Contacts of the helix formed by residues 367 - 400 (chain B) in PDB entry 4FE1
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 ASP 367 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 5.6 0.2 + - - -
84B ARG* 4.8 19.3 + - - +
85B PRO* 4.1 17.7 - - - +
116B TYR* 4.9 2.1 - - - -
121B HIS* 3.2 33.3 + - + +
363B PHE 3.8 1.2 + - - +
364B ILE 3.1 15.1 + - - +
366B GLN* 1.3 76.8 - - - +
368B HIS* 1.3 60.3 + - - +
369B THR* 3.8 6.9 + - - -
370B THR* 2.9 34.6 + - - +
371B MET* 3.1 19.0 + - - +
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Residues in contact with HIS 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B ALA 3.5 22.5 + - - -
366B GLN* 3.0 18.1 + - + +
367B ASP* 1.3 68.9 + - - +
369B THR* 1.3 61.3 + - - +
371B MET* 3.3 7.9 + - - +
372B ALA* 3.0 30.7 + - - +
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Residues in contact with THR 369 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 5.7 2.5 + - - -
116B TYR* 3.4 42.3 - - + -
367B ASP* 3.3 5.1 + - - -
368B HIS* 1.3 78.2 - - - +
370B THR* 1.3 58.8 + - - +
372B ALA* 3.4 7.2 + - + +
373B ALA* 3.0 28.0 + - + +
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Residues in contact with THR 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PRO* 5.7 0.2 - - + -
115B ALA 4.2 4.0 - - - +
116B TYR* 3.3 43.5 - - + -
118B GLY* 4.1 13.8 - - - +
121B HIS* 4.3 2.9 + - + +
364B ILE* 4.0 15.1 - - - +
367B ASP* 2.9 41.5 + - - +
368B HIS 3.3 0.4 - - - -
369B THR* 1.3 73.3 - - - +
371B MET* 1.3 62.7 + - - +
373B ALA* 3.8 0.7 - - - +
374B LEU* 2.9 36.0 + - - +
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Residues in contact with MET 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET 4.0 9.2 - - - +
356B TYR* 3.4 44.3 - - + +
359B PRO* 4.2 6.5 - - + -
364B ILE* 3.3 48.7 - - + +
365B ALA* 4.2 19.1 - - + +
367B ASP 3.1 8.0 + - - +
368B HIS* 3.3 9.6 + - - +
370B THR* 1.3 76.3 - - - +
372B ALA* 1.3 62.1 + - - +
374B LEU* 3.4 8.3 + - - +
375B TYR* 3.0 25.6 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B HIS 3.0 17.3 + - - +
369B THR* 3.6 7.4 - - + +
371B MET* 1.3 78.6 - - - +
373B ALA* 1.3 60.9 + - - +
375B TYR* 3.3 5.3 + - - +
376B THR* 2.8 32.0 + - - +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 3.7 27.6 - - + +
369B THR* 3.0 18.4 + - + +
370B THR 3.8 0.7 - - - +
372B ALA* 1.3 77.9 - - - +
374B LEU* 1.3 64.0 + - + +
376B THR* 4.0 3.7 - - - -
377B HIS* 3.0 28.5 + - - +
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR 4.9 0.4 - - - +
117B SER* 3.3 32.5 - - - +
118B GLY* 4.8 1.8 - - - -
352B ALA* 6.2 0.2 - - - -
355B MET* 5.8 13.2 - - + -
361B TYR* 5.3 7.2 - - + -
364B ILE* 3.9 27.1 - - + -
370B THR 2.9 25.9 + - - +
371B MET* 3.8 9.0 - - - +
373B ALA* 1.3 75.5 - - - +
375B TYR* 1.3 63.4 + - - +
377B HIS* 3.8 5.6 - - + +
378B HIS* 3.1 49.2 + - + +
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Residues in contact with TYR 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ALA* 3.2 46.4 - - + +
353B GLN* 3.3 22.3 + - - -
356B TYR* 4.1 21.8 - + + -
371B MET 3.0 16.6 + - - +
372B ALA* 3.8 4.7 - - - +
374B LEU* 1.3 77.3 - - - +
376B THR* 1.3 72.3 + - - +
378B HIS* 3.9 1.0 - - - +
379B GLN* 2.9 56.6 + - + +
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Residues in contact with THR 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ALA* 2.8 20.2 + - - +
373B ALA* 4.0 4.0 - - - -
375B TYR* 1.3 82.3 - - - +
377B HIS* 1.3 64.6 + - - +
379B GLN* 3.1 5.4 + - - +
380B TYR* 3.0 54.2 + - + -
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Residues in contact with HIS 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ALA 3.0 19.2 + - - +
374B LEU* 3.8 5.8 - - + +
376B THR* 1.3 78.5 - - - +
378B HIS* 1.3 94.3 + + - +
380B TYR* 3.2 6.3 + - - +
381B ILE* 3.0 48.1 + - + +
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Residues in contact with HIS 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B THR* 3.2 29.5 - - + +
351B VAL* 4.4 21.7 - - + +
352B ALA* 4.2 19.0 - - + -
355B MET* 5.4 6.8 - - - -
374B LEU* 3.1 40.1 + - + +
377B HIS* 1.3 101.9 + + - +
379B GLN* 1.3 58.6 + - - +
381B ILE* 3.5 6.2 + - + -
382B ALA* 3.0 23.4 + - - +
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Residues in contact with GLN 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B SER* 3.0 34.4 + - - -
352B ALA* 3.8 10.5 - - + +
353B GLN* 4.2 13.5 - - - +
375B TYR* 2.9 60.6 + - + +
376B THR* 3.6 5.4 - - - +
378B HIS* 1.3 74.9 - - - +
380B TYR* 1.3 68.4 + - + +
382B ALA* 3.2 5.1 + - - +
383B GLY* 3.0 18.9 + - - -
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Residues in contact with TYR 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B THR* 3.0 45.0 + - + -
377B HIS* 3.2 8.7 + - - +
379B GLN* 1.3 76.3 - - + +
381B ILE* 1.3 67.4 + - + +
383B GLY* 3.0 12.1 + - - -
384B PHE* 3.0 36.5 + + + -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B THR* 4.0 11.9 - - + +
377B HIS* 3.0 43.3 + - + +
378B HIS* 3.6 11.7 - - + +
379B GLN 3.3 0.2 - - - -
380B TYR* 1.3 76.2 - - + +
382B ALA* 1.3 64.2 + - - +
384B PHE* 3.2 10.7 + - + +
385B LEU* 3.0 44.8 + - + +
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B GLY* 3.6 22.4 - - - +
348B THR* 4.0 10.3 - - + -
349B SER* 3.6 19.3 - - - +
378B HIS 3.0 14.7 + - - +
379B GLN* 3.4 10.5 - - - +
380B TYR 3.1 0.4 - - - -
381B ILE* 1.3 77.7 - - - +
383B GLY* 1.3 57.3 + - - +
385B LEU* 3.4 4.5 + - - +
386B MET* 2.9 37.6 + - + +
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Residues in contact with GLY 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLN 3.0 10.0 + - - -
380B TYR* 3.0 8.5 + - - -
382B ALA* 1.3 75.7 - - - +
384B PHE* 1.3 63.9 + - - +
386B MET* 3.4 6.0 + - - +
387B VAL* 3.1 30.5 + - - +
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Residues in contact with PHE 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B TYR* 3.0 43.9 + + + -
381B ILE* 3.7 12.1 - - + +
383B GLY* 1.3 75.7 - - - +
385B LEU* 1.3 60.4 + - + +
387B VAL* 3.2 8.7 + - + +
388B GLY* 2.9 25.8 + - - -
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Residues in contact with LEU 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.7 31.9 - - + +
344B LEU* 3.7 28.0 - - + -
345B GLY* 3.7 30.3 - - - +
348B THR* 3.8 9.4 - - - +
381B ILE* 3.0 33.9 + - + +
382B ALA 3.7 3.6 - - - +
384B PHE* 1.3 79.6 - - + +
386B MET* 1.3 57.4 + - - +
388B GLY* 3.0 3.2 + - - -
389B ALA* 2.9 27.9 + - - +
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Residues in contact with MET 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU 4.9 0.2 - - - -
342B ALA* 3.8 35.9 - - + +
345B GLY* 4.0 5.2 - - - -
346B VAL* 3.9 25.4 - - + -
382B ALA* 2.9 27.3 + - + +
383B GLY* 3.8 6.3 - - - +
385B LEU* 1.3 75.6 - - - +
387B VAL* 1.3 63.3 + - + +
389B ALA* 3.2 15.6 + - + +
390B PHE* 3.2 34.4 + - + -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLY 3.1 19.4 + - - +
384B PHE* 3.5 10.8 - - + +
386B MET* 1.3 76.5 - - + +
388B GLY* 1.3 59.2 + - - +
390B PHE* 3.1 9.7 + - - +
391B ALA* 2.9 28.0 + - + +
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Residues in contact with GLY 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.3 23.0 - - - +
384B PHE 2.9 14.5 + - - -
385B LEU* 3.0 4.7 + - - -
387B VAL* 1.3 76.6 - - - +
389B ALA* 1.3 65.4 + - - +
391B ALA* 3.6 7.1 - - - +
392B HIS* 2.9 25.5 + - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B GLY* 3.1 32.9 - - - +
341B LEU* 3.6 4.2 - - - +
342B ALA* 3.4 30.1 - - + +
385B LEU 2.9 8.7 + - - +
386B MET* 3.2 12.8 + - + +
388B GLY* 1.3 74.7 - - - +
390B PHE* 1.3 63.5 + - + +
393B GLY* 3.0 24.8 + - - -
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Residues in contact with PHE 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B MET* 3.2 33.1 + - + -
387B VAL* 3.1 10.1 + - - +
388B GLY 3.1 0.4 - - - -
389B ALA* 1.3 84.6 - - + +
391B ALA* 1.3 58.6 + - - +
393B GLY* 3.7 1.6 - - - -
394B ALA* 3.0 28.1 + - - +
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Residues in contact with ALA 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B VAL* 2.9 20.0 + - + +
388B GLY* 3.0 9.8 + - - +
390B PHE* 1.3 75.8 - - - +
392B HIS* 1.3 64.6 + - + +
394B ALA* 3.1 7.8 + - - +
395B ILE* 3.0 37.3 + - + +
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Residues in contact with HIS 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B HIS* 3.0 59.1 + + - +
337B LEU* 3.4 32.1 - - + +
338B GLY* 3.9 10.1 - - - +
341B LEU* 4.0 8.3 - - + -
388B GLY* 2.9 19.8 + - - +
391B ALA* 1.3 79.3 - - + +
393B GLY* 1.3 60.8 - - - +
395B ILE* 3.7 15.9 - - + +
396B PHE* 2.9 23.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B HIS 4.9 1.6 - - - -
335B PHE* 5.7 2.2 - - - -
338B GLY* 5.2 2.5 - - - -
389B ALA 3.0 18.7 + - - -
390B PHE* 3.7 4.0 - - - -
391B ALA 3.1 0.4 - - - -
392B HIS* 1.3 79.3 - - - +
394B ALA* 1.3 59.0 + - - +
396B PHE* 3.4 10.5 + - - +
397B LEU* 3.4 25.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B PHE 3.0 14.0 + - - +
391B ALA* 3.6 8.5 - - - +
393B GLY* 1.3 75.1 - - - +
395B ILE* 1.3 65.3 + - + +
397B LEU* 3.2 14.1 + - - +
398B VAL* 3.1 26.9 + - + +
----------------------------------------------------------
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Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B HIS* 3.3 33.7 - - + +
391B ALA* 3.0 27.8 + - + +
392B HIS* 3.8 30.3 - - + +
394B ALA* 1.3 73.2 - - + +
396B PHE* 1.3 60.8 + - - +
398B VAL* 3.1 5.9 + - - +
399B ARG* 2.9 47.3 + - - +
----------------------------------------------------------
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Residues in contact with PHE 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B THR* 3.4 32.5 - - + -
332B SER* 3.0 29.4 - - - -
334B HIS* 3.8 15.0 - - + +
335B PHE* 3.4 38.8 - + + +
392B HIS 2.9 14.9 + - - +
393B GLY* 3.4 12.8 - - - +
394B ALA 3.2 0.2 - - - -
395B ILE* 1.3 76.5 - - - +
397B LEU* 1.3 79.1 + - + +
400B ASP* 2.8 15.7 + - + -
401B TYR* 2.7 57.1 + + + -
411B LEU* 3.8 7.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B GLY 3.4 13.0 + - - +
394B ALA* 3.2 14.6 + - - +
396B PHE* 1.3 102.9 - - + +
398B VAL* 1.3 63.2 + - + +
401B TYR* 3.6 39.6 + - + +
411B LEU* 4.4 7.2 - - + -
415B LEU* 4.3 28.9 - - + -
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Residues in contact with VAL 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ALA* 3.1 14.9 + - + +
395B ILE* 3.1 8.0 + - - +
397B LEU* 1.3 83.4 - - + +
399B ARG* 1.3 72.0 + - + +
400B ASP 3.7 0.2 - - - -
401B TYR 5.1 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ARG 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ASP* 2.8 40.4 + - - -
31B GLU* 2.9 34.4 + - - +
32B SER* 4.6 6.1 + - - +
334B HIS* 4.1 9.8 + - + -
395B ILE* 2.9 29.0 + - + +
398B VAL* 1.3 86.7 - - + +
400B ASP* 1.3 73.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP 400 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLU* 4.0 11.8 - - - +
328B THR* 6.0 0.2 - - - +
331B ASN 5.1 2.2 - - - -
332B SER* 2.9 43.3 + - - +
333B LEU 3.9 3.6 + - - -
334B HIS* 3.5 23.8 - - - -
396B PHE* 2.8 20.5 + - + +
399B ARG* 1.3 86.0 - - - +
401B TYR* 1.3 63.9 + - - +
402B ASP* 3.1 8.3 + - - +
----------------------------------------------------------
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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