Contacts of the helix formed by residues 219 - 244 (chain C) in PDB entry 4LML
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 219 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 4.2 5.2 - - - +
276B HIS* 4.7 8.4 + - - -
217C SER* 3.1 14.1 + - - -
218C THR* 1.3 75.8 - - - +
220C TYR* 1.3 66.1 + - - +
221C GLU* 4.7 4.0 - - - -
222C ALA* 3.7 17.7 - - - +
223C ASN* 3.0 22.8 + - - +
279C LYS* 5.6 0.7 - - - +
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Residues in contact with TYR 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A THR* 4.6 8.1 + - - +
214A ALA* 5.3 1.8 - - - -
217A SER* 3.2 37.9 - - - -
219A SER* 3.9 10.5 - - - +
222A ALA* 3.9 14.4 - - + -
223A ASN* 5.0 1.3 - - - -
226A LEU* 5.3 3.1 - - + +
218C THR 3.6 4.0 + - - -
219C SER* 1.3 71.0 - - - +
221C GLU* 1.3 59.2 + - - +
223C ASN* 2.8 24.2 + - + +
224C VAL* 2.9 33.6 + - + +
272C VAL* 3.2 37.4 - - + +
273C THR* 3.5 24.8 + - - +
275C GLN* 5.8 3.4 - - - +
276C HIS* 3.4 38.3 + + + +
279C LYS* 5.5 1.2 - - - +
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Residues in contact with GLU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 5.9 2.0 - - - +
221A GLU* 3.5 25.9 - - + +
222A ALA* 3.2 38.0 + - + +
225A THR* 3.5 10.4 + - - -
221B GLU* 3.4 33.9 - - + +
219C SER* 3.5 3.5 - - - -
220C TYR* 1.3 77.8 - - - +
222C ALA* 1.3 63.7 + - - +
224C VAL* 3.0 36.2 - - - +
225C THR* 3.1 11.5 + - - -
221D GLU* 4.9 0.5 - - - +
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 3.7 28.0 - - + -
221B GLU* 3.3 26.8 + - + +
224B VAL* 4.5 6.1 - - + -
219C SER* 3.7 21.9 + - - +
220C TYR 3.3 0.4 - - - -
221C GLU* 1.3 78.4 - - - +
223C ASN* 1.3 59.6 + - - +
225C THR* 3.4 2.1 + - - -
226C LEU* 3.0 35.0 + - - +
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Residues in contact with ASN 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 4.9 1.4 - - - -
214C ALA* 3.4 32.6 + - + +
217C SER* 3.3 34.5 + - - -
219C SER 3.0 16.7 + - - +
220C TYR* 2.8 13.4 + - - +
222C ALA* 1.3 80.2 - - - +
224C VAL* 1.3 61.4 + - - +
226C LEU* 4.0 0.6 - - - +
227C VAL* 3.4 27.9 + - - +
272C VAL* 3.7 30.9 - - + +
275C GLN* 4.0 11.3 - - - +
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Residues in contact with VAL 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA* 4.2 5.6 - - + -
225A THR* 3.6 19.3 - - + -
226A LEU* 3.5 26.0 - - + -
220C TYR* 2.9 47.9 + - + +
221C GLU* 3.0 38.3 + - - +
223C ASN* 1.3 76.0 - - - +
225C THR* 1.3 66.8 + - - +
227C VAL* 3.6 1.6 + - - +
228C VAL* 3.0 31.5 + - - +
272C VAL* 5.6 3.8 - - + -
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Residues in contact with THR 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 4.6 11.7 + - - +
221B GLU* 3.7 13.3 + - - +
224B VAL* 3.9 22.9 - - + +
225B THR* 4.6 14.7 + - - +
228B VAL* 5.3 4.9 - - + -
221C GLU* 3.1 16.3 + - - -
222C ALA 3.7 7.4 - - - -
224C VAL* 1.3 84.7 - - - +
226C LEU* 1.3 64.1 + - + +
228C VAL* 5.0 0.9 - - - -
229C SER* 3.0 35.9 + - - +
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Residues in contact with LEU 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B TYR* 5.2 3.1 - - + +
224B VAL* 3.6 35.4 - - + -
228B VAL* 4.5 15.4 - - + +
210C ILE* 3.3 37.7 - - + +
211C SER* 4.0 9.6 - - - +
213C THR* 4.0 16.8 - - + -
214C ALA* 4.4 11.0 - - + -
222C ALA 3.0 23.2 + - - +
223C ASN* 4.0 6.1 - - - +
224C VAL 3.2 0.2 - - - -
225C THR* 1.3 77.8 - - + +
227C VAL* 1.3 65.3 + - - +
229C SER* 3.8 1.1 - - - -
230C THR* 3.0 28.5 + - + +
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Residues in contact with VAL 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C SER* 4.2 18.6 - - - +
212C TRP* 6.0 0.2 - - - -
214C ALA* 5.0 6.5 - - + -
223C ASN 3.4 19.1 + - - +
224C VAL* 4.5 1.6 - - - +
226C LEU* 1.3 75.7 - - + +
228C VAL* 1.3 58.8 + - + +
230C THR* 2.9 18.3 + - - -
231C LEU* 3.0 18.2 + - + +
265C TYR* 3.9 24.6 - - + +
268C ALA* 4.1 17.7 - - + -
269C VAL* 3.9 26.5 - - + -
272C VAL* 4.8 14.4 - - + -
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Residues in contact with VAL 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE* 5.0 8.5 - - + -
225A THR* 5.1 5.4 - - + -
226A LEU* 4.4 26.9 - - + -
229A SER* 3.3 41.3 - - - +
230A THR* 5.2 5.2 - - + -
224C VAL* 3.0 22.2 + - - +
225C THR* 4.2 2.0 - - - +
227C VAL* 1.3 79.4 - - + +
229C SER* 1.3 63.5 + - - +
231C LEU* 3.0 24.9 + - + +
232C ALA* 3.0 15.0 + - + +
269C VAL* 5.5 3.6 - - + -
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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
----------------------------------------------------------
229A SER* 5.6 0.9 + - - -
228B VAL* 3.5 29.6 - - - +
229B SER* 5.5 1.9 + - - -
225C THR* 3.0 26.2 + - - +
226C LEU 4.2 0.7 - - - -
228C VAL* 1.3 81.3 - - - +
230C THR* 1.3 60.4 + - - +
232C ALA* 3.9 9.6 - - - +
233C ALA* 3.9 14.2 + - - +
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Residues in contact with THR 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B VAL* 5.4 6.1 - - + -
231B LEU* 5.9 2.9 - - + -
207C ILE* 3.4 27.8 - - + +
210C ILE* 4.5 11.4 - - + -
211C SER* 3.3 32.8 - - - +
226C LEU* 3.0 19.2 + - + +
227C VAL 2.9 17.8 + - - -
229C SER* 1.3 78.3 - - - +
231C LEU* 1.3 63.4 + - - +
232C ALA 3.2 1.8 - - - -
233C ALA* 3.1 8.9 + - - +
234C HIS 3.0 18.4 + - - -
265C TYR* 3.3 12.5 + - - -
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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
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206A PHE* 6.2 1.1 - - + -
207A ILE* 4.0 24.0 - - + -
210A ILE* 4.2 23.6 - - + -
230A THR* 6.3 2.0 - - + -
227C VAL* 3.0 15.1 + - + +
228C VAL* 3.0 14.6 + - + +
230C THR* 1.3 73.3 + - - +
232C ALA* 1.3 67.1 + - - +
234C HIS* 3.2 2.8 + - - +
235C ILE* 2.9 35.0 + - + +
262C TYR* 4.0 27.1 - - + -
265C TYR* 3.3 38.1 - - + -
269C VAL* 6.0 1.1 - - + -
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Residues in contact with ALA 232 (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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229A SER 6.1 0.4 - - - +
233A ALA* 5.9 3.4 - - + -
228C VAL* 3.0 15.1 + - + +
229C SER* 3.9 11.2 - - - +
231C LEU* 1.3 75.2 - - - +
233C ALA* 1.3 58.3 + - - +
235C ILE* 3.0 15.6 + - - +
236C ALA* 2.9 25.3 + - - +
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Residues in contact with ALA 233 (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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232B ALA* 6.0 2.7 - - + -
235B ILE* 3.8 27.4 - - + -
207C ILE* 3.7 16.2 - - + -
229C SER 3.9 8.4 + - - +
230C THR* 3.1 10.3 + - - +
232C ALA* 1.3 79.0 - - - +
234C HIS* 1.3 58.8 + - - +
236C ALA* 3.2 9.8 + - - +
237C PHE* 3.0 33.4 + - + -
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Residues in contact with HIS 234 (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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204C MET* 3.6 29.0 - - + -
207C ILE* 3.5 5.8 - - + +
230C THR 3.0 6.5 + - - -
231C LEU* 3.2 7.1 + - + +
233C ALA* 1.3 73.2 - - - +
235C ILE* 1.3 61.8 + - - +
237C PHE* 3.8 3.0 - - - +
238C ASN* 2.9 25.6 + - - +
258C ILE* 3.1 43.9 + - + +
261C ILE* 3.4 25.7 - - + +
262C TYR* 3.4 34.2 - + - -
265C TYR* 3.7 30.4 - + + +
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Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 4.2 8.3 - - + -
233A ALA* 3.7 30.5 - - + +
236A ALA* 5.6 5.2 - - + -
237A PHE* 3.6 34.1 - - + -
231C LEU* 2.9 34.5 + - + +
232C ALA* 3.3 9.0 - - - +
234C HIS* 1.3 75.5 - - - +
236C ALA* 1.3 58.3 + - - +
238C ASN* 3.3 0.9 + - - +
239C ILE* 2.9 42.8 + - + +
262C TYR* 3.2 26.2 - - + +
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Residues in contact with ALA 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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235B ILE* 5.7 2.9 - - + -
239B ILE* 4.8 16.7 - - + +
232C ALA 2.9 12.0 + - - +
233C ALA* 3.3 14.4 - - - +
234C HIS 3.2 0.2 - - - -
235C ILE* 1.3 78.0 - - - +
237C PHE* 1.3 57.1 + - + +
239C ILE* 3.3 5.9 + - - +
240C LEU* 2.9 30.6 + - - +
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Residues in contact with PHE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ILE* 3.7 40.4 - - + -
238B ASN* 4.8 4.7 - - - -
239B ILE* 5.4 6.3 - - + +
262B TYR* 4.0 2.5 - - - -
199C ASN 3.3 21.1 - - - -
200C ILE* 3.4 36.6 - - + -
203C PRO* 3.7 24.7 - - + -
204C MET* 4.5 24.9 - - + -
207C ILE* 4.4 11.9 - - + -
233C ALA 3.0 28.7 + - - +
234C HIS 3.8 4.7 - - - +
236C ALA* 1.3 73.0 - - + +
238C ASN* 1.3 66.4 + - - +
240C LEU* 3.3 6.3 + - + +
241C VAL* 3.0 30.9 + - - +
258C ILE* 4.6 0.9 - - - -
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Residues in contact with ASN 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PRO 4.3 2.1 - - - +
199A ASN* 3.7 28.8 + - - +
237A PHE* 5.0 1.2 - - - -
234C HIS 2.9 22.3 + - - +
235C ILE 3.4 3.6 - - - +
237C PHE* 1.3 72.4 - - - +
239C ILE* 1.3 64.2 + - - +
241C VAL* 3.4 1.9 + - - +
242C GLU* 2.9 48.3 + - - +
258C ILE* 3.3 41.8 - - + +
262C TYR* 3.6 28.1 + - + +
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Residues in contact with ILE 239 (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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236A ALA* 5.3 11.0 - - + +
237A PHE* 4.6 7.6 - - + -
240A LEU* 3.7 43.3 - - + -
235C ILE* 2.9 36.7 + - + +
236C ALA* 3.8 5.6 - - - +
238C ASN* 1.3 78.9 - - - +
240C LEU* 1.3 62.8 + - - +
242C GLU* 3.2 13.2 + - - +
243C THR* 2.9 44.6 + - - +
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Residues in contact with LEU 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ILE* 4.2 31.2 - - + -
242B GLU* 3.7 29.4 - - - +
243B THR* 5.2 6.1 - - - +
200C ILE* 3.8 19.1 - - + -
236C ALA 2.9 18.3 + - - +
237C PHE* 3.7 6.5 - - + +
239C ILE* 1.3 79.8 - - - +
241C VAL* 1.3 62.8 + - + +
243C THR* 3.4 17.1 + - + +
244C ASN* 3.7 17.1 + - - +
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C TYR* 3.8 34.4 + - + +
196C TYR* 5.9 3.6 - - + -
200C ILE* 3.9 34.8 - - + -
237C PHE 3.0 21.8 + - - +
238C ASN 4.0 2.5 - - - +
240C LEU* 1.3 73.8 - - + +
242C GLU* 1.3 64.1 + - - +
243C THR 3.0 5.5 + - - -
244C ASN* 3.3 13.4 + - - +
245C LEU* 3.6 15.2 + - + +
254C THR* 4.7 14.1 - - + -
258C ILE* 5.0 10.5 - - + -
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Residues in contact with GLU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN* 3.8 31.5 - - - +
200A ILE* 3.4 24.9 - - - +
240A LEU* 4.3 10.0 - - - +
238C ASN* 2.9 35.1 + - - +
239C ILE* 3.2 17.5 + - - +
241C VAL* 1.3 75.7 - - - +
243C THR* 1.3 59.4 + - - +
244C ASN 3.5 0.2 - - - -
245C LEU* 3.1 23.6 - - - +
247C LYS* 3.2 29.3 + - - +
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Residues in contact with THR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 5.0 7.1 - - - +
32C LYS* 3.7 23.1 + - - +
239C ILE* 2.9 29.3 + - - +
240C LEU* 3.5 11.2 - - + +
241C VAL 3.0 0.6 - - - -
242C GLU* 1.3 77.6 - - - +
244C ASN* 1.3 72.7 + - - +
245C LEU 3.1 8.8 + - - +
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Residues in contact with ASN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASP* 3.8 10.9 - - - +
32C LYS* 3.7 14.9 - - - +
118C TYR* 5.4 5.2 - - - +
240C LEU* 3.7 14.4 + - - +
241C VAL* 3.3 7.9 + - - +
243C THR* 1.3 91.0 - - - +
245C LEU* 1.3 70.1 + - + +
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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