Contacts of the helix formed by residues 317 - 349 (chain A) in PDB entry 5OC9
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 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU 5.4 0.2 - - - -
313A ARG* 3.4 14.9 + - + +
316A LEU* 1.3 88.9 - - + +
318A SER* 1.3 63.7 - - - +
320A PRO* 3.4 8.7 - - - +
321A PHE* 3.4 17.6 + - + +
384A LEU* 4.3 11.2 - - + -
387A TRP* 3.6 35.2 - - + -
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ARG 3.0 12.4 + - - -
314A ILE* 3.4 9.6 - - - -
317A VAL* 1.3 73.6 - - - +
319A LEU* 1.3 65.8 + - - +
321A PHE* 3.2 8.2 + - - +
322A VAL* 3.0 29.1 + - - +
384A LEU* 3.7 21.2 - - - +
387A TRP* 4.6 1.0 - - - -
388A GLU* 2.7 31.8 + - - +
403A LYS* 3.3 15.0 + - - +
710A 79M 4.0 3.4 - - - -
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 2.8 22.3 + - + +
315A TYR* 3.9 34.8 - - + +
318A SER* 1.3 70.9 - - - +
320A PRO* 1.4 68.1 - - + +
322A VAL* 3.3 6.5 + - - +
323A CYS* 3.2 36.7 + - - -
710A 79M 4.0 40.8 + - + +
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Residues in contact with PRO 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TYR 3.7 6.5 - - - +
316A LEU* 3.3 25.8 - - - +
317A VAL 3.4 17.0 - - - +
319A LEU* 1.4 95.0 - - + +
321A PHE* 1.4 55.1 + - - +
323A CYS* 3.4 8.6 + - + +
324A LEU* 3.0 38.2 + - + +
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Residues in contact with PHE 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A VAL* 3.4 13.6 + - + +
318A SER 3.2 9.8 + - - +
320A PRO* 1.4 75.0 - - - +
322A VAL* 1.4 71.5 + - + +
324A LEU* 3.2 17.1 + - + +
325A CYS* 3.1 43.4 + - - -
377A TYR* 4.3 9.0 - + - -
380A ALA* 3.7 22.2 - - + -
381A ALA* 5.2 1.1 - - - -
384A LEU* 3.5 25.8 - - + -
712A 79M 3.6 36.3 - - + -
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A SER 3.0 18.9 + - - +
319A LEU* 3.8 5.8 - - - +
321A PHE* 1.4 80.9 - - + +
323A CYS* 1.4 60.1 + - - +
325A CYS* 3.4 2.8 + - - +
326A LEU* 3.0 36.8 + - + +
377A TYR* 3.4 30.1 - - + +
403A LYS* 4.1 24.9 - - + +
406A VAL* 3.9 23.6 - - + -
710A 79M 4.2 21.3 - - + +
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Residues in contact with CYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LEU* 3.2 30.9 + - - +
320A PRO* 3.6 11.4 - - + +
321A PHE 3.3 0.2 - - - -
322A VAL* 1.4 76.6 - - - +
324A LEU* 1.3 59.1 + - + +
326A LEU* 3.6 1.1 + - - -
327A TYR* 3.1 24.1 + - - +
710A 79M 3.4 56.2 - - + +
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Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A PRO* 3.0 28.4 + - + +
321A PHE* 3.2 17.2 + - + +
323A CYS* 1.3 76.4 - - - +
325A CYS* 1.4 57.4 + - - +
327A TYR* 3.3 12.8 + - + +
328A PHE* 2.9 29.4 + - - +
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Residues in contact with CYS 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PHE* 3.1 48.7 + - - +
322A VAL 3.4 2.0 + - - +
324A LEU* 1.4 73.1 - - - +
326A LEU* 1.3 55.0 + - - +
328A PHE* 3.5 8.1 + - - +
329A SER* 2.7 37.5 + - - -
377A TYR* 3.6 34.3 - - + -
407A PHE* 3.8 9.0 - - + -
712A 79M 3.7 18.2 - - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 3.0 29.0 + - + +
323A CYS* 3.7 6.5 - - - +
324A LEU 3.3 0.2 - - - -
325A CYS* 1.3 75.3 - - - +
327A TYR* 1.4 62.0 + - - +
329A SER* 3.5 8.5 - - - -
330A LEU* 3.4 27.8 + - - +
377A TYR* 4.9 0.7 - - - +
406A VAL* 4.1 17.9 - - + +
407A PHE* 4.0 37.9 - - + +
410A LEU* 3.7 25.1 - - + +
710A 79M 3.9 49.6 - - + -
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Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A CYS 3.1 17.9 + - - +
324A LEU* 3.6 12.8 - - + +
326A LEU* 1.4 73.6 - - - +
328A PHE* 1.3 62.2 + - + +
330A LEU* 3.3 8.8 + - + +
331A TYR* 3.0 40.1 + + + +
710A 79M 3.6 44.3 - - + +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LEU 2.9 17.7 + - - +
325A CYS* 3.7 6.7 - - - +
326A LEU 3.4 0.2 - - - -
327A TYR* 1.3 75.8 - - - +
329A SER* 1.4 57.9 + - - +
331A TYR* 3.2 22.5 + + - +
332A VAL* 2.9 54.9 + - + +
369A VAL* 6.2 0.4 - - + -
373A MET* 3.7 18.4 - - + -
712A 79M 3.6 26.2 - - + -
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A CYS 2.7 21.8 + - - -
326A LEU* 3.5 9.3 - - - +
327A TYR 3.3 0.2 - - - -
328A PHE* 1.4 76.0 - - - +
330A LEU* 1.4 56.3 + - - +
332A VAL* 3.6 2.6 + - - +
333A MET* 3.0 28.3 + - - +
366A TYR* 4.5 2.9 + - - -
370A ILE* 5.7 0.2 - - - +
373A MET* 3.6 11.8 - - - +
407A PHE* 3.3 24.3 + - - -
410A LEU* 3.8 16.8 - - - +
411A ASN* 3.3 21.0 + - - +
414A ALA* 6.2 0.2 - - - -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU 3.4 16.1 + - - +
327A TYR* 3.3 9.5 + - + +
329A SER* 1.4 75.6 - - - +
331A TYR* 1.3 59.9 + - - +
333A MET* 3.6 12.5 - - + +
334A MET* 3.1 35.2 + - + +
410A LEU* 3.8 25.4 - - + -
414A ALA* 4.1 14.8 - - + -
710A 79M 3.8 37.7 - - + -
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Residues in contact with TYR 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 3.0 32.5 + + + +
328A PHE* 3.2 31.6 + + + +
330A LEU* 1.3 74.8 - - - +
332A VAL* 1.4 62.0 + - - +
334A MET* 3.4 11.1 + - + +
335A ILE* 3.3 46.0 + - + +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PHE* 2.9 53.9 + - + +
329A SER 3.9 4.5 - - - +
331A TYR* 1.4 71.5 - - - +
333A MET* 1.4 65.5 + - - +
335A ILE* 3.1 28.1 + - + +
336A TYR* 3.2 12.1 + - - +
366A TYR* 3.7 21.4 - - + -
369A VAL* 3.9 24.7 - - + -
370A ILE* 5.1 0.2 - - + -
373A MET* 4.2 11.0 - - - -
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Residues in contact with MET 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER 3.0 17.6 + - - +
330A LEU* 3.6 14.6 - - + +
332A VAL* 1.4 76.7 - - - +
334A MET* 1.4 90.2 + - + +
336A TYR* 3.1 5.0 + - - +
337A PHE* 3.1 60.7 + - + -
366A TYR* 3.3 31.2 - - + +
414A ALA* 3.6 39.9 - - + +
415A SER* 4.2 5.8 - - - +
418A TYR* 3.8 13.2 - - + -
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Residues in contact with MET 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.1 19.5 + - + +
331A TYR* 3.5 13.5 - - + +
333A MET* 1.4 94.0 - - + +
335A ILE* 1.4 57.6 + - + +
337A PHE* 3.5 5.2 + - + +
338A ASP* 3.0 47.3 + - - +
418A TYR* 3.8 29.8 - - + +
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Residues in contact with ILE 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TYR* 3.4 49.1 - - + +
332A VAL* 3.1 21.5 + - + +
334A MET* 1.4 75.8 - - + +
336A TYR* 1.4 50.5 + - - +
338A ASP* 3.2 11.2 + - + +
339A MET* 2.8 53.0 + - + +
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Residues in contact with TYR 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A VAL 3.2 4.4 + - - -
333A MET 3.1 6.6 + - - +
335A ILE* 1.4 76.8 - - - +
337A PHE* 1.3 94.6 + + - +
339A MET* 3.1 10.9 + - - +
340A GLU* 2.9 59.9 + - + +
362A PRO* 3.5 20.0 - - + -
363A SER* 3.5 33.7 + - - -
366A TYR* 3.6 47.8 - + + -
415A SER* 5.2 2.7 - - - -
419A ILE* 5.9 1.3 - - + -
428A LEU* 6.1 0.7 - - - +
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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
----------------------------------------------------------
333A MET* 3.1 59.6 + - + +
334A MET* 3.5 7.6 + - + +
335A ILE 3.4 0.2 - - - -
336A TYR* 1.3 96.8 - + - +
338A ASP* 1.4 60.1 + - - +
340A GLU* 4.0 11.0 + - + +
341A VAL* 3.3 24.9 + - - +
415A SER* 3.6 33.2 - - - -
418A TYR* 3.6 41.7 - + + +
419A ILE* 3.7 20.0 - - + -
423A LEU* 3.8 9.9 - - + -
428A LEU* 5.3 2.7 - - + -
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Residues in contact with ASP 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A MET* 3.0 36.1 + - - +
335A ILE* 3.4 10.7 - - + +
337A PHE* 1.4 77.1 - - - +
339A MET* 1.4 62.4 + - - +
340A GLU 3.4 0.7 - - - -
341A VAL* 3.5 11.8 - - - +
342A TRP* 3.3 19.6 + - - +
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Residues in contact with MET 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ILE* 2.8 39.8 + - + +
336A TYR* 3.1 10.1 + - - +
338A ASP* 1.4 75.4 - - - +
340A GLU* 1.4 57.6 + - - +
341A VAL 3.2 0.9 - - - -
342A TRP* 3.4 8.0 + - + +
343A ALA* 3.0 29.5 + - - +
361A VAL* 6.0 0.7 - - - -
362A PRO* 3.8 31.0 - - + +
365A ILE* 4.4 28.3 - - + -
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Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TYR* 2.9 53.6 + - + +
337A PHE* 4.1 13.1 - - + +
338A ASP 3.4 0.2 - - - -
339A MET* 1.4 74.4 - - - +
341A VAL* 1.4 57.3 + - + +
343A ALA* 3.9 5.9 - - - +
344A LEU* 3.2 27.4 + - - +
359A LEU 3.8 7.4 - - - +
362A PRO* 3.4 22.1 - - + +
363A SER* 3.5 11.4 + - - -
428A LEU* 5.3 12.5 - - - +
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Residues in contact with VAL 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE 3.3 17.5 - - - +
338A ASP* 3.5 13.9 - - - +
339A MET 3.2 0.2 - - - -
340A GLU* 1.4 75.6 - - + +
342A TRP* 1.4 59.1 + - - +
344A LEU* 3.3 7.6 + - - +
345A GLY* 3.1 24.3 + - - -
----------------------------------------------------------
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Residues in contact with TRP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ASP 3.3 10.8 + - - +
339A MET* 3.4 11.6 + - + +
341A VAL* 1.4 79.1 - - - +
343A ALA* 1.4 60.4 + - - +
345A GLY* 3.7 1.5 + - - +
346A LEU* 3.3 23.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A MET 3.0 16.8 + - - +
340A GLU* 3.9 7.0 - - - +
341A VAL 3.3 0.2 - - - -
342A TRP* 1.4 73.9 - - - +
344A LEU* 1.4 62.0 + - - +
346A LEU* 3.8 6.6 + - - +
347A HIS* 3.4 15.2 + - - +
355A THR 5.5 0.2 - - - +
358A LEU* 4.0 28.8 - - + +
359A LEU* 3.5 22.3 - - + +
362A PRO* 4.1 14.8 - - + -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU 3.2 18.4 + - - +
341A VAL* 3.3 8.5 + - - +
343A ALA* 1.4 74.4 - - - +
345A GLY* 1.3 59.6 + - - +
347A HIS* 3.4 4.7 + - - +
348A GLU* 3.1 27.1 + - - +
359A LEU* 4.5 9.6 - - + +
----------------------------------------------------------
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Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A VAL 3.1 14.4 + - - -
342A TRP* 3.7 2.4 + - - -
343A ALA 3.5 0.2 - - - -
344A LEU* 1.3 75.9 - - - +
346A LEU* 1.4 56.1 + - - +
348A GLU* 3.5 7.9 + - - +
349A ASN* 2.9 38.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A TRP 3.3 17.5 + - - +
343A ALA 3.9 5.8 - - - +
345A GLY* 1.4 72.8 - - - +
347A HIS* 1.4 63.9 + - - +
349A ASN* 3.4 24.5 + - - +
355A THR* 3.9 12.4 - - + +
358A LEU* 4.0 23.6 - - + -
----------------------------------------------------------
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Residues in contact with HIS 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ALA 3.4 11.6 + - - +
344A LEU* 3.4 9.1 + - - +
345A GLY 3.4 0.4 - - - -
346A LEU* 1.4 76.0 - - - +
348A GLU* 1.4 64.9 + - - +
349A ASN 3.5 3.6 + - - -
352A SER* 4.5 10.2 + - - -
355A THR* 3.1 39.2 + - - +
356A SER* 3.9 14.4 - - - -
358A LEU* 5.8 0.2 - - - +
359A LEU* 3.4 37.2 - - + +
----------------------------------------------------------
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU 3.1 13.3 + - - +
345A GLY* 3.6 13.2 - - - +
346A LEU 3.4 0.2 - - - -
347A HIS* 1.4 78.3 - - - +
349A ASN* 1.4 63.9 + - - +
----------------------------------------------------------
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Residues in contact with ASN 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A GLY* 2.9 23.8 + - - +
346A LEU* 3.4 18.3 + - - +
347A HIS 3.2 5.1 - - - -
348A GLU* 1.4 82.4 - - - +
355A THR* 5.7 3.4 - - - -
----------------------------------------------------------
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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
------------------------------------------------------------
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