Contacts of the helix formed by residues 220 - 243 (chain B) in PDB entry 6E8Z
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 GLY 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 4.3 15.2 + - - -
160A LYS* 5.9 3.0 - - - +
218B GLY 4.1 0.2 + - - -
219B PHE* 1.3 78.6 - - - +
221B ASP* 1.3 60.4 + - - -
222B ASN 3.3 2.9 - - - -
223B THR* 3.3 7.7 + - - -
224B LYS* 3.0 27.6 + - - +
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A GLU* 4.8 2.2 + - - -
263A THR* 3.6 20.3 + - - +
266A TYR* 4.4 20.4 - - - +
267A GLY* 4.8 6.2 - - - +
220B GLY* 1.3 69.5 - - - -
222B ASN* 1.3 60.8 + - - +
224B LYS* 3.8 9.4 - - - +
225B ALA* 2.8 30.5 + - - +
266B TYR* 3.9 27.2 + - - -
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Residues in contact with ASN 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA* 3.4 32.1 - - - +
151A ASN* 3.9 1.4 + - - -
152A ILE* 3.5 36.4 - - - +
155A GLU* 3.3 24.9 + - - +
161A PHE 4.5 2.0 - - - -
162A CYS* 4.4 8.3 - - + +
263A THR* 2.8 34.1 + - - +
405A EDO 4.4 2.3 - - - -
220B GLY 3.3 0.8 - - - -
221B ASP* 1.3 78.4 - - - +
223B THR* 1.3 62.4 + - - +
225B ALA* 3.4 5.2 + - - +
226B ALA* 3.1 21.1 + - - +
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 4.7 4.7 + - - -
160A LYS* 4.5 5.2 - - - +
161A PHE* 2.7 37.1 + - + +
214B CYS* 3.8 13.5 - - - -
219B PHE* 3.7 32.5 - - + +
220B GLY 3.3 11.4 + - - -
222B ASN* 1.3 79.1 - - - +
224B LYS* 1.3 63.1 + - - +
226B ALA* 3.0 6.4 + - - +
227B VAL* 2.9 21.1 + - - +
339B ILE* 4.1 17.9 - - + -
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA* 4.1 16.2 - - + +
214B CYS* 3.5 18.3 - - + -
215B ASP* 2.9 40.9 + - - +
220B GLY 3.0 16.5 + - - +
221B ASP* 3.8 11.0 - - - +
223B THR* 1.3 76.9 - - - +
225B ALA* 1.3 58.1 + - - +
227B VAL* 3.2 3.6 + - - +
228B ILE* 3.0 44.6 + - + +
265B CYS 3.2 27.8 + - - -
266B TYR* 3.8 34.0 + - + +
271B ARG* 3.9 3.4 - - - +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA* 4.3 7.4 - - + -
259A ALA* 3.9 33.2 - - + +
262A ILE* 4.2 19.5 - - + +
263A THR* 4.3 4.3 - - - -
221B ASP 2.8 18.1 + - - +
222B ASN* 3.6 5.8 - - - +
223B THR 3.2 0.2 - - - -
224B LYS* 1.3 77.4 - - - +
226B ALA* 1.3 57.1 + - - +
228B ILE* 3.5 3.1 + - - +
229B ARG* 3.0 30.5 + - - +
266B TYR* 4.7 2.6 + - - +
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ALA* 5.7 0.2 - - - +
161A PHE* 3.9 20.4 - - + -
162A CYS* 4.4 4.0 - - - -
163A GLU* 3.5 35.9 - - + +
259A ALA* 5.0 0.8 - - - +
222B ASN 3.1 12.2 + - - +
223B THR 3.0 10.1 + - - +
225B ALA* 1.3 74.3 - - - +
227B VAL* 1.3 65.8 + - - +
229B ARG* 3.3 0.7 + - - +
230B LEU* 2.9 32.1 + - + +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 5.5 0.9 - - + -
207B VAL* 4.2 3.8 - - + +
210B GLY* 4.0 27.8 - - - +
211B ALA* 4.0 7.9 - - - +
214B CYS* 4.3 11.0 - - + -
223B THR* 2.9 19.2 + - + +
224B LYS* 3.2 9.2 + - - +
226B ALA* 1.3 75.1 - - + +
228B ILE* 1.3 58.4 + - - +
230B LEU* 4.8 0.2 - - - -
231B GLY* 2.8 25.1 + - - -
321B LEU* 3.3 20.1 - - + +
338B PHE* 4.0 15.5 - - + -
339B ILE* 4.2 18.4 - - + -
342B LEU* 3.9 22.0 - - + -
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ILE* 4.2 16.6 - - + -
207B VAL* 4.0 6.5 - - + -
211B ALA* 4.4 8.5 - - + -
224B LYS* 3.0 29.2 + - + +
225B ALA 3.8 3.6 - - - +
227B VAL* 1.3 77.5 - - - +
229B ARG* 1.3 58.8 + - - +
231B GLY* 3.1 2.4 + - - -
232B LEU* 2.8 27.4 + - - +
261B LEU* 3.6 29.8 - - + +
262B ILE* 4.6 7.0 - - + -
265B CYS* 3.7 26.9 - - + -
266B TYR* 3.5 34.3 - - + +
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLU* 2.6 41.0 + - - +
189A THR* 4.2 5.3 + - - -
253A LEU 2.9 30.4 + - - +
254A GLU* 3.4 40.1 + - - +
255A SER* 3.4 10.7 - - - +
258A VAL* 4.0 13.5 - - + -
259A ALA* 4.0 8.3 - - + -
262A ILE* 6.2 0.9 - - + -
225B ALA 3.0 18.9 + - - +
226B ALA 3.8 2.2 - - - +
228B ILE* 1.3 78.6 - - - +
230B LEU* 1.3 71.1 + - - +
232B LEU* 3.0 9.1 + - + +
233B MET* 2.9 54.8 + - + +
347B GLU* 4.3 9.5 + - - +
348B HIS* 4.0 7.1 + - - -
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 4.5 9.0 - - + -
163A GLU* 3.6 20.0 - - - +
226B ALA 2.9 22.6 + - - +
227B VAL 3.9 2.9 - - - +
229B ARG* 1.3 84.6 - - - +
231B GLY* 1.3 66.4 + - - +
233B MET* 3.3 4.0 + - - +
234B GLU* 2.9 26.9 + - - +
321B LEU* 4.1 10.1 - - + -
342B LEU* 4.4 24.2 - - + -
345B HIS* 4.0 24.1 + - + +
347B GLU* 4.0 18.2 - - + -
348B HIS* 4.0 22.9 - - + -
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Residues in contact with GLY 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B VAL* 3.6 26.0 - - - +
227B VAL 2.8 16.6 + - - -
228B ILE 3.4 4.3 - - - -
230B LEU* 1.3 74.8 - - - +
232B LEU* 1.3 56.3 + - - +
234B GLU* 3.1 7.8 + - - +
235B MET* 2.8 31.2 + - - +
321B LEU* 3.4 11.9 - - - +
322B PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 4.0 26.7 - - + -
258A VAL* 4.9 12.6 - - + -
228B ILE 2.8 16.3 + - - +
229B ARG* 3.0 10.1 + - - +
231B GLY* 1.3 74.7 - - - +
233B MET* 1.3 66.7 + - + +
235B MET* 3.0 17.9 + - + +
236B ILE* 2.9 34.4 + - + +
252B PHE* 4.1 33.9 - - + +
257B GLY 5.0 0.4 - - - -
258B VAL* 4.8 22.9 - - + +
261B LEU* 3.9 19.9 - - + +
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Residues in contact with MET 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 3.7 31.4 - - + +
254A GLU* 5.4 3.4 - - - +
229B ARG* 2.9 42.9 + - + +
230B LEU* 3.6 6.5 - - - +
232B LEU* 1.3 87.3 - - + +
234B GLU* 1.3 57.0 + - - +
236B ILE* 3.2 28.1 + - + +
237B ALA* 2.9 31.0 + - - +
345B HIS* 5.3 0.2 - - + -
347B GLU* 3.7 39.0 - - + +
403B EDO 4.0 4.6 - - - -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU 2.9 18.2 + - - +
231B GLY* 3.5 5.6 - - - +
233B MET* 1.3 75.3 - - - +
235B MET* 1.3 57.0 + - - +
238B PHE* 2.8 33.4 + - - +
319B PHE* 3.5 19.5 - - + -
320B PRO* 3.1 3.3 - - - +
321B LEU* 2.7 31.5 + - - +
322B PHE* 2.8 46.2 + - + -
345B HIS* 2.8 28.0 + - + +
403B EDO 3.9 18.6 - - - -
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Residues in contact with MET 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B CYS* 4.2 42.4 - - + +
203B LEU* 3.7 26.4 - - + +
204B LYS* 4.0 17.5 - - + +
207B VAL* 4.0 18.8 - - + -
231B GLY 2.8 20.5 + - - +
232B LEU* 3.0 24.7 + - + +
234B GLU* 1.3 75.3 - - - +
236B ILE* 1.3 56.0 + - - +
238B PHE* 3.9 1.0 - - - +
239B ALA* 2.9 31.0 + - - +
252B PHE* 4.1 6.1 - - + -
257B GLY* 5.2 5.8 - - - +
261B LEU* 4.1 12.3 - - + -
322B PHE* 3.8 11.4 - - + -
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 3.6 30.5 - - + -
232B LEU* 2.9 16.3 + - + +
233B MET* 3.6 24.0 - - + +
235B MET* 1.3 73.2 - - - +
237B ALA* 1.3 67.1 + - - +
239B ALA* 3.2 3.1 + - - +
240B LYS* 2.9 52.8 + - + +
249B SER* 3.6 11.4 - - - +
252B PHE* 3.5 47.1 - - + -
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B MET 2.9 19.0 + - - +
236B ILE* 1.3 74.6 - - - +
238B PHE* 1.3 63.8 + - - +
240B LYS* 3.2 10.4 + - - +
241B LEU* 3.2 23.2 + - - +
319B PHE* 4.1 9.8 - - + -
403B EDO 3.8 27.6 - - - -
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LEU* 4.8 4.7 - - + -
199B ILE* 5.0 3.6 - - + -
203B LEU* 4.0 19.5 - - + -
234B GLU 2.8 19.5 + - - +
235B MET 4.0 2.5 - - - +
237B ALA* 1.3 77.1 - - - +
239B ALA* 1.3 59.2 + - - +
241B LEU* 3.2 19.3 + - + +
242B PHE* 3.0 64.0 + + + +
306B LEU* 3.3 33.9 - - + -
309B ILE* 4.3 16.4 - - + -
310B LEU* 4.0 28.5 - - + -
319B PHE* 3.6 15.4 - + + -
322B PHE* 4.1 8.3 - + + -
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B THR* 5.2 0.7 - - + -
199B ILE* 3.9 21.5 - - + -
203B LEU* 5.0 0.4 - - + -
235B MET 2.9 18.5 + - - +
236B ILE 3.7 4.0 - - - +
238B PHE* 1.3 82.1 - - - +
240B LYS* 1.3 62.5 + - - +
243B CYS* 3.1 37.5 + - - +
247B VAL* 3.7 12.3 - - + +
252B PHE* 3.9 19.3 - - + -
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Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ILE* 2.9 32.8 + - + +
237B ALA* 3.7 8.5 - - - +
238B PHE 3.2 0.4 - - - -
239B ALA* 1.3 77.9 - - - +
241B LEU* 1.3 59.3 + - - +
243B CYS 4.6 5.9 - - - +
247B VAL* 3.7 38.5 - - + +
248B SER* 4.9 0.2 - - - +
249B SER* 2.9 31.6 + - - +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ALA 3.2 11.4 + - - +
238B PHE* 3.2 25.0 + - + +
240B LYS* 1.3 78.9 - - - +
242B PHE* 1.3 72.1 + - + +
243B CYS 5.3 0.7 - - - -
309B ILE* 5.3 2.2 - - + -
310B LEU* 4.2 7.0 - - + -
313B LYS* 4.7 25.1 + - - +
315B LEU* 3.7 28.9 - - + -
319B PHE* 4.1 25.1 - - + -
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Residues in contact with PHE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLY 5.1 1.6 - - - -
129B LEU* 3.7 32.3 - - + -
130B LYS* 5.1 0.7 - - - -
131B LEU* 5.2 0.9 - - + -
199B ILE* 4.1 14.4 - - + -
238B PHE* 3.0 36.1 + + + +
239B ALA* 4.7 0.7 - - - +
241B LEU* 1.3 85.1 - - + +
243B CYS* 1.3 75.4 + - - +
244B SER 3.8 0.2 + - - -
309B ILE* 3.7 35.2 - - + -
313B LYS* 6.0 2.0 - - - +
402B PO4 3.2 41.6 + - - -
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Residues in contact with CYS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 5.4 1.1 - - - -
195B ASP* 3.9 26.9 - - + -
199B ILE* 4.1 26.5 - - - -
239B ALA* 3.1 31.8 + - - +
240B LYS 4.6 6.6 - - - +
241B LEU 5.3 0.2 - - - -
242B PHE* 1.3 93.7 - - - +
244B SER* 1.3 65.2 + - - +
245B GLY 3.5 4.4 - - - +
247B VAL* 4.0 11.4 - - + +
402B PO4 3.7 7.2 - - - -
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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