Contacts of the helix formed by residues 364 - 388 (chain A) in PDB entry 5HJP
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 364 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A SER 4.6 1.8 - - - +
363A LEU* 1.4 93.7 - - + +
365A LEU* 1.3 59.9 + - - +
366A ASP* 3.3 3.6 - - + +
367A ASP* 3.1 33.3 + - - +
368A GLN* 3.1 24.4 + - - +
455A SER* 4.3 7.9 - - - +
456A ASN* 5.8 4.9 - - + +
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Residues in contact with LEU 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A LEU 3.4 3.1 + - - -
364A PRO* 1.3 71.0 - - - +
366A ASP* 1.3 63.7 + - - +
368A GLN* 3.7 8.2 + - - +
369A VAL* 3.4 26.3 + - - +
544A HIS* 3.4 41.7 - - + +
547A LEU* 3.5 36.2 - - + +
548A GLN* 4.1 21.1 - - + +
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Residues in contact with ASP 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A PRO* 3.3 3.8 - - + +
365A LEU* 1.3 80.4 - - - +
367A ASP* 1.3 61.0 + - - +
369A VAL* 3.4 9.2 + - - +
370A ILE* 3.1 40.0 + - + +
455A SER* 6.3 1.3 - - - -
544A HIS* 5.2 8.8 + - - -
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Residues in contact with ASP 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 5.0 10.2 - - + +
364A PRO* 3.1 33.6 + - + +
366A ASP* 1.3 75.5 - - - +
368A GLN* 1.4 54.2 + - - +
370A ILE* 3.3 11.1 + - - +
371A LEU* 2.8 41.2 + - + +
454A LEU* 3.7 18.3 - - + +
455A SER* 2.7 48.5 + - - -
456A ASN* 4.0 7.8 + - - +
460A VAL* 5.5 1.3 - - + -
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A LYS* 5.7 2.4 - - - +
360A PHE* 2.8 54.8 + - + +
361A SER* 3.1 19.2 + - - +
363A LEU* 2.7 27.2 + - + +
364A PRO 3.1 14.7 + - - +
365A LEU* 3.8 13.3 - - - +
367A ASP* 1.4 71.9 - - - +
369A VAL* 1.4 59.6 + - - +
371A LEU* 4.9 0.7 - - - -
372A LEU* 3.2 36.4 + - - +
547A LEU* 3.5 33.8 - - + +
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Residues in contact with VAL 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU 3.4 14.5 + - - +
366A ASP* 3.4 12.9 + - - +
368A GLN* 1.4 74.0 - - - +
370A ILE* 1.3 58.5 + - + +
372A LEU* 3.2 1.7 + - - -
373A ARG* 2.8 52.1 + - - +
543A LEU* 3.7 27.8 - - + +
544A HIS* 4.7 21.1 - - + +
547A LEU* 3.7 15.9 - - + -
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A ASP* 3.1 31.3 + - + +
367A ASP* 3.5 15.3 - - - +
369A VAL* 1.3 78.6 - - + +
371A LEU* 1.4 55.6 + - - +
373A ARG* 3.3 5.9 + - - +
374A ALA* 3.0 29.3 + - - +
451A ALA* 3.6 20.2 - - + -
452A LYS 3.3 24.5 - - - +
453A GLY* 3.3 29.4 - - - +
454A LEU* 3.8 12.8 - - + -
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360A PHE* 3.9 26.2 - - + -
363A LEU* 4.0 22.4 - - + -
367A ASP 2.8 23.7 + - - +
368A GLN 4.1 3.8 - - - +
370A ILE* 1.4 69.3 - - - +
372A LEU* 1.3 63.6 + - - +
374A ALA* 3.6 4.0 + - - +
375A GLY* 3.3 18.7 + - - -
446A LEU* 3.4 35.3 - - + +
447A PHE* 4.3 5.4 - - + -
448A ASN* 3.4 29.6 - - + +
451A ALA* 4.1 5.4 - - + -
454A LEU* 4.0 12.1 - - + -
460A VAL* 3.9 17.5 - - + -
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.9 35.0 - - + +
351A VAL* 4.3 12.3 - - + -
354A ALA* 4.0 17.9 - - + -
360A PHE* 4.2 16.6 - - + -
368A GLN 3.2 21.7 + - - +
369A VAL 3.9 2.7 - - - +
371A LEU* 1.3 74.2 - - - +
373A ARG* 1.3 59.5 + - - +
375A GLY 4.8 0.2 - - - +
376A TRP* 3.1 36.0 + - - +
379A LEU* 4.8 1.3 - - + -
446A LEU* 4.2 10.3 - - + -
525A MET* 4.8 2.4 - - - +
543A LEU* 4.2 28.0 - - + -
547A LEU* 4.2 18.4 - - + -
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Residues in contact with ARG 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A VAL* 2.8 34.7 + - - +
370A ILE* 3.8 5.8 - - - +
372A LEU* 1.3 77.5 - - - +
374A ALA* 1.3 58.0 + - - +
376A TRP* 3.0 26.7 + - + -
377A ASN* 4.7 0.7 - - - +
524A GLU* 3.8 10.4 + - - +
525A MET* 3.4 28.4 + - + +
527A GLU 2.8 29.5 + - - -
528A ALA* 3.5 21.5 - - - +
543A LEU* 3.8 16.4 - - + -
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ILE 3.0 17.3 + - - +
371A LEU* 3.8 4.9 - - - +
372A LEU 3.3 0.2 - - - -
373A ARG* 1.3 77.8 - - - +
375A GLY* 1.3 57.6 + - - +
377A ASN* 3.3 15.4 + - - +
378A GLU* 5.2 3.1 - - - +
448A ASN* 4.9 10.8 - - + +
451A ALA* 3.9 25.4 - - + -
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Residues in contact with GLY 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A LEU 3.3 11.3 + - - -
374A ALA* 1.3 79.3 - - - +
376A TRP* 1.4 59.3 + - - +
377A ASN* 3.1 5.1 + - - -
378A GLU* 3.2 8.4 + - - +
379A LEU* 2.8 42.9 + - - +
445A ILE* 4.5 16.5 + - - -
446A LEU* 5.8 0.2 - - - -
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Residues in contact with TRP 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A ALA* 5.5 2.2 - - + -
347A LEU* 3.8 26.2 - - + -
350A LEU* 3.7 26.0 - - + -
372A LEU 3.1 20.5 + - - +
373A ARG* 3.0 30.0 + - - +
374A ALA 3.8 0.2 - - - -
375A GLY* 1.4 73.2 - - - +
377A ASN* 1.4 89.3 + - + +
379A LEU* 3.8 0.6 - - - +
380A LEU* 3.0 39.2 + - + +
504A LEU* 3.6 32.5 - - + +
507A LEU* 4.1 15.3 - - + -
522A LEU* 3.7 27.8 - - + -
525A MET* 3.6 43.6 + - + +
526A LEU* 4.3 4.7 - - + -
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Residues in contact with ASN 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ARG 4.7 0.5 - - - +
374A ALA 3.3 21.9 + - - +
375A GLY 4.0 0.3 - - - -
376A TRP* 1.4 110.3 + - + +
378A GLU* 1.3 75.0 + - - +
380A LEU* 3.3 2.4 + - - +
381A ILE* 3.0 39.7 + - + +
500A GLY* 3.6 32.7 + - - +
501A LEU* 5.3 2.2 - - - +
503A CYS* 5.9 0.2 - - + -
504A LEU* 4.5 21.0 - - + +
507A LEU* 6.2 0.7 - - + -
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Residues in contact with GLU 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A ALA 5.2 4.7 - - - +
375A GLY* 3.2 6.1 + - - +
377A ASN* 1.3 91.2 + - - +
379A LEU* 1.4 54.2 + - - +
381A ILE* 3.2 9.4 + - - +
382A ALA* 2.8 36.1 + - - +
445A ILE* 3.7 32.5 - - + +
493A LEU* 4.7 3.3 - - - +
496A LEU* 3.8 33.8 - - + +
497A ARG* 2.9 51.2 + - - +
500A GLY* 4.6 2.5 - - - -
426B VAL* 5.2 1.2 - - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A LEU* 3.8 30.5 - - + -
353A TRP* 3.8 17.0 - - + -
371A LEU 5.2 1.1 - - - +
372A LEU* 4.8 2.0 - - + -
375A GLY* 2.8 38.1 + - - +
376A TRP 3.8 5.6 - - - +
378A GLU* 1.4 71.2 - - - +
380A LEU* 1.3 57.0 + - - +
382A ALA* 3.6 3.6 - - - +
383A SER 3.2 12.5 + - - -
442A ARG* 3.0 67.0 + - + +
445A ILE* 3.9 11.4 - - + -
446A LEU* 4.1 25.1 - - + +
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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
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343A ALA* 3.8 31.6 - - + +
346A GLN* 3.6 36.8 - - + +
347A LEU* 3.9 19.3 - - + -
350A LEU* 4.5 14.1 - - + -
376A TRP* 3.0 30.4 + - + +
377A ASN* 3.9 2.7 - - - +
379A LEU* 1.3 72.9 - - - +
381A ILE* 1.4 56.1 + - - +
382A ALA 3.2 0.2 - - - -
383A SER* 3.0 8.2 + - - -
384A PHE* 2.8 51.9 + - + -
387A ARG* 5.9 0.2 - - - +
442A ARG* 4.6 7.4 - - - +
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A ASN* 3.0 29.7 + - + +
378A GLU* 3.6 4.9 - - - +
380A LEU* 1.4 74.1 - - + +
382A ALA* 1.4 56.5 + - - +
384A PHE* 3.4 10.9 + - + +
385A SER* 2.9 37.1 + - - +
420A VAL* 4.5 10.3 - - + +
424A LEU* 3.6 24.5 - - + -
496A LEU* 3.9 6.7 - - + -
499A ILE* 4.1 10.8 - - + -
500A GLY* 3.5 32.8 - - - +
503A CYS* 3.7 25.6 - - + -
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A GLU 2.8 17.3 + - - +
379A LEU* 3.6 7.0 - - - +
381A ILE* 1.4 76.7 - - - +
383A SER* 1.3 55.5 + - - +
385A SER* 3.8 2.0 - - - -
386A HIS* 3.1 28.8 + - - +
424A LEU* 5.1 0.7 - - - -
428A MET* 3.8 10.9 - - + +
438A LEU* 3.6 12.1 - - + +
441A LEU* 6.5 0.7 - - + -
442A ARG* 4.1 18.8 - - + -
445A ILE* 4.5 2.7 - - + -
496A LEU* 4.1 20.6 - - + +
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLU* 5.0 3.5 + - - -
346A GLN* 5.5 1.6 - - - -
379A LEU 3.2 7.8 + - - -
380A LEU* 3.0 14.2 + - - -
382A ALA* 1.3 73.5 - - - +
384A PHE* 1.4 59.6 + - - +
386A HIS* 3.4 5.3 + - - +
387A ARG* 3.0 52.9 + - - +
438A LEU* 5.1 2.8 - - - +
442A ARG* 3.0 35.1 + - - +
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Residues in contact with PHE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ILE* 5.5 6.5 - - + -
342A ALA 4.0 21.5 - - - -
343A ALA* 4.4 11.7 - - + -
346A GLN* 4.2 9.4 - - + -
380A LEU* 2.8 40.1 + - + +
381A ILE* 3.9 9.4 - - + +
383A SER* 1.4 71.5 - - - +
385A SER* 1.4 55.3 + - - +
387A ARG* 3.3 35.6 + - - +
388A SER* 2.7 34.0 + - - -
395A ILE* 4.0 19.4 - - + +
396A LEU 4.1 7.1 - - - +
397A LEU* 4.0 23.8 - - + -
398A ALA 3.9 15.9 - - - -
420A VAL* 6.3 0.7 - - + -
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ILE 2.9 22.4 + - - -
382A ALA 3.8 2.7 - - - -
383A SER 3.3 0.2 - - - -
384A PHE* 1.4 74.4 - - - +
386A HIS* 1.3 61.5 + - - +
388A SER 3.5 8.1 + - - -
389A ILE* 3.7 7.4 + - - +
395A ILE* 5.4 0.4 - - - -
420A VAL* 3.3 26.7 - - - +
424A LEU* 3.4 19.4 - - - +
425A VAL* 3.6 25.4 - - - +
428A MET* 3.7 23.6 - - - +
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Residues in contact with HIS 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ALA 3.1 17.3 + - - +
383A SER 3.4 3.3 + - - +
385A SER* 1.3 73.6 - - - +
387A ARG* 1.3 62.8 + - - +
389A ILE* 3.3 35.6 - - + +
390A ASP* 5.5 0.3 - - - +
428A MET* 3.6 7.2 - - + -
433A MET* 2.7 50.8 + - - -
434A ASP* 3.8 4.2 + - - -
435A LYS* 3.6 36.3 - - + +
438A LEU* 3.5 25.4 - - + +
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Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 4.8 11.3 - - - +
346A GLN* 3.2 30.5 - - - +
380A LEU* 5.9 0.8 - - - +
383A SER* 3.0 33.7 + - - +
384A PHE* 3.3 32.8 - - - +
385A SER 3.3 0.2 - - - -
386A HIS* 1.3 76.4 - - - +
388A SER* 1.3 57.4 + - - +
389A ILE 3.2 5.5 + - - -
390A ASP* 4.3 10.7 + - - +
391A VAL* 4.6 1.2 - - - +
396A LEU* 3.3 51.5 + - + +
397A LEU 4.6 1.6 - - - -
398A ALA* 3.9 17.1 - - - +
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PHE 2.7 23.4 + - - -
385A SER 3.5 4.9 + - - -
386A HIS 3.4 0.6 - - - -
387A ARG* 1.3 71.3 - - - +
389A ILE* 1.3 61.2 + - - +
390A ASP 3.3 2.7 - - - -
391A VAL* 3.1 30.4 + - - +
394A GLY 3.4 20.4 - - - -
395A ILE* 3.1 6.6 - - - +
396A LEU* 2.8 22.1 + - - -
425A VAL* 3.2 21.2 - - - +
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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