Contacts of the helix formed by residues 232 - 255 (chain D) in PDB entry 5Y1Z
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 HIS 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228D ASN* 3.5 40.4 + - + +
229D GLY 3.5 3.2 + - - -
230D GLY 3.6 0.4 - - - -
231D ASN* 1.3 81.3 - - - +
233D LYS* 1.3 73.4 + - + +
234D LEU* 3.1 48.4 + - + +
235D THR* 2.9 25.2 + - - +
236D GLN* 3.1 11.8 + - - +
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Residues in contact with LYS 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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91B PRO* 5.3 3.6 - - - +
92B ASP* 3.5 41.7 + - + +
93B ALA* 5.2 0.5 - - - +
231D ASN 3.6 2.2 + - - -
232D HIS* 1.3 79.7 + - + +
234D LEU* 1.3 63.2 + - + +
236D GLN* 3.2 19.1 + - - +
237D ILE* 3.1 25.7 + - - +
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Residues in contact with LEU 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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172D ALA* 3.5 32.3 - - + -
173D PHE* 3.1 18.7 - - + -
224D CYS* 3.5 14.4 - - - -
228D ASN* 3.9 17.7 - - - +
232D HIS* 3.1 27.9 + - + +
233D LYS* 1.3 75.4 - - + +
235D THR* 1.3 63.8 + - - +
237D ILE* 3.1 7.4 + - + +
238D ALA 2.9 18.4 + - - -
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Residues in contact with THR 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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221D LEU* 4.1 4.9 - - + -
224D CYS* 3.3 22.1 + - - -
225D ILE* 3.5 27.6 - - + +
229D GLY 2.7 21.4 + - - -
230D GLY 3.4 21.3 - - - +
232D HIS* 2.9 15.6 + - - +
234D LEU* 1.3 76.9 - - - +
236D GLN* 1.3 57.9 + - - +
238D ALA* 3.1 3.6 + - - +
239D LYS* 2.9 38.5 + - - +
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Residues in contact with GLN 236 (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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91B PRO* 5.8 4.9 - - - +
93B ALA* 3.7 24.7 - - + +
231D ASN* 3.4 35.3 + - - +
232D HIS 3.1 9.2 + - - +
233D LYS* 3.4 20.0 - - - +
234D LEU 3.2 0.2 - - - -
235D THR* 1.3 72.8 - - - +
237D ILE* 1.3 65.0 + - - +
239D LYS* 3.3 22.3 + - - +
240D VAL* 3.2 25.5 + - - +
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Residues in contact with ILE 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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92B ASP* 4.0 8.3 - - + +
93B ALA* 3.5 31.4 - - + +
96B CYS* 3.7 17.7 - - + -
169D GLY* 3.5 26.0 - - - +
170D THR* 3.8 20.6 - - + -
173D PHE* 3.7 18.6 - - + -
233D LYS 3.1 14.1 + - - +
234D LEU* 3.1 12.8 + - + +
236D GLN* 1.3 75.9 - - - +
238D ALA* 1.3 63.3 + - - +
240D VAL* 3.0 7.2 + - + +
241D VAL* 2.9 19.9 + - - +
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Residues in contact with ALA 238 (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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173D PHE* 3.8 20.1 - - + -
220D ILE* 4.5 5.6 - - + -
221D LEU* 3.9 29.6 - - + +
224D CYS* 4.2 7.0 - - + -
234D LEU 2.9 12.5 + - - +
235D THR 3.1 9.6 + - - +
237D ILE* 1.3 75.6 - - - +
239D LYS* 1.3 62.7 + - - +
241D VAL* 3.3 6.9 + - - +
242D ILE* 3.0 29.5 + - - +
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Residues in contact with LYS 239 (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 LEU* 3.9 24.9 - - + -
225D ILE* 6.0 1.3 - - - -
230D GLY 4.1 11.4 + - - -
231D ASN* 5.2 4.0 + - - -
235D THR* 2.9 34.4 + - - +
236D GLN* 3.6 23.0 - - - +
238D ALA* 1.3 74.1 - - - +
240D VAL* 1.3 66.1 + - + +
242D ILE* 3.4 2.1 + - - +
243D LYS* 3.0 32.7 + - + +
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Residues in contact with VAL 240 (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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-1B GLY 4.8 9.0 - - - +
93B ALA* 3.6 24.7 - - + +
96B CYS* 4.1 12.3 - - + -
97B ALA* 3.7 35.4 - - + +
236D GLN 3.2 14.2 + - - +
237D ILE* 3.0 10.8 + - - +
239D LYS* 1.3 76.6 - - + +
241D VAL* 1.3 64.2 + - - +
243D LYS* 3.1 8.4 + - + +
244D ILE* 2.9 39.4 + - + +
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Residues in contact with VAL 241 (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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165D MET* 4.0 28.9 - - + +
170D THR* 3.6 32.1 - - + -
173D PHE* 4.9 7.4 - - + -
195D LEU* 4.2 20.9 - - + -
217D ALA* 6.2 0.4 - - + -
220D ILE* 5.2 5.8 - - + -
237D ILE* 2.9 19.2 + - + +
238D ALA* 3.6 10.8 - - - +
240D VAL* 1.3 78.5 - - + +
242D ILE* 1.3 69.2 + - + +
244D ILE* 3.4 9.2 + - + +
245D CYS* 3.0 25.6 + - - +
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Residues in contact with ILE 242 (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* 4.6 3.8 - - + -
217D ALA* 3.7 27.8 - - + +
218D LYS* 4.0 34.3 - - + -
220D ILE* 4.5 8.1 - - + -
221D LEU* 4.2 25.6 - - + -
238D ALA 3.0 22.0 + - - +
239D LYS 4.1 3.1 - - - +
241D VAL* 1.3 85.7 - - + +
243D LYS* 1.3 68.4 + - + +
245D CYS* 3.1 6.1 + - + +
246D GLU* 2.9 40.3 + - - +
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Residues in contact with LYS 243 (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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-1B GLY 5.0 9.2 - - - +
0B SER* 4.2 12.8 - - - +
1B MET* 3.7 39.5 - - + +
239D LYS* 3.0 23.7 + - + +
240D VAL* 3.1 7.2 + - - +
242D ILE* 1.3 79.5 - - + +
244D ILE* 1.3 63.2 + - + +
246D GLU* 3.1 15.3 + - - +
247D HIS* 3.0 21.7 + - - +
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Residues in contact with ILE 244 (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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96B CYS* 5.0 0.7 - - - +
100B SER* 3.9 21.1 - - - +
164D LYS* 3.6 35.2 - - + +
165D MET* 4.0 13.7 - - + +
167D GLN* 3.7 30.3 - - + -
240D VAL* 2.9 35.2 + - + +
241D VAL* 3.7 7.2 - - + +
243D LYS* 1.3 75.5 - - + +
245D CYS* 1.3 64.3 + - - +
247D HIS* 3.0 8.8 + - + +
248D GLU* 2.9 27.5 + - + +
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Residues in contact with CYS 245 (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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165D MET* 3.5 25.8 - - - +
213D PHE* 3.8 35.0 - - - -
214D LEU* 3.6 25.4 - - + -
217D ALA* 4.1 8.5 - - + -
241D VAL 3.0 10.2 + - - +
242D ILE* 3.1 12.3 + - - +
244D ILE* 1.3 77.7 - - - +
246D GLU* 1.3 61.4 + - - +
248D GLU* 3.3 2.7 + - - +
249D MET* 2.9 32.4 + - - +
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Residues in contact with GLU 246 (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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1B MET* 3.7 33.8 - - + +
214D LEU* 3.5 30.0 - - + +
218D LYS* 4.2 12.3 + - - -
242D ILE* 2.9 32.6 + - - +
243D LYS* 3.1 13.4 + - - +
245D CYS* 1.3 75.3 - - - +
247D HIS* 1.3 58.5 + - - +
249D MET* 3.3 3.1 + - - +
250D ASN* 2.9 30.1 + - - +
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Residues in contact with HIS 247 (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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1B MET* 3.2 38.5 - - - +
2B ALA* 3.6 19.1 + - - -
3B GLY* 5.4 0.9 - - - -
104B LYS* 5.6 10.0 + - + +
243D LYS 3.0 9.8 + - - +
244D ILE* 3.0 11.9 + - + +
246D GLU* 1.3 77.4 - - - +
248D GLU* 1.3 78.7 + - - +
250D ASN* 3.3 4.8 + - + +
251D GLU* 3.0 56.9 + - + +
313D ARG* 5.7 0.9 + - - -
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Residues in contact with GLU 248 (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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161D ALA* 3.8 20.9 - - + +
164D LYS* 3.2 44.1 + - + +
244D ILE* 2.9 25.3 + - + +
245D CYS* 3.9 3.8 - - - +
247D HIS* 1.3 98.1 + - - +
249D MET* 1.3 68.8 - - + +
251D GLU* 3.1 5.6 + - - +
252D ILE* 2.9 27.5 + - - +
259D TYR* 2.9 39.8 + - - +
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Residues in contact with MET 249 (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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158D LEU* 3.9 13.7 - - + -
161D ALA* 3.7 22.7 - - + -
210D THR* 3.7 40.1 - - - +
213D PHE* 3.3 38.6 - - + -
214D LEU* 4.2 19.7 - - + -
245D CYS* 2.9 25.4 + - - +
246D GLU* 3.7 6.1 - - - +
248D GLU* 1.3 77.3 - - + +
250D ASN* 1.3 63.2 + - - +
252D ILE* 3.4 6.8 + - + +
253D GLU* 3.0 27.8 + - - +
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Residues in contact with ASN 250 (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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1B MET* 4.3 18.3 - - + +
246D GLU 2.9 17.4 + - - +
247D HIS* 3.5 7.0 - - + +
249D MET* 1.3 77.4 - - - +
251D GLU* 1.3 58.4 + - + +
253D GLU* 2.9 9.8 + - - +
254D VAL* 2.9 33.9 + - - +
297D ARG* 4.5 4.3 + - - +
313D ARG* 4.2 8.5 - - - +
504D SO4 3.3 41.5 + - - -
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Residues in contact with GLU 251 (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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247D HIS* 3.0 49.1 + - + +
248D GLU* 3.1 5.4 + - - +
250D ASN* 1.3 75.0 + - - +
252D ILE* 1.3 64.4 + - - +
254D VAL* 3.3 15.3 + - - +
255D CYS 3.3 16.1 + - - +
259D TYR* 3.5 26.4 - - + +
306D ARG* 5.6 7.7 + - - -
313D ARG* 3.0 38.6 + - - -
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Residues in contact with ILE 252 (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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145D ALA* 3.5 7.1 - - - +
146D MET* 4.7 10.1 - - + -
149D LEU* 4.7 4.3 - - + -
154D LEU* 4.7 2.0 - - + -
157D LEU* 3.9 36.8 - - + +
158D LEU* 4.2 21.3 - - + -
161D ALA* 4.9 0.4 - - + -
210D THR* 3.9 16.4 - - + -
248D GLU 2.9 23.0 + - - +
249D MET* 3.6 15.7 - - + +
251D GLU* 1.3 76.2 - - - +
253D GLU* 1.3 63.5 + - - +
255D CYS 4.7 0.2 - - - -
256D PRO* 3.4 18.2 - - + -
259D TYR* 3.6 36.1 - - + +
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Residues in contact with GLU 253 (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 SER* 2.8 32.2 + - - -
144D LYS* 6.0 0.5 - - - +
145D ALA* 3.4 21.4 + - - +
146D MET* 3.4 20.1 - - - +
210D THR* 2.8 26.9 + - + +
211D GLU* 4.5 7.3 - - - +
249D MET* 3.0 17.2 + - + +
250D ASN* 2.9 17.4 + - - +
252D ILE* 1.3 79.3 - - - +
254D VAL* 1.3 62.1 + - + +
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Residues in contact with VAL 254 (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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250D ASN* 2.9 26.6 + - - +
251D GLU* 3.3 10.7 + - - +
253D GLU* 1.3 79.8 - - + +
255D CYS* 1.3 62.7 + - + +
256D PRO* 4.9 0.2 - - - +
278D HIS* 5.3 0.7 - - - -
296D LEU* 4.0 31.9 - - + +
297D ARG* 3.3 53.1 - - - +
304D ASP* 3.8 9.0 - - - +
313D ARG* 3.9 14.6 - - - +
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Residues in contact with CYS 255 (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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148D MET* 5.7 2.5 - - - -
251D GLU 3.3 5.1 + - - +
252D ILE 3.7 2.9 - - - -
253D GLU 3.4 0.4 - - - -
254D VAL* 1.3 85.2 - - + +
256D PRO* 1.3 68.8 - - - +
257D GLU* 3.7 9.4 - - - -
258D CYS* 3.3 19.4 - - + +
259D TYR* 3.0 27.2 + - - +
274D CYS* 3.8 4.7 - - - -
278D HIS* 3.6 13.7 - - + +
296D LEU* 4.8 1.6 - - + -
503D ZN 2.2 37.7 - - - -
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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
------------------------------------------------------------
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