Contacts of the helix formed by residues 336 - 359 (chain N) in PDB entry 1OCR
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 PRO 336 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335N SER* 1.3 86.5 - - - +
337N ALA* 1.3 58.7 + - + +
339N MET* 2.8 26.7 + - + +
340N TRP* 3.0 22.5 + - + -
394N VAL* 4.0 14.4 - - + -
405N LEU* 6.5 0.2 - - + -
407N ASP* 3.7 37.9 - - - +
410N ALA* 3.7 36.1 - - + +
411N LYS* 4.1 15.2 - - + +
414N PHE* 6.0 0.9 - - + -
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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
----------------------------------------------------------
257N ILE* 3.7 12.4 - - + +
261N TYR* 3.8 25.8 - - + +
335N SER* 3.2 2.2 + - - +
336N PRO* 1.3 81.1 - - - +
338N MET* 1.3 61.9 + - - +
340N TRP* 3.2 8.3 + - - +
341N ALA 3.0 17.2 + - - -
391N GLY* 3.6 15.7 - - - +
394N VAL* 3.5 23.8 - - + +
395N HIS* 3.9 8.3 - - + -
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Residues in contact with MET 338 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257N ILE* 4.2 6.2 - - - +
258N VAL* 4.4 18.8 - - - +
261N TYR* 3.8 18.8 - - + +
262N SER* 4.0 9.6 - - - +
327N LEU* 3.3 34.8 - - + -
332N ILE* 4.3 20.4 - - + -
333N LYS 3.6 17.9 - - - +
334N TRP* 4.7 5.4 - - + -
335N SER* 2.9 22.8 + - - +
337N ALA* 1.3 76.3 - - - +
339N MET* 1.3 59.4 + - - +
341N ALA* 3.3 2.9 + - - +
342N LEU* 3.0 46.2 + - + +
46O LEU* 4.8 0.7 - - + -
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Residues in contact with MET 339 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334N TRP* 3.8 48.2 - - + +
335N SER 3.0 9.8 + - - +
336N PRO* 2.8 14.0 + - + +
338N MET* 1.3 77.6 - - - +
340N TRP* 1.3 59.5 + - - +
342N LEU* 3.3 9.3 + - - +
343N GLY 3.1 18.5 + - - -
411N LYS* 3.9 37.2 - - + +
414N PHE* 3.5 43.0 - - + -
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Residues in contact with TRP 340 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254N ILE* 5.2 0.2 - - - -
336N PRO* 3.0 33.6 + - + +
337N ALA* 3.2 7.2 + - - +
339N MET* 1.3 75.2 - - - +
341N ALA* 1.3 57.9 + - - +
343N GLY* 3.3 1.7 + - - -
344N PHE* 2.9 28.8 + - - +
387N PHE* 3.6 56.2 - + - +
390N MET* 3.5 30.6 - - + +
391N GLY* 3.6 28.9 - - - +
394N VAL* 4.4 12.6 - - + +
410N ALA* 4.9 2.6 + - - +
413N HIS* 3.5 31.3 + + - -
414N PHE* 3.7 32.5 - + + +
417N MET* 3.9 26.0 - - + -
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Residues in contact with ALA 341 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254N ILE* 3.9 22.8 - - + +
257N ILE* 3.8 19.3 - - + -
258N VAL* 4.0 19.7 - - + -
337N ALA 3.0 12.7 + - - +
338N MET* 3.6 8.7 - - - +
339N MET 3.2 0.2 - - - -
340N TRP* 1.3 75.4 - - - +
342N LEU* 1.3 64.4 + - - +
344N PHE* 3.4 2.1 + - - +
345N ILE* 3.1 29.7 + - - +
391N GLY* 5.4 0.2 - - - -
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Residues in contact with LEU 342 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258N VAL* 5.5 0.9 - - + -
327N LEU* 4.0 34.8 - - + -
334N TRP* 3.8 22.2 - - + -
338N MET* 3.0 35.5 + - + +
339N MET* 3.3 6.3 + - - +
341N ALA* 1.3 73.4 - - - +
343N GLY* 1.3 67.5 + - - +
345N ILE* 3.3 14.7 + - + +
346N PHE* 3.2 19.9 + - - +
42O ILE* 4.6 12.8 - - + +
46O LEU* 3.7 33.0 - - + -
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Residues in contact with GLY 343 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339N MET 3.1 14.4 + - - -
340N TRP 3.7 3.1 - - - -
342N LEU* 1.3 76.3 - - - +
344N PHE* 1.3 62.3 + - - +
346N PHE* 3.1 5.2 + - - +
347N LEU* 2.9 31.0 + - - +
387N PHE* 3.9 19.1 - - - -
414N PHE* 4.8 3.3 - - - -
418N PHE* 4.7 10.5 - - - -
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Residues in contact with PHE 344 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247N ILE* 4.1 8.5 - - + -
250N GLY 4.7 2.0 - - - -
251N PHE* 3.8 27.6 - + - -
254N ILE* 3.8 36.8 - - + -
323N TRP* 3.7 26.2 - + - -
340N TRP 2.9 14.6 + - - +
341N ALA 3.5 7.2 - - - +
342N LEU 3.3 0.2 - - - -
343N GLY* 1.3 74.0 - - - +
345N ILE* 1.3 70.5 + - + +
346N PHE 3.0 0.2 + - - -
348N PHE* 2.8 46.3 + + + +
383N MET 4.0 9.9 - - - -
384N GLY* 3.5 41.1 - - - -
387N PHE* 3.8 6.7 - - + -
388N ALA* 4.2 8.1 - - + -
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Residues in contact with ILE 345 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254N ILE* 4.5 3.4 - - + -
258N VAL* 4.3 16.4 - - + -
320N VAL* 4.3 16.7 - - + +
323N TRP* 4.0 38.6 - - + -
324N LEU* 3.9 20.6 - - + -
327N LEU* 4.8 3.4 - - + -
341N ALA 3.1 16.2 + - - +
342N LEU* 3.3 20.2 + - + +
344N PHE* 1.3 85.1 - - + +
346N PHE* 1.3 60.2 + - - +
348N PHE* 4.3 1.8 - - - +
349N THR* 2.8 26.3 + - - -
38O VAL* 5.0 2.6 - - + +
42O ILE* 3.9 17.0 - - + -
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Residues in contact with PHE 346 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342N LEU 3.2 8.5 + - - +
343N GLY* 3.1 7.6 + - - +
345N ILE* 1.3 79.6 - - - +
347N LEU* 1.3 78.5 + - + +
349N THR* 2.9 23.3 + - - -
350N VAL* 3.0 32.6 + - + +
418N PHE* 5.5 6.5 - + - -
35O SER* 3.9 26.2 - - - -
38O VAL* 4.7 12.3 - - + -
39O LEU* 4.0 39.9 - - + -
42O ILE* 4.5 9.4 - - + -
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Residues in contact with LEU 347 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343N GLY 2.9 17.9 + - - +
346N PHE* 1.3 92.9 - - + +
348N PHE* 1.3 61.5 + - - +
350N VAL* 3.2 8.3 + - + +
351N GLY* 2.9 20.3 + - - -
379N TYR* 3.7 15.4 - - + +
383N MET* 3.7 41.3 - - + +
387N PHE* 3.4 38.6 - - + -
418N PHE* 3.9 22.4 - - + -
422N ASN* 4.5 12.8 - - - +
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Residues in contact with PHE 348 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247N ILE* 4.2 8.7 - - + -
251N PHE* 3.6 30.3 - + - -
316N THR* 3.7 27.1 - - + -
320N VAL* 4.5 15.5 - - + -
323N TRP* 5.2 0.7 - + - -
344N PHE* 2.8 50.4 + + + +
345N ILE* 4.3 1.6 - - - +
347N LEU* 1.3 73.6 - - - +
349N THR* 1.3 63.3 + - - +
351N GLY 3.3 0.5 + - - -
352N GLY* 2.8 26.5 + - - -
379N TYR 5.0 4.0 - - - -
380N VAL* 4.2 22.4 - - + +
383N MET 4.7 1.9 + - - -
384N GLY* 5.0 2.7 - - - -
516N HEA 4.1 40.8 - - + -
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Residues in contact with THR 349 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320N VAL* 4.0 22.7 - - - +
345N ILE 2.8 17.7 + - - -
346N PHE* 2.9 14.2 + - + -
348N PHE* 1.3 84.0 - - - +
350N VAL* 1.3 57.0 + - + +
352N GLY* 3.3 0.5 + - - -
353N LEU* 3.0 46.7 + - + +
516N HEA 4.0 24.9 - - + +
34O ILE* 4.8 0.9 - - + -
35O SER* 4.9 5.2 - - - -
38O VAL* 4.3 19.7 - - + +
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Residues in contact with VAL 350 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346N PHE* 3.0 42.9 + - + +
347N LEU* 3.2 8.0 + - - +
349N THR* 1.3 76.2 - - - +
351N GLY* 1.3 65.0 + - - +
352N GLY 3.2 0.3 + - - -
353N LEU* 3.2 8.8 + - - +
354N THR* 3.1 23.5 + - - +
379N TYR* 3.5 29.8 - - + -
426N PHE* 5.9 3.4 - - + -
429N HIS* 5.2 10.3 - - + +
35O SER* 4.9 10.8 - - - -
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Residues in contact with GLY 351 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347N LEU 2.9 11.9 + - - -
350N VAL* 1.3 77.6 - - - +
352N GLY* 1.3 59.4 + - - +
354N THR* 3.4 6.4 - - - +
355N GLY 3.2 4.0 + - - -
376N HIS* 2.8 29.4 + - - -
379N TYR* 3.5 26.0 - - - +
380N VAL* 3.5 14.4 - - - -
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Residues in contact with GLY 352 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348N PHE* 2.8 17.6 + - - -
349N THR 3.8 0.2 - - - -
351N GLY* 1.3 76.2 - - - +
353N LEU* 1.3 63.3 + - - +
355N GLY* 3.1 10.6 + - - -
356N ILE* 3.3 7.8 + - - +
376N HIS* 4.9 1.1 - - - -
380N VAL* 3.8 5.8 - - - +
516N HEA 3.6 45.5 - - - +
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Residues in contact with LEU 353 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349N THR* 3.0 39.3 + - + +
350N VAL* 3.2 6.0 + - - +
352N GLY* 1.3 71.4 - - - +
354N THR* 1.3 61.5 + - - +
355N GLY 3.0 1.6 - - - -
356N ILE* 2.8 27.1 + - + +
357N VAL* 3.2 11.2 + - - +
516N HEA 3.9 46.4 - - + -
30O ILE* 6.5 0.2 - - + -
31O VAL* 3.9 32.1 - - + +
34O ILE* 4.0 20.0 - - + -
35O SER* 4.1 19.3 - - - +
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Residues in contact with THR 354 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350N VAL* 3.1 15.2 + - - +
351N GLY* 3.4 7.9 - - - +
353N LEU* 1.3 79.8 - - - +
355N GLY* 1.3 62.6 + - - +
357N VAL* 3.2 16.8 + - - +
358N LEU* 3.3 14.2 + - - +
372N TYR* 3.5 25.4 + - + +
376N HIS* 3.1 41.5 - - + +
429N HIS* 3.6 21.5 + - - +
31O VAL* 6.3 0.9 - - - -
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Residues in contact with GLY 355 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351N GLY 3.2 2.4 + - - -
352N GLY 3.1 7.4 + - - -
353N LEU 3.0 1.2 - - - -
354N THR* 1.3 81.0 - - - +
356N ILE* 1.3 61.3 + - - +
357N VAL 3.2 0.2 - - - -
358N LEU* 3.5 3.7 + - - +
359N ALA 3.1 15.8 + - - -
376N HIS* 3.3 28.3 - - - -
516N HEA 3.3 28.2 - - - +
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Residues in contact with ILE 356 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309N THR 4.9 0.2 - - - +
310N MET* 3.7 28.2 - - + +
313N ALA* 3.9 22.9 - - + +
352N GLY 3.3 12.8 + - - +
353N LEU* 2.8 13.4 + - + +
355N GLY* 1.3 74.7 - - - +
357N VAL* 1.3 61.2 + - - +
359N ALA* 3.2 10.7 + - - +
360N ASN* 2.9 19.9 + - - -
516N HEA 3.8 46.4 - - + -
27O THR* 5.4 3.1 - - + -
73O LEU* 4.6 4.3 - - + -
76O ILE* 4.0 26.7 - - + -
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Residues in contact with VAL 357 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353N LEU 3.2 11.9 + - - +
354N THR* 3.3 10.5 - - - +
356N ILE* 1.3 76.7 - - + +
358N LEU* 1.3 60.9 + - - +
360N ASN* 2.7 31.2 + - - +
363N LEU* 4.0 18.3 - - + +
367N LEU* 3.8 23.1 - - + -
372N TYR* 3.7 23.6 - - + +
24O HIS* 4.4 10.5 - - + +
27O THR* 3.7 24.5 - - + -
28O LEU* 5.6 3.8 - - + +
31O VAL* 4.3 11.9 - - + -
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Residues in contact with LEU 358 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293N PHE* 4.2 2.1 - - - -
354N THR 3.3 9.6 + - - +
355N GLY* 3.7 8.3 - - - +
356N ILE 3.2 0.4 - - - -
357N VAL* 1.3 77.9 - - - +
359N ALA* 1.3 61.4 + - - +
360N ASN 3.1 3.3 + - - -
364N ASP* 3.7 29.2 - - - +
367N LEU* 3.9 24.9 - - + -
372N TYR* 3.6 25.1 - - + -
373N VAL* 4.2 15.3 - - + -
376N HIS* 3.9 40.4 - - + -
516N HEA 3.4 37.6 - - + +
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Residues in contact with ALA 359 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293N PHE* 3.6 6.1 - - - -
306N THR* 2.8 29.2 - - - +
309N THR* 3.8 26.5 - - + -
310N MET* 4.0 20.6 - - + -
355N GLY 3.1 11.8 + - - +
356N ILE* 3.4 14.1 - - - +
357N VAL 3.1 1.6 + - - -
358N LEU* 1.3 75.9 - - - +
360N ASN* 1.3 62.3 + - - +
361N SER 3.1 1.0 + - - -
516N HEA 3.4 9.4 - - + -
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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