Contacts of the helix formed by residues 327 - 364 (chain A) in PDB entry 2IG7
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 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A LEU* 1.3 75.1 - - - +
328A GLN* 1.3 58.8 + - - +
329A GLU* 3.5 10.6 + - - +
330A GLU* 2.7 40.5 + - - +
331A GLN* 2.9 26.6 + - - +
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Residues in contact with GLN 328 (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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326A LEU 3.8 0.4 + - - +
327A SER* 1.3 71.4 - - - +
329A GLU* 1.3 64.0 + - - +
331A GLN* 3.7 12.7 - - - +
332A ARG* 3.1 44.0 + - + +
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Residues in contact with GLU 329 (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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327A SER* 3.5 10.2 + - - +
328A GLN* 1.3 76.7 - - - +
330A GLU* 1.3 65.3 + - + +
332A ARG* 3.2 7.0 + - - +
333A LYS* 3.1 22.3 + - + +
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Residues in contact with GLU 330 (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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325A THR 4.7 1.3 - - - +
326A LEU* 3.5 24.2 - - + +
327A SER* 2.7 44.9 + - - +
329A GLU* 1.3 80.3 - - + +
331A GLN* 1.3 64.1 + - - +
333A LYS* 3.2 8.8 + - - +
334A LEU* 3.0 30.1 + - + +
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Residues in contact with GLN 331 (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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314A ARG* 6.1 1.4 - - - +
317A LEU* 4.9 3.5 - - + +
326A LEU* 3.8 29.3 - - + +
327A SER 2.9 13.8 + - - +
328A GLN* 3.7 10.7 - - - +
330A GLU* 1.3 76.9 - - - +
332A ARG* 1.3 91.8 + - - +
334A LEU* 3.3 12.0 + - + +
335A GLU* 3.1 33.3 + - + +
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Residues in contact with ARG 332 (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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310A LEU* 6.3 0.4 - - - -
314A ARG* 4.9 10.8 - - - +
328A GLN* 3.1 34.5 + - + +
329A GLU* 3.8 4.7 - - - +
331A GLN* 1.3 119.7 - - - +
333A LYS* 1.3 56.5 + - - +
335A GLU* 2.8 42.7 + - - +
336A GLU* 3.0 45.7 + - + +
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Residues in contact with LYS 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLU* 3.1 14.0 + - + +
330A GLU* 3.4 11.9 - - - +
332A ARG* 1.3 76.0 - - - +
334A LEU* 1.3 60.8 + - + +
336A GLU* 3.7 17.8 + - - +
337A ASP* 2.6 67.4 + - - +
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Residues in contact with LEU 334 (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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273A ARG* 6.2 2.5 - - - +
317A LEU* 3.9 22.5 - - + +
321A LYS* 4.3 30.1 - - + +
326A LEU* 3.5 32.3 - - + -
330A GLU* 3.0 20.3 + - + +
331A GLN* 3.6 11.7 - - + +
333A LYS* 1.3 77.0 - - + +
335A GLU* 1.3 57.0 + - - +
337A ASP* 3.7 7.1 - - + +
338A LEU* 3.0 31.9 + - - +
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Residues in contact with GLU 335 (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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310A LEU* 3.6 28.0 - - + +
313A ILE* 4.1 11.6 - - + +
314A ARG* 3.3 28.8 - - + +
317A LEU* 4.1 14.6 - - + -
331A GLN* 3.1 15.7 + - + +
332A ARG* 2.8 56.4 + - - +
334A LEU* 1.3 74.4 - - - +
336A GLU* 1.3 59.6 + - + +
338A LEU* 3.5 2.1 + - - +
339A LEU* 3.0 35.5 + - - +
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Residues in contact with GLU 336 (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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332A ARG* 3.0 37.3 + - + +
333A LYS* 3.7 17.3 + - + +
335A GLU* 1.3 76.0 - - + +
337A ASP* 1.3 65.2 + - - +
339A LEU* 3.3 13.1 + - + +
340A VAL* 3.3 28.7 + - + +
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Residues in contact with ASP 337 (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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333A LYS* 2.6 59.9 + - - +
334A LEU* 3.7 8.4 - - + +
336A GLU* 1.3 76.1 - - - +
338A LEU* 1.3 60.7 + - - +
340A VAL* 3.4 7.5 + - - +
341A GLU* 3.0 30.0 + - - +
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Residues in contact with LEU 338 (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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273A ARG* 3.6 31.8 - - - +
277A ILE* 3.9 8.5 - - + -
313A ILE* 3.7 29.2 - - + -
316A TYR* 4.2 14.6 - - + -
317A LEU* 3.6 32.3 - - + -
334A LEU 3.0 17.2 + - - +
335A GLU 3.9 3.1 - - - +
337A ASP* 1.3 74.1 - - - +
339A LEU* 1.3 60.8 + - - +
341A GLU* 3.6 20.4 - - - +
342A VAL* 2.9 47.5 + - + +
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Residues in contact with LEU 339 (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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306A GLN* 4.3 31.4 - - + +
309A GLN* 3.2 46.9 - - + +
310A LEU* 3.9 25.6 - - + +
313A ILE* 3.6 17.0 - - + +
335A GLU 3.0 19.7 + - - +
336A GLU* 3.3 13.0 + - + +
338A LEU* 1.3 76.3 - - - +
340A VAL* 1.3 57.4 + - + +
342A VAL* 3.6 3.2 + - - +
343A SER* 3.1 27.0 + - - -
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Residues in contact with VAL 340 (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 THR* 5.5 1.8 - - + -
336A GLU* 3.3 15.8 + - + +
337A ASP* 3.7 7.9 - - - +
338A LEU 3.2 0.4 - - - -
339A LEU* 1.3 75.8 - - + +
341A GLU* 1.3 67.6 + - - +
343A SER* 2.8 23.6 + - - +
344A ARG* 3.3 32.2 + - - +
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Residues in contact with GLU 341 (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 THR* 3.9 12.1 - - + -
233A PRO 3.8 20.6 - - - +
234A SER* 2.6 32.3 + - - +
235A PRO* 3.7 0.7 - - - +
273A ARG* 2.9 39.8 + - - -
274A GLY* 3.5 12.2 + - - -
337A ASP* 3.0 17.3 + - - +
338A LEU* 3.4 19.1 + - - +
340A VAL* 1.3 79.4 - - - +
342A VAL* 1.3 62.4 + - - +
344A ARG* 3.3 1.2 + - - +
345A TYR* 3.0 31.4 + - + -
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Residues in contact with VAL 342 (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 GLY* 4.4 10.5 - - - -
277A ILE* 3.6 25.4 - - + -
278A GLY* 3.9 14.1 - - - +
281A PHE* 3.6 35.7 - - + -
303A TYR* 4.8 3.1 - - - +
309A GLN* 5.3 3.4 - - - +
313A ILE* 4.5 4.9 - - + -
338A LEU* 2.9 40.0 + - + +
339A LEU* 3.9 5.2 - - - +
341A GLU* 1.3 74.3 - - - +
343A SER* 1.3 60.4 + - - +
346A ALA* 2.8 30.1 + - - +
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Residues in contact with SER 343 (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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303A TYR* 5.1 4.0 - - - -
309A GLN* 5.7 3.6 + - - -
339A LEU 3.1 14.0 + - - -
340A VAL* 2.8 26.2 + - - +
342A VAL* 1.3 77.6 - - - +
344A ARG* 1.3 62.1 + - - +
346A ALA* 3.9 12.6 - - - +
347A LEU* 3.9 12.3 - - - +
384A GLN* 5.4 1.7 - - - +
388A LEU* 3.8 26.9 - - - +
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Residues in contact with ARG 344 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A LEU* 3.8 24.2 - - + +
229A LEU* 3.7 19.6 - - + +
231A SER* 3.7 21.4 + - - -
232A THR* 2.9 36.7 + - + +
340A VAL* 3.5 29.5 - - - +
341A GLU 3.3 6.4 + - - +
342A VAL 3.1 0.4 - - - -
343A SER* 1.3 82.3 + - - +
345A TYR* 1.3 63.5 + - - +
346A ALA 3.3 0.2 - - - -
347A LEU* 3.2 27.0 + - - +
348A ALA 3.9 0.5 + - - -
388A LEU* 4.2 17.3 - - + +
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Residues in contact with TYR 345 (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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188A LEU* 4.6 3.6 - - + -
229A LEU* 3.6 44.3 + - + +
232A THR* 3.2 31.9 + - + -
234A SER* 3.5 26.9 + - - -
272A TYR* 3.6 47.4 - + + -
274A GLY* 3.2 29.6 - - - +
275A PHE* 3.5 14.1 - - + +
278A GLY* 5.2 0.2 - - - -
341A GLU* 3.0 28.4 + - + +
344A ARG* 1.3 72.0 - - - +
346A ALA* 1.3 59.4 + - - +
347A LEU 3.1 1.8 - - - -
348A ALA* 2.9 26.2 + - + +
349A SER* 3.4 4.3 + - - -
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Residues in contact with ALA 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLY* 4.0 21.8 - - - -
282A CYS* 3.7 6.4 - - - -
303A TYR* 3.4 23.6 - - - +
342A VAL 2.8 19.5 + - - +
343A SER* 3.9 8.1 - - - +
344A ARG 3.3 0.2 - - - -
345A TYR* 1.3 75.1 - - - +
347A LEU* 1.3 61.2 + - - +
349A SER* 3.1 18.4 + - - -
350A HIS* 3.4 13.4 + - - -
384A GLN* 4.2 11.2 - - - +
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Residues in contact with LEU 347 (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 LEU* 4.1 5.6 - - + -
228A LEU* 3.7 19.7 - - + -
343A SER 3.9 11.7 - - - +
344A ARG 3.2 11.6 + - - +
345A TYR 3.1 0.6 - - - -
346A ALA* 1.3 77.5 - - - +
348A ALA* 1.3 61.6 + - - +
350A HIS* 3.4 5.8 + - + +
351A PHE* 3.2 18.0 + - - +
381A TYR* 3.3 44.4 - - + +
384A GLN* 3.5 36.3 - - + +
385A LYS* 3.8 20.2 - - + +
388A LEU* 3.7 22.2 - - + -
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Residues in contact with ALA 348 (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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188A LEU* 4.0 13.0 - - + -
192A MSE 4.5 1.4 - - + +
225A LEU* 4.0 14.7 - - + +
229A LEU* 4.0 25.8 - - + -
275A PHE* 3.7 15.7 - - + -
344A ARG 3.9 0.8 + - - -
345A TYR* 2.9 15.8 + - + +
347A LEU* 1.3 77.3 - - - +
349A SER* 1.3 53.4 - - - +
351A PHE* 3.9 0.2 - - - +
352A PHE* 2.8 36.6 + - - +
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Residues in contact with SER 349 (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 PHE* 3.6 14.3 - - - -
279A ASN* 2.6 49.3 + - - -
282A CYS* 3.8 4.9 - - - +
345A TYR 3.4 4.0 + - - -
346A ALA* 3.1 12.2 + - - -
348A ALA* 1.3 75.7 - - - +
350A HIS* 1.3 62.8 + - - +
353A TRP* 3.0 30.4 + - - +
377A ARG* 2.9 17.0 + - - -
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Residues in contact with HIS 350 (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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282A CYS* 3.4 23.1 - - + -
286A TYR* 4.8 0.7 - + - -
346A ALA 3.4 15.9 + - - -
347A LEU* 3.4 11.8 + - + +
348A ALA 3.3 0.4 - - - -
349A SER* 1.3 78.1 - - - +
351A PHE* 1.3 57.0 + - - +
354A GLY* 2.9 24.9 + - - -
377A ARG* 3.1 61.2 + - - +
378A PHE* 4.6 0.9 - - - -
380A PHE* 3.1 35.1 - + - +
381A TYR* 3.7 23.6 - - + -
384A GLN* 2.9 27.7 + - - -
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Residues in contact with PHE 351 (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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192A MSE 3.9 9.9 - - - -
218A LEU* 3.5 38.1 - - + -
221A GLU* 3.8 24.0 - - + -
222A MSE 3.7 37.5 - - + -
225A LEU* 3.9 16.4 - - + -
347A LEU 3.2 13.4 + - - +
348A ALA 3.9 1.1 - - - +
350A HIS* 1.3 76.5 - - - +
352A PHE* 1.3 67.1 + - - +
354A GLY* 3.8 0.5 - - - -
355A LEU* 3.1 44.9 + - + +
378A PHE* 3.7 20.9 - + - -
381A TYR* 3.9 22.4 - + - -
382A PHE* 5.9 0.2 - + - -
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Residues in contact with PHE 352 (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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187A TRP* 3.4 43.1 - + - -
188A LEU* 4.4 4.0 - - + -
191A THR* 3.7 26.5 - - + -
192A MSE 3.7 29.9 - - + -
195A TYR* 3.8 24.2 - + - -
267A TYR* 4.6 5.2 - + - -
275A PHE* 4.2 9.2 - + + -
348A ALA 2.8 19.1 + - - +
349A SER 3.8 2.5 - - - +
351A PHE* 1.3 78.0 - - - +
353A TRP* 1.3 105.5 + + - +
355A LEU* 3.3 2.9 + - - +
356A TRP* 2.9 24.9 + + + +
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Residues in contact with TRP 353 (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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241A ASN* 3.4 21.2 + - + -
242A ASP* 3.7 23.6 - - + -
267A TYR* 4.0 24.7 - + + -
275A PHE* 4.4 2.8 - - - -
279A ASN* 2.9 29.6 + - - +
283A GLU* 5.1 4.4 + - - -
349A SER* 3.0 28.9 + - - +
352A PHE* 1.3 97.0 - + - +
354A GLY* 1.3 60.8 + - - +
356A TRP* 3.5 56.9 - + - +
357A SER* 2.9 31.4 + - - -
373A TYR* 4.5 9.3 - + + -
377A ARG* 3.6 25.4 - - - +
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Residues in contact with GLY 354 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A HIS 2.9 18.7 + - - -
353A TRP* 1.3 78.5 - - - +
355A LEU* 1.3 60.9 + - - +
357A SER 3.3 0.7 + - - -
358A ILE* 3.1 27.7 + - - +
374A ALA* 3.6 10.2 - - - +
377A ARG* 4.1 12.2 - - - +
378A PHE* 3.4 23.1 - - - -
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Residues in contact with LEU 355 (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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192A MSE 3.7 28.0 - - + +
195A TYR* 4.3 13.7 - - + -
196A LEU* 4.1 17.0 - - + -
199A ILE* 3.6 26.8 - - + +
213A LEU* 4.6 0.2 - - + -
218A LEU* 4.1 25.1 - - + -
222A MSE 3.3 30.5 - - + -
351A PHE* 3.1 27.6 + - + +
352A PHE* 3.7 3.4 - - - +
354A GLY* 1.3 71.8 - - - +
356A TRP* 1.3 66.4 + - - +
358A ILE* 3.2 3.6 + - + -
359A LEU* 3.2 19.9 + - - +
378A PHE* 3.5 4.6 - - + -
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Residues in contact with TRP 356 (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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78A LEU* 3.6 33.4 - - + -
79A SER* 3.4 20.6 - - - -
109A ILE* 3.5 22.9 - - + +
195A TYR* 3.7 29.0 - + + -
267A TYR* 2.9 22.3 + + - -
352A PHE* 2.9 19.0 + + + +
353A TRP* 3.5 38.1 - + + +
354A GLY 3.4 0.2 - - - -
355A LEU* 1.3 78.5 - - - +
357A SER* 1.3 80.3 + - - +
359A LEU* 3.4 4.2 + - - +
360A GLN* 2.9 47.4 + - + +
370A TYR* 3.8 19.1 - + - -
373A TYR* 4.8 9.6 - + - -
1007A UNX 4.0 5.4 - - - -
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A TRP 2.9 18.9 + - - -
354A GLY 3.8 4.0 - - - -
355A LEU 3.2 0.2 - - - -
356A TRP* 1.3 83.1 - - - +
358A ILE* 1.3 65.8 + - - +
360A GLN* 3.3 2.6 + - - -
361A ALA* 3.0 19.2 + - - +
370A TYR* 2.7 51.0 + - - +
373A TYR* 3.3 25.2 - - - -
374A ALA* 4.0 4.7 - - - -
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Residues in contact with ILE 358 (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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199A ILE* 3.7 35.0 - - + -
202A LEU* 5.1 2.8 - - + +
212A LEU* 4.0 26.0 - - + -
213A LEU* 4.6 4.7 - - + -
218A LEU* 4.1 10.5 - - + -
354A GLY 3.1 15.5 + - - +
355A LEU* 3.2 6.5 + - - +
357A SER* 1.3 77.0 - - - +
359A LEU* 1.3 62.7 + - - +
361A ALA* 3.3 17.5 + - - +
362A SER* 3.8 3.5 + - - -
371A LEU* 4.2 16.1 - - + +
374A ALA* 3.8 13.7 - - + -
378A PHE* 3.9 19.1 - - + -
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE* 3.9 13.5 - - + -
195A TYR* 3.5 34.1 - - + -
198A GLN* 3.7 35.4 - - + +
199A ILE* 4.0 12.5 - - + +
202A LEU* 3.9 23.8 - - + -
355A LEU 3.2 9.6 + - - +
356A TRP* 3.7 8.1 - - - +
358A ILE* 1.3 80.1 - - - +
360A GLN* 1.3 55.6 - - - +
362A SER* 3.0 13.0 + - - -
363A MSE 2.9 50.5 + - + +
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Residues in contact with GLN 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU 3.1 25.9 + - - -
79A SER* 4.0 5.5 + - - +
107A GLY* 6.3 0.2 - - - -
108A ALA 5.8 0.3 + - - -
109A ILE* 3.5 36.7 + - + +
356A TRP* 2.9 45.5 + - + +
357A SER 3.6 0.4 - - - +
359A LEU* 1.3 70.5 - - - +
361A ALA* 1.3 64.6 + - - +
362A SER 3.0 2.0 - - - -
363A MSE 3.6 14.0 - - - +
364A SER* 2.8 45.1 + - - +
370A TYR* 3.5 25.3 - - + -
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A SER 3.0 10.5 + - - +
358A ILE 3.3 13.0 + - - +
360A GLN* 1.3 74.8 - - - +
362A SER* 1.3 57.9 + - - +
364A SER 4.8 3.3 - - - +
370A TYR* 3.7 16.3 - - + +
371A LEU* 3.5 35.7 - - + -
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Residues in contact with SER 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 2.8 43.0 - - - +
203A PRO* 6.3 1.3 - - - -
358A ILE 3.8 0.9 + - - -
359A LEU 3.0 11.7 + - - -
360A GLN 3.0 0.2 - - - -
361A ALA* 1.3 79.6 - - - +
363A MSE 1.3 61.9 + - - +
364A SER 3.7 3.5 - - - +
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Residues in contact with MSE 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.3 64.1 + - + +
109A ILE* 3.9 12.3 - - - +
198A GLN* 4.2 11.0 - - - +
202A LEU* 5.7 2.2 - - + -
359A LEU* 2.9 55.7 + - + +
360A GLN* 3.6 12.1 - - - +
362A SER* 1.3 74.5 - - - +
364A SER* 1.3 65.5 + - - +
365A THR* 3.9 5.7 + - - +
1009A UNX 4.5 5.4 - - - -
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Residues in contact with SER 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER 5.2 1.0 + - - -
108A ALA 6.1 0.7 - - - +
360A GLN* 2.8 40.5 + - - +
361A ALA 4.8 2.9 - - - +
362A SER 4.5 5.0 - - - +
363A MSE 1.3 76.4 - - - +
365A THR* 1.3 63.4 + - - +
366A ILE* 3.1 19.6 + - - +
370A TYR* 2.8 35.0 + - - -
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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