Contacts of the helix formed by residues 213 - 243 (chain A) in PDB entry 2LCK
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 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A THR* 3.3 20.2 - - + +
212A ASP* 1.3 80.1 - - - +
214A LEU* 1.3 62.2 + - - +
215A PRO* 3.4 8.5 - - + -
216A CYS* 2.7 49.1 - - + +
217A HIS* 3.6 2.9 + - - +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A LEU* 4.6 16.8 - - + -
211A THR 3.4 22.4 - - - +
212A ASP* 3.0 11.6 + - - +
213A ASP* 1.3 72.6 - - - +
215A PRO* 1.3 70.5 - - + +
217A HIS* 2.5 44.8 + - + +
218A PHE* 3.1 8.8 - - + -
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Residues in contact with PRO 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASP 4.8 1.1 - - - +
213A ASP* 3.4 6.7 - - + -
214A LEU* 1.3 96.5 - - + +
216A CYS* 1.3 63.1 + - + +
218A PHE* 3.4 10.7 + - + +
219A THR* 3.0 27.6 + - - -
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Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 6.2 0.2 - - - -
211A THR* 5.0 7.2 - - - -
213A ASP* 2.7 44.6 + - + +
214A LEU 3.1 0.4 - - - -
215A PRO* 1.3 84.7 - - + +
217A HIS* 1.3 74.6 + - - +
219A THR* 3.6 6.0 + - - -
220A SER* 3.4 19.1 + - - -
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Residues in contact with HIS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 3.6 43.4 - - + +
209A LEU* 5.0 11.6 - - + +
211A THR* 6.6 0.2 - - - -
213A ASP 4.1 0.9 + - - +
214A LEU* 2.5 42.9 + - + +
216A CYS* 1.3 89.2 - - - +
218A PHE* 1.3 124.3 + + - +
220A SER* 2.4 28.7 + - - -
221A ALA* 3.2 7.2 + - + +
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Residues in contact with PHE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.1 16.6 + - + -
215A PRO* 3.4 11.2 + - + +
216A CYS 3.3 0.4 - - - -
217A HIS* 1.3 120.2 - + - +
219A THR* 1.3 66.3 + - - +
221A ALA* 2.9 20.0 + - + +
222A PHE* 3.2 11.8 + - - +
291A TYR* 5.7 9.0 - + - -
294A LEU* 4.3 39.5 - - + -
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Residues in contact with THR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PRO* 3.0 15.8 + - - +
216A CYS* 4.0 6.4 - - - -
217A HIS 3.4 0.2 - - - -
218A PHE* 1.3 76.5 - - - +
220A SER* 1.3 64.2 + - - +
221A ALA 3.3 0.3 + - - -
222A PHE* 3.3 15.9 + - + +
223A GLY* 3.4 9.4 + - - -
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Residues in contact with SER 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 5.6 2.4 - - - +
216A CYS 3.4 10.0 + - - -
217A HIS* 2.4 29.3 + - - +
218A PHE 3.2 0.2 - - - -
219A THR* 1.3 79.7 - - - +
221A ALA* 1.3 62.7 + - - +
223A GLY* 3.6 1.0 + - - -
224A ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A HIS* 3.9 7.9 - - + +
218A PHE* 2.9 18.4 + - + +
220A SER* 1.3 84.4 + - - +
222A PHE* 1.3 50.4 + - - +
224A ALA* 3.1 8.6 + - - +
225A GLY* 2.3 35.7 + - - -
291A TYR* 5.3 14.2 + - + +
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Residues in contact with PHE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A PHE 3.2 8.1 + - - +
219A THR* 3.3 11.8 + - + +
221A ALA* 1.3 74.4 - - - +
223A GLY* 1.3 65.7 + - - +
225A GLY* 2.8 16.6 + - - +
226A PHE* 3.0 19.7 + + + +
288A PHE* 5.9 7.6 - + - -
291A TYR* 6.3 4.9 - + - -
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Residues in contact with GLY 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A THR 3.4 8.9 + - - -
220A SER 4.1 2.2 - - - -
221A ALA 3.3 0.2 - - - -
222A PHE* 1.3 84.6 - - - +
224A ALA* 1.3 61.8 + - - +
226A PHE* 3.4 12.7 + - - +
227A CYS* 3.6 16.3 + - - -
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Residues in contact with ALA 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A SER 3.1 16.9 + - - +
221A ALA* 3.1 15.0 - - - +
223A GLY* 1.3 77.8 - - - +
225A GLY* 1.3 58.3 + - - +
227A CYS* 3.2 10.7 + - - +
228A THR* 3.2 23.2 + - - +
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Residues in contact with GLY 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A ALA 2.3 24.1 + - - -
222A PHE* 2.8 8.5 + - - -
224A ALA* 1.3 67.2 - - - +
226A PHE* 1.3 61.4 + - - -
228A THR* 2.7 28.1 - - - +
229A THR* 3.3 15.0 + - - +
291A TYR* 5.6 5.2 - - - -
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Residues in contact with PHE 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A PHE* 3.0 16.9 + + + +
223A GLY* 3.8 9.2 - - - +
224A ALA 3.3 0.4 - - - -
225A GLY* 1.3 77.4 - - - +
227A CYS* 1.3 67.4 + - - +
229A THR* 2.3 29.9 + - + -
230A VAL* 3.6 19.6 + - + +
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Residues in contact with CYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLY 3.7 13.5 - - - -
224A ALA* 3.2 11.5 + - - +
226A PHE* 1.3 83.8 - - - +
228A THR* 1.3 62.1 + - - +
230A VAL* 3.3 16.4 + - - +
231A ILE* 3.3 18.5 - - - +
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Residues in contact with THR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A THR* 5.4 8.4 - - - +
224A ALA 3.2 13.3 + - - +
225A GLY* 2.7 33.7 - - - +
227A CYS* 1.3 73.2 - - - +
229A THR* 1.3 69.1 + - + +
231A ILE* 2.9 14.9 + - - +
232A ALA* 2.8 21.1 + - - +
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Residues in contact with THR 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLY 3.3 13.5 - - - +
226A PHE* 2.3 41.1 + - + -
228A THR* 1.3 78.9 - - + +
230A VAL* 1.3 61.1 + - - +
232A ALA* 2.9 19.5 + - + +
233A SER* 2.7 20.6 + - - -
280A LEU* 6.2 4.3 - - + -
283A TRP* 5.3 3.1 - - + -
284A ASN* 5.4 0.9 - - - +
287A MET* 3.8 30.5 - - + -
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A PHE* 3.8 30.5 - - + +
227A CYS* 3.3 10.3 + - - +
228A THR 3.1 0.6 - - - -
229A THR* 1.3 78.1 + - - +
231A ILE* 1.3 69.0 + - + +
233A SER* 3.2 18.3 + - - +
234A PRO* 3.3 12.0 - - - +
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A THR* 4.5 21.1 - - + +
199A LEU* 6.5 0.7 - - + -
227A CYS 3.3 17.0 - - - +
228A THR* 2.9 16.1 + - - +
230A VAL* 1.3 85.5 - - + +
232A ALA* 1.3 55.5 + - - +
234A PRO* 2.7 26.3 - - - +
235A VAL* 6.2 0.2 - - - +
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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
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228A THR* 2.8 13.8 + - - +
229A THR* 3.1 18.4 - - + +
231A ILE* 1.3 73.9 - - - +
233A SER* 1.3 55.2 + - - +
234A PRO* 3.1 6.7 - - - -
235A VAL* 3.0 30.9 - - - +
236A ASP* 3.3 5.6 - - - +
283A TRP* 4.5 24.5 - - + -
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Residues in contact with SER 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A THR 2.7 16.8 + - - -
230A VAL* 3.2 15.7 + - - -
232A ALA* 1.3 73.2 - - - +
234A PRO* 1.3 66.8 - - - +
236A ASP* 3.0 15.9 + - - +
237A VAL* 3.0 21.7 + - - +
280A LEU* 4.6 20.1 - - - +
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Residues in contact with PRO 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A VAL 3.3 10.1 - - - +
231A ILE* 2.7 32.3 - - - +
232A ALA 3.1 2.0 - - - +
233A SER* 1.3 81.6 - - - +
235A VAL* 1.3 67.4 + - + +
236A ASP 3.2 0.3 + - - -
237A VAL* 3.2 28.9 + - + +
238A VAL* 3.4 11.5 + - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 5.7 3.6 - - - +
188A ILE* 4.6 22.9 - - + -
189A VAL* 5.1 14.6 - - + -
192A ALA* 5.4 8.3 - - + -
231A ILE 5.2 0.4 + - - +
232A ALA* 3.0 22.7 - - - +
234A PRO* 1.3 77.3 - - + +
236A ASP* 1.3 70.1 + - - +
238A VAL* 3.9 4.4 + - - +
239A LYS* 3.2 36.6 + - - +
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Residues in contact with ASP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ARG* 5.9 1.0 + - - -
232A ALA 3.3 18.3 - - - +
233A SER* 3.0 13.2 + - - +
235A VAL* 1.3 85.9 - - - +
237A VAL* 1.3 57.1 + - - +
239A LYS* 3.6 16.1 + - - +
276A SER* 2.7 34.3 + - - +
279A ARG* 6.2 2.7 - - + -
280A LEU* 5.3 10.0 - - + +
283A TRP* 5.0 25.4 + - - -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A SER* 3.0 13.0 + - - +
234A PRO* 3.2 22.1 + - + +
236A ASP* 1.3 74.7 - - - +
238A VAL* 1.3 74.4 + - + +
240A THR* 2.7 27.7 - - + +
241A ARG* 3.8 6.4 + - - +
269A PHE* 5.1 11.0 - - + +
273A PHE* 4.7 18.2 - - + -
276A SER* 4.1 4.9 - - - -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PRO* 3.4 16.7 + - + +
235A VAL* 4.3 4.5 - - - +
236A ASP 3.5 0.2 - - - -
237A VAL* 1.3 90.6 - - + +
239A LYS* 1.3 65.5 + - + +
240A THR 3.5 0.2 + - - -
241A ARG* 3.5 20.8 + - + +
242A TYR* 3.9 3.8 + - - +
269A PHE* 5.1 22.2 - - + -
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ARG* 3.7 40.8 - - - +
188A ILE* 6.2 1.5 - - - +
235A VAL* 3.2 27.7 + - - +
236A ASP* 3.7 9.8 + - - +
237A VAL 3.2 0.4 - - - -
238A VAL* 1.3 81.6 - - + +
240A THR* 1.3 63.0 + - - +
242A TYR* 3.2 22.9 - - - +
243A MET* 4.4 1.2 + - - +
276A SER* 5.1 0.2 - - - +
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Residues in contact with THR 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ASP 3.8 0.8 + - - -
237A VAL* 2.7 29.4 - - - +
239A LYS* 1.3 73.2 - - - +
241A ARG* 1.3 66.4 + - + +
242A TYR 3.0 1.0 + - - -
243A MET* 3.0 26.7 + - - +
272A GLY 4.3 4.4 + - - +
273A PHE* 4.0 17.3 + - + -
275A PRO* 3.4 28.8 - - - +
276A SER* 2.9 38.1 + - - +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A VAL 4.4 7.4 - - - +
238A VAL* 3.5 13.2 + - + +
239A LYS 3.3 0.2 - - - -
240A THR* 1.3 82.1 - - - +
242A TYR* 1.3 58.4 + - - +
244A ASN* 2.5 56.6 + - - +
260A MET* 5.1 2.8 - - - +
264A GLU* 4.8 10.5 + - - +
265A GLY 4.8 0.8 + - - -
268A ALA* 3.2 48.8 + - - +
269A PHE* 3.3 59.8 - - + +
271A LYS 4.3 3.6 - - - -
272A GLY* 4.2 13.2 - - - +
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Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A VAL 3.9 3.3 + - - +
239A LYS* 3.2 17.8 + - - +
241A ARG* 1.3 77.2 - - - +
243A MET* 1.3 70.6 + - + +
244A ASN* 2.3 28.3 + - - +
245A SER* 2.7 39.5 + - - +
246A ALA* 3.4 23.1 - - + +
247A LEU* 4.0 10.3 + - - +
250A TYR* 5.8 6.1 - + - -
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Residues in contact with MET 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 5.7 8.1 - - - +
41A LEU 6.0 2.2 - - - +
42A GLN* 5.0 22.7 - - - +
239A LYS 4.4 0.9 + - - +
240A THR* 3.0 23.0 + - - +
242A TYR* 1.3 89.6 - - + +
244A ASN* 1.3 52.8 + - - +
245A SER* 2.4 23.5 + - - +
275A PRO* 5.3 11.0 - - + -
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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