Contacts of the helix formed by residues 197 - 232 (chain D) in PDB entry 1L0N
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 GLU 197 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C CYS* 4.3 10.1 - - - +
77C TRP* 3.6 53.9 - - + +
81C TYR* 3.0 34.7 + - + -
118D ARG* 4.0 1.0 + - - -
194D ALA 4.7 0.5 - - - +
195D GLU* 3.6 17.7 - - + +
196D PRO* 1.3 90.9 - - - +
198D HIS* 1.3 64.0 + - - +
199D ASP 3.1 1.9 + - - -
200D HIS* 3.2 8.3 + - - +
201D ARG* 2.9 31.3 + - + +
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Residues in contact with HIS 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D HIS* 3.5 23.3 + - + +
19D SER 3.0 28.7 - - - -
20D SER 2.8 18.3 + - - -
21D LEU* 3.5 13.5 - - + +
191D ARG* 4.4 14.8 - - + -
195D GLU* 3.2 28.2 + - + +
196D PRO 2.9 2.4 + - - +
197D GLU* 1.3 76.8 - - - +
199D ASP* 1.3 67.3 + - - +
201D ARG* 3.2 41.6 + - - +
202D LYS* 3.1 33.2 + - + +
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Residues in contact with ASP 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D SER* 2.7 29.3 - - - +
21D LEU* 3.6 11.8 - - - +
23D HIS* 2.6 33.1 + - - -
192D TRP* 6.0 0.4 - - - -
196D PRO 4.2 5.4 + - - +
197D GLU 3.1 1.0 + - - -
198D HIS* 1.3 78.1 + - - +
200D HIS* 1.3 66.3 + - - +
202D LYS* 3.0 14.6 + - - +
203D ARG* 3.0 10.1 + - - +
43J TYR* 3.3 20.3 + - + +
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Residues in contact with HIS 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C TYR* 4.2 17.6 - + - -
77C TRP* 3.9 12.6 + - + +
197D GLU* 3.2 9.8 + - - +
199D ASP* 1.3 76.3 - - - +
201D ARG* 1.3 67.5 + - - +
203D ARG* 3.0 30.1 + - + +
204D MET* 2.9 64.1 + - + +
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Residues in contact with ARG 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C TRP* 3.6 32.9 - - + -
81C TYR* 5.7 0.4 - - - -
243C VAL 4.6 1.1 - - - +
244C LEU* 2.4 39.2 + - - +
245C PHE* 3.0 27.1 + - - +
247C PRO* 3.9 12.6 - - - +
17D LEU* 6.1 0.2 - - - +
195D GLU* 2.8 43.6 + - - -
197D GLU* 2.9 16.4 + - + +
198D HIS* 3.2 31.2 - - - +
200D HIS* 1.3 79.8 - - - +
202D LYS* 1.3 88.0 + - - +
204D MET* 3.2 4.5 + - - +
205D GLY* 3.0 21.8 + - - -
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Residues in contact with LYS 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C LEU 5.4 0.4 - - - -
245C PHE* 4.9 8.5 - - + -
14D HIS 3.1 17.2 + - - -
15D ARG* 4.6 1.8 - - - +
16D GLY 4.4 2.4 + - - +
17D LEU* 3.0 31.4 + - - +
18D LEU* 4.0 17.4 - - - +
19D SER* 3.2 27.0 + - - +
198D HIS* 3.1 36.8 + - + +
199D ASP 3.0 7.9 + - - +
201D ARG* 1.3 109.3 - - - +
203D ARG* 1.3 60.1 + - - +
205D GLY* 3.7 4.8 - - - +
206D LEU* 3.2 22.2 + - - +
43J TYR* 4.0 8.3 - - - +
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Residues in contact with ARG 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ASP 3.0 9.8 + - - +
200D HIS* 3.0 35.1 + - + +
202D LYS* 1.3 74.1 - - - +
204D MET* 1.3 68.2 + - + +
206D LEU* 3.1 13.3 + - + +
207D LYS* 3.1 27.5 + - + +
39J ALA 5.6 0.7 - - - +
40J ASP* 3.1 54.2 + - - +
43J TYR* 3.6 41.0 - - + -
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Residues in contact with MET 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C TYR* 3.9 7.6 - - + -
77C TRP* 4.0 7.6 - - + -
78C ILE* 3.7 26.9 - - + -
244C LEU* 4.1 16.2 - - + -
200D HIS* 2.9 50.3 + - + +
201D ARG 3.6 6.3 - - - +
203D ARG* 1.3 75.8 - - + +
205D GLY* 1.3 51.7 + - - +
207D LYS* 2.9 15.1 + - + +
208D MET* 2.6 35.2 + - - +
57E GLN* 3.5 25.1 - - - +
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Residues in contact with GLY 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C LEU* 3.7 19.5 - - - +
245C PHE* 3.6 24.6 - - - -
201D ARG 3.0 14.2 + - - -
202D LYS 3.7 2.7 + - - -
203D ARG 3.1 0.2 - - - -
204D MET* 1.3 78.4 - - - +
206D LEU* 1.3 55.9 + - - +
208D MET* 3.5 1.8 - - - +
209D LEU* 2.9 34.1 + - - +
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Residues in contact with LEU 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LEU* 3.9 33.3 - - + +
202D LYS 3.2 13.4 + - - +
203D ARG* 3.1 11.7 + - + +
205D GLY* 1.3 74.7 - - - +
207D LYS* 1.3 57.1 + - - +
209D LEU* 3.3 7.0 + - + +
210D LEU* 3.0 46.5 + - + +
39J ALA* 3.4 36.1 - - + +
42J ILE* 4.7 12.1 - - + -
43J TYR* 4.2 24.0 - - + +
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Residues in contact with LYS 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ARG* 3.4 23.4 - - + +
204D MET* 2.9 13.3 + - + +
206D LEU* 1.3 75.4 - - + +
208D MET* 1.3 53.5 + - - +
210D LEU* 3.3 2.3 + - - +
211D MET* 2.8 41.2 + - - +
49E TYR* 3.6 17.7 - - + +
35J PHE* 3.9 16.4 - - + -
36J ASP* 2.6 37.3 + - - +
39J ALA* 3.5 24.0 - - + -
40J ASP* 2.6 31.0 + - - +
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Residues in contact with MET 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LEU* 3.7 22.0 - - - -
240C MET* 3.7 25.1 - - + +
241C LEU* 3.6 44.6 - - + +
244C LEU* 3.9 14.1 - - + -
245C PHE* 4.1 10.5 - - + -
204D MET 2.6 19.1 + - - +
205D GLY 3.5 2.9 - - - +
207D LYS* 1.3 73.2 - - - +
209D LEU* 1.3 57.7 + - + +
211D MET* 4.1 3.3 - - - +
212D MET* 2.9 48.7 + - + +
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LEU* 4.9 7.6 - - + -
241C LEU* 3.9 25.6 - - + -
245C PHE* 3.7 25.4 - - + -
17D LEU* 4.9 11.4 - - + -
18D LEU* 4.7 10.3 - - + -
205D GLY 2.9 16.0 + - - +
206D LEU* 3.3 6.7 + - + +
208D MET* 1.3 78.1 - - + +
210D LEU* 1.3 60.6 + - + +
212D MET* 4.2 2.2 - - + +
213D GLY* 2.9 25.8 + - - -
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D LEU* 3.0 45.7 + - + +
209D LEU* 1.3 76.3 - - + +
211D MET* 1.3 63.5 + - - +
213D GLY* 3.5 2.5 + - - -
214D LEU* 3.1 23.2 + - - +
35J PHE* 3.6 32.5 - - + -
39J ALA* 4.1 13.9 - - + -
42J ILE* 5.1 15.7 - - + -
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Residues in contact with MET 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D LYS 2.8 24.5 + - - +
208D MET* 4.1 3.8 - - - +
210D LEU* 1.3 72.3 - - - +
212D MET* 1.3 55.2 + - + +
214D LEU* 2.9 26.0 + - + +
215D LEU* 2.6 51.1 + - + +
46E GLY* 4.6 12.6 - - - +
49E TYR* 3.8 26.9 - - + -
50E ALA* 6.2 3.8 - - + -
31J PHE* 3.4 40.2 - - + -
35J PHE* 3.7 21.1 - - + -
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Residues in contact with MET 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 4.1 36.3 - - - +
236C ILE* 3.8 25.6 - - + -
237C LEU* 3.8 29.6 - - + -
208D MET* 2.9 46.2 + - + +
209D LEU* 4.2 3.1 - - + +
211D MET* 1.3 74.9 - - + +
213D GLY* 1.3 58.5 + - - +
214D LEU 2.9 1.6 + - - -
215D LEU* 4.4 7.6 - - - +
216D LEU* 2.8 53.9 + - + +
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Residues in contact with GLY 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D LEU 2.9 20.2 + - - -
210D LEU* 3.6 4.0 - - - -
211D MET 3.1 0.2 - - - -
212D MET* 1.3 77.2 - - - +
214D LEU* 1.3 55.8 + - - +
216D LEU* 5.2 1.1 - - - -
217D PRO* 3.4 20.1 - - - +
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Residues in contact with LEU 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D LEU 3.1 13.7 + - - +
211D MET* 2.9 24.9 + - + +
213D GLY* 1.3 79.4 - - - +
215D LEU* 1.3 67.7 + - + +
216D LEU 3.5 0.2 - - - -
217D PRO* 3.4 9.3 - - - +
218D LEU* 3.4 42.1 - - + +
42E THR* 4.8 11.9 - - + +
46E GLY* 5.7 2.2 - - - -
31J PHE* 5.4 10.5 - - + -
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Residues in contact with LEU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C LEU* 4.3 24.0 - - + -
211D MET* 2.6 35.9 + - + +
212D MET* 4.1 8.1 - - - +
214D LEU* 1.3 75.1 - - + +
216D LEU* 1.3 56.7 + - - +
218D LEU* 3.1 4.9 + - + +
219D VAL* 2.8 39.8 + - + +
42E THR 5.3 0.2 - - - +
43E THR* 3.7 18.2 - - + +
46E GLY* 3.7 22.0 - - - +
47E VAL* 3.7 35.0 - - + +
50E ALA* 5.5 8.7 - - + -
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C LEU* 4.0 12.2 - - + +
233C LEU* 3.9 23.5 - - + +
234C LEU* 3.8 32.5 - - + -
237C LEU* 3.8 29.8 - - + -
212D MET* 2.8 32.4 + - + +
213D GLY* 5.2 0.9 - - - -
215D LEU* 1.3 72.5 - - - +
217D PRO* 1.3 65.9 - - + +
219D VAL* 4.0 1.2 - - - +
220D TYR* 3.1 25.5 + - + +
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Residues in contact with PRO 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D GLY* 3.4 27.4 - - - +
214D LEU* 3.4 10.3 - - - +
216D LEU* 1.3 92.3 - - + +
218D LEU* 1.3 59.7 + - + +
220D TYR* 3.0 9.5 + - + +
221D ALA* 2.9 29.1 + - - +
26G PHE* 5.2 1.2 - - - -
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Residues in contact with LEU 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LEU* 3.4 30.0 + - + +
215D LEU* 3.1 10.1 + - + +
217D PRO* 1.3 81.6 - - + +
219D VAL* 1.3 57.0 + - - +
221D ALA* 3.3 7.3 + - + +
222D MET* 2.9 30.8 + - - +
39E VAL* 3.9 31.6 - - + +
42E THR* 3.9 32.8 - - + -
43E THR* 3.4 24.2 - - - +
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Residues in contact with VAL 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ILE* 4.1 3.1 - - + +
229C ILE* 4.2 14.1 - - + -
230C LEU* 3.7 38.6 - - + +
233C LEU* 3.8 20.9 - - + -
215D LEU* 2.8 26.9 + - + +
216D LEU 4.2 0.2 - - - +
218D LEU* 1.3 69.6 - - - +
220D TYR* 1.3 59.1 + - - +
222D MET* 3.2 15.3 + - + +
223D LYS* 2.9 27.7 + - - +
43E THR* 3.9 23.1 - - + -
47E VAL* 5.6 3.1 - - + -
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Residues in contact with TYR 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C LEU* 4.0 29.5 - - + +
216D LEU* 3.1 14.9 + - + +
217D PRO* 3.0 13.8 + - + +
219D VAL* 1.3 76.0 - - - +
221D ALA* 1.3 51.1 + - - +
223D LYS* 2.9 6.7 + - + +
224D ARG* 1.3 123.7 + - - -
26G PHE* 3.3 29.4 - + - -
29G TYR* 3.1 18.7 + - - -
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Residues in contact with ALA 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D PRO 2.9 13.0 + - - +
218D LEU* 3.8 9.9 - - + +
220D TYR* 1.3 76.9 - - - +
222D MET* 1.3 61.2 + - - +
224D ARG* 4.5 1.3 - - - +
225D HIS* 3.1 24.1 + - - +
35E PHE* 6.5 0.7 - - + -
39E VAL* 4.4 17.8 - - + +
25G ALA* 4.4 3.0 - - + +
26G PHE* 3.7 29.4 - - + -
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Residues in contact with MET 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ILE* 3.8 24.4 - - + +
229C ILE* 5.4 7.0 - - + -
218D LEU 2.9 17.3 + - - +
219D VAL* 3.4 18.8 - - + +
220D TYR 3.1 0.2 - - - -
221D ALA* 1.3 77.1 - - - +
223D LYS* 1.3 63.5 + - - +
225D HIS* 3.3 7.3 - - - +
226D LYS* 3.2 24.8 + - - +
39E VAL* 4.1 10.5 - - + -
40E THR* 3.7 43.5 - - + +
43E THR* 3.8 26.0 - - + +
44E THR* 6.1 1.1 - - - -
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Residues in contact with LYS 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ILE* 3.7 31.4 - - + +
227C LYS* 3.9 36.1 - - - +
230C LEU* 4.2 20.9 - - + -
219D VAL 2.9 12.5 + - - +
220D TYR* 2.9 9.2 + - + +
222D MET* 1.3 74.3 - - - +
224D ARG* 1.3 86.6 + - - +
226D LYS* 3.2 2.4 + - - +
227D TRP* 2.9 58.4 + - + +
231D LYS* 4.6 14.6 - - - +
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Residues in contact with ARG 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D TYR* 1.3 102.7 + - - +
223D LYS* 1.3 90.9 - - + +
225D HIS* 1.3 57.4 + - - +
227D TRP* 3.5 6.8 - - + +
228D SER* 2.8 33.1 + - - -
231D LYS* 5.6 12.2 - - + +
25G ALA* 3.3 34.1 + - + +
26G PHE* 4.1 7.0 - - + -
29G TYR* 4.0 17.4 + - - -
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Residues in contact with HIS 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ALA 3.1 20.3 + - - +
222D MET* 3.3 7.0 - - - +
224D ARG* 1.3 81.1 - - - +
226D LYS* 1.3 85.3 + - + +
228D SER* 3.1 19.5 + - - -
229D VAL 4.5 0.2 + - - -
15E ARG* 4.0 2.6 + - - -
36E SER* 3.6 27.4 + - - +
40E THR* 6.2 4.5 - - + -
20G PRO* 3.4 48.3 + - + +
21G PHE* 3.7 29.4 - + - -
25G ALA* 3.7 11.6 - - + +
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Residues in contact with LYS 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A ASN* 3.0 45.0 + - - +
439A SER* 4.9 11.3 + - - -
221C HIS* 6.3 0.6 - - - -
222C PRO* 3.6 33.9 - - + +
223C TYR* 3.1 9.7 - - + -
226C ILE* 4.9 14.8 - - + -
222D MET 3.2 8.1 + - - +
223D LYS 3.2 6.8 + - - +
225D HIS* 1.3 97.7 - - + +
227D TRP* 1.3 63.3 + - + +
228D SER 3.4 0.7 + - - -
229D VAL* 3.9 2.9 + - - +
21G PHE* 6.2 1.1 - - - -
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Residues in contact with TRP 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C SER 4.2 13.9 - - - -
27C ILE 5.3 0.9 - - - -
218C ILE* 4.1 6.1 - - + -
223C TYR* 2.8 50.1 + + + +
224C TYR* 3.5 39.7 - + - -
226C ILE* 4.4 4.4 - - + +
227C LYS* 4.3 11.0 - - + -
223D LYS* 2.9 53.8 + - + +
224D ARG* 3.5 7.6 - - + +
226D LYS* 1.3 78.6 - - + +
228D SER* 1.3 52.3 + - - +
229D VAL 3.2 0.7 - - - -
230D LEU* 2.9 22.9 + - + +
231D LYS* 2.8 61.3 + - + +
70F MET* 4.3 13.2 - - + -
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Residues in contact with SER 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D ARG 2.8 16.0 + - - -
225D HIS* 3.1 13.5 + - - -
226D LYS 3.2 1.6 - - - -
227D TRP* 1.3 75.6 - - - +
229D VAL* 1.3 60.5 + - - +
231D LYS* 4.2 8.1 - - - +
232D SER 3.0 24.0 + - - +
20G PRO* 3.6 8.3 + - - +
23G GLN* 2.9 43.9 + - - +
24G ARG 4.6 10.5 - - - -
25G ALA* 4.9 3.4 - - - -
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Residues in contact with VAL 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP* 4.8 2.7 - - - +
434A TYR* 4.1 18.6 - - + -
435A ASN* 3.3 25.6 - - - +
223C TYR* 3.7 15.3 - - - +
226D LYS 4.0 1.6 - - - +
227D TRP 3.2 0.2 - - - -
228D SER* 1.3 76.5 + - - +
230D LEU* 1.3 60.8 + - + +
232D SER 2.7 16.6 - - - +
233D ARG* 3.6 7.6 - - - +
17G SER* 3.6 30.9 + - - +
18G LEU 3.9 11.2 - - - +
20G PRO* 3.5 31.0 - - + -
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433A ASP* 4.4 7.4 - - - +
25C SER* 4.8 0.9 - - - -
218C ILE* 3.6 38.8 - - + -
223C TYR* 3.5 41.3 - - + +
227D TRP* 2.9 18.3 + - + +
229D VAL* 1.3 84.1 - - + +
231D LYS* 1.3 65.1 + - - +
232D SER 3.3 1.3 - - - -
233D ARG* 3.1 39.4 - - + +
67F ASP* 4.6 0.2 - - - +
70F MET* 3.3 30.8 - - + +
71F ARG* 5.3 0.3 + - - -
17G SER* 5.5 1.6 - - - +
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Residues in contact with LYS 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D LYS* 4.6 12.4 - - - +
224D ARG* 5.6 11.4 - - + +
227D TRP* 2.8 54.6 + - + +
228D SER* 4.4 6.1 - - - +
230D LEU* 1.3 73.8 - - - +
232D SER* 1.3 59.3 + - - +
233D ARG* 3.7 2.4 + - - +
13E TYR* 4.6 8.0 + - + -
70F MET* 3.7 34.0 + - + +
71F ARG* 3.7 43.1 + - + +
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Residues in contact with SER 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D SER 3.0 5.4 + - - +
229D VAL* 2.7 25.8 - - - +
231D LYS* 1.3 73.7 - - - +
233D ARG* 1.3 53.7 + - - +
10E PHE* 3.3 27.5 - - - -
13E TYR* 3.5 33.0 - - - -
18G LEU 5.1 2.1 + - - -
23G GLN* 3.1 31.7 + - - -
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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