.8 41.2 + - - +
225B VAL* 3.6 15.7 - - + -
226B ASP* 3.4 28.9 + - - +
227B LEU* 4.4 3.4 - - + -
229B ASP* 2.9 18.8 + - - +
231B ASP* 1.3 77.2 - - - +
233B LEU* 1.3 61.2 + - - +
235B ARG* 3.5 8.1 + - - +
236B TYR* 3.2 32.9 + - + -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A HIS* 5.1 0.2 - - - +
227B LEU* 3.3 55.4 - - + +
228B SER 5.0 3.6 - - - +
229B ASP 3.2 14.3 + - - +
230B ALA* 3.8 7.9 - - - +
232B THR* 1.3 74.6 - - - +
234B GLN* 1.3 56.5 + - - +
235B ARG 3.1 0.2 - - - -
236B TYR* 3.1 7.9 + - + +
237B LEU* 2.7 38.9 + - + +
266B LEU* 4.9 8.6 - - + +
269B ILE* 3.4 42.2 - - + +
270B SER* 4.0 12.8 - - - +
271B LYS* 4.7 4.9 - - + +
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Residues in contact with GLN 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ALA 2.8 21.6 + - - +
231B ASP* 3.2 5.1 + - - +
233B LEU* 1.3 72.0 - - - +
235B ARG* 1.3 57.6 + - + +
237B LEU* 4.5 12.4 - - - +
238B ASP* 3.0 38.2 + - + +
241B PHE* 5.2 2.2 - - - -
270B SER* 4.6 4.5 + - - -
272B ARG* 3.5 47.1 - - - +
273B ALA 3.8 7.3 - - - +
274B PRO* 3.8 26.8 - - - +
275B LYS 4.7 2.6 - - - +
278B THR* 5.7 0.8 + - - -
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Residues in contact with ARG 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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173B ALA 5.5 0.6 + - - -
176B GLU* 2.6 45.7 + - - +
177B ILE* 3.7 33.5 - - - +
180B SER* 3.9 30.1 + - - +
229B ASP* 4.8 0.6 + - - -
231B ASP* 3.1 31.5 + - - +
232B THR* 3.6 17.8 + - - +
233B LEU 3.1 0.2 - - - -
234B GLN* 1.3 75.6 - - + +
236B TYR* 1.3 66.9 + - + +
238B ASP* 3.2 7.6 + - - +
239B GLN* 3.0 30.0 + - - +
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Residues in contact with TYR 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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171B ASN* 4.0 15.3 + - - -
176B GLU* 4.9 7.6 + - + +
179B TYR* 4.2 24.3 - + - -
210B LEU* 4.1 17.3 - - + -
213B ALA* 4.9 1.0 - - + +
225B VAL* 3.5 26.3 - - + +
227B LEU* 3.7 32.5 - - + -
232B THR* 3.2 23.9 + - + -
233B LEU* 3.1 10.4 + - + +
235B ARG* 1.3 79.8 - - + +
237B LEU* 1.3 62.6 + - - +
239B GLN* 3.2 20.5 + - - -
240B ARG* 3.1 39.6 + - - +
266B LEU* 3.6 15.5 - - + -
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A TYR* 4.6 1.8 - - - +
233B LEU* 2.7 21.9 + - + +
234B GLN* 4.0 11.2 - - - +
236B TYR* 1.3 69.9 - - - +
238B ASP* 1.3 59.4 - - - +
240B ARG* 3.3 1.4 + - + +
241B PHE* 2.9 54.9 + - + -
263B VAL* 3.6 24.5 - - + +
266B LEU* 3.6 30.0 - - + +
267B MET* 3.7 25.4 - - + +
270B SER* 4.0 25.1 - - - +
274B PRO* 4.7 7.2 - - + -
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Residues in contact with ASP 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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180B SER* 5.6 1.3 - - - +
234B GLN* 3.0 27.5 + - - +
235B ARG* 3.3 8.7 - - - +
237B LEU* 1.3 77.4 - - - +
239B GLN* 1.3 62.2 + - + +
241B PHE* 3.5 13.9 + - - +
242B GLN* 3.3 21.1 + - - +
278B THR* 5.2 13.0 - - - +
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Residues in contact with GLN 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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179B TYR* 3.9 16.4 + - - -
180B SER* 3.1 42.2 + - - +
183B VAL* 4.0 30.4 - - + +
184B LYS 5.9 0.2 - - - +
187B MET* 4.0 5.1 - - - +
206B LEU* 4.5 3.1 - - + +
235B ARG* 3.0 16.7 + - - +
236B TYR* 3.4 20.8 - - - +
237B LEU 3.2 0.4 - - - -
238B ASP* 1.3 75.2 - - + +
240B ARG* 1.3 85.2 + - - +
242B GLN* 3.0 12.8 + - - +
243B GLN* 2.9 26.1 + - - +
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B TYR* 5.6 1.8 + - - -
206B LEU* 3.3 39.3 + - - +
207B ARG* 5.2 1.6 - - - +
209B HIS* 5.6 0.8 - - - +
210B LEU* 3.6 34.0 - - - +
236B TYR* 3.1 34.0 + - - +
237B LEU* 3.3 4.0 + - - +
239B GLN* 1.3 101.7 + - - +
241B PHE* 1.3 65.2 + - - +
243B GLN* 3.1 29.0 + - + +
244B VAL* 3.0 19.4 + - - +
259B SER* 4.8 0.6 - - - +
262B ASP* 4.7 13.9 - - + +
263B VAL* 3.5 30.4 - - + +
266B LEU* 3.6 21.3 - - + +
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Residues in contact with PHE 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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234B GLN* 5.2 2.2 - - - -
237B LEU* 2.9 47.4 + - + +
238B ASP* 3.5 13.5 - - - +
239B GLN 3.2 0.2 - - - -
240B ARG* 1.3 75.5 - - - +
242B GLN* 1.3 61.8 + - - +
244B VAL* 3.3 6.7 + - - +
245B ASP* 3.1 19.6 + - - +
263B VAL* 3.6 20.1 - - + +
267B MET* 4.4 5.8 - - - -
274B PRO* 4.0 22.9 - - + -
278B THR* 4.5 19.3 - - - +
279B LEU* 4.0 20.2 - - + -
282B TYR* 3.4 50.4 - + + -
285B ASN* 5.1 1.0 + - - -
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Residues in contact with GLN 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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183B VAL* 5.5 0.5 - - - +
184B LYS* 3.4 42.1 + - - +
187B MET* 3.3 33.8 - - - +
188B HIS* 4.0 7.1 - - - +
238B ASP* 3.3 9.2 + - - +
239B GLN* 3.0 13.0 + - - +
241B PHE* 1.3 77.4 - - - +
243B GLN* 1.3 61.8 + - - +
245B ASP* 3.0 9.9 + - + +
246B VAL* 2.9 36.4 + - + +
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Residues in contact with GLN 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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187B MET* 3.7 17.0 - - + +
199B PHE* 3.4 18.0 - - + -
203B ALA* 3.4 28.4 + - + +
206B LEU* 3.5 30.7 - - - +
207B ARG* 3.6 2.6 + - - +
239B GLN 2.9 10.5 + - - +
240B ARG* 3.2 26.6 - - - +
242B GLN* 1.3 77.3 - - - +
244B VAL* 1.3 60.9 + - - +
247B SER* 2.9 29.6 + - - -
259B SER* 2.9 24.1 + - - +
262B ASP* 3.5 16.1 - - - +
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Residues in contact with VAL 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 ARG 3.0 6.3 + - - -
241B PHE 3.6 7.9 - - - +
242B GLN 3.2 0.2 - - - -
243B GLN* 1.3 76.4 - - - +
245B ASP* 1.3 63.4 + - - +
247B SER* 3.3 6.0 + - - -
248B VAL* 3.1 26.5 + - + +
256B ALA* 4.3 3.4 - - + +
259B SER* 3.3 42.4 - - - +
260B ILE* 3.7 17.5 - - + +
263B VAL* 3.7 15.9 - - + -
282B TYR* 4.1 16.4 - - + -
285B ASN* 4.1 23.6 - - + +
286B LEU* 4.8 1.8 - - + -
289B VAL* 5.6 0.2 - - + -
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Residues in contact with ASP 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 PHE 3.1 11.3 + - - +
242B GLN* 3.0 15.7 + - + +
244B VAL* 1.3 77.4 - - - +
246B VAL* 1.3 63.8 + - + +
248B VAL* 3.2 4.7 + - - +
249B LYS* 3.0 54.7 + - - +
281B ASN* 3.5 17.9 + - - +
285B ASN* 2.9 31.9 + - - +
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Residues in contact with VAL 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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187B MET* 4.0 30.3 - - + +
188B HIS* 5.7 0.2 - - - -
191B LEU* 4.2 24.0 - - + -
199B PHE* 3.4 29.4 - - + -
242B GLN* 2.9 28.2 + - + +
245B ASP* 1.3 73.2 - - + +
247B SER* 1.3 53.8 + - - +
249B LYS* 3.1 7.7 + - + +
250B LEU* 2.8 56.0 + - + +
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Residues in contact with SER 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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199B PHE* 3.2 21.5 - - - -
243B GLN 2.9 22.4 + - - -
244B VAL 3.3 6.3 - - - -
245B ASP 3.2 0.2 - - - -
246B VAL* 1.3 77.4 - - - +
248B VAL* 1.3 59.9 + - - +
250B LEU* 3.4 1.6 + - - -
251B GLU 3.2 3.1 + - - -
252B LEU* 3.0 36.4 + - - +
255B GLU* 3.7 13.2 - - - +
256B ALA* 3.5 27.8 + - - -
259B SER* 3.9 3.5 + - - -
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Residues in contact with VAL 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 VAL* 3.1 15.5 + - + +
245B ASP 3.2 6.7 + - - +
247B SER* 1.3 77.5 - - - +
249B LYS* 1.3 60.8 + - + +
251B GLU* 3.0 21.3 + - - +
253B TRP* 3.5 31.1 - - + -
256B ALA* 4.3 3.6 - - + -
285B ASN* 4.1 24.7 - - + +
288B LYS* 3.9 25.6 - - + +
289B VAL* 3.7 28.3 - - + -
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Residues in contact with LYS 249 (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 LEU* 3.6 41.2 - - + +
194B GLN* 5.5 1.7 + - - +
245B ASP* 3.0 45.0 + - - +
246B VAL* 3.1 3.6 + - + +
248B VAL* 1.3 79.9 - - + +
250B LEU* 1.3 61.9 + - - +
251B GLU* 3.2 5.8 + - - +
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Residues in contact with LEU 250 (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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190B CYS 4.2 15.5 - - - +
191B LEU* 3.7 18.2 - - + -
194B GLN* 3.8 33.0 - - - +
196B LYS* 3.3 34.9 + - + +
199B PHE* 4.0 27.1 - - + -
246B VAL* 2.8 39.0 + - + +
247B SER 4.1 0.2 - - - +
249B LYS* 1.3 75.0 - - - +
251B GLU* 1.3 71.0 + - - +
252B LEU* 3.0 23.3 + - + +
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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