Contacts of the helix formed by residues 227 - 253 (chain E) in PDB entry 4PHZ
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 227 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225E GLY 3.2 0.8 + - - -
226E ASP* 1.3 70.2 + - - +
228E ASP* 1.3 65.6 + - - +
229E ARG 3.2 0.4 - - - -
230E ARG* 3.5 33.1 + - + +
231E ILE* 3.3 29.1 + - + +
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Residues in contact with ASP 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E PHE* 5.9 0.2 - - - -
202E TRP* 3.7 20.2 - - + -
206E LYS* 2.7 33.3 + - - -
223E VAL 3.5 0.9 - - - +
224E ILE* 3.5 23.2 - - + -
225E GLY 2.7 35.7 + - - +
227E ASP* 1.3 76.7 + - - +
229E ARG* 1.3 58.3 + - - +
231E ILE* 3.3 13.3 + - - +
232E GLY 3.1 21.5 + - - -
141F LEU* 3.9 4.6 - - + +
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Residues in contact with ARG 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221E ASP* 5.4 3.2 + - - -
224E ILE* 3.5 23.6 + - + +
225E GLY* 3.2 12.1 - - - -
226E ASP* 2.9 46.3 + - + +
228E ASP* 1.3 76.2 - - - +
230E ARG* 1.3 60.2 + - - +
233E ALA* 3.0 25.1 + - - +
85F TRP* 5.8 0.8 - - - -
141F LEU* 3.8 26.8 + - + +
142F LEU* 3.3 42.9 + - + +
144F GLY* 6.2 1.4 - - - -
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Residues in contact with ARG 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ASP* 5.1 11.7 + - + -
227E ASP* 3.5 33.5 + - + +
228E ASP 3.3 0.6 - - - -
229E ARG* 1.3 75.7 - - - +
231E ILE* 1.3 65.8 + - + +
233E ALA* 3.2 5.6 + - - +
234E ILE* 2.9 36.2 + - + +
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Residues in contact with ILE 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TRP* 5.1 0.9 - - + -
201E PHE* 3.7 39.9 - - + -
202E TRP* 4.5 5.4 - - + -
205E ARG* 4.7 9.0 - - - +
227E ASP* 3.3 19.3 - - + +
228E ASP* 3.3 18.5 + - - +
230E ARG* 1.3 76.0 - - + +
232E GLY* 1.3 57.7 + - - +
234E ILE* 3.2 8.3 + - + +
235E VAL* 2.9 40.8 + - + +
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Residues in contact with GLY 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E TRP* 4.2 15.9 - - - -
202E TRP* 4.9 0.4 - - - -
228E ASP 3.1 10.9 + - - -
229E ARG 3.9 2.5 - - - -
231E ILE* 1.3 77.3 - - - +
233E ALA* 1.3 55.4 + - - +
235E VAL* 3.3 0.3 + - - -
236E LEU* 2.9 32.7 + - - +
138F VAL* 3.7 10.6 - - - +
141F LEU* 4.0 20.8 - - - +
142F LEU* 4.8 0.4 - - - -
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Residues in contact with ALA 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E ARG 3.0 19.1 + - - +
230E ARG* 3.2 6.9 + - - +
232E GLY* 1.3 74.6 - - - +
234E ILE* 1.3 62.6 + - + +
236E LEU* 4.1 4.5 - - - +
237E ALA* 3.2 24.8 + - - +
142F LEU* 4.1 23.1 - - + +
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Residues in contact with ILE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ARG* 2.9 28.6 + - + +
231E ILE* 3.7 7.4 - - + +
233E ALA* 1.3 81.2 - - + +
235E VAL* 1.3 70.6 + - + +
237E ALA* 2.9 8.3 + - + +
238E LEU* 2.8 41.4 + - + +
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Residues in contact with VAL 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E VAL* 5.8 5.4 - - + -
198E TRP* 3.8 38.8 - - + -
231E ILE* 2.9 33.0 + - + +
232E GLY 3.9 1.6 - - - +
234E ILE* 1.3 77.3 - - + +
236E LEU* 1.3 59.2 + - - +
238E LEU* 3.2 11.8 + - + +
239E THR* 2.8 41.3 + - - +
134F ILE* 4.6 12.8 - - + -
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Residues in contact with LEU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232E GLY 2.9 17.8 + - - +
233E ALA* 4.1 4.9 - - - +
235E VAL* 1.3 79.1 - - - +
237E ALA* 1.3 62.8 + - - +
239E THR* 3.1 8.6 + - + -
240E ILE* 3.0 35.8 + - + +
134F ILE* 4.5 7.6 - - + -
135F TRP* 3.7 57.7 - - + +
138F VAL* 3.7 26.0 - - + +
139F ILE* 5.1 7.2 - - + -
142F LEU* 4.8 8.5 - - + -
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Residues in contact with ALA 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E ALA 3.2 13.8 + - - +
234E ILE* 2.9 13.4 + - + +
236E LEU* 1.3 79.7 - - - +
238E LEU* 1.3 63.4 + - + +
240E ILE* 3.6 7.7 + - - +
241E LEU* 3.0 25.2 + - - +
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Residues in contact with LEU 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ILE* 2.8 35.7 + - + +
235E VAL* 3.4 14.4 - - + +
237E ALA* 1.3 75.3 - - + +
239E THR* 1.3 56.7 + - - +
241E LEU* 3.3 14.9 + - + +
242E ALA* 2.8 32.5 + - - +
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Residues in contact with THR 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E TRP* 3.6 29.6 - - + -
194E VAL* 5.5 1.4 - - - +
235E VAL* 2.8 31.4 + - - +
236E LEU* 3.1 11.4 + - + -
238E LEU* 1.3 73.8 - - - +
240E ILE* 1.3 66.3 + - + +
241E LEU 3.2 0.2 + - - -
242E ALA* 3.3 4.0 + - - +
243E THR* 2.9 25.5 + - - -
131F VAL* 3.8 24.7 - - + +
134F ILE* 4.0 23.7 - - + +
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Residues in contact with ILE 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E LEU* 3.0 34.2 + - + +
237E ALA* 4.0 6.7 - - - +
239E THR* 1.3 77.0 - - + +
241E LEU* 1.3 64.3 + - - +
243E THR* 3.2 8.6 + - + -
244E ILE* 2.9 43.2 + - + +
131F VAL* 6.0 1.3 - - + -
135F TRP* 4.0 28.9 - - + -
160F LEU* 5.2 13.9 - - + -
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Residues in contact with LEU 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E ALA 3.0 19.4 + - - +
238E LEU* 3.4 16.2 - - + +
240E ILE* 1.3 78.9 - - - +
242E ALA* 1.3 59.5 - - - +
244E ILE* 2.9 14.2 + - + +
245E VAL* 2.8 42.1 + - + +
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Residues in contact with ALA 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E TRP* 3.8 9.6 - - + -
191E TRP* 4.0 19.7 - - + -
238E LEU 2.8 21.2 + - - +
239E THR 3.6 4.7 - - - +
241E LEU* 1.3 75.5 - - - +
243E THR* 1.3 56.6 + - - +
245E VAL* 3.9 8.4 - - - +
246E GLY* 3.0 25.9 + - - -
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Residues in contact with THR 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E TRP* 4.7 8.0 - - - -
191E TRP* 4.1 3.1 - - - -
239E THR 2.9 17.5 + - - -
240E ILE* 3.5 8.3 - - - +
241E LEU 3.0 0.2 - - - -
242E ALA* 1.3 76.8 - - - +
244E ILE* 1.3 66.1 + - + +
246E GLY* 4.1 0.5 - - - -
247E TYR* 3.1 23.2 + - - +
131F VAL* 3.5 28.1 - - - +
160F LEU* 4.2 22.2 - - + -
163F PRO* 4.5 20.3 - - + +
164F ASN* 4.5 11.3 - - + +
167F PRO* 5.6 0.3 - - - +
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Residues in contact with ILE 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E ILE* 2.9 35.7 + - + +
241E LEU* 3.6 13.5 - - + +
243E THR* 1.3 76.2 - - + +
245E VAL* 1.3 67.9 + - + +
247E TYR* 3.3 7.2 + - - +
248E ALA* 3.0 26.2 + - + +
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Residues in contact with VAL 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E LEU* 2.8 38.7 + - + +
242E ALA* 3.9 8.1 - - - +
244E ILE* 1.3 73.0 - - + +
246E GLY* 1.3 58.4 + - - +
247E TYR 3.1 0.5 + - - -
248E ALA* 3.2 6.6 + - - +
249E VAL* 2.8 46.2 + - + +
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Residues in contact with GLY 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E TRP* 4.0 19.7 - - - -
242E ALA 3.0 22.2 + - - -
245E VAL* 1.3 76.9 - - - +
247E TYR* 1.3 57.9 + - - +
249E VAL* 4.0 5.4 - - - +
250E THR* 2.9 33.8 + - - +
167F PRO* 3.7 8.1 - - - +
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Residues in contact with TYR 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E THR* 3.1 19.4 + - + +
244E ILE* 3.4 7.0 - - + +
245E VAL 3.1 0.6 - - - -
246E GLY* 1.3 76.5 - - - +
248E ALA* 1.3 64.1 + - + +
250E THR* 2.9 19.5 + - - -
251E ASN* 2.9 35.5 + - - +
162F TYR* 5.8 3.9 - + - -
163F PRO* 4.1 28.3 - - + +
166F TRP* 3.4 45.3 + + + -
167F PRO* 4.3 3.7 - - - +
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Residues in contact with ALA 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E ILE* 3.0 17.2 + - + +
245E VAL* 3.7 4.7 - - - +
247E TYR* 1.3 79.4 - - + +
249E VAL* 1.3 68.2 + - - +
251E ASN* 3.1 21.1 - - - +
252E SER* 3.1 11.6 + - - -
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Residues in contact with VAL 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ARG* 5.2 3.8 - - - +
245E VAL* 2.8 34.2 + - + +
246E GLY* 4.0 5.6 - - - +
248E ALA* 1.3 71.7 - - + +
250E THR* 1.3 62.3 + - + +
252E SER* 2.6 31.2 + - - -
253E THR* 3.1 19.3 + - - +
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Residues in contact with THR 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E ARG* 3.5 25.6 - - + +
246E GLY 2.9 21.2 + - - +
247E TYR* 2.9 10.4 + - - -
249E VAL* 1.3 81.5 - - + +
251E ASN* 1.3 51.7 + - - +
253E THR* 2.7 28.0 - - - +
254E PHE* 3.5 14.5 - - - +
166F TRP* 3.6 14.5 + - - -
167F PRO* 3.5 40.9 - - + +
170F ALA* 4.5 8.5 - - - +
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Residues in contact with ASN 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E TYR* 2.9 31.1 + - - +
248E ALA* 3.1 17.6 - - - +
249E VAL 2.8 0.4 + - - -
250E THR* 1.3 73.8 - - - +
252E SER* 1.3 55.5 + - - +
253E THR 2.9 11.0 - - - +
254E PHE 4.3 4.2 - - - +
255E PRO* 3.3 24.0 - - - +
166F TRP* 3.5 20.5 + - - +
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Residues in contact with SER 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E ALA 3.1 9.4 + - - -
249E VAL* 2.6 18.3 + - - -
251E ASN* 1.3 68.4 - - - +
253E THR* 1.3 67.4 + - - +
255E PRO* 3.4 18.8 - - - +
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Residues in contact with THR 253 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183E ARG* 3.5 30.1 + - - +
249E VAL* 3.1 16.7 + - - +
250E THR* 2.7 18.7 - - - +
251E ASN 2.9 1.4 - - - -
252E SER* 1.3 82.4 - - - +
254E PHE* 1.3 92.3 + - + +
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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
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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