Contacts of the helix formed by residues 211 - 234 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ASN* 3.4 46.7 - - + +
5A ARG 5.1 1.4 + - - -
6A MSE 3.9 23.8 - - + -
209A GLY 3.7 11.4 - - - +
210A ALA* 1.3 74.8 - - - +
212A ALA* 1.3 73.1 + - + +
213A LEU* 3.4 43.1 - - + -
214A THR* 3.2 20.5 + - + +
215A ASP* 2.9 28.6 + - - -
256A ASN 5.4 0.4 + - - -
257A VAL* 3.8 13.0 - - + +
14B PHE* 3.5 36.1 - + + -
245B LEU* 4.1 15.7 - - + -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TRP* 1.3 81.4 - - + +
213A LEU* 1.3 62.8 + - - +
215A ASP* 3.6 6.6 + - - +
216A ALA* 3.1 22.3 + - - +
224B ILE* 6.2 0.7 - - + -
245B LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MSE 3.9 33.2 - - + -
211A TRP* 3.4 36.5 - - + -
212A ALA* 1.3 78.2 - - - +
214A THR* 1.3 62.0 + - - +
216A ALA* 3.4 8.8 + - + +
217A LEU* 3.2 33.1 + - + +
14B PHE* 4.2 14.4 - - + -
217B LEU* 5.6 2.7 - - + -
220B LYS* 6.6 0.2 - - + -
245B LEU* 4.3 9.6 - - + +
249B VAL* 4.1 25.6 - - + -
252B MSE 4.6 18.4 - - + -
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Residues in contact with THR 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MSE 4.0 18.8 - - + -
210A ALA* 3.9 3.8 - - - -
211A TRP* 3.2 34.4 + - - +
213A LEU* 1.3 73.7 - - - +
215A ASP* 1.3 62.4 + - - +
217A LEU* 3.3 7.2 + - - +
218A HIS* 2.8 51.5 + - - -
253A GLY* 3.8 17.0 - - - +
257A VAL* 3.5 29.4 - - + +
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Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 3.5 27.2 - - + +
210A ALA* 3.5 9.5 - - - +
211A TRP* 2.9 25.7 + - - +
212A ALA* 3.6 7.5 + - - +
214A THR* 1.3 79.4 + - - +
216A ALA* 1.3 55.5 + - - +
219A ILE* 3.0 32.3 + - - +
299A LYS* 3.2 38.1 + - - -
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Residues in contact with ALA 216 (chain A).
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 3.1 13.6 + - - +
213A LEU* 3.6 15.0 - - + +
214A THR 3.2 0.2 - - - -
215A ASP* 1.3 77.8 - - - +
217A LEU* 1.3 64.1 + - + +
219A ILE* 3.5 9.4 - - - +
220A LYS* 3.3 23.0 + - - +
220B LYS* 4.2 35.9 - - + +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A MSE 4.1 23.1 - - + -
213A LEU* 3.2 24.3 + - + +
214A THR* 3.8 6.1 - - - +
215A ASP 3.3 0.2 - - - -
216A ALA* 1.3 79.3 - - + +
218A HIS* 1.3 56.6 + - - +
220A LYS* 3.3 3.7 + - - +
221A ALA* 2.9 24.5 + - - +
249A VAL* 3.3 36.2 - - + +
252A MSE 4.0 43.3 - - + -
253A GLY* 4.2 6.5 - - - +
213B LEU* 5.5 3.8 - - + -
217B LEU* 4.5 20.0 - - + -
252B MSE 5.8 2.2 - - + -
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Residues in contact with HIS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A HIS 4.0 2.0 - - - -
201A ALA* 3.6 26.0 + - - +
204A GLY* 3.3 33.9 + - - -
205A TYR* 3.6 13.9 - - + -
214A THR* 2.8 35.3 + - - +
217A LEU* 1.3 70.6 - - - +
219A ILE* 1.3 66.8 + - - +
221A ALA* 3.0 6.5 + - - +
222A ILE* 2.9 28.5 + - - +
250A ALA* 3.3 16.4 + - - -
253A GLY* 3.3 7.8 - - - -
254A PHE* 2.9 43.8 + - + -
257A VAL* 3.9 3.2 - - - +
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 3.9 25.7 - - + +
215A ASP 3.0 20.4 + - - +
216A ALA* 3.5 11.7 - - - +
218A HIS* 1.3 76.9 - - - +
220A LYS* 1.3 67.7 + - + +
222A ILE* 3.6 11.8 + - + -
223A GLU* 3.2 22.3 + - - +
302A ASP* 3.8 39.0 - - + +
306A VAL* 3.9 21.0 - - + +
220B LYS* 6.4 0.7 - - - -
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Residues in contact with LYS 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA 3.3 15.0 + - - +
217A LEU* 3.3 6.0 + - - +
218A HIS 3.1 0.6 - - - -
219A ILE* 1.3 82.6 - - + +
221A ALA* 1.3 65.5 + - - +
223A GLU* 2.8 30.8 + - - +
224A ILE* 3.0 49.6 + - + +
249A VAL* 4.8 6.7 - - + -
213B LEU* 6.4 1.1 - - + -
216B ALA* 4.1 32.0 - - + +
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ALA* 4.0 4.9 - - + -
217A LEU 2.9 14.0 + - - +
218A HIS 3.5 8.1 - - - +
220A LYS* 1.3 77.6 - - - +
222A ILE* 1.3 55.9 + - - +
224A ILE* 3.3 6.6 + - - +
225A ILE* 2.9 38.5 + - + +
246A GLY 3.6 22.0 - - - +
249A VAL* 4.1 5.4 - - + -
250A ALA* 3.7 25.6 - - + +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 4.1 19.9 - - + +
201A ALA* 3.5 27.4 - - + +
202A ILE* 4.0 15.9 - - + -
205A TYR* 4.4 5.6 - - + -
218A HIS 2.9 21.7 + - - +
219A ILE* 3.7 16.6 - - + +
220A LYS 3.3 0.2 - - - -
221A ALA* 1.3 74.5 - - - +
223A GLU* 1.3 57.7 + - - +
225A ILE* 4.0 0.4 - - - +
226A ALA* 2.9 35.3 + - - +
303A ILE* 3.9 30.7 - - + -
306A VAL* 3.5 20.0 - - + -
307A MSE 4.1 12.1 - - + -
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ILE 3.2 10.6 + - - +
220A LYS* 2.8 41.7 + - + +
222A ILE* 1.3 78.8 - - - +
224A ILE* 1.3 64.8 + - + +
226A ALA* 4.1 0.9 - - - +
227A GLY* 3.1 20.4 + - - -
306A VAL* 3.8 38.4 - - + +
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LYS* 3.0 44.8 + - + +
221A ALA* 3.7 4.7 - - - +
223A GLU* 1.3 78.8 - - + +
225A ILE* 1.3 63.0 + - - +
227A GLY* 3.4 1.2 + - - -
228A ALA* 3.1 22.9 + - - +
242A GLU* 3.3 40.0 - - + +
243A MSE 5.1 0.2 - - - -
245A LEU* 4.4 21.3 - - + -
246A GLY* 3.7 18.4 - - - +
249A VAL* 4.8 6.1 - - + -
212B ALA* 6.3 0.7 - - + -
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A GLY 3.8 20.0 - - - +
197A ALA* 3.8 33.7 - - + +
198A LEU* 3.9 20.6 - - + +
201A ALA* 4.7 1.8 - - + -
221A ALA* 2.9 28.0 + - + +
222A ILE* 4.0 2.0 - - - +
224A ILE* 1.3 73.3 - - - +
226A ALA* 1.3 65.5 + - - +
228A ALA 3.2 0.3 + - - -
229A LEU* 2.9 33.3 + - + +
243A MSE 3.8 24.2 - - + -
246A GLY* 3.8 29.8 - - - +
247A GLN* 4.4 0.2 - - - -
250A ALA* 4.7 0.4 - - + -
330A LEU* 5.8 0.2 - - + -
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LEU* 4.8 3.1 - - + +
222A ILE* 2.9 23.1 + - + +
225A ILE* 1.3 76.6 - - - +
227A GLY* 1.3 60.4 + - - +
229A LEU* 4.5 3.5 + - - +
230A ARG* 3.7 22.2 + - - +
306A VAL 4.1 4.0 - - - +
307A MSE 3.6 45.8 - - + -
330A LEU* 5.1 10.0 - - - +
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU 3.1 16.4 + - - -
224A ILE 3.8 1.3 - - - -
225A ILE 3.1 0.8 - - - -
226A ALA* 1.3 80.0 - - - +
228A ALA* 1.3 59.0 + - - +
230A ARG* 5.4 1.9 + - - +
231A GLY 5.4 1.4 + - - -
242A GLU* 4.8 3.6 - - - +
306A VAL 5.2 1.1 + - - -
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ILE 3.1 14.8 + - - +
227A GLY* 1.3 77.7 - - - +
229A LEU* 1.3 66.2 + - - +
230A ARG 3.4 2.2 - - - -
231A GLY 3.2 4.6 + - - +
232A SER* 2.9 20.6 + - - -
239A ALA* 3.5 28.2 - - - +
242A GLU* 3.3 29.4 - - + +
243A MSE 4.2 7.4 - - + -
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LYS* 3.6 23.8 - - + +
191A ALA 4.2 2.9 - - - +
194A GLY* 3.8 21.3 - - - +
195A VAL* 4.0 18.2 - - + +
225A ILE* 2.9 20.5 + - + +
226A ALA 4.5 1.5 + - - +
227A GLY 3.9 0.6 - - - -
228A ALA* 1.3 75.3 - - - +
230A ARG* 1.3 64.5 + - - +
232A SER* 3.1 3.7 + - - -
233A VAL* 2.9 34.1 + - + +
243A MSE 3.7 30.0 - - + -
330A LEU* 4.2 26.2 - - + -
334A VAL* 4.2 12.1 - - + -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ALA* 3.7 19.0 + - - +
227A GLY 5.4 1.5 + - - +
228A ALA 3.4 0.4 - - - -
229A LEU* 1.3 77.2 - - - +
231A GLY* 1.3 62.9 + - - +
233A VAL* 3.4 3.3 + - - +
234A ALA* 3.0 22.9 + - - +
307A MSE 6.1 1.2 - - - +
326A ALA 4.8 1.6 + - - -
329A ALA* 4.2 4.8 - - - +
330A LEU* 3.5 47.8 - - + +
333A ASP* 2.9 39.6 + - + +
334A VAL* 4.4 10.1 - - + -
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLY 5.4 1.2 + - - -
228A ALA* 3.2 7.9 + - - +
230A ARG* 1.3 79.0 - - - +
232A SER* 1.3 60.8 + - - +
234A ALA* 3.2 9.0 + - - +
235A GLY 3.1 5.4 + - - -
236A ASP* 2.9 29.3 + - - +
239A ALA* 3.6 12.3 - - - -
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A MSE 5.7 1.7 - - - +
190A LYS* 3.2 36.5 + - - +
228A ALA 2.9 16.8 + - - -
229A LEU* 3.6 6.5 - - - -
231A GLY* 1.3 72.5 - - - +
233A VAL* 1.3 62.6 + - - +
235A GLY* 2.8 16.5 + - - -
236A ASP 4.1 5.2 - - - -
239A ALA* 3.3 13.1 - - - +
240A GLY* 3.6 15.6 - - - -
243A MSE 3.8 20.5 - - - +
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Residues in contact with VAL 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A PRO* 3.6 41.4 - - + +
190A LYS* 4.2 10.2 + - + +
191A ALA* 3.9 25.6 - - - +
229A LEU* 2.9 27.5 + - + +
230A ARG 3.7 5.2 - - - +
232A SER* 1.3 75.9 - - - +
234A ALA* 1.3 61.1 + - - +
235A GLY* 3.1 1.3 + - - -
333A ASP 5.8 0.4 - - - +
334A VAL* 3.8 36.3 - - + +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ARG 3.0 13.0 + - - +
231A GLY* 3.4 13.9 - - - +
232A SER 3.0 0.4 - - - -
233A VAL* 1.3 77.7 - - - +
235A GLY* 1.3 56.7 + - - +
236A ASP* 3.6 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
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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