Contacts of the helix formed by residues 211 - 234 (chain B) in PDB entry 1RRM
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 TRP 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A PHE* 3.5 37.7 - + + -
245A LEU* 4.2 14.6 - - + -
4B ASN* 3.5 45.5 - - + +
5B ARG 5.1 2.0 + - - -
6B MSE 3.8 23.7 - - + -
209B GLY 3.7 6.3 - - - +
210B ALA* 1.3 73.7 - - - +
212B ALA* 1.3 73.2 + - + +
213B LEU* 3.2 41.8 + - + -
214B THR* 3.2 19.0 + - + +
215B ASP* 2.9 27.3 + - - -
256B ASN 5.3 0.6 + - - -
257B VAL* 3.6 20.8 - - + +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ILE* 6.3 0.4 - - + -
245A LEU* 3.8 21.8 - - + -
211B TRP* 1.3 80.1 - - + +
213B LEU* 1.3 63.0 + - - +
215B ASP* 3.4 7.5 + - - +
216B ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.3 13.2 - - + -
217A LEU* 5.5 2.7 - - + -
220A LYS* 6.4 0.9 - - + -
245A LEU* 4.4 10.9 - - + +
249A VAL* 4.1 25.6 - - + -
252A MSE 4.8 17.5 - - + -
6B MSE 3.9 34.1 - - + -
8B LEU* 6.3 0.2 - - + -
211B TRP* 3.4 35.8 - - + -
212B ALA* 1.3 78.6 - - - +
214B THR* 1.3 61.5 + - - +
216B ALA* 3.3 9.0 + - + +
217B LEU* 3.2 33.9 + - + +
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Residues in contact with THR 214 (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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6B MSE 3.9 18.4 - - + -
210B ALA* 3.8 4.5 - - - +
211B TRP* 3.2 34.5 + - - +
213B LEU* 1.3 72.5 - - - +
215B ASP* 1.3 63.8 + - - +
217B LEU* 3.7 6.9 - - - +
218B HIS* 2.8 52.8 + - - -
253B GLY* 3.8 15.5 - - - +
257B VAL* 3.5 29.2 - - + +
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Residues in contact with ASP 215 (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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205B TYR* 3.5 23.6 - - + +
210B ALA* 3.4 15.5 - - - +
211B TRP* 2.9 23.8 + - - +
212B ALA* 3.6 7.9 + - - +
213B LEU 3.2 0.2 - - - -
214B THR* 1.3 79.5 + - - +
216B ALA* 1.3 61.9 + - - +
218B HIS* 4.6 0.4 - - - -
219B ILE* 3.0 28.0 + - - +
299B LYS* 3.1 39.0 + - - -
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS* 4.1 36.3 - - + +
212B ALA 3.1 10.4 + - - +
213B LEU* 3.6 15.0 - - + +
214B THR 3.2 0.2 - - - -
215B ASP* 1.3 80.0 - - - +
217B LEU* 1.3 62.9 + - + +
219B ILE* 3.6 9.0 - - - +
220B LYS* 3.4 23.6 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LEU* 5.6 3.1 - - + -
217A LEU* 4.5 21.1 - - + -
252A MSE 5.8 2.2 - - + -
6B MSE 3.9 24.5 - - + -
213B LEU* 3.2 24.1 + - + +
214B THR* 3.7 5.8 - - - +
216B ALA* 1.3 78.0 - - + +
218B HIS* 1.3 59.1 + - - +
220B LYS* 3.3 3.3 + - - +
221B ALA* 2.9 24.4 + - - +
249B VAL* 3.4 36.4 - - + +
252B MSE 3.9 41.7 - - + -
253B GLY* 4.1 5.8 - - - +
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Residues in contact with HIS 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ALA* 3.6 33.0 - - - +
204B GLY* 3.2 31.1 + - - -
205B TYR* 3.5 13.5 + - + -
214B THR* 2.8 27.4 + - - +
215B ASP* 4.7 0.2 - - - -
217B LEU* 1.3 74.5 - - - +
219B ILE* 1.3 56.6 + - - +
221B ALA* 3.2 4.9 + - - +
222B ILE* 2.9 34.3 + - - +
250B ALA* 3.4 17.1 + - - -
253B GLY* 3.2 12.8 - - - -
254B PHE* 2.7 39.0 + - - +
257B VAL* 3.9 7.6 - - + -
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LYS* 6.4 0.7 - - - +
205B TYR* 3.8 26.4 - - + +
215B ASP 3.0 22.6 + - - +
216B ALA* 3.6 11.9 - - - +
218B HIS* 1.3 76.5 - - - +
220B LYS* 1.3 65.4 + - + +
222B ILE* 3.6 11.8 + - + -
223B GLU* 3.2 21.8 + - - +
302B ASP* 3.8 38.6 - - + +
303B ILE 4.2 0.4 - - - +
306B VAL* 4.0 19.0 - - + +
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Residues in contact with LYS 220 (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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213A LEU* 6.6 0.2 - - + -
216A ALA* 4.2 30.3 - - + +
216B ALA 3.4 15.0 + - - +
217B LEU* 3.3 6.0 + - - +
218B HIS 3.2 0.4 - - - -
219B ILE* 1.3 80.3 - - + +
221B ALA* 1.3 66.5 + - - +
223B GLU* 2.8 32.4 + - - +
224B ILE* 2.9 50.4 + - + +
249B VAL* 4.8 7.6 - - + -
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Residues in contact with ALA 221 (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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201B ALA* 4.0 4.3 - - + -
217B LEU 2.9 13.6 + - - +
218B HIS 3.5 8.7 - - - +
220B LYS* 1.3 77.7 - - - +
222B ILE* 1.3 56.9 + - - +
224B ILE* 3.3 6.4 + - - +
225B ILE* 2.9 37.6 + - + +
246B GLY 3.7 22.0 - - - +
249B VAL* 4.1 5.8 - - + +
250B ALA* 3.7 26.0 - - + +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.1 19.2 - - + +
201B ALA* 3.5 27.4 - - + +
202B ILE* 3.9 21.8 - - + -
205B TYR* 4.4 5.6 - - + -
218B HIS 2.9 22.8 + - - +
219B ILE* 3.8 14.6 - - + +
221B ALA* 1.3 75.4 - - - +
223B GLU* 1.3 58.1 + - - +
225B ILE* 4.0 0.2 - - - +
226B ALA* 2.8 35.2 + - - +
303B ILE* 3.9 25.1 - - + -
306B VAL* 3.5 20.6 - - + -
307B MSE 4.2 12.6 - - + -
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Residues in contact with GLU 223 (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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219B ILE 3.2 11.3 + - - +
220B LYS* 2.8 41.9 + - + +
222B ILE* 1.3 81.0 - - - +
224B ILE* 1.3 63.1 + - + +
226B ALA* 4.3 0.7 - - - +
227B GLY* 3.1 20.3 + - - -
306B VAL* 3.7 36.2 - - + +
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Residues in contact with ILE 224 (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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212A ALA* 6.2 1.1 - - + -
220B LYS* 2.9 45.0 + - + +
221B ALA* 3.7 4.7 - - - +
223B GLU* 1.3 78.2 - - + +
225B ILE* 1.3 63.9 + - - +
227B GLY* 3.4 0.7 + - - -
228B ALA* 3.1 23.4 + - - +
242B GLU* 3.2 38.8 - - + +
245B LEU* 4.4 20.9 - - + -
246B GLY* 3.7 18.8 - - - +
249B VAL* 4.9 5.4 - - + -
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Residues in contact with ILE 225 (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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194B GLY 3.8 19.7 - - - +
197B ALA* 3.7 35.0 - - + +
198B LEU* 3.8 20.2 - - + +
201B ALA* 4.5 2.7 - - + -
221B ALA* 2.9 28.6 + - + +
222B ILE* 4.0 2.2 - - - +
224B ILE* 1.3 76.2 - - - +
226B ALA* 1.3 59.6 + - - +
229B LEU* 2.9 38.2 + - + +
243B MSE 3.8 24.0 - - + -
246B GLY* 4.0 27.1 - - - +
247B GLN* 4.6 0.2 - - - -
250B ALA* 4.7 0.7 - - + -
330B LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 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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198B LEU* 4.9 2.4 - - + +
222B ILE* 2.8 23.1 + - + +
225B ILE* 1.3 76.4 - - - +
227B GLY* 1.3 60.1 + - - +
228B ALA 3.7 0.2 + - - -
229B LEU* 4.6 3.2 + - - +
230B ARG* 3.9 20.6 + - - -
306B VAL 4.0 9.9 - - - +
307B MSE 3.7 41.7 - - + -
330B LEU* 5.1 9.4 - - - +
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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
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223B GLU 3.1 17.9 + - - -
224B ILE 3.8 1.6 - - - -
226B ALA* 1.3 80.2 - - - +
228B ALA* 1.3 58.3 + - - +
230B ARG* 5.5 1.0 + - - +
231B GLY 5.4 1.7 + - - -
242B GLU* 4.9 3.7 - - - +
306B VAL 5.2 1.1 + - - -
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Residues in contact with ALA 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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224B ILE 3.1 14.4 + - - +
227B GLY* 1.3 78.1 - - - +
229B LEU* 1.3 65.3 + - - +
230B ARG 3.4 2.5 - - - -
231B GLY* 3.2 4.2 + - - +
232B SER* 2.9 20.4 + - - -
239B ALA* 3.5 18.5 - - - +
242B GLU* 3.4 38.8 - - + +
243B MSE 4.1 8.7 - - + -
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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
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190B LYS* 3.6 24.2 - - + +
191B ALA 4.2 2.7 - - - +
194B GLY* 3.8 20.4 - - - +
195B VAL* 3.9 28.3 - - + -
198B LEU* 5.9 0.2 - - + -
225B ILE* 2.9 21.3 + - + +
226B ALA 4.6 1.5 + - - +
227B GLY 3.9 0.6 - - - -
228B ALA* 1.3 76.8 - - - +
230B ARG* 1.3 63.4 + - - +
232B SER* 3.2 3.3 + - - -
233B VAL* 2.9 35.1 + - + +
243B MSE 3.7 18.1 - - + -
330B LEU* 4.2 25.4 - - + -
334B VAL* 4.2 13.0 - - + -
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Residues in contact with ARG 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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226B ALA* 3.9 19.4 + - - +
227B GLY 5.5 1.3 + - - +
228B ALA 3.4 0.8 - - - -
229B LEU* 1.3 76.5 - - - +
231B GLY* 1.3 63.2 + - - +
233B VAL* 3.4 3.2 + - - +
234B ALA* 3.0 22.9 + - - +
307B MSE 5.9 2.2 + - - +
326B ALA 4.8 1.8 + - - -
329B ALA* 4.2 4.8 - - - +
330B LEU* 3.4 47.1 - - + +
333B ASP* 2.8 36.8 + - + +
334B VAL* 4.4 13.7 - - + -
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Residues in contact with GLY 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 5.4 1.4 + - - -
228B ALA* 3.2 7.5 + - - +
230B ARG* 1.3 81.5 - - - +
232B SER* 1.3 58.7 + - - +
234B ALA* 3.3 9.2 + - - +
235B GLY 3.2 4.5 + - - -
236B ASP* 2.9 30.1 + - - +
239B ALA* 3.7 12.1 - - - -
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LYS* 3.1 35.5 + - - +
228B ALA 2.9 16.6 + - - -
229B LEU* 3.7 6.5 - - - -
231B GLY* 1.3 71.8 - - - +
233B VAL* 1.3 61.3 + - - +
234B ALA 3.0 1.1 - - - -
235B GLY* 2.8 16.6 + - - -
236B ASP 4.2 4.7 - - - -
239B ALA* 3.4 13.4 - - - +
240B GLY* 3.6 16.5 - - - -
243B MSE 3.8 21.2 - - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO* 3.7 39.7 - - + +
190B LYS* 4.1 10.0 + - + +
191B ALA* 3.9 30.3 - - - +
229B LEU* 2.9 27.4 + - + +
230B ARG 3.7 5.2 - - - +
232B SER* 1.3 75.9 - - - +
234B ALA* 1.3 61.6 + - - +
235B GLY* 3.1 1.1 + - - -
333B ASP 5.8 0.2 - - - +
334B VAL* 3.9 31.2 - - + +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ARG 3.0 13.4 + - - +
231B GLY* 3.4 15.5 - - - +
232B SER 3.0 0.6 - - - -
233B VAL* 1.3 77.9 - - - +
235B GLY* 1.3 56.2 + - - +
236B ASP* 3.6 1.8 - - + +
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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