Contacts of the helix formed by residues 186 - 207 (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 PRO 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A GLY 3.5 6.7 - - - +
185A MSE 1.3 84.6 - - - +
187A PRO* 1.3 75.6 - - + +
188A ALA* 4.4 6.7 - - + +
189A LEU* 2.8 35.2 + - + +
190A LYS* 3.0 9.9 + - - +
389A APR 4.0 11.0 - - + +
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Residues in contact with PRO 187 (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 3.5 3.1 - - - +
186A PRO* 1.3 83.5 - - + +
188A ALA* 1.3 56.4 + - - +
190A LYS* 3.2 14.7 + - + +
191A ALA* 2.9 27.7 + - - +
233A VAL* 3.6 36.2 - - + +
334A VAL 5.9 0.2 - - - -
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Residues in contact with ALA 188 (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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186A PRO* 3.1 5.5 + - + +
187A PRO* 1.3 79.0 - - - +
189A LEU* 1.3 58.3 + - - +
191A ALA* 3.4 8.0 + - - +
192A ALA* 2.9 28.1 + - - +
334A VAL 5.4 2.0 - - - -
336A ILE* 5.7 0.3 - - - +
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Residues in contact with LEU 189 (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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141A THR* 4.5 2.0 - - + -
185A MSE 3.6 28.7 - - + -
186A PRO* 2.8 26.8 + - + +
188A ALA* 1.3 75.4 - - - +
190A LYS* 1.3 61.7 + - - +
191A ALA 3.1 0.2 - - - -
192A ALA* 4.4 7.2 - - + +
193A THR* 2.8 52.9 + - + +
389A APR 3.5 55.2 - - + +
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Residues in contact with LYS 190 (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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142A ALA* 5.0 1.0 - - - +
182A MSE 4.4 4.5 - - - -
183A ASP* 3.9 22.1 + - - +
185A MSE 3.4 48.0 + - + +
186A PRO 3.0 10.1 + - - +
187A PRO* 3.5 12.1 - - + +
189A LEU* 1.3 76.2 - - - +
191A ALA* 1.3 57.4 + - - +
193A THR* 3.6 6.0 + - - -
194A GLY* 2.9 28.2 + - - -
229A LEU* 3.6 6.6 - - + +
232A SER* 3.2 42.4 + - - +
233A VAL* 4.2 14.7 + - + -
235A GLY* 4.1 14.5 + - - -
236A ASP 5.6 1.0 + - - -
240A GLY* 6.3 0.4 - - - -
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Residues in contact with ALA 191 (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 2.9 13.0 + - - +
188A ALA* 3.4 11.9 - - - +
189A LEU 3.1 0.2 - - - -
190A LYS* 1.3 77.7 - - - +
192A ALA* 1.3 57.9 + - - +
194A GLY* 3.8 0.5 - - - -
195A VAL* 3.0 34.1 + - - +
229A LEU* 4.2 2.9 - - - +
233A VAL* 3.9 10.5 - - + +
334A VAL* 3.4 40.8 - - + +
336A ILE* 4.0 8.3 - - + -
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Residues in contact with ALA 192 (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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188A ALA 2.9 17.4 + - - +
189A LEU* 3.9 8.7 - - + +
191A ALA* 1.3 76.2 - - - +
193A THR* 1.3 63.9 + - + +
195A VAL* 3.3 1.2 + - - -
196A ASP 3.0 17.8 + - - -
276A PRO* 5.5 3.6 - - + -
278A GLY* 3.3 19.0 - - - +
279A VAL* 3.9 31.9 - - + +
336A ILE* 4.2 11.1 - - + +
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Residues in contact with THR 193 (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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141A THR* 3.8 14.8 - - - -
142A ALA 3.4 14.7 + - - -
143A GLY* 2.9 29.2 - - - -
185A MSE 3.5 15.8 - - - +
189A LEU* 2.8 45.8 + - + +
190A LYS* 3.6 2.6 + - - -
192A ALA* 1.3 73.3 - - + +
194A GLY* 1.3 59.6 + - - +
196A ASP* 3.3 7.7 + - - +
197A ALA 3.0 13.7 + - - -
278A GLY* 5.1 0.9 - - - -
389A APR 3.4 24.7 - - - +
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Residues in contact with GLY 194 (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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142A ALA 3.6 11.2 - - - -
190A LYS 2.9 20.0 + - - -
191A ALA 3.8 1.1 - - - -
193A THR* 1.3 76.8 + - - +
195A VAL* 1.3 59.6 + - - +
197A ALA* 3.3 4.6 + - - +
198A LEU* 3.0 24.1 + - - +
225A ILE* 3.8 7.1 - - - +
229A LEU* 3.8 9.9 - - - -
243A MSE 3.6 15.0 - - - -
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Residues in contact with VAL 195 (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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191A ALA 3.0 18.2 + - - +
192A ALA 4.0 3.1 - - - +
194A GLY* 1.3 73.8 - - - +
196A ASP* 1.3 61.4 + - - +
198A LEU* 3.3 8.9 + - + +
199A THR* 2.8 38.8 + - - +
229A LEU* 4.0 15.3 - - + -
278A GLY 4.6 0.4 - - - +
282A ALA* 3.5 35.4 - - + +
285A LEU* 4.4 11.2 - - + -
327A VAL* 5.9 0.2 - - + -
330A LEU* 4.8 7.4 - - + -
331A ASN* 3.6 14.1 - - - +
334A VAL* 4.5 4.3 - - + -
336A ILE* 3.6 15.9 - - + -
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Residues in contact with ASP 196 (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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143A GLY 3.5 11.8 - - - +
144A THR* 3.6 15.2 - - - +
192A ALA 3.0 13.6 + - - +
193A THR* 3.3 12.5 - - - +
194A GLY 3.2 0.2 - - - -
195A VAL* 1.3 76.9 - - - +
197A ALA* 1.3 55.9 + - - +
199A THR* 3.1 4.7 + - - -
200A HIS* 2.9 33.6 + - - -
277A HIS* 3.4 14.1 - - - -
278A GLY* 3.9 12.9 - - - +
281A ASN* 3.0 15.8 + - - +
387A ZN 2.3 34.5 - - - -
389A APR 4.9 2.4 + - - +
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Residues in contact with ALA 197 (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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142A ALA 4.2 2.0 - - - +
143A GLY* 3.4 20.1 + - - +
193A THR 3.0 11.2 + - - +
194A GLY* 3.5 10.1 - - - +
195A VAL 3.2 0.2 - - - -
196A ASP* 1.3 73.6 - - - +
198A LEU* 1.3 65.3 + - - +
200A HIS* 3.1 9.5 + - - +
201A ALA* 3.1 21.3 + - - +
225A ILE* 3.8 15.0 - - + +
243A MSE 4.8 0.7 - - + -
247A GLN* 3.7 26.9 - - + +
250A ALA* 4.0 2.1 - - - +
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Residues in contact with LEU 198 (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 3.0 14.2 + - - +
195A VAL* 3.3 13.0 + - + +
197A ALA* 1.3 76.2 - - - +
199A THR* 1.3 58.8 + - - +
201A ALA* 3.2 3.3 + - - +
202A ILE* 2.9 45.5 + - + +
222A ILE* 4.1 33.9 - - + +
225A ILE* 3.9 22.3 - - + +
226A ALA* 4.8 3.6 - - + +
285A LEU* 4.4 12.1 - - + -
307A MSE 4.3 14.4 - - + -
327A VAL* 4.7 4.7 - - + -
330A LEU* 3.5 30.7 - - + -
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Residues in contact with THR 199 (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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195A VAL* 2.8 20.9 + - - +
196A ASP 3.3 9.9 - - - -
198A LEU* 1.3 76.8 - - - +
200A HIS* 1.3 55.9 + - - +
202A ILE 4.5 0.2 - - - +
203A GLU* 2.8 39.1 + - + +
262A VAL* 3.5 23.3 - - + -
263A HIS* 3.4 28.5 - - + +
281A ASN* 3.6 15.1 - - - +
285A LEU* 3.6 26.7 - - + +
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Residues in contact with HIS 200 (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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143A GLY 3.2 27.7 + - - -
144A THR* 3.4 19.8 + - - -
145A ALA* 5.0 1.2 - - - +
196A ASP* 2.9 18.8 + - - -
197A ALA* 3.1 9.0 + - - +
199A THR* 1.3 76.3 - - - +
201A ALA* 1.3 57.3 + - - +
204A GLY* 2.9 28.4 + - - -
218A HIS* 4.0 0.3 - - - -
247A GLN 5.4 0.4 + - - -
250A ALA* 4.2 6.4 - - + +
254A PHE* 3.4 39.0 - + + +
259A LEU* 3.6 13.4 - - + +
263A HIS* 3.0 23.1 + + - -
387A ZN 2.2 30.5 - - - -
390A PGO 3.3 6.7 + - - -
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Residues in contact with ALA 201 (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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197A ALA 3.1 9.2 + - - +
198A LEU* 3.2 8.7 + - - +
200A HIS* 1.3 77.1 - - - +
202A ILE* 1.3 59.9 + - - +
205A TYR* 2.9 31.0 + - - +
218A HIS* 3.6 23.2 - - - +
221A ALA* 4.0 17.3 - - + -
222A ILE* 3.5 26.2 - - + +
225A ILE* 4.7 0.7 - - + -
250A ALA* 4.1 3.1 - - + +
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Residues in contact with ILE 202 (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* 2.9 39.0 + - + +
199A THR 4.1 1.6 - - - +
201A ALA* 1.3 73.1 - - - +
203A GLU* 1.3 68.4 + - + +
205A TYR* 3.2 11.9 + - - +
206A ILE* 3.2 21.8 + - + +
222A ILE* 4.0 22.7 - - + -
285A LEU* 4.3 14.4 - - + -
289A MSE 4.1 35.9 - - + -
300A TYR* 5.6 0.2 - - + -
303A ILE* 4.0 29.8 - - + -
307A MSE 4.7 0.4 - - - -
327A VAL* 4.2 11.9 - - + -
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Residues in contact with GLU 203 (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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199A THR* 2.8 29.8 + - + +
202A ILE* 1.3 73.1 - - + +
204A GLY* 1.3 57.3 + - - +
206A ILE* 3.3 11.2 + - + +
207A THR* 2.9 32.3 + - - -
259A LEU* 3.6 18.9 - - + +
260A GLY* 3.0 25.7 + - - -
261A LEU 3.2 1.4 + - - -
262A VAL* 2.9 40.1 + - + +
263A HIS* 2.8 36.6 + - - -
285A LEU* 5.1 2.7 - - + -
288A VAL* 4.9 0.5 - - - +
292A ASN* 5.5 1.0 + - - -
366A ASN* 4.5 1.6 - - - +
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Residues in contact with GLY 204 (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 2.9 17.6 + - - -
203A GLU* 1.3 78.4 - - - +
205A TYR* 1.3 61.0 + - - +
207A THR* 3.3 17.2 - - - +
210A ALA* 4.0 5.7 - - - +
218A HIS* 3.3 30.4 + - - -
254A PHE* 4.2 0.2 - - - -
257A VAL* 4.0 1.3 - - - +
258A GLY 3.5 19.0 + - - -
259A LEU* 4.1 0.2 - - - +
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Residues in contact with TYR 205 (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 2.9 19.9 + - - +
202A ILE* 3.2 7.8 + - - +
204A GLY* 1.3 78.2 - - - +
206A ILE* 1.3 54.3 + - + +
210A ALA* 3.8 1.0 - - - +
215A ASP* 3.5 49.8 - - + +
218A HIS* 3.6 13.7 - - + -
219A ILE* 3.9 24.0 - - + +
222A ILE* 4.4 6.1 - - + -
299A LYS* 2.7 82.1 + - + +
302A ASP* 2.7 26.1 + - - +
303A ILE* 4.1 17.3 - - + -
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Residues in contact with ILE 206 (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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202A ILE* 3.4 22.2 - - + +
203A GLU* 3.6 11.2 - - + +
205A TYR* 1.3 83.2 - - + +
207A THR* 1.3 70.0 + - - +
210A ALA* 4.8 0.2 - - - -
289A MSE 5.7 2.0 - - + -
292A ASN* 4.1 12.3 - - - +
295A PHE 5.1 0.9 - - - +
296A THR* 3.9 40.6 - - + -
299A LYS* 4.1 21.1 - - + +
300A TYR* 4.1 20.4 - - + +
303A ILE* 4.9 2.5 - - + -
367A PRO* 3.5 32.7 - - + +
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Residues in contact with THR 207 (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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203A GLU 2.9 15.4 + - - -
204A GLY 3.3 17.0 - - - +
205A TYR 3.6 0.4 - - - -
206A ILE* 1.3 81.5 - - - +
208A ARG* 1.3 62.5 + - - +
209A GLY 3.9 2.4 + - - +
210A ALA* 3.1 30.5 + - - +
257A VAL* 3.7 26.5 + - + +
258A GLY 3.6 13.0 - - - +
259A LEU 2.8 21.8 + - - -
299A LYS* 5.4 0.2 + - - -
365A GLY* 3.0 18.7 + - - -
367A PRO* 4.6 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
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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