Contacts of the helix formed by residues 221 - 245 (chain C) in PDB entry 4DQM
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 ASP 221 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C ASN* 3.4 22.5 - - - +
213C SER* 2.9 28.9 + - - +
218C VAL* 3.4 9.2 - - + +
220C LEU* 1.3 70.1 - - - +
222C ILE* 1.3 58.5 + - - +
223C ASP* 2.7 18.9 + - - +
224C LEU* 3.2 14.2 + - + -
225C TRP* 3.0 24.8 + - - +
299C ASN* 2.9 20.9 + - + +
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Residues in contact with ILE 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C LEU* 3.5 11.2 + - + +
221C ASP* 1.3 73.5 + - - +
223C ASP* 1.3 63.8 + - + +
225C TRP* 3.5 28.3 - - + -
226C ASP* 2.9 39.1 + - - +
401C GLU 5.2 1.8 - - - +
402C ILE* 4.2 7.4 - - + -
403C PRO* 3.4 37.2 - - + -
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Residues in contact with ASP 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C ASN* 3.1 24.9 + - - +
221C ASP* 2.7 11.6 + - - +
222C ILE* 1.3 80.0 - - - +
224C LEU* 1.3 58.4 + - - +
226C ASP* 3.3 14.4 + - - +
227C LYS* 3.1 53.9 + - - +
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Residues in contact with LEU 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C THR* 4.6 7.2 - - + -
212C ASN* 3.7 24.9 + - + +
213C SER* 3.6 23.8 - - - +
221C ASP* 3.2 16.2 + - + +
223C ASP* 1.3 73.1 - - - +
225C TRP* 1.3 60.0 + - - +
227C LYS* 3.3 10.4 + - + +
228C PHE* 2.8 34.9 + - - +
290C LEU* 6.2 0.9 - - + -
292C LEU* 3.8 33.9 - - + -
296C GLN* 3.7 27.8 - - + +
299C ASN* 3.9 6.1 - - + +
300C ALA* 3.8 14.1 - - + -
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Residues in contact with TRP 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C LEU* 4.0 9.4 - - + -
221C ASP 3.0 18.1 + - - +
222C ILE* 3.5 29.4 - - + +
224C LEU* 1.3 74.5 - - - +
226C ASP* 1.3 73.0 + - - +
228C PHE* 4.3 3.6 - + - -
229C SER* 2.8 54.6 + - - -
300C ALA* 3.5 29.6 - - - +
301C GLY* 5.0 0.7 - - - -
398C LEU* 3.7 27.1 - - + -
402C ILE* 3.7 28.0 - - + +
403C PRO* 5.2 1.9 - - + +
405C SER 4.7 2.4 + - - -
406C MET* 3.7 32.1 - - + -
407C PRO* 4.2 9.4 - - + -
410C ILE* 5.7 2.0 - - + -
501C LUF 4.1 23.3 - - + -
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Residues in contact with ASP 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222C ILE* 2.9 35.0 + - - +
223C ASP* 3.5 18.1 - - - +
224C LEU 3.3 0.4 - - - -
225C TRP* 1.3 89.6 + - - +
227C LYS* 1.3 66.9 + - + +
229C SER* 3.2 13.3 + - - -
230C GLU* 3.2 18.3 + - - +
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208C TYR* 6.5 1.1 - - - -
210C THR* 5.3 17.4 + - + -
212C ASN* 4.9 4.2 + - - +
223C ASP* 3.1 41.9 + - - +
224C LEU* 3.8 9.4 - - + +
226C ASP* 1.3 80.8 - - + +
228C PHE* 1.3 64.2 + - - +
230C GLU* 3.2 9.1 + - - +
231C LEU* 3.0 28.4 + - + +
290C LEU* 4.2 26.7 - - + -
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Residues in contact with PHE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C LEU 2.8 21.2 + - - +
225C TRP* 3.9 4.7 - + - +
227C LYS* 1.3 68.6 - - - +
229C SER* 1.3 66.8 + - - +
230C GLU 2.9 6.3 + - - -
231C LEU* 3.2 10.8 + - - +
232C SER* 2.9 43.5 + - - -
286C PHE* 3.5 34.8 - + + -
290C LEU* 5.2 1.3 - - + +
292C LEU* 5.5 4.5 - - + -
300C ALA* 3.6 34.8 - - + -
302C PHE* 3.5 30.5 - + - -
501C LUF 3.2 50.9 - - + -
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Residues in contact with SER 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C TRP* 2.8 66.3 + - - -
226C ASP* 3.2 10.4 + - - -
228C PHE* 1.3 79.3 - - - +
230C GLU* 1.3 57.4 + - - +
232C SER* 4.2 4.7 - - - -
233C THR* 3.2 23.4 + - - -
407C PRO* 4.4 15.6 - - - +
410C ILE* 3.5 11.5 - - - +
501C LUF 6.0 0.4 - - - -
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Residues in contact with GLU 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ASP* 3.3 18.7 - - - +
227C LYS* 3.3 7.2 - - - +
228C PHE 2.9 1.2 - - - -
229C SER* 1.3 79.2 + - - +
231C LEU* 1.3 65.5 + - + +
232C SER 3.0 1.3 - - - -
233C THR* 2.9 20.1 + - - +
234C LYS* 3.5 29.3 + - - +
407C PRO* 6.0 0.7 - - - -
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C LYS* 3.0 20.5 + - + +
228C PHE* 3.5 8.3 - - - +
230C GLU* 1.3 75.1 - - - +
232C SER* 1.3 61.0 + - - +
234C LYS* 3.2 19.1 + - + +
235C CYS 3.1 9.4 + - - -
286C PHE* 3.7 36.6 - - + -
287C SER* 5.9 0.7 - - - -
288C ASP* 3.5 36.1 - - + +
290C LEU* 3.3 34.3 - - + -
501C LUF 2.8 22.5 + - - +
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Residues in contact with SER 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C PHE* 2.9 40.1 + - - -
229C SER* 3.6 9.6 - - - -
230C GLU 3.0 0.4 - - - -
231C LEU* 1.3 74.4 - - - +
233C THR* 1.3 67.5 + - - +
235C CYS* 3.0 9.4 - - - +
236C ILE* 3.0 28.0 + - - +
410C ILE* 4.0 13.7 - - - -
501C LUF 3.5 25.4 - - - +
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Residues in contact with THR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C SER 3.2 13.5 + - - -
230C GLU* 2.9 12.3 + - - -
232C SER* 1.3 78.8 - - - +
234C LYS* 1.3 65.2 + - + +
236C ILE* 3.4 1.2 + - - -
237C ILE* 3.2 28.0 + - + +
407C PRO* 4.1 11.4 - - + +
408C PRO* 6.1 2.5 - - + -
409C LEU* 3.8 33.5 - - + +
410C ILE* 4.0 14.5 - - - +
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C GLU* 3.5 30.5 + - - +
231C LEU* 3.2 19.0 + - + +
232C SER 3.1 0.8 - - - -
233C THR* 1.3 78.5 - - + +
235C CYS* 1.3 53.7 + - - +
237C ILE* 2.9 16.4 + - + +
238C LYS* 2.8 40.7 + - + +
287C SER* 6.6 0.4 - - - -
501C LUF 5.7 1.1 - - - +
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Residues in contact with CYS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C PHE* 5.3 2.0 - - - -
231C LEU 3.1 4.9 + - - -
232C SER* 3.0 11.7 - - - +
234C LYS* 1.3 77.3 - - - +
236C ILE* 1.3 57.3 - - + +
238C LYS* 3.2 10.5 + - - +
239C THR* 2.9 32.0 + - - -
269C LEU* 3.8 16.3 - - + +
272C ARG* 4.2 4.2 + - - -
501C LUF 1.5 89.5 - - + +
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C SER* 3.0 17.3 + - - +
233C THR* 3.8 4.5 - - - +
234C LYS 3.2 0.2 - - - -
235C CYS* 1.3 80.2 - - - +
237C ILE* 1.3 57.0 + - - +
239C THR* 3.0 9.0 + - - -
240C VAL* 2.9 34.5 + - + +
265C CYS* 4.1 10.8 - - - -
269C LEU* 3.9 23.1 - - + -
409C LEU* 4.0 18.4 - - + -
410C ILE* 3.9 35.2 - - + +
413C MET* 3.8 39.7 - - + -
414C LEU* 6.2 0.4 - - + -
501C LUF 5.7 1.1 - - + -
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C THR* 3.2 18.5 + - + +
234C LYS* 2.9 18.1 + - + +
236C ILE* 1.3 77.2 - - - +
238C LYS* 1.3 58.7 + - + +
239C THR 3.1 0.2 + - - -
240C VAL* 3.2 8.9 + - - +
241C GLU* 2.8 48.8 + - + +
409C LEU* 3.7 18.4 - - + -
1438D LEU* 3.9 26.0 - - + -
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Residues in contact with LYS 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C GLU 4.3 13.3 + - - -
198C THR* 3.4 35.5 + - - +
199C PHE* 6.0 0.2 - - + -
200C PRO* 6.1 2.2 - - - +
234C LYS* 2.8 23.9 + - + +
235C CYS* 3.2 10.7 + - - +
237C ILE* 1.3 76.1 - - - +
239C THR* 1.3 57.3 + - - +
241C GLU* 3.3 23.9 + - - +
242C PHE* 2.8 29.3 + - - +
272C ARG* 3.8 5.6 - - - +
287C SER* 6.0 3.1 - - - +
501C LUF 6.4 0.7 - - + -
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Residues in contact with THR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C CYS 2.9 14.7 + - - -
236C ILE* 3.0 12.3 + - - +
238C LYS* 1.3 74.5 - - - +
240C VAL* 1.3 62.7 + - - +
242C PHE* 3.2 9.0 - - + +
243C ALA* 2.9 26.5 + - - +
261C LEU* 4.4 11.0 - - + -
265C CYS* 3.9 22.2 - - + -
268C ILE* 4.2 25.7 - - + +
269C LEU* 3.3 16.3 - - - +
272C ARG* 3.4 16.2 + - - +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C ILE* 2.9 28.4 + - + +
237C ILE* 3.5 8.5 - - - +
239C THR* 1.3 75.1 - - - +
241C GLU* 1.3 68.3 + - + +
243C ALA* 3.2 7.5 + - - +
244C LYS* 2.9 27.2 + - + +
261C LEU* 4.4 20.4 - - + -
265C CYS* 6.1 0.2 - - - -
409C LEU* 6.2 0.2 - - + -
413C MET* 5.6 4.0 - - + -
1435D LEU* 5.3 6.7 - - + +
1438D LEU* 4.0 32.8 - - + +
1439D LEU* 3.9 27.6 - - + -
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Residues in contact with GLU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C THR* 3.9 13.3 - - + +
237C ILE* 2.8 38.5 + - + +
238C LYS* 3.3 31.9 + - - +
240C VAL* 1.3 80.5 - - + +
242C PHE* 1.3 64.0 + - - +
244C LYS* 3.2 21.6 + - - +
245C GLN* 3.4 16.6 + - - +
1438D LEU* 5.7 2.5 - - + +
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Residues in contact with PHE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL 4.4 2.0 - - - -
194C ALA* 3.6 28.3 - - + -
195C HIS* 3.6 28.7 - - + -
198C THR* 3.4 15.3 - - - +
238C LYS 2.8 17.7 + - - +
239C THR* 3.2 13.9 - - - +
241C GLU* 1.3 70.5 - - - +
243C ALA* 1.3 69.6 + - + +
245C GLN* 3.1 18.3 + - - +
246C LEU* 3.6 32.8 + - + +
268C ILE* 4.8 12.1 - - + -
272C ARG* 3.8 10.5 - - - +
327C GLY* 3.5 26.0 - - - -
330C SER* 3.9 22.4 - - - -
331C ALA* 4.4 1.8 - - - -
334C LEU* 4.9 3.6 - - + -
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C THR 2.9 16.7 + - - +
240C VAL* 3.4 8.5 - - - +
242C PHE* 1.3 74.4 - - - +
244C LYS* 1.3 57.9 + - - +
246C LEU* 2.8 29.0 + - - +
249C PHE* 3.5 28.4 - - + +
261C LEU* 4.1 11.9 - - + -
334C LEU* 3.7 30.5 - - + -
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Residues in contact with LYS 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C VAL* 2.9 24.9 + - + +
241C GLU* 3.2 15.2 + - - +
243C ALA* 1.3 72.2 - - - +
245C GLN* 1.3 59.8 + - + +
246C LEU 3.2 4.5 + - - +
249C PHE* 4.0 9.9 - - + -
250C THR* 3.6 31.4 + - + +
257C GLN* 5.1 0.9 - - - +
1438D LEU 2.9 25.6 + - - +
1439D LEU* 3.6 41.7 + - + +
1441D GLU 3.8 18.0 - - - -
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Residues in contact with GLN 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C LYS* 4.6 12.6 + - - +
193C LYS* 4.4 10.1 - - - +
194C ALA* 3.5 33.5 - - + +
197C GLU* 3.2 27.1 + - - +
198C THR* 4.0 19.3 - - - +
241C GLU* 3.4 9.0 + - - +
242C PHE 3.1 11.0 + - - +
243C ALA 2.8 1.0 + - - -
244C LYS* 1.3 78.5 - - + +
246C LEU* 1.3 60.1 + - - +
247C PRO* 3.8 5.9 - - - +
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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