Contacts of the helix formed by residues 186 - 207 (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 PRO 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B GLY 3.5 7.9 - - - +
185B MSE 1.3 86.9 - - - +
187B PRO* 1.3 75.7 - - + +
188B ALA* 4.3 7.2 - - + +
189B LEU* 2.8 37.8 + - + +
190B LYS 3.0 7.6 + - - -
389B APR 4.0 10.1 - - + +
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Residues in contact with PRO 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B MSE 3.5 2.9 - - - +
186B PRO* 1.3 84.0 - - + +
188B ALA* 1.3 61.5 + - - +
190B LYS* 3.2 14.1 + - + +
191B ALA* 3.0 22.7 + - - +
233B VAL* 3.7 35.5 - - + +
334B VAL 5.9 0.2 - - - -
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO* 3.1 5.7 - - + -
187B PRO* 1.3 79.7 - - - +
189B LEU* 1.3 57.8 + - - +
191B ALA* 3.5 7.3 + - - +
192B ALA* 3.1 27.9 + - - +
334B VAL 5.5 2.2 - - - -
336B ILE* 5.7 0.7 - - - +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 4.7 0.4 - - + -
185B MSE 3.1 32.1 - - + +
186B PRO* 2.8 30.9 + - + +
188B ALA* 1.3 76.0 - - - +
190B LYS* 1.3 68.2 + - - +
191B ALA 3.1 0.2 - - - -
192B ALA* 4.6 5.6 - - + -
193B THR* 2.9 33.9 + - + +
276B PRO* 6.5 1.3 - - + -
389B APR 3.3 58.6 - - + +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA* 5.0 1.8 - - - +
182B MSE 4.4 5.2 - - - -
183B ASP* 3.9 23.0 + - - +
185B MSE 3.5 46.2 - - + +
186B PRO 3.0 9.6 + - - +
187B PRO* 3.5 11.8 - - + +
189B LEU* 1.3 76.0 - - - +
191B ALA* 1.3 58.1 + - - +
193B THR* 3.6 1.3 + - - -
194B GLY* 2.9 27.2 + - - -
229B LEU* 3.6 6.8 - - + +
232B SER* 3.1 41.6 + - - +
233B VAL* 4.1 15.2 + - + +
235B GLY* 4.0 15.0 - - - -
236B ASP 5.6 0.8 + - - -
240B GLY* 6.2 0.6 - - - -
243B MSE 5.3 0.2 - - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B PRO 3.0 13.0 + - - +
188B ALA* 3.6 10.3 - - - +
190B LYS* 1.3 77.2 - - - +
192B ALA* 1.3 58.5 + - - +
194B GLY* 3.3 0.7 + - - -
195B VAL* 3.0 35.0 + - - +
229B LEU* 4.2 3.5 - - - +
233B VAL* 3.9 9.8 - - + +
334B VAL* 3.4 41.5 - - + +
336B ILE* 4.1 8.3 - - + -
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ALA 3.1 17.0 + - - +
189B LEU* 4.0 7.6 - - + +
191B ALA* 1.3 76.1 - - - +
193B THR* 1.3 64.8 + - + +
195B VAL* 3.4 1.7 + - - -
196B ASP 3.0 17.0 + - - -
276B PRO* 5.4 3.4 - - + -
278B GLY* 3.3 19.5 - - - +
279B VAL* 3.9 32.5 - - + +
336B ILE* 4.3 11.6 - - + +
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Residues in contact with THR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B THR* 3.8 7.4 - - + +
142B ALA* 3.4 13.5 + - - +
143B GLY* 2.9 31.5 - - - -
185B MSE 3.1 35.8 - - + +
189B LEU* 2.9 24.2 + - + +
190B LYS* 3.6 3.5 + - - -
192B ALA* 1.3 79.0 - - + +
194B GLY* 1.3 58.2 + - - +
196B ASP* 3.4 7.0 - - - +
197B ALA 3.0 13.0 + - - -
278B GLY* 5.1 1.1 - - - -
389B APR 3.3 26.2 - - - +
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Residues in contact with GLY 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA 3.6 10.8 - - - -
190B LYS 2.9 21.3 + - - -
191B ALA 3.7 0.9 - - - -
193B THR* 1.3 78.8 + - - +
195B VAL* 1.3 56.7 + - - +
197B ALA* 3.2 5.2 + - - +
198B LEU* 2.9 24.4 + - - +
225B ILE* 3.8 6.4 - - - +
229B LEU* 3.8 10.5 - - - -
243B MSE 3.6 14.6 - - - -
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Residues in contact with VAL 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA 3.0 16.1 + - - +
192B ALA 4.0 3.4 - - - +
194B GLY* 1.3 74.4 - - - +
196B ASP* 1.3 61.5 + - - +
198B LEU* 3.6 9.8 - - + +
199B THR* 2.8 37.9 + - - +
229B LEU* 3.9 15.9 - - + -
278B GLY 4.6 0.2 - - - +
282B ALA* 3.5 35.2 - - + -
285B LEU* 4.4 11.7 - - + -
330B LEU* 4.8 7.9 - - + -
331B ASN* 3.6 13.7 - - - +
334B VAL* 4.5 4.3 - - + -
336B ILE* 3.6 15.9 - - + -
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Residues in contact with ASP 196 (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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143B GLY 3.4 11.8 - - - +
144B THR* 3.5 15.9 - - - +
192B ALA 3.0 14.3 + - - +
193B THR* 3.4 12.1 - - - +
194B GLY 3.2 0.2 - - - -
195B VAL* 1.3 76.7 - - - +
197B ALA* 1.3 58.5 + - - +
199B THR* 3.2 3.9 + - - -
200B HIS* 2.9 33.7 + - - -
277B HIS* 3.4 15.0 - - - -
278B GLY* 3.8 11.8 - - - -
281B ASN* 2.9 19.1 + - - +
387B ZN 2.3 35.2 - - - -
389B APR 4.8 2.2 + - - +
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ALA 4.1 2.0 - - - +
143B GLY* 3.4 25.1 + - - +
193B THR 3.0 11.2 + - - +
194B GLY* 3.3 10.5 - - - +
195B VAL 3.1 0.2 - - - -
196B ASP* 1.3 78.3 - - - +
198B LEU* 1.3 62.1 + - - +
200B HIS* 3.1 8.2 + - - +
201B ALA* 3.0 18.5 + - - +
225B ILE* 3.7 19.5 - - + +
243B MSE 4.7 1.1 - - + -
247B GLN* 3.7 19.7 - - + -
250B ALA* 4.0 2.4 - - - +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B GLY 2.9 14.0 + - - +
195B VAL* 3.2 13.4 + - + +
197B ALA* 1.3 76.1 - - - +
199B THR* 1.3 58.5 + - - +
201B ALA* 3.2 1.3 + - - +
202B ILE* 2.8 51.8 + - + +
222B ILE* 4.1 31.0 - - + +
225B ILE* 3.8 21.9 - - + +
226B ALA* 4.9 2.5 - - + +
285B LEU* 4.5 11.4 - - + -
307B MSE 4.1 15.3 - - + -
327B VAL* 4.7 4.5 - - + -
330B LEU* 3.6 31.2 - - + -
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Residues in contact with THR 199 (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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195B VAL* 2.8 21.8 + - - +
196B ASP 3.4 9.6 - - - -
198B LEU* 1.3 73.1 - - - +
200B HIS* 1.3 61.1 + - - +
202B ILE 4.5 0.2 - - - +
203B GLU* 2.8 39.4 + - + +
262B VAL* 3.6 23.3 - - + -
263B HIS* 3.4 28.9 - - + +
281B ASN* 3.6 14.1 - - - +
285B LEU* 3.6 26.6 - - + +
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Residues in contact with HIS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLY 3.1 29.0 + - - -
144B THR* 3.5 18.9 + - - -
145B ALA* 5.0 1.0 - - - +
196B ASP* 2.9 17.7 + - - -
197B ALA* 3.1 8.6 + - - +
199B THR* 1.3 76.1 - - - +
201B ALA* 1.3 57.1 + - - +
204B GLY* 2.9 28.2 + - - -
218B HIS* 4.1 0.3 + - - -
247B GLN 5.4 0.2 + - - -
250B ALA* 4.2 5.5 - - + +
254B PHE* 3.4 40.6 - + + +
259B LEU* 3.5 15.2 - - + +
263B HIS* 3.0 16.8 + + - -
387B ZN 2.1 36.4 - - - -
390B PGO 3.2 6.4 + - - -
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Residues in contact with ALA 201 (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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197B ALA 3.0 9.5 + - - +
198B LEU 3.2 6.0 + - - +
200B HIS* 1.3 81.7 - - - +
202B ILE* 1.3 57.0 + - - +
205B TYR* 2.9 30.1 + - - +
218B HIS* 3.6 23.6 - - + +
221B ALA* 4.0 17.3 - - + -
222B ILE* 3.5 26.4 - - + +
225B ILE* 4.5 2.7 - - + -
250B ALA* 4.1 3.8 - - + +
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Residues in contact with ILE 202 (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* 2.8 45.7 + - + +
199B THR* 4.0 2.9 - - - +
201B ALA* 1.3 70.4 - - - +
203B GLU* 1.3 67.9 + - + +
205B TYR* 3.2 11.2 + - - +
206B ILE* 3.3 23.7 + - + +
222B ILE* 3.9 20.9 - - + -
285B LEU* 4.3 13.0 - - + -
289B MSE 4.2 34.5 - - + -
300B TYR* 5.5 0.2 - - + -
303B ILE* 4.0 28.5 - - + -
307B MSE 4.8 0.9 - - - -
327B VAL* 4.2 11.4 - - + -
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Residues in contact with GLU 203 (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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199B THR* 2.8 28.7 + - + +
202B ILE* 1.3 73.8 - - + +
204B GLY* 1.3 58.0 + - - +
206B ILE* 3.3 11.2 + - + +
207B THR* 2.9 32.2 + - - -
259B LEU* 3.7 19.0 - - + +
260B GLY* 3.0 23.0 + - - -
261B LEU 3.2 1.0 + - - -
262B VAL* 2.9 40.1 + - + +
263B HIS* 2.8 39.8 + - - +
285B LEU* 5.1 3.6 - - + -
288B VAL* 4.9 0.3 - - - +
292B ASN* 5.5 0.5 + - - -
366B ASN* 4.5 2.4 + - - -
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Residues in contact with GLY 204 (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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200B HIS 2.9 17.8 + - - -
203B GLU* 1.3 78.1 - - - +
205B TYR* 1.3 59.7 + - - +
207B THR* 3.3 17.2 - - - +
210B ALA* 4.0 6.1 - - - +
218B HIS* 3.2 31.1 + - - -
254B PHE* 4.3 0.7 - - - -
257B VAL* 4.1 0.3 - - - +
258B GLY 3.5 17.3 - - - -
259B LEU* 4.0 0.8 - - - +
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Residues in contact with TYR 205 (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 2.9 19.5 + - - +
202B ILE* 3.2 7.4 + - - +
204B GLY* 1.3 78.2 - - - +
206B ILE* 1.3 55.5 - - + +
210B ALA* 3.7 1.6 - - - +
215B ASP* 3.5 50.6 - - + +
218B HIS* 3.5 12.1 + - + -
219B ILE* 3.8 21.9 - - + +
222B ILE* 4.4 5.4 - - + -
299B LYS* 2.7 79.8 + - + +
302B ASP* 2.8 29.3 + - + +
303B ILE* 4.1 17.3 - - + -
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Residues in contact with ILE 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B ILE* 3.3 23.1 + - + +
203B GLU* 3.7 10.8 - - + +
205B TYR* 1.3 83.3 - - + +
207B THR* 1.3 68.6 + - - +
208B ARG* 4.6 0.2 - - - -
210B ALA* 4.9 0.2 - - - -
289B MSE 5.7 1.8 - - + -
292B ASN* 4.1 18.8 - - - +
295B PHE 5.3 0.3 - - - +
296B THR* 4.0 33.7 - - + -
299B LYS* 4.2 23.1 - - + +
300B TYR* 4.1 24.7 - - + +
303B ILE* 4.8 2.7 - - + -
367B PRO* 3.6 27.0 - - + +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU 2.9 16.4 + - - -
204B GLY 3.3 16.6 - - - +
205B TYR 3.5 0.4 - - - -
206B ILE* 1.3 81.7 - - - +
208B ARG* 1.3 64.8 + - - +
209B GLY 4.3 0.3 + - - -
210B ALA* 3.0 32.0 + - - +
257B VAL* 3.7 20.1 + - + +
258B GLY* 3.5 21.7 - - - +
259B LEU 2.7 20.8 + - - -
365B GLY* 3.1 16.4 + - - -
367B PRO* 4.7 1.1 - - - -
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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