Contacts of the helix formed by residues 197 - 219 (chain X) in PDB entry 1XDM
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 197 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198X LEU* 1.3 70.0 + - - +
199X GLU* 3.4 26.6 + - - +
200X HIS* 3.1 30.0 + - - +
201X CYS* 3.3 11.6 + - - +
235X ALA* 4.6 9.0 - - - +
239X CYS* 4.6 13.3 - - - +
241X LYS* 5.7 2.2 - - + -
243X TYR* 2.8 29.4 - - + +
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Residues in contact with LEU 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197X ASP* 1.3 73.3 - - - +
199X GLU* 1.3 68.4 + - - +
200X HIS 2.7 1.4 + - - -
201X CYS* 2.8 8.6 + - - -
202X GLN* 2.6 26.8 + - - +
233X VAL* 4.6 8.7 - - + +
234X THR* 4.2 4.5 - - - -
235X ALA 3.7 15.9 - - - +
243X TYR* 3.2 51.3 + - + -
247X GLN* 3.8 24.5 - - + +
248X VAL* 4.1 4.7 - - + +
251X ALA* 3.5 31.9 - - + -
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Residues in contact with GLU 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197X ASP* 3.4 22.6 - - - +
198X LEU* 1.3 76.7 - - - +
200X HIS* 1.3 55.8 + - - +
202X GLN* 3.4 14.9 - - - +
203X TYR* 2.7 37.8 + - + +
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Residues in contact with HIS 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192X PRO* 3.8 28.7 - - + +
197X ASP* 3.1 23.7 + - - +
198X LEU 2.7 4.8 + - - -
199X GLU* 1.3 77.5 - - - +
201X CYS* 1.3 54.7 + - - +
202X GLN 2.7 14.4 + - - -
203X TYR* 2.9 17.9 + + - +
204X VAL* 2.9 28.0 + - + +
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Residues in contact with CYS 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X VAL* 4.1 19.3 - - - -
192X PRO* 4.5 20.2 - - + -
197X ASP 3.3 5.5 + - - +
198X LEU 2.8 7.7 + - - +
200X HIS* 1.3 77.6 - - - +
202X GLN* 1.3 52.4 + - - +
204X VAL* 4.0 7.7 - - - +
205X THR* 2.6 38.6 + - - -
231X ASN* 4.6 3.4 - - - -
232X MET 5.2 0.4 - - - -
233X VAL* 3.5 16.6 - - + -
234X THR 3.4 31.9 - - - +
235X ALA 5.3 0.9 - - - -
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Residues in contact with GLN 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198X LEU* 2.6 21.0 + - - +
199X GLU* 3.4 17.6 - - - +
200X HIS 2.7 0.8 + - - -
201X CYS* 1.3 70.8 - - - +
203X TYR* 1.3 68.3 + - - +
204X VAL 3.1 1.1 + - - -
205X THR* 3.2 3.8 + - - -
206X GLU* 3.0 32.9 + - - +
233X VAL* 3.5 11.9 - - + +
251X ALA* 3.7 38.5 - - + +
254X THR* 3.9 12.5 - - - -
255X ALA* 4.1 11.0 + - + -
258X ARG* 3.9 6.1 + - - -
364X SO4 3.4 24.5 + - - -
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Residues in contact with TYR 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217W ASN 5.9 2.0 - - - -
220W HIS* 4.0 35.9 - + + -
199X GLU* 2.7 23.5 + - + +
200X HIS* 3.5 11.2 - + - +
202X GLN* 1.3 74.5 - - - +
204X VAL* 1.3 74.1 + - + +
206X GLU* 3.2 24.9 + - + +
207X LYS* 3.3 40.6 + - + +
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Residues in contact with VAL 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X ILE* 5.6 4.7 - - + -
190X VAL* 4.4 13.5 - - + -
191X ILE* 5.5 3.1 - - + +
192X PRO* 5.1 7.4 - - + -
200X HIS* 2.9 41.0 + - + +
201X CYS* 4.0 7.4 - - - +
203X TYR* 1.3 78.1 - - + +
205X THR* 1.3 69.5 + - - +
206X GLU 2.7 3.8 + - - -
207X LYS* 2.7 19.7 + - + +
208X VAL* 3.1 27.3 + - + +
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Residues in contact with THR 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X VAL* 3.6 20.4 - - + +
201X CYS* 2.6 22.1 + - - -
202X GLN* 3.2 6.7 + - - -
204X VAL* 1.3 78.3 - - - +
206X GLU* 1.3 57.8 + - - +
208X VAL* 3.8 2.2 - - - +
209X LEU* 2.9 56.5 + - + +
230X PRO* 5.9 1.6 - - + -
231X ASN* 3.4 30.9 + - - +
233X VAL* 4.1 9.4 - - + +
255X ALA* 4.7 11.9 - - + -
256X LEU* 5.2 3.6 - - + -
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Residues in contact with GLU 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217W ASN* 3.9 9.1 + - - +
220W HIS* 5.2 6.1 - - - -
202X GLN* 3.0 23.8 + - - +
203X TYR* 3.2 26.7 - - + +
204X VAL 2.7 4.8 + - - -
205X THR* 1.3 71.6 - - - +
207X LYS* 1.3 65.0 + - + +
209X LEU* 3.3 1.3 + - - -
210X ALA* 3.0 20.8 + - - +
255X ALA* 3.6 31.8 - - + +
258X ARG* 2.9 40.6 + - - +
259X THR* 3.4 19.6 - - + +
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Residues in contact with LYS 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214W LYS* 4.7 0.9 + - - -
217W ASN* 4.1 17.0 + - - +
218W ASP* 4.6 19.8 + - - +
160X SER* 4.8 16.8 - - - -
163X ILE* 4.6 17.2 - - + +
203X TYR* 3.3 45.4 + - + +
204X VAL* 2.7 14.8 + - - +
206X GLU* 1.3 74.1 - - + +
208X VAL* 1.3 54.5 + - + +
210X ALA* 3.1 4.9 + - - +
211X ALA* 2.8 35.4 + - - +
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Residues in contact with VAL 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X ILE* 3.7 38.1 - - + +
188X PRO* 3.8 24.9 - - + -
189X GLU* 4.1 24.2 - - - +
190X VAL* 4.7 5.2 - - + -
204X VAL* 3.4 26.7 - - + +
205X THR* 3.8 9.0 - - - +
207X LYS* 1.3 75.5 - - - +
209X LEU* 1.3 57.2 + - + +
211X ALA* 3.5 1.4 + - - +
212X VAL* 3.0 37.7 + - + +
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Residues in contact with LEU 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188X PRO* 3.8 29.2 - - + -
190X VAL* 6.1 0.7 - - + -
205X THR* 2.9 42.4 + - + +
206X GLU 3.8 0.7 - - - +
208X VAL* 1.3 73.9 - - + +
210X ALA* 1.3 60.5 + - - +
212X VAL* 3.4 2.1 + - - +
213X TYR* 2.8 40.7 + - + +
228X LEU* 4.1 17.3 - - + -
230X PRO* 5.0 6.3 - - + -
231X ASN* 5.9 1.8 - - - +
255X ALA 4.7 3.4 - - - +
256X LEU* 3.6 29.8 - - + -
259X THR* 3.5 29.8 - - - +
260X VAL* 3.9 5.8 - - + -
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Residues in contact with ALA 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214W LYS* 3.5 16.6 - - + +
217W ASN* 3.7 30.5 - - + +
218W ASP* 5.5 0.2 - - - +
206X GLU 3.0 13.2 + - - +
207X LYS 3.3 7.9 - - - +
209X LEU* 1.3 72.9 - - - +
211X ALA* 1.3 68.0 + - - +
212X VAL 3.0 1.1 - - - -
213X TYR* 3.1 3.6 + - - -
214X LYS* 2.6 28.1 + - - +
259X THR* 4.3 7.5 - - + +
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Residues in contact with ALA 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214W LYS* 3.2 16.5 - - - +
163X ILE* 3.2 46.2 - - + +
164X GLN* 5.3 1.3 - - - -
167X ALA* 3.3 5.0 - - + +
207X LYS 2.8 14.1 + - - +
208X VAL 3.5 2.5 - - - +
210X ALA* 1.3 71.7 - - - +
212X VAL* 1.3 58.5 + - + +
214X LYS* 3.6 2.1 - - - +
215X ALA* 2.9 29.8 + - - +
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Residues in contact with VAL 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163X ILE* 5.6 0.7 - - + +
166X ASN* 6.3 0.4 - - + -
167X ALA* 3.8 23.6 - - + +
170X LEU* 4.5 12.8 - - + -
186X VAL* 3.9 20.0 - - + -
188X PRO* 3.6 27.6 - - + -
208X VAL* 3.0 25.3 + - + +
209X LEU 3.5 4.9 - - - +
210X ALA 3.0 0.8 + - - -
211X ALA* 1.3 71.7 - - + +
213X TYR* 1.3 69.0 + - + +
214X LYS 2.9 5.1 + - - -
215X ALA* 2.9 3.8 + - - +
216X LEU* 2.9 46.3 + - + +
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Residues in contact with TYR 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210W ALA* 5.5 1.4 - - - +
186X VAL* 4.2 4.5 - - + +
209X LEU* 2.8 35.2 + - + +
210X ALA* 4.2 2.9 - - - +
212X VAL* 1.3 78.4 - - + +
214X LYS* 1.3 59.5 + - - +
216X LEU* 3.6 16.8 - - + +
217X ASN* 3.5 18.7 + - - +
223X LEU* 3.5 27.6 - - + +
226X THR* 4.8 5.9 - - + +
228X LEU* 2.8 53.0 + - + +
259X THR 4.7 3.4 - - - +
260X VAL* 3.8 30.6 - - + +
261X PRO* 3.5 25.4 - - + +
264X VAL* 3.5 22.5 - - + +
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Residues in contact with LYS 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207W LYS* 5.7 2.0 - - - -
210W ALA* 3.5 28.7 - - + +
211W ALA* 4.5 15.9 - - - +
214W LYS* 3.4 34.3 - - + +
210X ALA 2.6 21.3 + - - +
211X ALA 3.6 3.4 - - - +
213X TYR* 1.3 70.3 - - - +
215X ALA* 1.3 71.4 + - - +
217X ASN* 2.9 15.5 + - - +
218X ASP* 2.9 45.8 + - - +
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Residues in contact with ALA 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167X ALA* 3.5 34.3 - - + +
168X ASN* 3.7 10.8 - - - +
171X ALA* 3.7 4.7 - - + -
211X ALA 2.9 14.3 + - - +
212X VAL 3.2 7.6 - - - +
214X LYS* 1.3 75.1 - - - +
216X LEU* 1.3 55.0 + - - +
218X ASP* 2.7 35.1 + - - +
219X HIS* 3.0 19.1 + - - -
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Residues in contact with LEU 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170X LEU* 4.8 0.7 - - + +
171X ALA* 3.9 15.2 - - - +
174X ALA* 3.9 14.6 - - + -
186X VAL* 4.5 18.4 - - + -
212X VAL* 2.9 50.7 + - + +
213X TYR* 3.6 27.6 - - + +
215X ALA* 1.3 72.8 - - - +
217X ASN* 1.3 59.5 + - - +
220X HIS 3.4 2.1 + - - -
221X VAL* 2.9 68.0 + - + +
223X LEU* 4.9 9.6 - - + -
226X THR* 5.5 2.0 - - + -
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Residues in contact with ASN 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203W TYR* 5.6 7.6 - - - -
206W GLU* 3.7 19.7 + - - +
207W LYS* 4.1 18.0 + - - +
210W ALA* 3.0 33.0 - - + +
258W ARG* 4.7 6.5 + - - +
259W THR* 4.5 6.5 - - - +
213X TYR 3.5 11.4 + - - +
214X LYS* 2.9 12.0 + - + +
215X ALA 2.9 0.2 + - - -
216X LEU* 1.3 76.2 - - - +
218X ASP* 1.3 69.4 + - - +
219X HIS 3.1 0.2 - - - -
220X HIS* 3.0 15.7 + - - +
221X VAL 5.0 0.9 - - - +
223X LEU* 5.5 9.8 - - + +
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Residues in contact with ASP 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203W TYR* 5.6 1.4 + - - -
207W LYS* 5.2 11.8 - - - +
168X ASN* 4.9 2.6 - - - +
214X LYS* 2.9 48.1 + - - +
215X ALA* 2.7 20.1 + - - +
217X ASN* 1.3 75.7 - - - +
219X HIS* 1.3 61.1 + - + +
220X HIS* 3.2 4.6 + - - +
161Y LEU* 3.5 39.5 - - + +
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Residues in contact with HIS 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168X ASN* 3.1 41.7 + - - -
171X ALA* 3.4 18.0 - - + +
172X ARG* 3.6 23.9 + - + +
175X SER* 4.0 14.1 + - - +
215X ALA 3.0 25.5 + - - +
216X LEU 3.4 5.8 + - - +
217X ASN 3.1 0.4 - - - -
218X ASP* 1.3 85.4 - - + +
220X HIS* 1.3 69.5 + - - +
221X VAL* 2.9 15.3 + - + +
161Y LEU* 4.6 10.7 - - + +
165Y GLU* 4.1 17.8 - - + -
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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