Contacts of the helix formed by residues 210 - 238 (chain D) in PDB entry 5IJO
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 SER 210 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D GLU* 5.0 6.0 - - - +
209D GLY* 1.4 71.1 - - - -
211D GLU* 1.3 63.8 + - - +
212D LYS 3.4 2.5 - - - +
213D HIS* 4.3 15.0 - - - +
214D ARG* 3.8 15.8 + - - +
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Residues in contact with GLU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D GLY 3.8 3.4 + - - -
210D SER* 1.3 71.5 - - - +
212D LYS* 1.3 67.2 + - - +
214D ARG* 3.0 10.2 + - - +
215D LYS* 2.9 21.4 + - - +
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D SER 3.4 0.4 - - - -
211D GLU* 1.3 76.9 - - - +
213D HIS* 1.3 67.3 + - - +
215D LYS* 3.2 7.8 + - - +
216D GLU* 3.1 22.2 + - - +
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Residues in contact with HIS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D SER* 3.9 17.9 + - - +
211D GLU 3.3 0.6 - - - -
212D LYS* 1.3 78.3 - - - +
214D ARG* 1.3 61.3 + - - +
216D GLU* 3.3 8.7 - - - +
217D VAL* 3.3 18.7 + - - +
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Residues in contact with ARG 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D GLU* 6.1 4.9 - - + -
210D SER 3.8 9.8 + - - +
211D GLU* 3.0 12.6 + - - +
213D HIS* 1.3 75.5 - - - +
215D LYS* 1.3 60.7 + - - +
216D GLU 3.0 1.6 - - - -
217D VAL* 3.0 7.0 + - - +
218D SER* 2.7 31.3 + - - -
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Residues in contact with LYS 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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211D GLU 2.9 13.0 + - - +
212D LYS* 3.2 10.3 + - - +
214D ARG* 1.3 75.7 - - - +
216D GLU* 1.3 63.7 + - - +
218D SER* 3.8 6.9 - - - -
219D ASP* 2.9 25.3 + - - +
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Residues in contact with GLU 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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212D LYS 3.1 11.1 + - - +
213D HIS* 3.3 13.7 - - - +
214D ARG 3.0 0.2 - - - -
215D LYS* 1.3 80.0 - - - +
217D VAL* 1.4 61.8 + - - +
219D ASP* 3.2 6.9 + - - +
220D LEU* 3.2 19.2 + - - +
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Residues in contact with VAL 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D GLU* 6.3 2.9 - - + -
213D HIS 3.3 8.5 + - - +
214D ARG* 3.0 9.1 + - - +
216D GLU* 1.4 73.0 - - - +
218D SER* 1.3 68.5 + - - +
219D ASP 3.0 1.1 - - - -
220D LEU* 3.1 8.0 + - - +
221D ILE* 3.0 23.1 + - - +
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Residues in contact with SER 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D ARG* 2.7 20.7 + - - -
215D LYS* 3.9 7.6 - - - -
217D VAL* 1.3 73.5 - - - +
219D ASP* 1.3 62.1 + - - +
221D ILE* 3.5 6.3 + - - +
222D LYS* 3.1 23.6 + - - +
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Residues in contact with ASP 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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215D LYS 2.9 14.7 + - - +
216D GLU* 3.3 12.3 - - - +
217D VAL 3.0 0.2 - - - -
218D SER* 1.3 73.4 - - - +
220D LEU* 1.3 67.3 + - - +
222D LYS* 3.1 6.8 + - - +
223D GLU* 3.1 22.0 + - - +
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Residues in contact with LEU 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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136D TRP* 3.9 28.0 - - + -
216D GLU 3.2 8.1 + - - +
217D VAL* 3.1 10.1 + - - +
219D ASP* 1.3 79.3 - - - +
221D ILE* 1.3 57.2 + - - +
223D GLU* 3.4 7.7 + - - +
224D CYS* 3.0 24.8 + - - +
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Residues in contact with ILE 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ILE* 5.1 20.1 - - + +
217D VAL 3.0 14.8 + - - +
218D SER* 3.9 6.5 - - - +
220D LEU* 1.3 75.1 - - - +
222D LYS* 1.3 65.5 + - - +
224D CYS* 2.9 10.5 + - - +
225D ARG* 2.9 22.1 + - - +
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Residues in contact with LYS 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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218D SER 3.1 17.2 + - - +
219D ASP* 3.1 6.5 + - - +
221D ILE* 1.3 74.8 - - - +
223D GLU* 1.3 64.5 + - - +
225D ARG* 3.1 10.6 + - - +
226D GLN* 3.0 23.1 + - - +
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Residues in contact with GLU 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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140D ARG* 6.5 0.9 - - + -
219D ASP 3.1 12.5 + - - +
220D LEU* 3.5 10.8 - - - +
222D LYS* 1.3 77.8 - - - +
224D CYS* 1.3 56.6 + - - +
226D GLN* 3.1 8.7 + - - +
227D SER* 2.9 30.2 + - - -
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Residues in contact with CYS 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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139D LYS* 6.3 3.4 - - + -
140D ARG* 6.4 2.9 - - - +
193D ILE* 5.6 6.7 - - + -
220D LEU 3.0 13.4 + - - +
221D ILE* 2.9 13.6 + - - +
223D GLU* 1.3 77.0 - - - +
225D ARG* 1.3 56.4 + - - +
227D SER* 3.4 6.6 + - - -
228D LEU* 2.9 29.1 + - - +
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Residues in contact with ARG 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D ILE* 5.9 7.2 - - + -
221D ILE 2.9 11.3 + - - +
222D LYS* 3.1 12.3 + - - +
224D CYS* 1.3 75.9 - - - +
226D GLN* 1.3 58.2 + - - +
228D LEU* 3.1 10.1 - - - +
229D ALA* 2.9 25.6 + - - +
270D ALA* 4.7 12.9 - - + +
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Residues in contact with GLN 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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222D LYS 3.0 12.0 + - - +
223D GLU* 3.4 12.1 - - - +
225D ARG* 1.3 77.8 - - - +
227D SER* 1.4 59.4 + - - +
229D ALA* 3.1 22.1 + - - +
230D GLU* 3.5 5.0 + - - +
270D ALA* 5.8 1.3 - - - -
384D GLN* 4.4 13.1 - - + +
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Residues in contact with SER 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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140D ARG 5.8 0.4 - - - -
143D ALA* 4.1 28.4 - - - +
144D ASN* 5.0 4.7 - - - -
147D LYS* 4.5 7.6 - - - +
223D GLU 2.9 15.8 + - - -
224D CYS* 3.9 4.9 - - - -
226D GLN* 1.4 74.3 - - - +
228D LEU* 1.3 64.8 + - - +
230D GLU* 3.2 17.5 + - - +
231D SER* 3.3 12.1 + - - -
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Residues in contact with LEU 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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143D ALA* 5.5 1.8 - - - +
189D LEU* 6.0 4.9 - - + +
190D VAL* 5.7 12.6 - - + +
224D CYS 2.9 14.5 + - - +
225D ARG* 3.1 17.5 - - - +
227D SER* 1.3 75.8 - - - +
229D ALA* 1.3 62.7 + - - +
231D SER* 3.3 8.5 + - - -
232D LEU* 3.2 20.4 + - - +
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Residues in contact with ALA 229 (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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225D ARG 2.9 11.3 + - - +
226D GLN* 3.2 14.8 - - - +
227D SER 3.1 0.4 - - - -
228D LEU* 1.3 77.7 - - - +
230D GLU* 1.3 62.5 + - - +
232D LEU* 3.3 7.2 + - - +
233D PHE* 3.1 22.7 + - - +
270D ALA* 3.5 35.0 - - + +
273D MET* 5.5 5.3 - - + +
274D ALA* 5.4 0.9 + - - +
384D GLN* 4.6 12.6 - - + -
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Residues in contact with GLU 230 (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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147D LYS* 4.5 15.3 - - + +
151D GLN* 5.3 5.1 - - + +
226D GLN 3.5 4.3 + - - +
227D SER* 3.2 13.7 + - - +
229D ALA* 1.3 79.2 - - - +
231D SER* 1.3 57.2 + - - +
233D PHE* 3.4 7.1 + - - +
234D ALA* 2.9 30.2 + - - +
384D GLN* 5.2 9.8 - - + +
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Residues in contact with SER 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ALA 5.7 0.9 - - - -
146D LEU* 5.4 8.1 - - - -
147D LYS* 4.8 15.8 - - - +
150D ILE* 4.8 5.1 - - - +
186D VAL* 6.2 4.0 - - - -
227D SER 3.3 9.8 + - - -
228D LEU* 3.7 11.2 - - - -
229D ALA 3.3 0.2 - - - -
230D GLU* 1.3 76.7 - - - +
232D LEU* 1.4 65.9 + - - +
234D ALA* 3.2 7.6 + - - +
235D TRP* 2.9 21.8 + - - +
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Residues in contact with LEU 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 LEU 3.2 10.2 + - - +
229D ALA* 3.3 8.9 + - - +
231D SER* 1.4 77.3 - - - +
233D PHE* 1.3 64.3 + - - +
235D TRP* 3.1 17.0 + - - +
236D ALA* 3.1 12.0 + - - +
271D LEU* 6.4 1.6 - - + -
274D ALA* 3.9 19.1 - - + +
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Residues in contact with PHE 233 (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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229D ALA 3.1 11.9 + - - +
230D GLU* 3.7 10.1 - - - +
232D LEU* 1.3 77.2 - - - +
234D ALA* 1.3 64.3 + - - +
236D ALA* 2.9 15.9 + - - +
237D CYS* 3.0 11.5 + - - +
273D MET* 4.5 20.6 - - + +
274D ALA* 4.2 15.2 - - - +
277D TYR* 5.9 4.1 - - + +
387D PHE* 4.9 10.5 - - + -
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Residues in contact with ALA 234 (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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147D LYS 4.9 0.4 - - - +
150D ILE* 3.4 43.6 - - + +
151D GLN* 3.6 13.7 - - + +
230D GLU 2.9 19.1 + - - +
231D SER* 3.5 3.6 - - - +
233D PHE* 1.3 75.3 - - - +
235D TRP* 1.3 64.8 + - - +
237D CYS* 3.1 8.3 + - - +
238D GLN* 2.9 24.1 + - - +
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Residues in contact with TRP 235 (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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150D ILE* 4.9 3.3 - - - +
231D SER 2.9 13.9 + - - +
232D LEU* 3.1 13.0 + - - +
234D ALA* 1.3 77.5 - - - +
236D ALA* 1.3 56.7 + - - +
238D GLN* 2.5 33.9 - - - +
239D SER* 3.3 3.5 + - - -
240D PRO* 3.9 10.3 - - + -
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Residues in contact with ALA 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D LEU 3.1 9.7 + - - +
233D PHE* 2.9 12.5 + - - +
235D TRP* 1.3 73.2 - - - +
237D CYS* 1.3 67.2 + - - +
239D SER* 3.2 18.4 + - - +
240D PRO 5.4 0.4 - - - -
274D ALA* 4.4 18.8 - - + +
277D TYR* 5.2 6.7 - - + -
278D CYS* 4.8 16.2 - - + +
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Residues in contact with CYS 237 (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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233D PHE 3.0 11.0 + - - +
234D ALA* 3.7 10.1 - - - +
236D ALA* 1.3 76.7 - - - +
238D GLN* 1.4 59.1 + - + +
239D SER* 3.1 6.6 + - - -
277D TYR* 6.3 0.2 - - - +
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Residues in contact with GLN 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 4.8 11.0 - - + +
234D ALA 2.9 15.1 + - - +
235D TRP* 2.5 18.1 - - - +
237D CYS* 1.4 73.1 - - - +
239D SER* 1.3 63.5 + - - +
240D PRO 3.3 1.0 - - - -
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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