Contacts of the helix formed by residues 324 - 349 (chain N) in PDB entry 5A31
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 TRP 324 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297N VAL* 4.4 10.8 - - + -
300N LEU* 3.6 44.2 - - + -
301N GLY* 4.1 4.9 - - - -
304N PHE* 3.0 54.7 - + + -
321N LEU* 3.3 53.1 + - + +
322N ARG 3.2 1.0 + - - -
323N ARG* 1.3 81.9 - - + +
325N ARG* 1.3 66.9 + - - +
326N CYS 3.2 0.9 - - - -
327N HIS* 3.4 7.5 + - + +
328N VAL* 3.1 26.9 + - - +
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Residues in contact with ARG 325 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290N HIS 5.0 3.4 + - - -
293N ILE* 4.5 9.0 - - + +
294N GLU* 4.0 28.2 - - - +
297N VAL* 3.6 25.3 - - + +
321N LEU 4.4 4.4 + - - +
322N ARG* 3.1 17.8 + - - +
324N TRP* 1.3 77.9 - - - +
326N CYS* 1.3 59.4 + - - +
328N VAL* 3.3 2.6 + - - +
329N GLN* 2.9 44.2 + - - +
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Residues in contact with CYS 326 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322N ARG* 3.1 16.1 + - - +
323N ARG* 4.6 26.2 - - - +
324N TRP 3.2 0.2 - - - -
325N ARG* 1.3 79.3 - - - +
327N HIS* 1.3 64.9 + - - +
329N GLN* 3.4 11.0 + - - +
330N ARG* 3.1 38.8 + - - +
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Residues in contact with HIS 327 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262N THR* 4.7 8.4 + - - -
265N LEU* 5.8 1.3 - - + -
266N HIS* 4.0 25.3 + + - -
323N ARG 3.9 13.4 + - - +
324N TRP* 3.4 12.6 + + + +
325N ARG 3.4 0.4 - - - -
326N CYS* 1.3 78.3 - - - +
328N VAL* 1.3 75.0 + - + +
330N ARG* 3.4 20.0 - - + +
331N PHE* 3.1 30.1 + - + +
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Residues in contact with VAL 328 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265N LEU* 3.9 37.5 - - + -
269N THR* 5.6 1.8 - - + -
292N TRP* 5.5 4.0 - - + -
293N ILE* 4.0 28.0 - - + -
296N VAL* 4.6 14.8 - - + -
297N VAL* 5.1 2.7 - - + -
300N LEU* 4.8 9.6 - - + -
324N TRP 3.1 15.7 + - - +
325N ARG* 4.1 2.5 - - - +
327N HIS* 1.3 83.8 - - + +
329N GLN* 1.3 61.2 + - - +
331N PHE* 3.6 6.0 - - + +
332N PHE* 2.8 30.9 + - + +
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Residues in contact with GLN 329 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290N HIS* 4.1 21.3 - - + +
293N ILE* 4.1 25.7 - - + +
325N ARG* 2.9 33.4 + - + +
326N CYS* 3.7 10.6 - - - +
328N VAL* 1.3 76.1 - - - +
330N ARG* 1.3 58.5 + - - +
332N PHE* 3.2 2.4 + - - +
333N TYR* 2.9 58.7 + - + +
367N ARG* 4.0 14.3 + - - +
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Residues in contact with ARG 330 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323N ARG* 5.2 8.3 - - - +
326N CYS* 3.1 24.8 + - - +
327N HIS* 3.4 23.1 - - + +
329N GLN* 1.3 76.5 - - - +
331N PHE* 1.3 65.9 + - - +
333N TYR* 3.4 8.1 + - - +
334N ARG* 3.0 58.9 + - - +
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Residues in contact with PHE 331 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265N LEU* 4.1 10.5 - - + -
266N HIS* 3.2 64.6 - + + -
269N THR* 4.1 12.1 - - + -
270N ARG* 4.6 7.9 - - - -
327N HIS* 3.1 26.0 + + + +
328N VAL* 3.6 9.0 - - + +
330N ARG* 1.3 76.7 - - + +
332N PHE* 1.3 70.6 + - - +
334N ARG* 3.4 15.7 + - + +
335N ILE* 3.3 45.6 + - + +
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Residues in contact with PHE 332 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269N THR* 4.4 14.6 - - + -
273N MET* 3.1 31.4 - - + -
285N PHE 4.9 1.6 - - - -
286N LEU* 5.3 6.1 - - + -
289N PHE* 3.1 55.4 - + + -
290N HIS* 5.6 2.0 - + - -
293N ILE* 3.7 21.8 - - + -
328N VAL* 2.8 24.2 + - + +
329N GLN 3.5 2.2 - - - +
331N PHE* 1.3 77.7 - - - +
333N TYR* 1.3 97.8 + + - +
335N ILE* 3.0 11.6 + - - +
336N TYR* 3.0 34.2 + + + -
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Residues in contact with TYR 333 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286N LEU* 5.0 4.5 - - + -
290N HIS* 3.1 23.4 + + - -
293N ILE* 6.0 0.2 - - + -
329N GLN* 2.9 41.9 + - + +
330N ARG* 3.8 8.1 - - - +
332N PHE* 1.3 101.1 - + - +
334N ARG* 1.3 67.3 + - - +
336N TYR* 3.2 1.6 + + - +
337N ALA* 2.9 23.0 + - - +
363N TYR* 3.6 14.5 - + - -
364N CYS* 3.1 31.3 - - - -
367N ARG* 2.8 68.5 + - + +
368N THR 4.9 3.1 - - - +
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Residues in contact with ARG 334 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330N ARG* 3.0 62.7 + - - +
331N PHE* 3.8 10.5 - - + +
332N PHE 3.3 0.2 - - - -
333N TYR* 1.3 76.6 - - - +
335N ILE* 1.3 64.2 + - + +
337N ALA* 3.5 5.6 + - - +
338N SER* 3.1 24.3 + - - -
367N ARG 5.0 1.8 + - - -
368N THR* 4.0 33.4 + - - +
369N ASP* 4.9 11.8 + - - +
370N GLN* 3.9 9.9 - - + +
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Residues in contact with ILE 335 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266N HIS 4.6 4.3 - - - +
269N THR* 4.8 4.7 - - + -
270N ARG* 3.7 50.9 - - + +
273N MET* 3.3 21.1 - - + -
331N PHE* 3.3 51.1 - - + +
332N PHE* 3.0 7.5 + - - +
334N ARG* 1.3 76.8 - - + +
336N TYR* 1.3 63.4 + - - +
338N SER* 2.6 24.2 + - - +
339N LEU* 3.1 16.4 + - + +
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Residues in contact with TYR 336 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273N MET* 3.4 24.2 - - + +
277N CYS* 4.1 14.1 - - - -
281N TYR* 3.8 0.7 + - - -
284N SER* 2.9 20.8 + - - -
285N PHE* 4.5 12.6 - - + -
286N LEU* 4.1 14.6 - - + -
289N PHE* 5.7 0.9 - + - -
332N PHE* 3.0 24.1 + + + +
333N TYR* 3.2 5.8 + + - +
335N ILE* 1.3 75.1 - - - +
337N ALA* 1.3 64.6 + - - +
339N LEU* 3.3 2.2 + - + -
340N ARG* 2.7 74.1 + - + +
360N ASP* 3.6 30.7 - - + +
364N CYS* 4.1 19.5 - - + -
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Residues in contact with ALA 337 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333N TYR 2.9 16.6 + - - +
334N ARG* 3.7 2.5 - - - +
336N TYR* 1.3 76.2 - - - +
338N SER* 1.3 64.2 + - - +
340N ARG* 3.2 3.9 + - - +
341N ILE* 2.9 25.9 + - + +
361N LEU* 4.4 8.5 - - - -
364N CYS* 3.8 15.0 - - - +
365N LEU* 4.4 18.8 - - + -
368N THR 5.5 3.6 - - - +
370N GLN* 3.2 21.8 - - + +
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Residues in contact with SER 338 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334N ARG 3.1 14.1 + - - -
335N ILE* 2.6 28.4 + - - +
337N ALA* 1.3 74.3 - - - +
339N LEU* 1.3 62.6 + - - +
341N ILE* 3.0 19.6 + - - +
342N GLU* 3.1 23.9 + - - +
370N GLN* 3.5 18.5 + - - +
373N GLN* 5.7 2.0 - - - -
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Residues in contact with LEU 339 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270N ARG* 5.9 3.8 - - + +
273N MET* 3.8 32.3 - - + -
274N GLU* 4.1 26.9 - - + +
277N CYS* 3.8 22.4 - - + -
278N ARG* 4.8 11.8 + - - +
335N ILE* 3.1 19.8 + - + +
336N TYR* 3.9 4.3 - - + +
338N SER* 1.3 78.5 + - - +
340N ARG* 1.3 71.5 + - - +
342N GLU* 3.4 11.9 + - + +
343N GLU* 3.3 26.2 + - - +
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Residues in contact with ARG 340 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277N CYS* 3.3 33.7 + - - +
280N GLU* 4.3 6.3 - - - +
281N TYR* 5.2 1.9 - - - -
284N SER* 4.3 3.0 + - - -
285N PHE* 4.1 6.3 - - - -
336N TYR* 2.7 67.6 + - + +
339N LEU* 1.3 79.6 + - - +
341N ILE* 1.3 53.1 + - - +
343N GLU* 2.5 31.1 + - - +
344N LEU* 2.7 34.5 + - - +
347N ILE* 3.4 19.9 - - + +
357N ALA* 3.7 23.3 + - - +
361N LEU* 3.4 34.3 - - + +
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Residues in contact with ILE 341 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337N ALA* 2.9 18.6 + - + +
338N SER* 3.0 9.6 + - - +
340N ARG* 1.3 75.4 - - - +
342N GLU* 1.3 67.5 + - - +
344N LEU* 2.7 27.9 - - + +
345N PHE 3.8 1.4 + - - -
361N LEU* 3.9 12.3 - - + -
365N LEU* 5.0 1.6 - - + -
370N GLN* 3.3 36.1 - - + +
373N GLN* 5.0 3.8 - - - +
374N LEU* 3.7 43.3 - - + -
377N SER* 3.4 34.4 + - - +
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Residues in contact with GLU 342 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278N ARG* 5.9 3.8 - - - +
338N SER* 3.1 22.7 + - - +
339N LEU* 3.9 13.2 - - + +
340N ARG 3.3 0.4 - - - -
341N ILE* 1.3 88.0 - - - +
343N GLU* 1.3 63.8 + - + +
344N LEU 3.0 1.2 + - - -
345N PHE* 3.4 12.8 + - - +
346N SER* 3.8 5.7 + - - -
373N GLN* 5.2 3.3 - - - +
377N SER* 3.6 16.5 + - - -
385N ARG* 4.7 3.5 + - - -
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Residues in contact with GLU 343 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277N CYS* 5.2 0.7 - - - +
278N ARG* 2.8 53.5 + - - +
280N GLU* 2.7 38.8 - - - +
339N LEU* 3.3 12.1 + - - +
340N ARG* 2.5 30.0 + - - -
342N GLU* 1.3 79.4 - - + +
344N LEU* 1.3 49.6 - - - +
345N PHE 3.5 0.2 - - - -
346N SER* 2.7 11.3 - - - -
347N ILE* 2.0 50.9 + - + +
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Residues in contact with LEU 344 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340N ARG 2.7 17.5 + - - +
341N ILE* 2.7 19.7 - - + +
342N GLU 3.0 1.0 - - - -
343N GLU* 1.3 68.4 - - - +
345N PHE* 1.3 65.8 + - - +
347N ILE* 3.6 6.5 - - + -
348N VAL* 2.8 39.8 + - + +
358N ILE* 4.6 9.9 - - + -
361N LEU* 4.0 24.5 - - + -
374N LEU* 3.3 30.1 - - + -
378N LEU* 3.6 31.4 - - + -
407N LEU* 4.4 18.4 - - + -
410N ILE* 5.0 1.8 - - + -
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Residues in contact with PHE 345 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341N ILE 3.8 1.6 + - - -
342N GLU 3.4 6.7 + - - +
344N LEU* 1.3 84.1 - - - +
346N SER* 1.3 56.2 + - - +
348N VAL* 3.4 5.0 + - - +
349N ARG* 3.2 23.4 + - + -
378N LEU* 5.9 3.4 - - + -
381N ALA* 4.1 24.5 - - + -
382N LEU* 3.4 35.0 - - + -
385N ARG* 2.9 66.9 - - + +
386N LEU* 3.8 22.4 - - + -
399N LEU* 3.6 24.6 - - + +
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Residues in contact with SER 346 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280N GLU* 3.8 11.8 + - - +
342N GLU 3.8 1.9 + - - -
343N GLU* 2.7 20.5 + - - -
345N PHE* 1.3 83.4 - - - +
347N ILE* 1.3 61.7 + - - +
349N ARG* 3.3 20.6 + - - +
350N ASP* 3.7 9.7 - - - +
385N ARG* 3.8 16.5 + - - +
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Residues in contact with ILE 347 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280N GLU* 3.4 21.8 - - + +
340N ARG* 3.4 48.9 - - + +
343N GLU* 2.0 34.6 + - + +
344N LEU* 3.1 8.5 + - + +
346N SER* 1.3 68.0 - - - +
348N VAL* 1.3 65.1 + - + +
350N ASP* 3.5 12.4 + - - +
351N PHE* 3.7 2.7 - - + +
354N SER* 2.7 38.6 + - - +
357N ALA* 4.0 10.8 - - + -
358N ILE* 3.3 33.7 - - + -
361N LEU* 5.9 0.7 - - + -
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Residues in contact with VAL 348 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344N LEU* 2.8 32.4 + - + +
345N PHE* 3.8 5.4 - - - +
347N ILE* 1.3 82.3 - - + +
349N ARG* 1.3 49.7 + - - +
350N ASP 2.6 27.2 - - - +
351N PHE* 3.4 5.1 + - - +
358N ILE* 5.2 0.4 - - + -
399N LEU* 4.2 16.9 - - + +
402N SER* 3.6 9.2 - - - +
403N ALA* 3.4 40.4 - - + +
406N ALA* 3.7 21.8 - - + -
407N LEU* 5.1 7.0 - - + -
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Residues in contact with ARG 349 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345N PHE* 3.2 19.2 + - + +
346N SER* 3.3 18.3 + - - +
348N VAL* 1.3 70.0 - - - +
350N ASP* 1.3 65.9 + - - +
385N ARG* 5.2 3.1 - - - +
399N LEU* 4.6 14.3 - - + +
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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