Contacts of the helix formed by residues 312 - 345 (chain A) in PDB entry 5TIN
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 THR 312 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ALA* 2.7 22.1 + - + +
311A GLY* 1.3 75.9 - - - +
313A LYS* 1.3 66.4 + - - +
314A VAL* 3.9 7.8 - - - +
315A PHE* 3.0 32.6 + - - -
316A ILE* 3.0 22.1 + - - +
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLY 4.2 1.0 + - - -
312A THR* 1.3 72.3 - - - +
314A VAL* 1.3 57.1 + - - +
316A ILE* 3.8 5.8 - - - +
317A ASP* 2.9 43.3 + - - +
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A THR* 3.9 7.6 - - - +
313A LYS* 1.3 79.2 - - - +
315A PHE* 1.3 85.8 + - + +
317A ASP* 3.7 7.3 + - - +
318A ARG* 3.2 43.7 + - - +
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Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 3.4 30.9 - - + +
308A SER* 4.2 2.1 - - - -
310A ALA* 3.9 23.3 - - + +
312A THR* 3.0 26.0 + - - +
314A VAL* 1.3 91.0 - - + +
316A ILE* 1.3 66.3 + - - +
317A ASP 3.2 1.1 - - - -
318A ARG* 3.3 40.6 + - - +
319A ALA* 3.1 23.4 + - - +
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Residues in contact with ILE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 4.0 17.7 - - + +
247A ASP* 6.0 1.3 - - - +
308A SER* 4.1 26.2 - - - +
311A GLY* 4.0 18.2 - - - +
312A THR 3.0 24.6 + - - +
313A LYS* 3.8 6.5 - - - +
315A PHE* 1.3 76.9 - - - +
317A ASP* 1.3 62.0 + - - +
319A ALA* 3.4 6.3 + - - +
320A LYS* 2.9 29.3 + - + +
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LYS* 2.9 30.6 + - - +
314A VAL* 3.8 7.9 - - - +
316A ILE* 1.3 79.4 - - - +
318A ARG* 1.3 60.4 + - - +
320A LYS* 3.3 8.2 + - - +
321A LYS* 3.0 28.2 + - - +
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A VAL* 4.5 15.0 - - + -
314A VAL* 3.2 34.2 + - - +
315A PHE* 3.3 42.7 - - - +
316A ILE 3.3 0.4 - - - -
317A ASP* 1.3 78.6 - - - +
319A ALA* 1.3 61.9 + - - +
321A LYS* 3.3 8.0 + - + +
322A ILE* 3.2 30.9 + - + +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 3.8 13.4 - - + +
304A VAL* 3.7 24.4 - - + +
307A VAL* 3.6 25.9 - - + +
308A SER* 3.8 9.9 - - - -
315A PHE 3.1 13.1 + - - +
316A ILE 3.6 4.7 - - - +
318A ARG* 1.3 78.0 - - - +
320A LYS* 1.3 60.7 + - - +
322A ILE* 3.3 9.6 + - - +
323A ASP* 3.3 17.8 + - - +
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A MET* 3.7 13.6 - - + +
316A ILE* 2.9 20.1 + - + +
317A ASP* 3.7 10.8 - - - +
318A ARG 3.3 0.2 - - - -
319A ALA* 1.3 77.2 - - - +
321A LYS* 1.3 57.0 + - - +
323A ASP* 3.4 7.0 + - - +
324A THR* 3.1 33.5 + - + +
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Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A ASP 3.0 16.7 + - - +
318A ARG* 3.6 8.7 - - + +
319A ALA 3.2 0.2 - - - -
320A LYS* 1.3 73.0 - - - +
322A ILE* 1.3 67.0 + - + +
324A THR* 3.0 10.7 + - - +
325A ILE* 3.0 37.4 + - + +
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A GLU* 3.5 27.8 - - + +
303A ALA* 4.6 15.0 - - + -
304A VAL* 3.7 11.7 - - + -
307A VAL* 4.2 29.6 - - + -
318A ARG* 3.2 20.6 + - + +
319A ALA* 3.3 8.5 + - - +
321A LYS* 1.3 77.1 - - - +
323A ASP* 1.3 59.0 + - - +
325A ILE* 3.9 7.0 - - - +
326A SER* 2.8 29.2 + - - +
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Residues in contact with ASP 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 4.0 10.0 - - - +
244A ILE 4.6 2.9 - - - +
246A MET* 4.5 11.8 + - - +
252A ARG* 2.6 35.7 + - - -
300A GLU* 2.8 25.4 - - - +
304A VAL* 3.7 17.2 - - - +
319A ALA 3.3 6.3 + - - +
320A LYS* 3.6 9.9 - - - +
321A LYS 3.2 0.6 - - - -
322A ILE* 1.3 79.6 - - - +
324A THR* 1.3 62.1 + - - +
326A SER* 3.2 2.8 + - - -
327A ARG* 3.0 43.9 + - - +
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LYS* 3.1 18.8 + - + +
321A LYS* 3.0 18.5 + - - +
323A ASP* 1.3 75.8 - - - +
325A ILE* 1.3 62.5 + - - +
327A ARG* 3.6 40.6 + - - +
328A ALA* 3.8 6.6 + - - +
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Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LYS* 3.0 30.5 + - + +
322A ILE* 3.9 6.3 - - + +
324A THR* 1.3 77.9 - - - +
326A SER* 1.3 56.2 + - - +
328A ALA* 3.0 6.9 + - - +
329A CYS* 2.8 55.3 + - + +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 3.8 21.9 - - - -
300A GLU* 3.0 29.5 + - - +
322A ILE* 2.8 23.8 + - - +
323A ASP 3.2 4.9 + - - -
325A ILE* 1.3 78.6 - - - +
327A ARG* 1.3 61.7 + - - +
329A CYS* 4.4 1.8 - - - +
330A PHE* 3.2 43.5 + - - +
331A PRO* 3.6 0.7 - - - +
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Residues in contact with ARG 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 2.9 40.8 + - + -
243A TRP* 3.6 61.2 + - + +
244A ILE 5.6 0.8 + - - -
323A ASP* 3.0 28.3 + - - +
324A THR* 3.6 35.9 - - - +
325A ILE 3.2 0.4 - - - -
326A SER* 1.3 76.4 - - - +
328A ALA* 1.3 56.9 + - - +
331A PRO* 3.4 20.7 - - - +
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Residues in contact with ALA 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR 3.8 6.7 + - - +
325A ILE* 3.0 8.1 + - - +
327A ARG* 1.3 79.6 - - - +
329A CYS* 1.3 64.1 + - - +
330A PHE 3.5 0.4 - - - -
331A PRO* 3.5 4.2 - - - +
332A LEU* 3.1 32.6 + - + +
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Residues in contact with CYS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 2.8 42.3 + - + +
326A SER* 4.7 2.2 - - - +
328A ALA* 1.3 75.9 - - - +
330A PHE* 1.3 59.8 + - + +
332A LEU* 3.7 11.1 - - - +
333A ALA* 2.7 38.2 + - + +
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.7 21.5 - + - +
242A PHE* 3.7 22.0 - + + -
293A PHE* 3.5 40.1 - + - -
296A SER* 3.7 29.8 - - - -
297A ALA* 3.6 13.5 - - + -
300A GLU* 4.4 5.8 - - + -
326A SER* 3.2 33.6 + - - +
329A CYS* 1.3 81.4 - - + +
331A PRO* 1.3 70.9 - - + +
333A ALA* 4.7 2.5 - - - -
334A PHE* 3.0 26.5 + - - +
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Residues in contact with PRO 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.6 41.9 - - + -
242A PHE* 5.4 0.7 - - + -
243A TRP* 5.4 5.4 - - + -
326A SER 3.6 2.5 - - - +
327A ARG* 3.4 26.7 - - - +
328A ALA 3.5 4.9 - - - +
330A PHE* 1.3 94.9 - - + +
332A LEU* 1.3 55.6 + - - +
334A PHE* 3.5 1.7 + - - +
335A LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ALA* 3.1 23.9 + - + +
329A CYS* 3.7 11.7 - - - +
330A PHE 3.2 0.2 - - - -
331A PRO* 1.3 77.0 - - - +
333A ALA* 1.3 58.1 + - - +
335A LEU* 3.3 18.8 + - + +
336A ILE* 3.0 48.0 + - + +
----------------------------------------------------------
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.6 18.3 - - + -
329A CYS 2.7 22.6 + - - +
330A PHE* 4.0 2.0 - - - +
332A LEU* 1.3 73.5 - - - +
334A PHE* 1.3 58.0 + - - +
336A ILE* 3.4 12.4 + - - +
337A PHE* 3.0 27.9 + - - +
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Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 3.5 27.8 - - + -
235A VAL* 4.1 20.6 - - + -
236A ILE* 6.1 0.2 - - + -
239A TRP* 3.7 24.7 - + + -
286A TRP* 4.3 4.9 - + - -
290A CYS* 4.1 27.4 - - - -
293A PHE* 3.5 33.8 - + + -
330A PHE 3.0 18.6 + - - +
331A PRO 3.8 2.5 - - - +
333A ALA* 1.3 76.2 - - - +
335A LEU* 1.3 64.4 + - - +
337A PHE* 3.5 17.1 + + - +
338A ASN* 3.1 48.8 + - - -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PRO 3.0 18.3 + - - +
332A LEU* 3.6 18.8 - - + +
334A PHE* 1.3 73.9 - - - +
336A ILE* 1.3 68.1 + - + +
338A ASN* 3.3 11.2 + - + +
339A ILE* 3.0 42.5 + - + +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 3.0 40.3 + - + +
333A ALA* 3.6 11.4 - - - +
335A LEU* 1.3 77.3 - - + +
337A PHE* 1.3 62.7 + - - +
339A ILE* 3.2 10.0 + - + +
340A PHE* 3.2 43.2 + - + -
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Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE* 4.7 5.8 - - + -
286A TRP* 3.7 33.2 - + - -
289A VAL* 3.5 50.3 - - + -
290A CYS 5.3 0.2 - - - -
293A PHE* 4.7 4.3 - - + -
333A ALA 3.0 16.7 + - - +
334A PHE* 3.7 22.2 - + - +
335A LEU 3.3 0.2 - - - -
336A ILE* 1.3 77.6 - - - +
338A ASN* 1.3 61.4 + - - +
340A PHE* 3.2 9.2 + - + +
341A TYR* 2.8 55.0 + + + +
----------------------------------------------------------
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Residues in contact with ASN 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.8 4.0 - - - +
286A TRP* 3.7 16.7 - - - -
334A PHE* 3.1 53.4 + - - +
335A LEU* 3.4 17.5 - - + +
337A PHE* 1.3 76.3 - - - +
339A ILE* 1.3 69.4 + - + +
341A TYR* 4.4 2.9 - - - -
342A TRP* 2.9 57.6 + - + +
----------------------------------------------------------
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 3.0 39.9 + - + +
336A ILE* 3.2 10.5 + - + +
338A ASN* 1.3 77.7 - - + +
340A PHE* 1.3 71.6 + - + +
342A TRP* 4.4 1.0 - - - +
343A VAL* 3.1 39.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ILE* 3.2 37.5 + - + +
337A PHE* 3.6 11.2 - - + +
339A ILE* 1.3 86.5 - - + +
341A TYR* 1.3 63.2 + - - +
343A VAL* 4.0 2.8 - - - +
344A ILE* 2.9 43.9 + - + +
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Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A MET* 3.6 15.0 - - + +
228A TYR* 2.7 39.3 + + - -
282A ALA 2.8 31.0 + - - -
285A ILE* 4.3 7.9 - - + -
286A TRP* 3.7 27.9 - + + +
337A PHE* 2.8 44.8 + + + +
338A ASN* 3.8 6.3 - - - +
340A PHE* 1.3 75.0 - - - +
342A TRP* 1.3 83.2 + + - +
344A ILE* 3.7 2.5 - - - +
345A TYR* 3.3 49.9 + + - -
----------------------------------------------------------
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Residues in contact with TRP 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A MET* 3.8 17.9 - - + -
220A MET* 3.5 33.9 - - + -
224A LEU* 4.5 9.4 - - + -
228A TYR* 3.8 36.3 - + + -
286A TRP* 4.1 7.8 - + - -
338A ASN* 2.9 49.6 + - + +
339A ILE* 4.4 1.6 - - - +
341A TYR* 1.3 88.2 - + - +
343A VAL* 1.3 67.2 + - + +
345A TYR* 3.2 19.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ILE* 3.1 35.7 + - + +
340A PHE* 4.0 3.1 - - - +
342A TRP* 1.3 79.7 - - + +
344A ILE* 1.3 68.9 + - + +
345A TYR 4.1 2.9 - - - +
----------------------------------------------------------
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PHE* 2.9 41.5 + - + +
341A TYR* 3.7 5.2 - - - +
342A TRP 3.3 0.2 - - - -
343A VAL* 1.3 81.7 - - + +
345A TYR* 1.3 80.4 + - + +
----------------------------------------------------------
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Residues in contact with TYR 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LYS 4.8 1.4 + - - -
144A ASN* 3.6 30.5 - - + -
147A MET* 3.6 34.0 - - + +
281A LYS 4.9 0.5 - - - -
282A ALA* 3.5 31.6 + - + -
285A ILE* 4.0 14.6 - - + +
341A TYR* 3.3 59.6 + + - +
342A TRP* 3.2 15.0 - - - +
343A VAL 3.4 3.1 - - - +
344A ILE* 1.3 94.7 - - + +
----------------------------------------------------------
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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