Contacts of the helix formed by residues 269 - 292 (chain A) in PDB entry 2Q8F
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 VAL 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A MET* 4.7 1.1 - - - -
193A MET* 3.8 33.0 - - + -
218A SER* 3.6 24.9 - - - +
219A ILE* 4.0 11.4 - - + -
268A TYR* 1.3 92.6 - - + +
270A PRO* 1.3 68.7 - - + +
271A SER* 3.8 11.2 - - - +
272A HIS* 3.0 47.2 + - + +
273A LEU 3.3 0.7 + - - -
369A PHE* 4.4 10.1 - - + -
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Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A HIS* 4.0 13.7 - - + +
218A SER 3.3 16.4 - - - +
220A ASN* 3.7 25.8 - - + +
223A CYS* 4.2 22.2 - - - -
228A VAL* 4.1 13.5 - - + +
268A TYR 3.2 9.8 - - - +
269A VAL* 1.3 83.1 - - + +
271A SER* 1.3 56.1 + - - +
273A LEU* 3.2 5.7 + - + +
274A TYR* 2.8 29.7 + - - +
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Residues in contact with SER 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A SER* 5.8 0.5 - - - -
269A VAL* 3.8 14.0 - - - +
270A PRO* 1.3 79.4 - - - +
272A HIS* 1.3 65.3 + - - +
274A TYR* 3.7 10.2 - - - +
275A HIS* 3.0 29.1 + - - +
365A TYR* 5.6 0.6 - - - -
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Residues in contact with HIS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ILE* 4.3 4.5 + - + +
193A MET* 4.4 8.4 - - - +
268A TYR* 3.8 14.7 + - + +
269A VAL* 3.0 43.6 + - + +
271A SER* 1.3 83.7 + - - +
273A LEU* 1.3 65.9 + - - +
275A HIS* 3.4 4.8 + - - +
276A MET* 3.2 28.9 + - - +
365A TYR* 3.6 49.3 + + + +
368A TYR* 4.0 29.7 - + - -
369A PHE* 4.6 6.0 - + - -
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Residues in contact with LEU 273 (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 CYS* 4.1 17.5 - - - -
225A VAL* 4.2 25.8 - - + +
228A VAL* 3.7 26.7 - - + -
229A ILE* 5.4 0.7 - - + -
266A VAL* 6.0 0.9 - - + -
268A TYR* 3.8 17.6 - - + -
269A VAL 3.3 2.2 + - - +
270A PRO* 3.2 9.9 + - + +
272A HIS* 1.3 77.8 - - - +
274A TYR* 1.3 65.4 + - - +
276A MET* 3.4 19.7 + - + +
277A VAL* 3.0 39.4 + - + +
312A LEU* 5.6 1.3 - - + -
314A VAL* 5.0 9.4 - - + -
387A ILE* 4.8 3.8 - - + -
389A ILE* 4.1 15.3 - - + -
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 3.6 15.4 - - + +
231A ASP* 3.5 27.1 - - + -
232A GLY* 3.5 30.1 - - - -
235A ASN* 2.9 32.5 + - - +
270A PRO 2.8 20.3 + - - +
271A SER* 3.7 10.1 - - - +
273A LEU* 1.3 73.8 - - - +
275A HIS* 1.3 62.6 + - + +
277A VAL* 3.2 3.3 + - - +
278A PHE* 2.8 63.5 + + + +
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Residues in contact with HIS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A SER 3.0 17.4 + - - +
272A HIS 3.6 4.5 - - - +
273A LEU 3.3 0.2 - - - -
274A TYR* 1.3 82.5 - - + +
276A MET* 1.3 63.2 + - - +
278A PHE* 3.9 4.9 - + - -
279A GLU* 2.9 47.2 + - + +
358A GLY* 3.4 18.1 - - - -
361A ILE* 3.9 17.1 - - + +
362A SER* 3.2 27.7 + - - -
365A TYR* 3.7 26.5 - + + -
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Residues in contact with MET 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TYR* 3.8 19.3 - - - +
272A HIS 3.2 8.8 + - - +
273A LEU* 3.6 30.1 - - + +
274A TYR 3.3 0.2 - - - -
275A HIS* 1.3 79.1 + - - +
277A VAL* 1.3 62.9 + - - +
279A GLU* 4.0 1.4 - - - +
280A LEU* 3.0 29.1 + - - +
362A SER* 3.5 30.1 + - - +
365A TYR* 4.1 5.2 - - + -
366A ALA* 3.6 35.9 - - - +
373A LEU* 4.7 2.2 - - + -
387A ILE* 3.8 22.9 - - + -
389A ILE* 3.9 17.3 - - + -
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 4.1 6.7 - - + +
229A ILE* 4.0 37.9 - - + +
232A GLY* 4.2 7.4 - - - -
273A LEU* 3.0 32.0 + - + +
274A TYR* 3.5 14.6 - - - +
276A MET* 1.3 75.7 - - - +
278A PHE* 1.3 62.9 + - - +
280A LEU* 3.3 3.9 + - - +
281A PHE* 2.9 44.8 + - + -
314A VAL* 4.6 7.9 - - + -
316A MET* 3.8 5.5 - - + +
387A ILE* 3.7 23.3 - - + -
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Residues in contact with PHE 278 (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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232A GLY* 3.7 25.1 - - - -
235A ASN* 3.8 14.1 - - + -
236A ALA* 3.5 19.3 - - - -
239A LEU* 3.7 14.4 - - + -
274A TYR* 2.8 52.7 + + + +
275A HIS* 4.0 4.9 - + - +
277A VAL* 1.3 74.4 - - - +
279A GLU* 1.3 74.7 + - + +
281A PHE* 3.4 2.7 + - - +
282A LYS* 3.1 58.9 + - + +
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Residues in contact with GLU 279 (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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275A HIS* 2.9 36.3 + - + +
278A PHE* 1.3 85.3 - - + +
280A LEU* 1.3 62.0 + - - +
282A LYS* 2.9 39.0 + - - +
283A ASN* 3.1 22.0 + - - +
352A LEU 5.4 0.5 - - - +
358A GLY* 3.3 29.2 - - - +
359A LEU* 3.8 10.8 + - + +
362A SER* 3.3 22.9 - - - +
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Residues in contact with LEU 280 (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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276A MET 3.0 17.9 + - - +
279A GLU* 1.3 78.0 - - + +
281A PHE* 1.3 56.9 + - - +
283A ASN* 3.2 10.0 + - - +
284A ALA* 2.8 29.1 + - - +
314A VAL* 5.7 0.7 - - + +
316A MET* 3.5 24.0 - - + +
332A PHE* 6.4 0.2 - - + -
359A LEU* 4.0 17.5 - - + -
362A SER* 5.6 0.7 - - - -
373A LEU* 4.0 25.1 - - + -
375A LEU* 4.2 6.5 - - + -
385A ALA* 3.7 34.5 - - + +
387A ILE* 3.6 37.9 - - + -
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Residues in contact with PHE 281 (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 ILE* 3.4 32.5 - - + -
232A GLY 3.7 2.7 - - - -
233A TYR* 3.4 39.5 - + + -
236A ALA* 3.5 19.1 - - + -
250A LEU* 3.8 12.6 - - + -
277A VAL* 2.9 28.2 + - + +
278A PHE 3.6 1.6 - - - +
280A LEU* 1.3 71.8 - - - +
282A LYS* 1.3 61.0 + - - +
284A ALA* 3.2 0.9 + - - +
285A MET* 2.8 41.7 + - + +
301A ILE* 3.8 24.2 - - + -
303A VAL* 3.7 20.2 - - + -
316A MET* 3.5 22.0 - - + -
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Residues in contact with LYS 282 (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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236A ALA* 4.0 13.0 - - + -
239A LEU* 4.1 10.2 - - + +
278A PHE* 3.1 50.7 + - + +
279A GLU* 2.9 42.7 + - - +
281A PHE* 1.3 75.6 - - - +
283A ASN* 1.3 57.0 + - - +
285A MET* 4.5 0.4 - - - -
286A ARG* 3.0 31.9 + - - +
352A LEU* 3.6 52.2 - - + +
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Residues in contact with ASN 283 (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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279A GLU 3.1 13.1 + - - +
280A LEU* 3.2 12.0 + - - +
282A LYS* 1.3 76.3 - - - +
284A ALA* 1.3 66.0 + - - +
286A ARG* 3.0 35.6 + - - +
287A ALA* 3.3 20.3 + - - +
318A ASP* 4.9 5.5 + - - -
331A LEU* 4.2 15.8 - - - +
352A LEU 5.1 0.9 + - - -
359A LEU* 3.8 30.6 - - + +
375A LEU* 4.9 13.7 - - - +
383A THR* 5.2 8.5 - - - +
385A ALA* 5.7 2.0 - - - +
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Residues in contact with ALA 284 (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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280A LEU 2.8 17.0 + - - +
281A PHE 3.7 1.8 - - - +
283A ASN* 1.3 79.8 - - - +
285A MET* 1.3 54.6 + - - +
287A ALA* 3.6 2.8 + - - +
288A THR* 2.8 36.9 + - - -
301A ILE* 3.6 20.9 - - + -
316A MET* 3.9 15.3 - - + -
318A ASP* 3.7 29.6 - - + +
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Residues in contact with MET 285 (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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233A TYR* 3.4 41.5 - - + +
236A ALA* 3.7 32.3 - - + +
237A ARG* 3.8 18.2 - - + +
240A CYS* 3.8 16.4 - - - -
248A PRO* 3.9 17.0 - - + +
281A PHE* 2.8 23.3 + - + +
284A ALA* 1.3 74.1 - - - +
286A ARG* 1.3 59.2 + - - +
288A THR* 3.2 0.9 + - - -
289A MET* 2.8 36.8 + - - +
301A ILE* 3.3 18.8 - - + -
352A LEU* 3.7 14.4 - - + -
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Residues in contact with ARG 286 (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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244A TYR* 3.4 28.5 - - - +
282A LYS 3.0 18.0 + - - +
283A ASN* 3.0 37.5 + - - +
285A MET* 1.3 75.5 - - - +
287A ALA* 1.3 80.6 + - - +
289A MET* 3.9 0.3 - - - -
290A GLU* 3.0 46.7 + - - +
331A LEU* 5.0 10.9 - - - +
352A LEU* 3.8 11.9 - - + +
353A ALA* 3.7 30.3 - - - +
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Residues in contact with ALA 287 (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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283A ASN* 3.3 15.6 + - - +
284A ALA 3.9 3.4 - - - +
286A ARG* 1.3 99.5 - - - +
288A THR* 1.3 57.4 + - - +
290A GLU* 4.0 2.3 - - - +
291A HIS* 2.9 33.6 + - - +
318A ASP* 4.4 7.9 - - - +
320A GLY* 3.4 23.1 - - - +
322A GLY 5.7 0.7 - - - +
383A THR* 6.0 1.6 - - - +
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Residues in contact with THR 288 (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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248A PRO* 4.0 16.4 - - + -
284A ALA 2.8 22.3 + - - -
285A MET 3.2 4.0 + - - -
287A ALA* 1.3 77.9 - - - +
289A MET* 1.3 61.5 + - - +
292A HIS* 3.1 28.4 + - + +
298A TYR* 3.8 7.5 - - + -
299A PRO* 3.6 41.4 + - + +
301A ILE* 4.4 5.5 - - - +
318A ASP* 3.8 16.3 - - - +
319A ARG 4.3 3.1 + - - +
320A GLY* 3.7 10.3 + - - -
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Residues in contact with MET 289 (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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240A CYS* 3.5 19.7 - - - -
244A TYR* 3.5 37.4 - - + +
246A ASN* 3.7 25.6 - - + +
247A SER* 4.0 2.9 - - - -
248A PRO* 3.9 23.1 - - - -
285A MET 2.8 20.3 + - - +
288A THR* 1.3 73.1 - - - +
290A GLU* 1.3 65.4 + - - +
293A ALA* 3.3 25.5 + - - +
298A TYR* 3.5 53.7 + - + +
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A TYR* 4.9 4.0 - - - -
244A TYR* 2.9 32.6 + - + +
286A ARG* 3.0 37.9 + - - +
287A ALA* 4.2 3.1 - - - +
289A MET* 1.3 75.7 - - - +
291A HIS* 1.3 67.3 + - - +
293A ALA* 3.8 12.6 - - - +
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Residues in contact with HIS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ALA 2.9 19.1 + - - +
289A MET 3.4 0.2 - - - -
290A GLU* 1.3 81.1 - - - +
292A HIS* 1.3 86.2 + + + +
293A ALA 3.4 1.8 + - - -
294A ASN* 4.8 1.7 + - - +
295A ARG* 2.9 35.9 + - - -
319A ARG 3.9 0.9 - - - -
320A GLY* 3.4 16.1 + - - +
321A GLY* 3.7 28.2 - - - -
380A GLY* 4.3 13.1 + - - -
381A TYR 5.0 1.3 + - - -
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Residues in contact with HIS 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A THR* 3.1 21.7 + - + +
291A HIS* 1.3 85.0 - + + +
293A ALA* 1.3 64.2 + - - +
294A ASN 3.2 3.4 - - - -
295A ARG* 3.0 55.7 + - - +
296A GLY 3.0 10.6 + - - -
297A VAL 3.6 17.1 + - - +
298A TYR* 3.6 11.1 - - + -
299A PRO* 3.5 33.4 - - + +
319A ARG* 2.7 33.6 + - + +
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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