Contacts of the helix formed by residues 180 - 211 (chain D) in PDB entry 4DAJ
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 THR 180 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D VAL* 3.9 11.2 - - - +
177D ALA 5.7 1.3 - - - +
178D LYS 3.5 8.9 + - - +
179D ARG* 1.3 79.2 - - - +
181D THR* 1.3 65.2 + - - +
182D LYS* 3.8 11.5 + - - +
183D ARG* 3.2 28.7 + - - +
184D ALA* 3.2 17.3 + - - +
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Residues in contact with THR 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D PHE* 6.0 0.2 - - + -
99D LYS* 5.4 3.8 - - + -
100D THR* 4.2 7.9 - - - +
101D VAL* 4.1 23.1 - - + +
104D TYR* 3.7 34.3 + - + -
180D THR* 1.3 72.0 - - - +
182D LYS* 1.3 60.7 + - - +
184D ALA* 3.2 10.1 - - - +
185D GLY* 2.9 23.4 + - - -
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Residues in contact with LYS 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D THR* 3.1 10.7 - - - +
181D THR* 1.3 78.7 + - - +
183D ARG* 1.3 63.5 + - + +
185D GLY* 3.3 2.4 + - - -
186D VAL* 3.0 43.7 + - + +
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Residues in contact with ARG 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C VAL* 5.4 11.1 + - - +
174D THR 5.0 2.8 + - - -
175D TYR* 3.8 31.9 + - - -
178D LYS* 2.9 43.8 + - - +
179D ARG* 3.9 7.0 - - + +
180D THR* 3.2 21.4 + - - +
182D LYS* 1.3 78.2 - - + +
184D ALA* 1.3 57.8 + - - +
186D VAL* 3.4 8.6 + - - +
187D MET* 2.9 47.9 + - + +
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Residues in contact with ALA 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D VAL* 4.4 6.1 - - + -
104D TYR* 3.9 20.4 - - + -
105D PHE* 3.7 30.1 - - + -
180D THR 3.2 7.3 + - - +
181D THR* 3.2 20.9 - - - +
183D ARG* 1.3 73.4 - - - +
185D GLY* 1.3 66.0 + - - +
187D MET* 3.3 2.5 + - - +
188D ILE* 2.9 29.7 + - - +
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Residues in contact with GLY 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D TYR* 4.1 19.2 - - - -
181D THR 2.9 14.3 + - - -
182D LYS* 3.3 4.2 + - - -
184D ALA* 1.3 75.9 - - - +
186D VAL* 1.3 63.2 + - - +
188D ILE* 3.2 3.5 + - - +
189D GLY* 2.9 22.5 + - - -
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Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE* 3.4 35.9 - - + -
182D LYS* 3.0 29.4 + - + +
183D ARG* 3.6 10.1 - - - +
184D ALA 3.3 0.2 - - - -
185D GLY* 1.3 73.4 - - - +
187D MET* 1.3 60.4 + - + +
189D GLY* 4.0 0.5 - - - -
190D LEU* 2.9 27.9 + - - +
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Residues in contact with MET 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C PHE* 5.4 8.5 - - + -
105D PHE* 4.6 9.2 - - + -
160D VAL* 3.8 39.3 - - + +
163D PHE* 6.4 1.6 - - + -
164D ASP* 5.4 1.3 - - + +
175D TYR* 4.5 23.1 - - + +
183D ARG* 2.9 33.7 + - - +
184D ALA* 3.8 3.4 - - - +
186D VAL* 1.3 76.9 - - + +
188D ILE* 1.3 66.5 + - - +
190D LEU* 3.2 9.7 + - - +
191D ALA* 2.9 22.8 + - - +
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Residues in contact with ILE 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D TYR* 3.7 36.8 - - + +
105D PHE* 3.9 18.8 - - + -
108D SER* 3.1 43.1 - - - +
157D ASN* 4.5 5.2 - - - +
160D VAL* 5.6 4.3 - - + -
184D ALA 2.9 20.1 + - - +
185D GLY* 3.8 3.8 - - - +
187D MET* 1.3 70.4 - - - +
189D GLY* 1.3 65.2 + - - +
191D ALA* 2.9 18.7 + - - +
192D TRP* 3.0 30.8 + - + +
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Residues in contact with GLY 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D GLY 2.9 15.2 + - - -
186D VAL 4.0 0.7 - - - -
188D ILE* 1.3 76.6 - - - +
190D LEU* 1.3 64.1 + - - +
191D ALA 3.0 0.5 + - - -
192D TRP* 3.0 7.7 + - - +
193D VAL* 2.9 29.7 + - - +
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Residues in contact with LEU 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C TRP* 6.2 3.4 - - + -
209C PHE* 4.2 26.7 - - + -
186D VAL 2.9 19.9 + - - +
187D MET* 3.2 9.6 + - - +
189D GLY* 1.3 74.6 - - - +
191D ALA* 1.3 58.3 + - - +
193D VAL* 3.4 18.2 - - + +
194D ILE* 3.0 48.9 + - + +
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Residues in contact with ALA 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ALA* 4.7 2.5 - - - +
156D MET* 4.1 24.8 - - + +
157D ASN* 5.0 6.3 - - - +
160D VAL* 4.9 11.7 - - + -
187D MET 2.9 11.2 + - - +
188D ILE* 2.9 17.4 + - - +
190D LEU* 1.3 77.9 - - + +
192D TRP* 1.3 61.0 + - + +
194D ILE* 3.3 6.8 + - - +
195D SER* 2.9 33.5 + - - -
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Residues in contact with TRP 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D SER* 3.8 8.6 + - - +
111D CYS* 4.3 11.7 - - + -
112D ALA* 3.8 28.9 - - + -
115D ILE* 3.9 38.8 - - + -
149D VAL* 4.3 12.7 - - + +
150D ALA* 4.7 11.7 - - - -
153D ALA* 4.1 21.4 - - + +
157D ASN* 4.1 7.2 + - - -
188D ILE* 3.0 39.8 + - + +
189D GLY* 3.8 7.2 - - - +
191D ALA* 1.3 76.0 - - + +
193D VAL* 1.3 57.5 + - + +
195D SER* 3.9 0.5 - - - -
196D PHE* 2.9 33.8 + - - +
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Residues in contact with VAL 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189D GLY 2.9 18.0 + - - +
190D LEU* 3.4 22.4 - - + +
192D TRP* 1.3 77.4 - - - +
194D ILE* 1.3 59.8 + - + +
196D PHE* 3.9 4.8 - - - +
197D VAL* 2.9 44.7 + - + +
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Residues in contact with ILE 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D MET* 3.7 30.7 - - + -
190D LEU* 3.0 41.4 + - + +
191D ALA 3.3 5.3 + - - +
193D VAL* 1.3 77.8 - - + +
195D SER* 1.3 60.6 + - - +
197D VAL* 3.9 3.5 - - - +
198D LEU* 2.9 47.6 + - + +
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Residues in contact with SER 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D VAL* 3.3 26.2 - - - -
152D ASN* 3.2 24.6 + - - +
153D ALA* 3.1 22.2 - - - -
156D MET* 3.4 4.9 - - - -
191D ALA 2.9 17.4 + - - -
192D TRP 3.9 2.5 - - - -
194D ILE* 1.3 76.7 - - - +
196D PHE* 1.3 64.1 + - - +
198D LEU* 4.9 0.4 - - - -
199D TRP* 2.9 31.8 + - - +
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Residues in contact with PHE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D VAL* 3.4 22.5 - - + +
192D TRP 2.9 19.1 + - - +
193D VAL* 3.9 4.9 - - + +
195D SER* 1.3 76.4 - - - +
197D VAL* 1.3 90.9 + - + +
199D TRP 3.1 0.5 + - - -
200D ALA* 2.9 53.5 + - + +
201D PRO* 3.0 11.3 - - + +
204D LEU* 5.9 0.9 - - + -
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C VAL* 5.4 12.6 - - + -
193D VAL* 2.9 31.8 + - + +
194D ILE* 3.9 5.6 - - - +
196D PHE* 1.3 94.2 - - + +
198D LEU* 1.3 68.2 + - + +
201D PRO* 3.0 27.1 - - + +
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Residues in contact with LEU 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C VAL* 6.0 1.8 - - + -
198C LEU* 4.2 26.5 - - + -
152D ASN* 5.4 6.7 - - - +
156D MET* 6.1 0.4 - - - -
194D ILE* 2.9 35.8 + - + +
195D SER 3.9 2.7 - - - +
197D VAL* 1.3 87.1 - - + +
199D TRP* 1.3 72.4 + - + +
201D PRO* 5.0 0.2 - - - +
202D ALA* 3.8 14.9 + - - +
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Residues in contact with TRP 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D TYR* 3.5 39.0 - + + -
149D VAL* 3.7 11.9 - - + +
152D ASN* 3.0 39.4 + - + +
195D SER* 2.9 28.2 + - - +
198D LEU* 1.3 83.5 - - + +
200D ALA* 1.3 68.5 + - - +
202D ALA* 2.9 16.5 + - + +
203D ILE* 2.9 34.4 + - + +
222D ILE* 4.5 4.3 - - + -
224D PHE* 4.3 21.5 - + - -
225D LEU* 5.1 2.5 - - + -
234D THR* 3.6 31.4 - - + -
238D ALA* 4.5 4.7 - - + -
2000D 0HK 3.4 26.2 - - + -
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Residues in contact with ALA 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D SER* 4.2 13.0 - - - -
149D VAL* 3.9 7.5 - - + +
196D PHE* 2.9 45.8 + - + +
199D TRP* 1.3 73.4 - - - +
201D PRO* 1.3 68.5 - - + +
203D ILE* 4.6 0.2 - - - -
204D LEU* 2.9 46.7 + - + +
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Residues in contact with PRO 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D PHE* 3.0 33.9 - - + +
197D VAL* 3.0 26.5 - - + +
198D LEU 5.0 0.2 - - - +
199D TRP 3.4 2.9 - - - -
200D ALA* 1.3 81.2 - - + +
202D ALA* 1.3 56.0 + - - +
204D LEU* 5.2 1.3 - - + -
205D PHE* 2.8 52.6 + - + +
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D LEU 3.8 12.0 + - - +
199D TRP* 2.9 10.6 + - + +
201D PRO* 1.3 78.3 - - - +
203D ILE* 1.3 66.5 + - - +
205D PHE 5.3 0.2 - - - -
206D TRP* 2.9 38.3 + - + +
224D PHE* 3.8 23.3 - - + -
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Residues in contact with ILE 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ASP* 4.3 27.5 - - - +
144D LEU* 4.2 12.1 - - + -
145D SER* 3.5 33.0 - - - +
148D TYR* 4.1 15.7 - - + -
199D TRP* 2.9 30.0 + - + +
200D ALA 3.8 2.7 - - - +
202D ALA* 1.3 77.1 - - - +
204D LEU* 1.3 62.1 + - - +
206D TRP* 4.1 7.3 + - - +
207D GLN* 5.0 3.5 + - - +
222D ILE* 3.9 35.3 - - + +
223D GLN* 5.6 4.7 + - - +
224D PHE* 4.2 13.2 - - + -
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 6.5 0.7 - - + -
141D ASP* 3.4 43.5 - - + +
142D LEU* 4.3 12.6 - - + +
145D SER* 3.9 18.6 - - - +
196D PHE* 5.9 1.3 - - + -
200D ALA* 2.9 34.6 + - + +
201D PRO* 5.2 0.4 - - + -
203D ILE* 1.3 77.0 - - + +
205D PHE* 1.3 73.7 + - + +
206D TRP 3.3 2.0 + - - -
207D GLN* 3.7 25.8 + - - +
208D TYR* 3.8 6.1 - - - -
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Residues in contact with PHE 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PRO* 2.8 34.2 + - + +
202D ALA 3.8 0.7 - - - -
204D LEU* 1.3 90.4 - - + +
206D TRP* 1.3 59.1 + - - +
207D GLN 3.5 1.3 - - - -
208D TYR* 3.7 16.9 + + + +
209D PHE* 2.9 30.3 + - - +
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Residues in contact with TRP 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C MET* 6.5 0.9 - - + -
190C LEU* 6.5 0.4 - - + -
202D ALA* 2.9 26.1 + - + +
203D ILE 4.1 6.3 - - - +
204D LEU 3.3 1.4 - - - -
205D PHE* 1.3 76.1 - - - +
207D GLN* 1.3 60.3 + - - +
209D PHE* 3.3 34.2 + + + +
210D VAL* 2.9 45.3 + - + +
223D GLN* 3.1 48.9 - - + +
224D PHE* 3.2 43.4 - + + +
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Residues in contact with GLN 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141D ASP* 3.8 16.8 + - - -
203D ILE 5.0 2.9 + - - +
204D LEU 3.7 12.6 + - - +
206D TRP* 1.3 76.2 - - - +
208D TYR* 1.3 94.9 + - + +
210D VAL 3.3 0.9 + - - -
211D GLY* 2.7 32.4 + - - -
212D LYS 3.4 16.2 + - - +
213D ARG* 2.8 45.0 + - + +
223D GLN* 3.0 26.0 + - - +
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Residues in contact with TYR 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU 3.8 11.2 - - - -
205D PHE* 3.7 16.3 + + + +
206D TRP 3.3 0.4 - - - -
207D GLN* 1.3 108.5 + - + +
209D PHE* 1.3 65.9 + - - +
211D GLY* 3.6 10.1 + - - +
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Residues in contact with PHE 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ARG* 5.2 2.4 + - - -
186C VAL* 4.0 28.3 - - + -
187C MET* 4.9 14.8 - - + -
190C LEU* 4.1 33.0 - - + -
205D PHE 2.9 19.8 + - - +
206D TRP* 3.5 39.7 - + + +
207D GLN 3.2 0.2 - - - -
208D TYR* 1.3 81.5 - - - +
210D VAL* 1.3 64.2 + - + +
----------------------------------------------------------
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Residues in contact with VAL 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C ARG* 3.5 28.7 + - - +
206D TRP* 2.9 53.6 + - + +
207D GLN 3.9 2.5 - - - +
209D PHE* 1.3 80.5 - - + +
211D GLY* 1.3 59.3 + - - +
212D LYS* 4.0 16.8 - - + +
214D THR* 5.8 0.7 - - - +
223D GLN* 4.1 9.0 - - - +
----------------------------------------------------------
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Residues in contact with GLY 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D GLN 2.7 17.1 + - - -
208D TYR* 3.6 9.6 + - - -
209D PHE 3.3 1.8 - - - -
210D VAL* 1.3 74.4 - - - +
212D LYS* 1.3 57.2 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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