Contacts of the helix formed by residues 366 - 393 (chain A) in PDB entry 4IKV
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 366 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLN 3.6 3.1 + - - +
365A PRO* 1.3 75.4 - - - +
367A ILE* 1.3 60.0 + - - +
368A PRO* 3.5 11.1 - - - +
369A GLN* 2.9 35.1 + - - +
370A LYS* 2.9 26.3 + - - +
485A ALA* 4.9 4.2 + - - +
489A GLY* 5.2 7.9 - - - -
613A PG4 3.3 9.2 - - - -
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A THR* 1.3 76.1 - - - +
368A PRO* 1.4 68.4 - - + +
370A LYS* 3.0 7.5 + - - +
371A PHE* 3.0 25.7 + - + -
419A VAL* 3.9 23.6 - - + -
422A SER* 3.6 26.9 - - - +
423A ALA* 3.6 27.8 - - + +
426A LYS* 3.7 24.5 - - + -
492A MET* 4.0 12.1 - - + -
613A PG4 3.4 29.1 + - - +
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Residues in contact with PRO 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.2 17.5 - - + -
366A THR* 3.5 12.1 - - - +
367A ILE* 1.4 95.9 - - + +
369A GLN* 1.3 59.7 + - - +
371A PHE* 3.3 4.2 + - - +
372A ALA* 3.1 21.8 + - - +
481A LEU* 3.9 6.3 - - + +
485A ALA* 3.7 24.7 - - + +
488A ILE* 3.5 31.4 - - + -
489A GLY* 3.6 16.4 - - - +
492A MET* 3.9 13.9 - - + -
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Residues in contact with GLN 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLN 4.7 0.3 - - - +
365A PRO* 3.3 18.9 - - + +
366A THR* 2.9 39.5 + - - +
367A ILE 3.2 0.6 - - - -
368A PRO* 1.3 79.5 - - - +
370A LYS* 1.3 56.6 + - - +
372A ALA* 3.2 8.7 + - - +
373A LEU* 2.9 34.4 + - + +
482A LEU* 4.1 9.9 - - + +
485A ALA* 3.9 9.3 - - + +
486A PRO* 5.7 2.2 - - - +
612A OLB 2.9 44.8 + - - +
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Residues in contact with LYS 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TRP* 3.8 40.9 - - + +
364A GLN* 2.8 25.7 + - - -
365A PRO* 3.5 17.5 - - + -
366A THR 2.9 12.3 + - - +
367A ILE 3.0 7.8 + - - +
369A GLN* 1.3 73.9 - - - +
371A PHE* 1.3 65.0 + - - +
373A LEU* 3.4 7.1 + - + -
374A GLY 3.0 18.2 + - - -
415A CYS* 3.4 32.8 - - + +
416A LEU 3.8 0.3 + - - -
419A VAL* 4.0 19.7 - - + +
613A PG4 3.1 42.0 + - - +
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Residues in contact with PHE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 5.5 2.9 - + - -
298A LEU* 3.3 46.2 - - + -
301A ALA* 4.3 4.1 - - + +
302A SER* 4.1 13.2 - - - -
367A ILE* 3.0 24.1 + - + -
368A PRO 3.4 9.2 - - - +
370A LYS* 1.3 75.6 - - - +
372A ALA* 1.3 63.7 + - - +
374A GLY* 3.1 3.3 + - - -
375A LEU* 3.0 21.5 + - - +
416A LEU* 3.7 31.4 - - + +
419A VAL* 3.8 22.4 - - + -
420A GLY* 3.9 15.5 - - - -
423A ALA* 3.7 31.9 - - + -
440A TRP* 4.3 6.1 - + - -
481A LEU* 3.7 13.2 - - + +
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Residues in contact with ALA 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A PRO 3.1 10.3 + - - +
369A GLN 3.3 9.0 - - - +
371A PHE* 1.3 79.8 - - - +
373A LEU* 1.3 57.6 + - - +
375A LEU* 3.2 7.3 + - - +
376A LEU* 2.9 33.9 + - - +
478A GLY* 3.6 21.0 - - - +
481A LEU* 3.7 10.5 - - + +
482A LEU* 3.7 29.8 - - + +
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TRP* 5.2 1.6 - - + -
365A PRO* 3.9 29.4 - - + -
369A GLN* 2.9 20.3 + - + +
370A LYS* 3.7 7.2 - - - +
371A PHE 3.3 0.2 - - - -
372A ALA* 1.3 75.0 - - + +
374A GLY* 1.3 62.6 + - - +
376A LEU* 3.3 12.9 + - + +
377A PHE* 3.1 33.4 + - + -
415A CYS* 3.9 16.6 - - - -
482A LEU* 5.4 8.5 - - + -
609A OLA 4.6 20.4 - - + -
610A OLA 3.6 37.7 - - + -
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 3.4 17.8 - - - -
370A LYS 3.0 13.8 + - - -
371A PHE 3.1 4.4 + - - -
373A LEU* 1.3 77.4 - - - +
375A LEU* 1.3 57.9 + - - +
377A PHE* 3.4 2.1 + - - +
378A ALA 2.9 23.2 + - - -
412A GLY* 3.4 27.6 - - - -
415A CYS* 3.9 1.3 - - - +
416A LEU* 4.1 6.5 - - - -
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ALA* 3.8 29.2 - - + +
304A MET* 3.4 28.7 - - + -
305A PHE* 3.6 23.5 - - + +
371A PHE 3.0 11.7 + - - +
372A ALA* 3.2 8.0 + - - +
374A GLY* 1.3 73.6 - - - +
376A LEU* 1.3 58.7 + - - +
378A ALA* 3.2 4.8 + - + +
379A GLY* 2.9 27.7 + - - -
416A LEU* 4.7 0.6 - - - +
474A ALA* 3.4 20.5 - - + +
477A LEU* 3.7 17.9 - - + +
478A GLY* 3.6 24.2 - - - +
481A LEU* 5.5 1.1 - - + -
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Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ALA 2.9 20.9 + - - +
373A LEU* 3.7 20.4 - - + +
375A LEU* 1.3 74.8 - - - +
377A PHE* 1.3 58.8 + - - +
379A GLY 3.3 0.9 + - - -
380A LEU* 2.9 28.9 + - - +
474A ALA 4.9 0.2 - - - -
475A LEU* 3.5 43.4 - - + +
478A GLY* 4.0 3.1 - - - -
479A LEU* 3.7 23.6 - - + +
482A LEU* 4.2 25.1 - - + -
610A OLA 3.8 27.7 - - + +
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Residues in contact with PHE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 3.1 26.3 + - + -
376A LEU* 1.3 73.9 - - - +
378A ALA* 1.3 67.2 + - - +
380A LEU* 3.2 8.8 + - + -
381A SER* 2.9 20.6 + - - -
408A ILE* 3.2 27.3 - - + +
411A LEU* 3.8 28.9 - - + -
412A GLY* 3.5 33.9 - - - +
415A CYS* 4.2 8.3 - - - -
609A OLA 3.9 35.4 - - + -
610A OLA 3.8 39.9 - - + -
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A PHE* 3.6 24.8 - - + -
308A ILE* 3.7 34.0 - - + +
309A GLN 5.7 0.2 - - - +
374A GLY 2.9 17.8 + - - +
375A LEU* 3.5 9.6 - - + +
377A PHE* 1.3 76.3 - - - +
379A GLY* 1.3 62.2 + - - +
381A SER* 2.7 26.4 + - - -
382A PHE 3.5 2.4 + - - -
409A VAL* 5.0 4.9 - - + +
412A GLY* 5.0 0.2 - - - -
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Residues in contact with GLY 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 4.2 0.4 - - - -
375A LEU 2.9 12.1 + - - -
376A LEU 3.7 2.7 - - - -
378A ALA* 1.3 76.9 - - - +
380A LEU* 1.3 61.5 + - - +
382A PHE 3.2 3.3 + - - -
383A ILE* 3.1 22.3 + - - +
471A GLY* 3.4 30.1 - - - -
474A ALA* 3.6 12.0 - - - +
475A LEU* 4.2 8.1 - - - -
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU 2.9 16.4 + - - +
377A PHE* 3.5 13.2 - - + +
379A GLY* 1.3 75.6 - - - +
381A SER* 1.3 63.2 + - - +
383A ILE* 3.1 15.8 + - + -
384A VAL* 2.9 33.2 + - + +
408A ILE* 4.0 27.6 - - + -
475A LEU* 3.9 4.0 - - + +
610A OLA 3.9 37.0 - - + -
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Residues in contact with SER 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 3.8 6.6 - - - +
377A PHE 2.9 11.9 + - - -
378A ALA 2.7 18.1 + - - -
380A LEU* 1.3 76.6 - - - +
382A PHE* 1.3 62.5 + - - +
384A VAL* 3.6 4.2 + - - +
385A ILE* 3.3 14.9 + - - +
405A SER* 3.0 45.6 + - - +
408A ILE* 4.0 8.7 - - - -
409A VAL* 3.1 26.4 - - - +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A ILE* 3.9 31.2 - - + -
311A GLN* 3.4 35.4 - - + -
315A ILE* 5.5 0.4 - - + -
316A LEU* 4.8 17.3 - - + -
378A ALA 3.5 2.0 + - - +
379A GLY 3.2 9.0 + - - +
380A LEU 3.2 0.2 - - - -
381A SER* 1.3 82.6 + - - +
383A ILE* 1.3 66.0 + - - +
384A VAL 3.2 0.2 - - - -
385A ILE* 3.2 20.5 - - + +
386A LEU* 3.3 6.9 + - - +
405A SER* 5.0 1.8 - - - -
409A VAL* 6.2 0.4 - - + -
466A TYR* 4.2 3.6 - + - -
467A PHE* 3.6 62.0 - + - +
470A ILE* 3.7 31.0 - - + -
471A GLY* 3.7 5.6 - - - -
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Residues in contact with ILE 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLY 3.1 14.2 + - - +
380A LEU* 3.1 17.1 + - + +
382A PHE* 1.3 76.5 - - - +
384A VAL* 1.3 64.6 + - + +
386A LEU* 3.3 33.2 - - + +
387A VAL* 3.5 14.1 - - + +
468A GLY* 4.2 4.3 - - - +
471A GLY* 4.3 1.6 - - - -
472A GLY 4.2 17.3 - - - +
475A LEU* 3.9 17.7 - - + -
611A OLA 3.8 39.3 - - + -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 2.9 30.1 + - + +
381A SER* 3.7 7.0 - - - +
382A PHE 3.2 0.2 - - - -
383A ILE* 1.3 77.9 - - + +
385A ILE* 1.3 61.0 + - - +
387A VAL* 3.3 17.2 + - - +
388A PRO* 3.4 10.6 - - - +
401A TRP* 3.7 28.8 - - + +
404A LEU* 3.8 29.6 - - + -
405A SER* 4.6 3.4 - - - +
408A ILE* 3.7 21.3 - - + -
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LEU* 4.3 15.9 - - + -
319A TYR* 3.7 46.3 + - + +
381A SER 3.3 7.2 + - - +
382A PHE* 3.2 26.0 - - + +
384A VAL* 1.3 80.8 - - - +
386A LEU* 1.3 62.4 + - - +
387A VAL 3.4 0.3 + - - -
388A PRO* 3.4 10.6 - - - +
389A GLY 4.7 0.7 + - - -
401A TRP* 4.0 25.4 - - + +
402A LEU* 4.0 14.4 - - + +
405A SER* 4.1 7.4 - - - +
463A GLU* 5.2 0.5 - - - +
467A PHE* 3.6 28.9 - - + -
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A PHE 3.3 12.9 + - - +
383A ILE* 3.3 25.8 - - + +
385A ILE* 1.3 78.7 - - - +
387A VAL* 1.3 72.6 + - + +
388A PRO 3.6 0.4 - - - -
389A GLY* 3.7 1.9 + - - -
390A HIS* 3.2 26.6 + - + +
463A GLU* 5.1 5.1 - - - +
464A THR* 4.1 32.1 + - + +
467A PHE* 3.8 20.2 - - + -
468A GLY* 3.5 35.4 - - - +
608A OLA 5.4 1.8 - - + -
611A OLA 5.2 5.6 - - + -
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ILE* 3.5 21.8 - - + +
384A VAL* 3.3 7.6 + - - +
385A ILE 3.2 0.4 - - - -
386A LEU* 1.3 85.4 - - + +
388A PRO* 1.3 74.8 - - + +
390A HIS* 3.1 5.6 + - + +
391A LEU* 2.9 47.3 + - + +
401A TRP* 4.1 19.3 - - + -
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Residues in contact with PRO 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TYR* 4.0 9.0 - - - +
384A VAL 3.4 13.9 - - - +
385A ILE* 3.4 11.9 - - + +
387A VAL* 1.3 93.8 - - + +
389A GLY* 1.3 57.5 + - - +
391A LEU* 3.8 4.7 - - + +
392A SER* 2.9 33.4 + - - -
397A VAL* 3.8 16.8 - - + +
401A TRP* 3.5 52.0 - - + +
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Residues in contact with GLY 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A TYR* 4.6 2.0 + - - -
323A ARG* 3.6 26.0 + - - -
385A ILE 4.7 0.2 + - - -
386A LEU 3.7 3.0 + - - -
387A VAL 3.3 0.8 - - - -
388A PRO* 1.3 82.0 - - - +
390A HIS* 1.3 60.1 + - - +
392A SER* 3.0 18.7 + - - -
393A GLY* 3.3 10.0 + - - -
394A GLY 4.2 1.7 + - - -
397A VAL* 3.8 4.7 - - - +
463A GLU* 4.1 9.6 - - - -
464A THR* 5.4 1.8 - - - -
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LEU* 3.2 25.3 + - + +
387A VAL* 3.1 8.1 + - + +
389A GLY* 1.3 75.9 - - - +
391A LEU* 1.3 76.0 + - + +
393A GLY* 3.9 6.8 + - - -
464A THR* 4.3 27.3 + - + +
----------------------------------------------------------
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL* 2.9 38.5 + - + +
388A PRO* 3.8 5.2 - - + +
390A HIS* 1.3 90.1 - - + +
392A SER* 1.3 66.0 + - - +
393A GLY* 4.6 0.2 - - - -
401A TRP* 5.7 5.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ARG* 5.1 0.2 + - - -
388A PRO 2.9 15.3 + - - -
389A GLY* 3.0 16.5 + - - -
391A LEU* 1.3 80.3 - - - +
393A GLY* 1.3 66.1 + - - +
394A GLY 3.1 26.3 + - - +
395A GLY 4.4 3.2 + - - -
396A LEU 5.6 2.0 - - - -
397A VAL* 4.6 6.6 - - - +
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Residues in contact with GLY 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A GLY 3.3 9.9 + - - -
390A HIS 3.9 5.1 + - - -
391A LEU 3.4 2.4 - - - -
392A SER* 1.3 80.9 + - - +
394A GLY* 1.3 55.7 + - - +
----------------------------------------------------------
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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