Contacts of the helix formed by residues 219 - 244 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A SER* 3.0 16.4 + - - -
218A THR* 1.3 76.0 - - - +
220A TYR* 1.3 62.3 + - - +
221A GLU* 4.8 2.0 - - - -
222A ALA* 3.3 21.0 - - - +
223A ASN* 3.0 27.9 + - - +
220C TYR* 3.9 6.0 - - - +
221C GLU* 6.1 1.8 - - - -
276C HIS* 4.5 9.9 + - - -
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Residues in contact with TYR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A THR 3.6 4.2 + - - -
219A SER* 1.3 69.2 - - - +
221A GLU* 1.3 66.1 + - - +
223A ASN* 2.9 7.0 + - + +
224A VAL* 2.9 44.4 + - + +
272A VAL* 3.4 31.4 - - + -
273A THR* 2.9 33.7 + - + +
275A GLN* 5.1 4.2 - - - +
276A HIS* 3.4 44.2 - + + +
279A LYS* 5.6 3.2 - - - +
213D THR* 4.2 9.2 + - - +
214D ALA* 5.2 1.2 - - - -
217D SER* 3.4 30.6 - - - -
219D SER* 4.0 1.6 - - - +
222D ALA* 3.6 28.7 - - + -
223D ASN* 4.6 1.1 - - - -
226D LEU* 4.9 2.0 - - + +
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Residues in contact with GLU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 3.5 2.1 - - - -
220A TYR* 1.3 77.9 - - - +
222A ALA* 1.3 62.8 + - - +
224A VAL* 3.1 22.7 - - - +
225A THR* 3.0 31.0 + - - -
221C GLU* 3.5 30.4 - - + +
219D SER* 6.2 0.7 - - - -
221D GLU* 2.8 33.5 - - + +
222D ALA* 3.1 37.9 - - + +
225D THR* 3.3 12.1 + - - -
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 3.3 24.4 + - - +
220A TYR 3.3 0.8 - - - -
221A GLU* 1.3 78.8 - - - +
223A ASN* 1.3 59.6 + - - +
225A THR* 3.4 1.7 - - - -
226A LEU* 2.9 35.0 + - - +
220C TYR* 3.9 24.0 - - + -
221C GLU* 3.2 25.6 + - + +
224C VAL* 4.2 9.0 - - + -
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Residues in contact with ASN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A ALA* 3.3 40.2 + - + +
217A SER* 3.4 25.1 + - - -
219A SER 3.0 19.9 + - - +
220A TYR* 2.9 7.3 + - - +
222A ALA* 1.3 79.7 - - - +
224A VAL* 1.3 61.9 + - - +
226A LEU* 3.9 1.1 - - - +
227A VAL* 3.2 29.5 + - - +
272A VAL* 3.5 27.6 - - + +
275A GLN* 3.5 17.2 - - - +
220C TYR* 5.0 1.0 - - - -
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Residues in contact with VAL 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 2.9 48.6 + - + +
221A GLU* 3.1 38.8 - - - +
223A ASN* 1.3 75.9 - - - +
225A THR* 1.3 66.5 + - - +
227A VAL* 5.2 1.3 - - - -
228A VAL* 3.0 32.7 + - - +
269A VAL* 6.1 1.6 - - + -
272A VAL* 5.3 4.3 - - + -
222D ALA* 4.3 2.5 - - + +
225D THR* 3.8 15.5 - - + -
226D LEU* 3.4 30.3 - - + -
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Residues in contact with THR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLU* 3.0 22.6 + - - -
222A ALA 3.4 8.3 - - - -
224A VAL* 1.3 79.7 - - - +
226A LEU* 1.3 59.0 + - + +
228A VAL* 4.9 0.9 - - - -
229A SER* 2.9 46.9 + - - +
221C GLU* 3.5 9.5 + - - -
224C VAL* 3.6 29.4 - - + +
225C THR* 4.5 14.8 + - - +
228C VAL* 5.1 4.3 - - + -
225D THR* 4.6 10.5 + - - +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ILE* 3.2 45.3 - - + +
211A SER 4.1 7.6 - - - +
213A THR* 4.2 12.3 - - + -
214A ALA* 4.2 12.6 - - + -
222A ALA 2.9 21.9 + - - +
223A ASN* 4.1 4.7 - - - +
224A VAL 3.3 0.4 - - - -
225A THR* 1.3 78.5 - - + +
227A VAL* 1.3 55.7 + - - +
229A SER* 3.9 0.3 - - - -
230A THR* 2.5 41.6 + - + +
220C TYR* 5.3 3.4 - - + +
224C VAL* 3.5 34.3 - - + -
228C VAL* 4.4 11.9 - - + -
269C VAL* 5.7 0.7 - - + -
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER* 3.8 22.4 - - - +
212A TRP* 5.8 0.2 - - - -
214A ALA* 5.0 2.9 - - + -
215A PHE* 6.4 0.9 - - + -
223A ASN 3.2 19.5 + - - +
224A VAL* 4.6 0.9 - - - +
226A LEU* 1.3 74.4 - - + +
228A VAL* 1.3 57.9 + - - +
230A THR* 2.9 17.3 + - - -
231A LEU* 2.9 20.4 + - + +
265A TYR* 3.4 31.0 - - + +
268A ALA* 3.6 21.3 - - + -
269A VAL* 3.5 18.4 - - + -
272A VAL* 4.5 16.2 - - + -
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A VAL* 3.0 25.8 + - + +
225A THR* 4.2 0.9 - - - +
227A VAL* 1.3 78.0 - - - +
229A SER* 1.3 63.6 + - - +
231A LEU* 3.0 12.4 + - + +
232A ALA* 2.9 28.4 + - + +
269A VAL* 4.7 6.5 - - + -
210D ILE* 4.6 11.7 - - + -
225D THR* 5.4 4.3 - - + +
226D LEU* 4.4 26.9 - - + -
229D SER* 3.3 39.7 - - - +
230D THR* 5.2 4.5 - - + -
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Residues in contact with SER 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 2.9 25.3 + - - +
226A LEU 4.4 0.4 - - - -
228A VAL* 1.3 81.7 - - - +
230A THR* 1.3 60.1 - - - +
232A ALA* 4.0 10.1 - - - +
233A ALA* 3.8 16.3 + - - +
228C VAL* 3.3 32.4 - - - +
229C SER* 5.6 1.0 + - - -
232C ALA* 6.1 0.7 - - - +
229D SER* 5.2 2.8 + - - -
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Residues in contact with THR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.2 44.5 - - + +
210A ILE* 4.0 15.7 - - + -
211A SER* 3.1 19.5 - - - +
226A LEU* 2.5 27.8 + - + +
227A VAL 2.9 12.0 + - - -
229A SER* 1.3 76.1 - - - +
231A LEU* 1.3 58.5 + - - +
232A ALA 3.2 0.2 - - - -
233A ALA* 3.3 4.8 + - - -
234A HIS* 3.0 24.3 + - - +
265A TYR* 3.1 12.0 - - - -
228C VAL* 5.2 5.4 - - + -
231C LEU* 6.3 1.8 - - + -
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL 2.9 20.6 + - - +
228A VAL* 3.2 11.9 - - + +
230A THR* 1.3 73.6 - - - +
232A ALA* 1.3 59.9 + - - +
234A HIS* 3.3 4.8 + - - +
235A ILE* 2.9 40.9 + - + +
262A TYR* 4.2 27.6 - - + +
265A TYR* 3.2 35.6 - - + +
269A VAL* 5.7 0.4 - - + -
206D PHE* 6.4 0.4 - - + -
207D ILE* 4.1 17.5 - - + -
210D ILE* 3.7 32.1 - - + -
230D THR* 6.1 2.0 - - + -
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 2.9 16.1 + - + +
229A SER* 4.0 11.7 - - - +
230A THR 3.2 0.2 - - - -
231A LEU* 1.3 76.0 - - - +
233A ALA* 1.3 57.7 + - - +
235A ILE* 3.0 17.2 + - - +
236A ALA* 2.9 25.9 + - - +
229D SER 5.9 3.1 - - - +
233D ALA* 5.7 4.5 - - + -
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ILE* 3.7 16.8 - - + -
229A SER 3.8 10.5 + - - +
230A THR* 3.3 9.0 + - - +
232A ALA* 1.3 78.3 - - - +
234A HIS* 1.3 58.2 + - - +
236A ALA* 3.3 9.7 - - - +
237A PHE* 3.0 33.8 + - - -
232C ALA* 5.9 3.6 - - + -
235C ILE* 3.7 28.3 - - + -
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MET* 3.7 24.4 - - + -
207A ILE* 3.3 10.9 - - + +
230A THR 3.0 14.0 + - - +
231A LEU* 3.5 12.6 - - - +
232A ALA 3.1 0.4 - - - -
233A ALA* 1.3 75.6 - - - +
235A ILE* 1.3 61.1 + - - +
237A PHE* 3.5 3.2 + - - +
238A ASN* 2.9 27.2 + - - +
258A ILE* 3.1 38.0 + - + +
261A ILE* 3.2 28.5 - - + +
262A TYR* 3.4 40.4 + + - -
265A TYR* 4.1 9.4 - + + -
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 2.9 28.9 + - + +
232A ALA* 3.3 9.0 - - - +
234A HIS* 1.3 71.1 - - - +
236A ALA* 1.3 61.2 + - - +
238A ASN* 3.3 1.4 + - - +
239A ILE* 2.9 41.4 + - + +
262A TYR* 3.6 26.5 - - + +
207D ILE* 4.1 21.1 - - + -
233D ALA* 3.8 28.9 - - + +
236D ALA* 5.9 2.5 - - + -
237D PHE* 3.6 31.0 - - + -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA 2.9 11.4 + - - +
233A ALA* 3.3 15.0 - - - +
234A HIS 3.2 0.2 - - - -
235A ILE* 1.3 78.6 - - - +
237A PHE* 1.3 58.5 + - + +
239A ILE* 3.3 6.7 + - - +
240A LEU* 2.9 29.4 + - - +
235C ILE* 5.6 4.5 - - + -
239C ILE* 5.3 11.1 - - + +
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Residues in contact with PHE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASN 3.6 19.3 - - - -
200A ILE* 3.9 33.9 - - + -
203A PRO* 3.7 26.5 - - + -
204A MET* 4.5 24.0 - - + -
207A ILE* 4.6 9.0 - - + -
233A ALA 3.0 28.9 + - - +
234A HIS 3.9 4.3 - - - +
236A ALA* 1.3 76.0 - - - +
238A ASN* 1.3 64.5 + - - +
240A LEU* 3.2 15.5 + - + +
241A VAL* 3.0 29.0 + - - +
258A ILE* 4.7 1.1 - - - -
235C ILE* 3.6 43.5 - - + -
238C ASN* 5.0 0.7 - - - -
239C ILE* 4.6 5.2 - - + -
262C TYR* 3.9 4.7 - - - -
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Residues in contact with ASN 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A HIS 2.9 19.0 + - - +
235A ILE 3.3 5.7 + - - +
237A PHE* 1.3 76.2 - - - +
239A ILE* 1.3 61.5 + - - +
241A VAL* 3.3 1.9 + - - +
242A GLU* 2.9 50.4 + - - +
258A ILE* 3.2 45.8 - - + +
262A TYR* 3.2 28.7 + - + +
198D PRO 4.6 1.4 - - - +
199D ASN* 3.8 20.5 + - - +
237D PHE* 4.9 1.4 - - - -
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ILE* 2.9 37.7 + - + +
236A ALA* 3.7 6.1 - - - +
238A ASN* 1.3 74.2 - - - +
240A LEU* 1.3 62.7 + - - +
242A GLU* 3.3 11.3 + - - +
243A THR* 2.9 45.8 + - - +
236D ALA* 5.2 13.2 - - + +
237D PHE* 4.8 8.7 - - + -
240D LEU* 3.7 40.6 - - + -
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ILE* 3.5 32.3 - - + -
236A ALA 2.9 14.8 + - - +
237A PHE* 3.4 13.2 - - + +
239A ILE* 1.3 80.4 - - - +
241A VAL* 1.3 62.1 + - + +
243A THR* 3.5 16.5 - - + +
244A ASN* 3.8 16.1 + - - +
239C ILE* 3.7 46.0 - - + -
242C GLU* 4.3 9.0 - - - +
243C THR* 5.0 6.7 - - - +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 4.2 29.6 + - + +
200A ILE* 4.1 28.7 - - + -
237A PHE 3.0 16.9 + - - +
238A ASN 4.0 2.5 - - - +
240A LEU* 1.3 78.7 - - + +
242A GLU* 1.3 63.9 + - - +
243A THR 3.0 5.6 + - - -
244A ASN* 3.3 13.1 + - - +
245A LEU* 3.7 15.2 + - + +
254A THR* 4.9 16.2 - - + -
258A ILE* 5.0 11.0 - - + -
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASN* 2.9 35.5 + - - +
239A ILE* 3.7 13.4 - - - +
241A VAL* 1.3 76.3 - - - +
243A THR* 1.3 57.9 + - - +
244A ASN 3.6 0.2 - - - -
245A LEU* 3.2 24.2 - - - +
247A LYS* 3.4 26.5 + - - +
199D ASN* 3.6 28.9 - - - +
200D ILE* 3.2 28.8 - - - +
240D LEU* 4.1 10.4 - - - +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 3.8 19.4 + - - -
239A ILE* 2.9 31.7 + - - +
240A LEU* 3.5 9.8 - - + +
241A VAL 3.0 0.2 - - - -
242A GLU* 1.3 76.8 - - - +
244A ASN* 1.3 72.5 + - - +
245A LEU 3.1 9.0 + - - +
240D LEU* 4.9 8.0 - - - +
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Residues in contact with ASN 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ASP* 4.1 9.2 - - - +
32A LYS* 3.6 16.2 + - - +
118A TYR* 5.4 6.7 - - - +
240A LEU* 3.8 14.2 + - - +
241A VAL* 3.3 7.8 + - - +
243A THR* 1.3 92.6 - - - +
245A LEU* 1.3 68.1 + - + +
32C LYS* 6.0 2.4 - - - +
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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