Contacts of the helix formed by residues 359 - 396 (chain A) in PDB entry 1AM9
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 LYS 359 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASN* 2.7 32.6 + - - +
343A ILE* 4.1 31.1 - - + +
358A ASN* 1.3 72.2 - - - +
360A SER* 1.3 64.0 + - - +
362A VAL* 3.2 3.9 + - - +
363A LEU* 3.1 28.3 + - - +
335B TYR* 4.1 1.9 + - - +
339B ILE* 3.8 23.6 - - + -
46G G 3.1 40.1 + - - +
47G G 2.7 27.0 + - - -
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ASN* 3.3 16.4 + - - +
359A LYS* 1.3 78.7 - - - +
361A ALA* 1.3 55.4 + - - +
363A LEU* 3.5 5.5 + - - +
364A ARG* 2.9 28.6 + - - +
335B TYR* 5.6 1.4 - - - -
338B SER* 3.1 47.3 + - - -
339B ILE* 4.1 6.3 - - - +
342B LYS* 3.4 11.6 - - - -
45G T 4.7 6.2 + - - -
46G G 4.7 2.3 + - - -
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU* 3.4 20.4 - - + -
358A ASN* 3.1 27.9 + - - +
360A SER* 1.3 77.5 + - - +
362A VAL* 1.3 62.7 + - - +
364A ARG* 3.8 8.6 - - - +
365A LYS* 3.0 34.9 + - + +
----------------------------------------------------------
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Residues in contact with VAL 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 3.4 32.8 - - + +
346A LEU* 3.8 11.7 - - + +
347A LYS* 3.5 43.1 - - + +
350A VAL* 4.2 2.5 - - - +
357A LEU* 3.8 21.1 - - + +
358A ASN 3.0 18.2 + - - +
359A LYS* 3.4 9.4 - - - +
361A ALA* 1.3 77.7 - - - +
363A LEU* 1.3 58.8 + - + +
365A LYS* 3.1 6.2 + - - +
366A ALA* 2.8 26.5 + - - +
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Residues in contact with LEU 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ILE* 4.2 15.7 - - + -
346A LEU* 3.9 11.9 - - + -
359A LYS 3.1 16.0 + - - +
360A SER 3.9 1.6 - - - +
362A VAL* 1.3 74.8 - - + +
364A ARG* 1.3 66.2 + - - +
366A ALA* 3.5 4.0 - - - +
367A ILE* 3.0 30.5 + - - +
339B ILE* 3.6 45.5 - - + +
342B LYS* 3.5 16.2 - - + -
343B ILE* 3.7 13.0 - - + -
346B LEU* 3.9 11.7 - - + -
363B LEU* 3.8 26.9 - - + -
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Residues in contact with ARG 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER 2.9 18.3 + - - +
361A ALA* 3.8 10.1 - - - +
363A LEU* 1.3 76.8 - - - +
365A LYS* 1.3 64.0 + - + +
367A ILE* 3.2 24.8 + - - +
368A ASP* 3.1 42.2 + - - +
342B LYS* 3.7 25.5 - - - +
345B GLU* 3.1 40.1 + - - -
----------------------------------------------------------
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Residues in contact with LYS 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL* 3.8 18.4 - - + +
351A VAL* 3.7 23.9 - - + +
357A LEU* 3.5 31.9 - - + -
361A ALA* 3.0 23.1 + - - +
362A VAL 3.4 4.9 - - - +
364A ARG* 1.3 78.1 - - + +
366A ALA* 1.3 54.8 + - - +
368A ASP* 3.4 5.7 + - - +
369A TYR* 2.7 36.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.1 29.4 - - + -
350A VAL* 3.6 13.2 - - + +
362A VAL 2.8 13.6 + - - +
363A LEU* 3.5 12.8 - - - +
365A LYS* 1.3 74.8 - - - +
367A ILE* 1.3 57.0 + - - +
369A TYR* 3.3 2.3 + - - +
370A ILE* 2.8 35.7 + - - +
346B LEU* 4.0 16.2 - - + -
370B ILE* 4.4 3.8 - - + -
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Residues in contact with ILE 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU 3.0 15.3 + - - +
364A ARG* 3.2 36.3 - - - +
366A ALA* 1.3 75.5 - - - +
368A ASP* 1.3 62.0 + - - +
370A ILE* 3.5 2.9 + - - +
371A ARG* 3.2 27.3 + - + +
342B LYS* 3.5 18.6 - - + +
345B GLU* 3.4 38.4 - - + +
346B LEU* 3.7 24.9 - - + +
349B LEU* 3.8 16.3 - - + +
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Residues in contact with ASP 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ARG* 3.1 50.4 + - - +
365A LYS* 3.9 5.3 - - - +
367A ILE* 1.3 73.6 - - - +
369A TYR* 1.3 61.7 + - - +
371A ARG* 3.5 8.0 + - - +
372A PHE* 2.9 27.5 + - - +
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Residues in contact with TYR 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU 3.7 13.0 - - - -
350A VAL* 3.9 22.0 - - + -
365A LYS 2.7 23.3 + - - +
366A ALA 3.6 4.3 - - - +
368A ASP* 1.3 72.0 - - - +
370A ILE* 1.3 53.9 + - - +
372A PHE* 3.0 22.0 + + + +
373A LEU* 2.7 61.4 + - + +
370B ILE* 3.8 20.2 - - + -
374B GLN* 2.5 39.9 + - - +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A ALA 2.8 21.1 + - - +
367A ILE 3.7 4.0 - - - +
369A TYR* 1.3 74.9 - - - +
371A ARG* 1.3 64.8 + - - +
373A LEU* 2.8 11.8 + - + +
374A GLN* 2.8 34.1 + - + +
346B LEU* 3.7 25.4 - - + -
349B LEU* 3.7 20.0 - - + -
350B VAL* 4.7 3.6 - - + -
366B ALA* 4.3 13.2 - - + +
369B TYR* 3.8 34.1 - - + -
370B ILE* 3.4 29.8 - - + -
373B LEU* 4.7 0.9 - - + -
----------------------------------------------------------
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Residues in contact with ARG 371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 3.2 16.8 + - + +
368A ASP* 3.7 10.8 - - - +
370A ILE* 1.3 78.1 - - - +
372A PHE* 1.3 58.4 + - - +
374A GLN* 2.7 34.3 + - - +
375A HIS* 3.0 55.1 + - + -
349B LEU* 3.1 29.1 - - + +
----------------------------------------------------------
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Residues in contact with PHE 372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A ASP 2.9 15.1 + - - +
369A TYR* 3.0 35.2 + + - +
371A ARG* 1.3 79.4 - - - +
373A LEU* 1.3 66.9 + - + +
375A HIS* 3.3 8.0 + - + +
376A SER* 2.9 49.0 + - - -
381B LYS* 5.8 4.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A TYR* 2.7 54.2 + - + +
370A ILE* 3.3 9.2 - - - +
372A PHE* 1.3 77.0 - - + +
374A GLN* 1.3 60.7 + - - +
376A SER* 4.2 0.4 - - - -
377A ASN* 2.9 27.0 + - - +
370B ILE* 3.8 50.7 - - + +
373B LEU* 3.6 18.6 - - + +
374B GLN* 4.2 10.1 - - + -
377B ASN* 3.0 24.0 + - + +
----------------------------------------------------------
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 2.8 23.5 + - - +
371A ARG* 2.7 46.9 + - - +
373A LEU* 1.3 76.9 - - - +
375A HIS* 1.3 68.7 + - + +
377A ASN* 3.4 6.7 + - - +
378A GLN* 3.2 21.0 + - - +
349B LEU* 3.8 8.8 + - - +
369B TYR* 3.0 29.1 + - - +
373B LEU* 3.8 17.7 - - + -
----------------------------------------------------------
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Residues in contact with HIS 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ARG* 3.0 44.8 + - + +
372A PHE* 3.7 8.9 - - + +
374A GLN* 1.3 81.8 - - + +
376A SER* 1.3 56.3 + - - +
378A GLN* 3.4 8.1 + - - +
379A LYS* 3.0 38.3 + - + +
----------------------------------------------------------
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Residues in contact with SER 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 2.9 42.3 + - - -
373A LEU* 3.6 4.9 - - - -
375A HIS* 1.3 74.9 - - - +
377A ASN* 1.3 56.5 + - - +
379A LYS* 2.9 12.7 + - - +
380A LEU* 2.6 54.3 + - - +
377B ASN* 3.8 7.9 + - - -
381B LYS* 4.6 9.0 + - - -
----------------------------------------------------------
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Residues in contact with ASN 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU 2.9 16.3 + - - +
374A GLN* 3.6 7.6 - - - +
376A SER* 1.3 75.0 - - - +
378A GLN* 1.3 63.9 + - - +
380A LEU* 3.1 4.1 + - - +
381A LYS* 2.8 58.4 + - - +
373B LEU* 4.4 13.2 - - + +
376B SER* 3.6 22.6 - - - -
377B ASN* 2.7 29.4 + - - +
380B LEU* 3.8 11.5 - - - +
----------------------------------------------------------
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Residues in contact with GLN 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLN 3.2 10.7 + - - +
375A HIS* 3.5 10.5 - - - +
376A SER 3.2 0.4 - - - -
377A ASN* 1.3 80.7 + - - +
379A LYS* 1.3 68.1 + - - +
381A LYS* 3.3 7.3 + - + +
382A GLN* 3.0 31.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A HIS* 3.0 23.3 + - + +
376A SER* 2.9 14.3 + - - +
378A GLN* 1.3 82.2 - - - +
380A LEU* 1.3 58.2 + - + +
382A GLN* 3.2 7.7 + - - +
383A GLU* 3.0 29.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A SER* 2.6 29.9 + - - +
377A ASN 3.5 3.6 - - - +
379A LYS* 1.3 71.5 - - + +
381A LYS* 1.3 59.7 + - - +
383A GLU* 4.2 11.7 - - - +
384A ASN* 2.8 27.4 + - - +
377B ASN* 3.4 52.7 - - + +
380B LEU* 3.9 12.6 - - + +
381B LYS* 3.4 31.4 - - + -
384B ASN* 3.2 23.1 + - - +
----------------------------------------------------------
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 2.8 43.9 + - - +
378A GLN* 3.8 6.7 - - + +
380A LEU* 1.3 73.0 - - - +
382A GLN* 1.3 67.9 + - - +
384A ASN* 3.2 8.3 + - - +
385A LEU* 3.0 22.9 + - - +
376B SER* 5.5 2.4 - - - -
380B LEU* 3.5 24.6 - - + +
----------------------------------------------------------
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Residues in contact with GLN 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLN* 3.0 21.7 + - - +
379A LYS* 3.6 9.0 - - - +
381A LYS* 1.3 77.4 - - - +
383A GLU* 1.3 63.1 + - - +
385A LEU* 3.2 12.5 + - - +
386A SER* 3.0 29.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LYS 3.0 16.2 + - - +
380A LEU* 3.5 16.4 - - - +
382A GLN* 1.3 74.8 - - - +
384A ASN* 1.3 60.8 + - - +
386A SER* 3.2 6.8 + - - +
387A LEU* 2.8 40.1 + - + +
384B ASN* 2.6 21.0 - - - +
388B ARG* 2.5 43.6 + - - +
----------------------------------------------------------
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Residues in contact with ASN 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU 2.8 15.3 + - - +
381A LYS* 3.4 6.5 - - - +
383A GLU* 1.3 76.6 - - - +
385A LEU* 1.3 56.8 + - - +
387A LEU* 3.4 3.5 + - - +
388A ARG* 2.9 63.2 + - - +
380B LEU* 4.0 15.0 - - + +
383B GLU* 2.6 27.8 + - - +
384B ASN* 2.7 30.8 + - - +
387B LEU* 3.3 5.1 - - - +
----------------------------------------------------------
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Residues in contact with LEU 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A LYS 3.0 13.0 + - - +
382A GLN* 3.5 13.7 - - - +
383A GLU 3.2 0.2 - - - -
384A ASN* 1.3 76.5 - - - +
386A SER* 1.3 56.1 + - - +
388A ARG* 3.0 15.7 + - + +
389A THR* 2.7 49.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLN* 3.0 22.9 + - - +
383A GLU* 3.7 9.9 - - - -
385A LEU* 1.3 76.0 - - - +
387A LEU* 1.3 65.2 + - - +
389A THR* 3.3 6.8 + - - +
390A ALA* 2.9 23.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLU* 2.8 28.1 + - + +
384A ASN 3.6 4.0 - - - +
386A SER* 1.3 74.4 - - - +
388A ARG* 1.3 57.8 + - - +
390A ALA* 3.1 8.9 + - + +
391A VAL* 2.9 35.0 + - - +
384B ASN* 3.2 48.0 - - + +
387B LEU* 3.7 15.5 - - + -
388B ARG* 3.5 38.6 - - + +
391B VAL* 4.3 7.4 - - + +
----------------------------------------------------------
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASN* 2.9 45.3 + - - +
385A LEU* 3.0 15.7 + - + +
387A LEU* 1.3 77.8 - - - +
389A THR* 1.3 60.5 + - - +
391A VAL* 3.6 4.2 + - - +
392A HIS* 3.2 22.9 + - - +
383B GLU* 2.7 29.7 + - - +
387B LEU* 3.8 22.5 - - + +
----------------------------------------------------------
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Residues in contact with THR 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A LEU* 2.7 35.9 + - - +
386A SER* 3.9 6.7 - - - -
388A ARG* 1.3 70.7 - - - +
390A ALA* 1.3 63.1 + - - +
392A HIS* 3.7 9.1 - - + +
393A LYS* 3.4 21.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER 2.9 13.8 + - - +
387A LEU* 3.1 16.2 - - + +
389A THR* 1.3 75.7 - - - +
391A VAL* 1.3 66.6 + - - +
393A LYS* 3.1 8.4 + - - +
394A SER* 2.9 22.0 + - - -
391B VAL* 4.4 15.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU 2.9 16.0 + - - +
388A ARG* 3.9 5.8 - - - +
390A ALA* 1.3 73.6 - - - +
392A HIS* 1.3 66.2 + - - +
394A SER* 3.0 23.5 + - - -
395A LYS* 3.5 24.2 - - + +
387B LEU* 4.0 24.5 - - + +
390B ALA* 4.9 9.0 - - + -
391B VAL* 3.3 27.1 - - + +
----------------------------------------------------------
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Residues in contact with HIS 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ARG 3.2 16.1 + - - +
389A THR* 3.7 11.7 - - + +
390A ALA 3.1 0.2 - - - -
391A VAL* 1.3 78.7 - - - +
393A LYS* 1.3 55.1 + - - +
395A LYS* 2.9 21.2 + - - +
396A SER* 2.7 51.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A THR* 3.4 10.2 + - + +
390A ALA* 3.1 10.1 + - - +
392A HIS* 1.3 75.2 - - + +
394A SER* 1.3 52.9 + - - +
395A LYS 2.5 17.9 + - - -
396A SER* 3.2 16.1 + - - -
397A LEU* 3.5 17.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ALA 2.9 13.2 + - - -
391A VAL* 3.0 19.9 + - - -
393A LYS* 1.3 72.5 - - - +
395A LYS* 1.3 63.7 + - - +
397A LEU* 5.8 0.9 - - - -
391B VAL* 6.0 7.0 - - - -
394B SER* 5.7 11.3 - - - -
----------------------------------------------------------
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Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A VAL* 3.5 29.2 - - + +
392A HIS* 4.0 15.5 + - - +
393A LYS 2.5 6.4 + - - -
394A SER* 1.3 85.0 - - - +
396A SER* 1.3 52.1 + - - +
397A LEU* 2.5 27.7 + - - +
----------------------------------------------------------
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Residues in contact with SER 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A HIS* 2.7 48.7 + - - -
393A LYS* 3.2 7.2 + - - -
395A LYS* 1.3 69.4 - - - +
397A LEU* 1.3 56.3 + - - -
398A LYS* 3.2 11.6 + - - +
----------------------------------------------------------
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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