Contacts of the helix formed by residues 275 - 299 (chain A) in PDB entry 1KL1
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 GLN 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLY 3.5 16.5 + - - +
272A GLU* 3.1 10.8 + - - +
274A LEU* 1.3 84.0 + - - +
276A ASP* 1.3 66.4 + - - +
277A ASP* 3.4 20.6 - - - +
278A PHE* 3.1 13.3 + - - +
279A LYS* 3.2 14.9 + - - +
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Residues in contact with ASP 276 (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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274A LEU 4.0 1.9 + - - +
275A GLN* 1.3 74.7 - - - +
277A ASP* 1.3 63.0 + - - +
279A LYS* 3.0 23.5 + - - +
280A ALA* 3.1 11.4 + - - +
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Residues in contact with ASP 277 (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 ARG* 5.8 3.4 + - - -
272A GLU 4.2 1.4 - - - +
275A GLN* 3.4 19.0 - - - +
276A ASP* 1.3 78.8 - - - +
278A PHE* 1.3 76.5 + - - +
280A ALA* 3.3 9.6 + - + +
281A TYR* 2.9 27.0 + - - +
284A ARG* 4.9 2.1 + - - -
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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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203A GLY* 3.6 30.1 - - - -
206A ALA* 4.6 3.4 - - + -
207A ALA* 4.5 6.5 - - + -
227A THR 3.5 23.6 - - - -
228A LEU* 4.0 16.8 - - - -
229A ARG* 3.9 22.0 - - + +
272A GLU* 3.3 24.0 - - + +
273A ALA* 3.5 33.7 - - + -
275A GLN 3.1 6.5 + - - +
277A ASP* 1.3 82.9 + - - +
279A LYS* 1.3 60.4 + - - +
281A TYR* 3.3 27.9 + + - +
282A ALA* 2.9 29.2 + - + +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 4.4 6.5 - - - +
206A ALA 2.8 32.7 + - - -
207A ALA* 3.9 26.9 - - + +
209A LEU* 4.5 1.4 - - - +
273A ALA 2.9 23.6 + - - +
274A LEU* 4.1 11.7 - - - +
275A GLN 3.2 18.2 - - - +
276A ASP* 3.0 14.2 + - - +
278A PHE* 1.3 77.1 - - - +
280A ALA* 1.3 61.3 + - - +
282A ALA* 3.4 3.3 + - - +
283A LYS* 3.1 22.0 + - - +
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Residues in contact with ALA 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 ASP 3.1 11.1 + - - +
277A ASP* 3.6 11.9 - - + +
279A LYS* 1.3 72.4 - - - +
281A TYR* 1.3 65.5 + - - +
283A LYS* 3.4 7.7 + - - +
284A ARG* 3.1 41.8 + - - +
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Residues in contact with TYR 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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33A ASN* 3.0 14.9 + - - -
227A THR* 4.3 9.4 + - - -
229A ARG* 3.4 27.4 - - - +
277A ASP 2.9 14.4 + - - +
278A PHE* 3.4 37.0 - + - +
280A ALA* 1.3 76.3 - - - +
282A ALA* 1.3 73.7 + - + +
284A ARG* 3.0 24.0 + - - +
285A VAL* 2.9 40.7 + - + +
361A ALA* 2.8 24.9 + - - +
364A THR* 3.7 10.3 - - + -
365A THR* 2.9 37.1 + - - -
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Residues in contact with ALA 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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203A GLY 4.2 9.2 - - - +
204A LEU* 4.1 8.4 - - + +
207A ALA* 3.4 33.2 - - + -
209A LEU* 3.4 11.5 - - + +
278A PHE* 2.9 18.0 + - + +
279A LYS 3.8 0.7 - - - +
280A ALA 3.3 0.2 - - - -
281A TYR* 1.3 82.5 - - + +
283A LYS* 1.3 61.4 + - - +
285A VAL* 3.1 17.3 + - - +
286A VAL* 3.2 13.7 + - - +
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.3 22.7 - - + +
279A LYS 3.1 13.7 + - - +
280A ALA* 3.7 10.8 - - - +
281A TYR 3.3 0.2 - - - -
282A ALA* 1.3 75.7 - - - +
284A ARG* 1.3 57.1 + - + +
286A VAL* 3.3 4.0 + - + +
287A ASP* 2.7 65.8 + - - +
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Residues in contact with ARG 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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277A ASP 4.9 1.8 + - - -
280A ALA* 3.1 33.4 + - - +
281A TYR* 3.0 34.6 + - - +
283A LYS* 1.3 72.8 - - + +
285A VAL* 1.3 60.0 + - - +
287A ASP* 4.1 9.2 - - + +
288A ASN* 2.8 40.2 + - - +
364A THR* 3.7 19.8 + - + +
367A GLY* 6.3 0.8 - - - -
368A PHE 5.4 5.5 + - - -
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Residues in contact with VAL 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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204A LEU* 4.4 9.0 - - + -
227A THR* 5.0 2.5 - - + -
281A TYR* 2.9 56.1 + - + +
282A ALA* 3.1 11.8 + - - +
284A ARG* 1.3 77.0 - - - +
286A VAL* 1.3 57.2 + - - +
288A ASN* 3.6 0.2 - - - +
289A ALA* 3.0 16.6 + - - +
311A HIS* 3.6 25.8 - - + -
360A THR* 2.9 30.4 + - - +
361A ALA* 4.1 10.8 - - + -
364A THR* 3.7 14.4 - - - -
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Residues in contact with VAL 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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204A LEU* 3.7 35.2 - - + -
209A LEU* 4.6 16.6 - - + +
282A ALA 3.2 6.2 + - - +
283A LYS* 3.9 6.7 - - + +
285A VAL* 1.3 73.2 - - - +
287A ASP* 1.3 69.3 + - - +
289A ALA 3.2 0.5 + - - -
290A LYS* 2.9 59.5 + - + +
309A ASP 3.9 9.6 - - - +
310A ASN* 3.7 15.5 - - - +
311A HIS 4.5 0.4 - - - +
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Residues in contact with ASP 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 LYS* 2.7 63.0 + - - +
284A ARG* 3.9 9.5 - - + +
286A VAL* 1.3 75.7 - - - +
288A ASN* 1.3 57.7 + - - +
290A LYS* 3.4 8.5 + - - +
291A ARG* 2.9 28.2 + - - +
370A LEU* 3.9 15.4 - - + +
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Residues in contact with ASN 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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284A ARG* 2.8 24.0 + - - +
285A VAL 3.6 4.3 - - - +
287A ASP* 1.3 73.4 - - - +
289A ALA* 1.3 60.7 + - - +
291A ARG* 4.3 1.1 - - - -
292A LEU* 2.8 32.7 + - - +
360A THR* 3.9 4.5 - - - -
364A THR* 2.9 28.0 + - - +
368A PHE 3.0 26.4 + - - -
369A GLY* 3.4 22.1 - - - +
370A LEU* 3.6 9.5 + - - +
373A MET* 3.3 27.4 - - + +
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Residues in contact with ALA 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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285A VAL 3.0 15.6 + - - +
286A VAL 3.2 1.3 + - - +
288A ASN* 1.3 76.4 - - - +
290A LYS* 1.3 59.5 + - - +
292A LEU* 3.5 2.5 + - - +
293A ALA* 2.9 29.6 + - - +
308A THR* 3.6 8.6 - - + +
310A ASN 3.1 28.3 - - - +
311A HIS 3.9 11.7 - - - +
312A LEU* 5.2 1.8 - - - -
313A LEU* 3.9 4.8 - - + +
360A THR* 3.7 17.9 - - + +
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Residues in contact with LYS 290 (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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286A VAL* 2.9 44.4 + - + +
287A ASP* 3.6 11.4 - - - +
289A ALA* 1.3 76.9 - - - +
291A ARG* 1.3 57.8 + - - +
293A ALA* 3.4 3.5 + - - +
294A SER* 3.0 29.6 + - - -
308A THR* 3.1 31.6 - - + +
309A ASP* 3.3 3.2 - - - -
310A ASN 2.7 39.8 + - - +
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Residues in contact with ARG 291 (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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287A ASP 2.9 17.5 + - - +
288A ASN 3.6 4.3 - - - +
290A LYS* 1.3 74.2 - - - +
292A LEU* 1.3 60.1 + - - +
294A SER* 3.3 9.2 + - - -
295A ALA* 2.8 29.3 + - - +
370A LEU* 3.7 53.3 - - + +
371A GLU* 3.9 13.3 + - - -
373A MET* 3.8 5.8 - - + -
374A ASP* 2.6 42.2 + - - +
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Residues in contact with LEU 292 (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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28A LEU* 4.9 4.3 - - + -
288A ASN 2.8 22.4 + - - +
289A ALA* 3.8 4.7 - - - +
291A ARG* 1.3 74.8 - - - +
293A ALA* 1.3 55.2 + - - +
295A ALA* 3.4 2.6 + - - -
296A LEU* 2.9 44.4 + - + +
313A LEU* 4.0 8.3 - - + -
358A ILE* 3.6 30.3 - - + -
360A THR* 4.0 17.9 - - + -
373A MET* 3.6 35.4 - - + +
376A ILE* 4.0 16.8 - - + -
377A ALA* 3.9 17.9 - - + +
380A ILE* 5.2 0.2 - - + -
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Residues in contact with ALA 293 (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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289A ALA 2.9 18.8 + - - +
290A LYS* 3.5 6.1 - - - +
292A LEU* 1.3 76.5 - - - +
294A SER* 1.3 57.8 + - - +
296A LEU* 3.2 2.5 + - - +
297A GLN* 2.9 34.2 + - - +
303A LEU* 3.5 26.3 - - + +
307A GLY* 4.4 8.1 - - - -
308A THR* 4.1 13.5 - - + -
313A LEU* 3.8 12.0 - - + +
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Residues in contact with SER 294 (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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290A LYS 3.0 17.7 + - - -
291A ARG* 3.6 9.9 - - - -
293A ALA* 1.3 75.5 - - - +
295A ALA* 1.3 58.1 + - - +
297A GLN* 3.2 16.5 + - - +
298A ASN* 2.9 27.4 + - - +
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Residues in contact with ALA 295 (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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291A ARG* 2.8 21.2 + - - +
292A LEU 3.8 2.0 - - - +
294A SER* 1.3 73.3 - - - +
296A LEU* 1.3 61.1 + - - +
298A ASN* 3.2 11.4 - - - +
299A GLU* 3.1 24.9 + - - +
373A MET 4.4 0.9 - - - +
374A ASP* 3.8 27.6 - - - +
377A ALA* 3.4 22.4 - - + -
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Residues in contact with LEU 296 (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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292A LEU* 2.9 32.6 + - + +
293A ALA 3.7 3.8 - - - +
295A ALA* 1.3 72.3 - - - +
297A GLN* 1.3 65.1 + - - +
299A GLU* 3.1 8.2 + - - -
301A PHE* 3.0 61.0 + - + -
303A LEU* 4.4 5.6 - - + -
313A LEU* 3.9 29.8 - - + -
315A VAL* 4.3 10.8 - - + -
358A ILE* 4.5 7.2 - - + -
377A ALA* 3.9 20.6 - - + +
380A ILE* 3.9 21.1 - - + -
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Residues in contact with GLN 297 (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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293A ALA* 2.9 20.9 + - - +
294A SER* 3.2 17.3 + - - +
296A LEU* 1.3 75.2 - - - +
298A ASN* 1.3 57.6 + - - +
300A GLY* 3.0 19.9 + - - -
301A PHE 3.6 18.7 + - - +
303A LEU* 3.7 21.1 + - + +
306A GLY* 3.1 31.4 + - - +
307A GLY* 5.3 0.4 - - - -
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Residues in contact with ASN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A SER 2.9 13.8 + - - +
295A ALA* 3.2 17.0 - - - +
297A GLN* 1.3 76.1 - - - +
299A GLU* 1.3 65.6 + - - +
300A GLY 3.4 0.3 + - - -
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Residues in contact with GLU 299 (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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295A ALA 3.4 14.3 - - - +
296A LEU* 3.1 12.4 + - - +
298A ASN* 1.3 85.2 - - - +
300A GLY* 1.3 57.4 + - - +
301A PHE* 3.6 16.8 - - + -
377A ALA* 3.6 20.8 - - + +
378A ALA* 3.8 25.9 + - - +
381A GLY* 3.8 10.5 - - - -
385A LYS* 2.6 46.4 + - - +
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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
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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) + - + + + + + -
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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