Contacts of the helix formed by residues 225 - 247 (chain B) in PDB entry 1U54
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 LEU 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B HIS* 2.7 23.3 + - + +
224B PHE* 1.3 75.8 - - - +
226B LEU* 1.3 68.3 + - - +
227B GLY 3.2 4.5 - - - +
228B THR* 3.1 28.4 + - - +
229B LEU* 3.3 7.6 + - - +
263B ARG* 6.2 2.0 - - - +
326B TYR* 5.2 0.9 - - - -
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Residues in contact with LEU 226 (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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225B LEU* 1.3 75.0 - - - +
227B GLY* 1.3 57.5 + - - +
229B LEU* 3.5 5.9 + - + +
230B SER* 3.0 33.2 + - - +
324B PHE* 3.8 30.4 - - + -
326B TYR* 4.4 15.3 - - - +
355B ASP* 3.9 22.0 - - + +
356B CYS* 4.6 0.7 - - - -
357B PRO* 3.9 26.7 - - + -
360B ILE* 5.9 1.8 - - + -
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Residues in contact with GLY 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.2 3.0 - - - +
226B LEU* 1.3 76.3 - - - +
228B THR* 1.3 65.4 + - - +
230B SER* 3.8 5.5 - - - -
231B ARG* 3.2 35.9 + - - +
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Residues in contact with THR 228 (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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223B HIS* 5.0 8.9 - - + -
224B PHE* 4.3 18.1 - - + -
225B LEU* 3.1 29.1 + - - +
227B GLY* 1.3 76.9 - - - +
229B LEU* 1.3 63.2 + - - +
231B ARG* 3.2 9.5 + - - +
232B TYR* 3.1 58.6 + - + +
263B ARG* 4.7 6.2 + - + +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B LEU* 4.2 15.0 - - + -
224B PHE* 4.2 16.2 - - + -
225B LEU 3.3 11.7 + - - +
226B LEU* 4.0 5.2 - - - +
228B THR* 1.3 77.0 - - - +
230B SER* 1.3 60.4 + - - +
232B TYR* 3.1 22.7 + - + -
233B ALA* 2.8 26.7 + - - +
323B MET* 3.2 45.5 - - + +
324B PHE* 3.9 32.3 - - + -
326B TYR* 3.9 24.7 - - + +
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.0 18.6 + - - +
227B GLY* 3.8 8.5 - - - -
228B THR 3.4 0.2 - - - -
229B LEU* 1.3 76.7 - - - +
231B ARG* 1.3 59.5 + - - +
233B ALA* 3.2 8.7 + - - +
234B VAL* 3.0 33.3 + - - +
324B PHE* 4.5 2.9 - - - -
360B ILE* 3.6 25.5 - - - +
385B LEU* 5.1 12.7 + - - +
388B ALA 5.4 2.4 + - - -
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Residues in contact with ARG 231 (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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227B GLY* 3.2 19.6 + - - +
228B THR* 3.5 9.6 - - - +
229B LEU 3.2 0.2 - - - -
230B SER* 1.3 81.1 - - - +
232B TYR* 1.3 61.0 + - + +
234B VAL* 3.3 7.2 + - - +
235B GLN* 2.9 39.3 + - - +
264B ASP* 5.1 11.3 + - - +
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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
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213B LEU* 3.9 30.7 - - + -
216B ARG* 4.6 1.4 + - - -
224B PHE* 4.7 6.0 - + - -
228B THR* 3.1 36.4 + - + +
229B LEU* 3.1 18.3 + - + +
231B ARG* 1.3 76.4 - - + +
233B ALA* 1.3 62.0 + - - +
235B GLN* 3.5 13.0 - - - -
236B VAL* 3.1 30.1 + - - +
258B LEU* 6.5 0.2 - - + -
260B LEU* 3.2 17.7 - - + +
263B ARG* 2.0 34.1 + - - +
264B ASP* 3.2 24.0 - - - -
266B VAL* 3.8 18.0 - - + +
323B MET* 3.4 17.0 - - + +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU 2.8 19.0 + - - +
230B SER* 3.5 8.7 - - - +
232B TYR* 1.3 73.2 - - - +
234B VAL* 1.3 62.7 + - - +
236B VAL* 4.9 0.9 - - - -
237B ALA* 3.1 23.6 + - - +
316B PHE* 3.6 5.0 - - - -
320B LEU* 3.3 30.3 - - + -
323B MET* 3.5 7.4 - - + +
324B PHE* 5.0 4.3 - - + -
385B LEU* 3.4 21.5 - - + +
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Residues in contact with VAL 234 (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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230B SER* 3.0 20.3 + - - +
231B ARG* 3.8 6.5 - - - +
233B ALA* 1.3 74.4 - - - +
235B GLN* 1.3 60.7 + - + +
237B ALA* 3.5 6.2 - - - +
238B GLU* 2.8 50.4 + - - +
382B ARG* 4.0 16.4 - - + +
385B LEU* 3.8 27.4 - - + +
386B LEU* 3.9 30.5 - - + -
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Residues in contact with GLN 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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187B ARG* 4.7 5.6 + - - +
188B ASN* 3.5 27.3 - - - +
231B ARG* 2.9 20.3 + - - +
232B TYR* 3.5 9.1 - - - -
233B ALA 3.2 0.4 - - - -
234B VAL* 1.3 80.6 - - + +
236B VAL* 1.3 62.6 + - - +
238B GLU* 3.2 14.8 + - - +
239B GLY 3.0 17.7 + - - -
264B ASP* 3.1 22.9 + - - +
265B LEU* 3.9 12.5 - - + +
266B VAL* 3.0 45.3 - - + +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B TYR 3.1 18.3 + - - +
233B ALA* 4.9 0.4 - - - -
235B GLN* 1.3 71.5 - - - +
237B ALA* 1.3 70.4 + - - +
239B GLY* 2.8 14.4 + - - -
240B MET* 2.9 22.8 + - + -
253B LEU* 4.5 13.7 - - + -
258B LEU* 3.6 37.7 - - + -
266B VAL* 4.2 11.0 - - + -
268B ILE* 3.9 12.6 - - + +
316B PHE* 3.5 30.1 - - + -
319B THR* 5.4 1.6 - - + -
323B MET* 5.3 2.5 - - + -
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Residues in contact with ALA 237 (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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233B ALA 3.1 17.2 + - - +
234B VAL* 3.5 8.7 - - - +
236B VAL* 1.3 82.6 - - - +
238B GLU* 1.3 56.4 + - - +
240B MET* 3.3 3.3 + - - +
241B GLY* 2.8 26.7 + - - -
316B PHE* 4.1 13.0 - - + -
378B PHE* 4.0 23.8 - - + +
381B LEU* 4.7 0.7 - - + -
382B ARG* 4.3 19.5 - - + +
385B LEU* 4.2 8.1 - - + -
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Residues in contact with GLU 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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186B HIS* 4.1 17.8 + - + +
187B ARG* 5.4 4.7 + - - -
188B ASN* 4.3 4.1 - - - +
234B VAL* 2.8 40.4 + - - +
235B GLN* 3.5 17.2 - - - +
236B VAL 2.8 1.2 + - - -
237B ALA* 1.3 69.4 - - - +
239B GLY* 1.3 70.0 + - - +
241B GLY* 3.0 9.6 + - - +
242B TYR* 3.2 12.8 + - - +
382B ARG* 4.0 25.5 + - - +
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Residues in contact with GLY 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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186B HIS* 3.9 17.8 - - - -
188B ASN* 4.0 3.1 - - - -
189B LEU* 4.0 12.7 - - - +
235B GLN 3.0 8.4 + - - -
236B VAL 2.8 12.4 + - - -
238B GLU* 1.3 74.7 - - - +
240B MET* 1.3 59.3 + - - -
241B GLY 3.1 0.3 + - - -
242B TYR* 3.1 18.2 - - - +
243B LEU* 3.3 7.3 + - - +
268B ILE* 3.8 15.0 - - - -
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Residues in contact with MET 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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236B VAL* 2.9 17.5 + - + +
237B ALA 3.4 9.2 - - - +
239B GLY* 1.3 71.2 - - - +
241B GLY* 1.3 64.2 + - - +
243B LEU* 3.3 21.6 + - + +
244B GLU* 3.0 21.3 + - - +
250B HIS* 4.0 13.9 - - + -
253B LEU* 3.6 37.2 - - + -
268B ILE* 4.1 10.0 - - - +
312B ASP* 3.5 28.3 - - - +
378B PHE* 3.5 42.3 - - + -
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Residues in contact with GLY 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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237B ALA 2.8 17.8 + - - -
238B GLU* 3.0 5.7 + - - -
240B MET* 1.3 69.1 - - - +
242B TYR* 1.3 56.7 + - - +
244B GLU* 2.7 27.9 + - - +
245B SER* 3.0 12.4 + - - -
378B PHE* 3.7 18.4 - - - -
379B VAL* 5.3 4.7 - - - -
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Residues in contact with TYR 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 SER 3.9 1.9 + - - -
184B LEU* 4.1 5.4 - - + -
185B ASP* 3.3 46.8 + - - +
186B HIS* 3.9 24.0 - + + -
189B LEU* 3.5 22.2 - - + -
238B GLU 3.2 8.8 + - - +
239B GLY 3.1 11.4 - - - +
241B GLY* 1.3 70.8 - - - +
243B LEU* 1.3 67.6 + - + +
245B SER* 2.5 27.0 + - - -
246B LYS* 3.1 46.9 + - + +
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Residues in contact with LEU 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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184B LEU* 3.6 36.1 - - + -
189B LEU* 3.9 18.8 - - + -
239B GLY 3.3 9.3 + - - +
240B MET* 3.3 31.0 + - + +
241B GLY 3.2 1.4 - - - -
242B TYR* 1.3 77.5 - - + +
244B GLU* 1.3 58.9 + - - +
246B LYS* 2.9 8.4 + - - -
247B ARG 2.7 25.6 + - - -
248B PHE* 3.2 24.6 + - + +
250B HIS* 4.1 25.1 - - + +
271B PHE* 5.1 3.1 - - + -
274B MET* 4.1 15.7 - - + -
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Residues in contact with GLU 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 MET 3.0 12.7 + - - +
241B GLY* 2.7 17.8 + - - +
243B LEU* 1.3 72.7 - - - +
245B SER* 1.3 58.8 + - - +
247B ARG* 3.1 15.9 + - - +
248B PHE 4.2 0.4 + - - -
309B HIS* 3.0 55.3 + - + +
313B THR* 5.0 0.7 + - - -
377B THR* 3.7 24.3 - - - +
378B PHE* 3.0 39.8 + - + +
379B VAL* 4.3 3.6 + - - +
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Residues in contact with SER 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 GLY 3.0 6.4 + - - -
242B TYR* 2.5 33.8 + - - -
244B GLU* 1.3 74.5 - - - +
246B LYS* 1.3 61.3 + - - +
247B ARG* 3.1 4.5 + - - +
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Residues in contact with LYS 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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183B SER* 3.2 31.3 + - - +
184B LEU* 4.8 2.5 - - + -
242B TYR* 3.1 54.3 + - + +
243B LEU* 2.9 7.5 + - - +
245B SER* 1.3 80.2 - - - +
247B ARG* 1.3 68.4 + - - +
248B PHE* 3.4 32.4 + - + -
276B ALA* 6.0 0.3 - - - +
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Residues in contact with ARG 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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243B LEU 2.7 5.9 + - - -
244B GLU 3.1 14.4 + - - +
245B SER 3.1 2.7 - - - +
246B LYS* 1.3 83.7 - - - +
248B PHE* 1.3 60.2 + - - -
276B ALA* 4.9 2.2 - - + -
277B LEU* 3.2 56.3 + - - +
278B PRO 2.8 28.1 + - - -
279B GLN* 3.6 20.8 + - - +
280B ASN* 5.1 0.2 - - - +
281B ASP 3.0 23.6 + - - +
282B ASP* 4.9 1.8 - - - +
309B HIS* 4.0 15.0 + - - +
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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
------------------------------------------------------------
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