Contacts of the helix formed by residues 361 - 386 (chain B) in PDB entry 5NC5
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 ASN 361 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET 5.4 0.2 - - - +
356B TYR* 3.7 10.2 - - - -
359B LEU* 3.2 11.3 + - - +
360B GLN* 1.3 82.3 + - - +
362B PHE* 1.3 64.1 + - - +
363B ARG* 3.3 30.8 + - - +
364B ALA* 3.3 13.6 + - - +
365B THR* 3.5 14.2 + - - -
417B GLU* 3.3 25.2 + - - -
497B LEU* 4.8 2.1 - - - +
498B LYS* 5.0 11.7 + - - +
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Residues in contact with PHE 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 4.3 26.9 - + - -
356B TYR* 3.3 48.0 - + - -
361B ASN* 1.3 71.1 - - - +
363B ARG* 1.3 67.2 + - + +
365B THR* 3.0 26.1 + - + +
366B LEU* 3.0 13.5 + - + +
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Residues in contact with ARG 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASN* 3.3 12.0 + - - +
362B PHE* 1.3 80.3 - - + +
364B ALA* 1.3 64.2 + - - +
366B LEU* 3.3 12.7 + - - +
367B ILE* 3.6 13.3 - - - +
495B THR 5.2 1.4 + - - -
496B MET* 2.8 52.3 + - + +
497B LEU* 4.0 6.7 - - + +
498B LYS* 3.7 46.8 - - - +
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Residues in contact with ALA 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B MET* 3.8 6.4 - - + +
359B LEU* 3.7 27.8 - - + -
361B ASN* 3.3 24.2 + - - +
362B PHE 3.4 0.4 - - - -
363B ARG* 1.3 78.4 - - - +
365B THR* 1.3 63.3 + - - +
367B ILE* 3.2 15.8 + - - +
368B PRO* 3.2 11.4 - - - +
413B VAL* 4.1 6.0 - - + +
417B GLU* 4.1 3.1 - - - +
497B LEU* 3.3 22.3 - - + +
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Residues in contact with THR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 5.6 0.2 - - - +
352B PHE* 3.0 64.3 + - + -
355B MET* 3.6 18.2 - - - +
356B TYR* 3.7 7.5 + - - +
361B ASN 3.5 5.8 + - - -
362B PHE* 3.0 28.1 + - + +
364B ALA* 1.3 79.4 - - - +
366B LEU* 1.3 72.9 + - + +
367B ILE 3.4 0.5 + - - -
368B PRO* 3.5 9.2 - - - +
369B THR* 3.5 13.7 + - - -
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 5.1 3.6 - - + -
362B PHE* 3.0 15.0 + - + +
363B ARG* 3.7 1.6 - - - +
364B ALA 3.2 0.6 - - - -
365B THR* 1.3 95.2 - - + +
367B ILE* 1.3 65.0 + - - +
369B THR* 2.9 22.7 + - + -
370B ILE* 3.0 25.5 + - + +
496B MET* 3.6 28.7 - - + -
1110B D10 5.3 10.1 - - + -
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Residues in contact with ILE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B ARG 3.6 14.1 - - - +
364B ALA 3.7 2.9 - - - +
366B LEU* 1.3 75.7 - - - +
368B PRO* 1.3 66.1 - - + +
370B ILE* 3.1 6.4 + - - +
371B ALA* 2.9 25.5 + - - +
409B ALA* 6.1 0.2 - - + -
413B VAL* 3.4 21.5 - - + -
489B THR* 4.0 16.4 - - + +
492B LEU* 4.0 29.7 - - + +
493B CYS* 3.7 39.5 - - - +
496B MET* 4.4 11.2 - - + -
497B LEU* 3.9 18.2 - - + -
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Residues in contact with PRO 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 3.6 29.4 - - + -
355B MET* 3.7 23.8 - - + -
364B ALA 3.2 15.0 - - - +
365B THR 3.5 7.9 - - - +
367B ILE* 1.3 91.9 - - + +
369B THR* 1.3 55.8 + - - +
371B ALA* 4.2 1.8 - - + +
372B VAL* 2.8 38.4 + - + +
409B ALA* 3.7 32.3 - - + -
410B ILE 5.1 0.7 - - - +
413B VAL* 4.7 2.9 - - + -
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Residues in contact with THR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ILE* 3.9 35.5 + - + +
351B VAL* 5.4 0.7 - - - +
352B PHE* 4.2 14.1 + - + +
365B THR 3.5 12.3 + - - -
366B LEU* 2.9 20.2 + - + +
368B PRO* 1.3 78.9 - - - +
370B ILE* 1.3 58.0 + - + +
373B PRO* 3.4 20.1 - - - +
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Residues in contact with ILE 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TRP* 4.1 30.5 - - + -
20B MET* 5.4 1.5 - - + +
366B LEU* 3.0 26.3 + - + +
367B ILE* 3.6 5.2 - - - +
369B THR* 1.3 80.8 - - + +
371B ALA* 1.3 66.9 + - - +
372B VAL 3.3 0.4 + - - -
373B PRO* 3.6 4.1 - - - +
374B VAL* 3.2 28.7 + - + +
488B LEU* 4.1 11.4 - - + -
492B LEU* 3.9 28.7 - - + -
496B MET* 4.6 11.9 - - + -
1110B D10 4.2 31.0 - - + -
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ILE 2.9 15.5 + - - +
368B PRO* 4.1 5.6 - - + +
370B ILE* 1.3 77.1 - - - +
372B VAL* 1.3 65.2 + - + +
374B VAL* 3.2 4.7 + - - +
375B VAL* 3.1 24.8 + - - +
409B ALA* 4.5 7.0 - - + -
484B VAL* 4.1 11.1 - - + +
488B LEU* 4.3 10.3 - - + -
489B THR* 3.5 32.8 - - + -
492B LEU* 5.1 0.7 - - + -
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Residues in contact with VAL 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ILE* 3.6 26.5 - - + -
351B VAL* 6.0 2.0 - - + -
368B PRO* 2.8 22.9 + - + +
371B ALA* 1.3 71.8 - - - +
373B PRO* 1.3 73.9 - - + +
375B VAL* 3.0 8.9 + - - +
376B LEU* 3.0 31.2 + - + +
405B LEU* 4.2 29.9 - - + +
406B VAL* 4.3 22.0 - - + -
409B ALA* 4.5 10.5 - - + -
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Residues in contact with PRO 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B MET* 5.4 7.2 - - + -
348B ILE* 3.7 21.5 - - + -
368B PRO 3.8 1.1 - - - +
369B THR 3.4 25.8 - - - +
370B ILE* 3.6 5.2 - - - +
372B VAL* 1.3 99.9 - - + +
374B VAL* 1.3 56.1 + - + +
376B LEU* 3.7 10.8 - - + +
377B LEU* 2.8 39.6 + - + +
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Residues in contact with VAL 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TRP* 6.2 0.4 - - + -
16B ALA* 4.3 16.8 - - + +
19B ILE* 3.4 22.1 - - + +
20B MET* 4.0 34.1 - - + -
370B ILE* 3.2 19.1 - - + +
371B ALA 3.2 8.7 + - - +
372B VAL 3.2 0.8 - - - -
373B PRO* 1.3 76.2 - - - +
375B VAL* 1.3 59.6 + - - +
377B LEU* 4.1 0.2 - - - +
378B GLY* 2.9 23.2 + - - -
480B LEU* 5.2 0.2 - - - +
484B VAL* 3.9 21.3 - - + +
488B LEU* 4.1 20.9 - - + -
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ALA 3.1 8.7 + - - +
372B VAL* 3.0 10.7 + - - +
374B VAL* 1.3 75.5 - - - +
376B LEU* 1.3 56.4 + - - +
378B GLY 3.8 0.9 - - - -
379B THR* 2.7 40.1 + - - +
405B LEU* 3.9 26.5 - - + -
477B ALA 3.7 23.1 - - - +
480B LEU* 3.6 7.6 - - + +
481B SER* 3.5 23.1 - - - +
484B VAL* 3.3 33.4 - - + -
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.7 48.2 - - + -
348B ILE* 4.6 7.4 - - + -
372B VAL* 3.0 28.6 + - + +
373B PRO* 3.7 11.0 - - + +
375B VAL* 1.3 74.1 - - - +
377B LEU* 1.3 66.2 + - + +
379B THR* 3.2 13.3 + - - -
380B PHE* 2.9 31.3 + - + -
398B MET* 3.8 26.5 - - + +
405B LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE 4.1 8.1 - - - +
20B MET* 3.7 47.8 - - + +
23B GLY* 3.4 14.2 - - - -
24B GLY* 4.1 3.1 - - - +
27B ILE* 3.7 24.7 - - + -
373B PRO* 2.8 24.5 + - + +
374B VAL 4.1 2.7 - - - +
376B LEU* 1.3 71.3 - - + +
378B GLY* 1.3 65.6 + - - +
379B THR 2.9 1.7 + - - -
380B PHE* 2.9 19.7 + - + -
381B ALA 3.2 8.5 + - - -
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Residues in contact with GLY 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE* 3.3 28.6 - - - +
374B VAL 2.9 14.3 + - - -
375B VAL 3.9 1.3 - - - -
377B LEU* 1.3 76.6 - - - +
379B THR* 1.3 56.2 + - - +
381B ALA* 3.3 8.3 + - - +
382B VAL* 3.1 23.2 + - - +
480B LEU* 3.3 19.7 - - - +
1118B D10 5.0 2.6 - - - +
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Residues in contact with THR 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B VAL 2.7 22.9 + - - -
376B LEU* 3.5 6.9 - - - -
377B LEU 3.0 0.4 - - - -
378B GLY* 1.3 75.1 - - - +
380B PHE* 1.3 60.7 + - - +
382B VAL* 3.2 2.6 + - - +
383B LEU* 2.8 35.4 + - + +
398B MET* 3.5 22.9 - - + -
473B THR* 4.2 7.4 - - + +
476B SER* 4.4 4.9 - - - -
477B ALA* 3.3 43.8 - - + +
480B LEU* 3.6 11.6 - - - +
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Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.3 9.4 - - + +
27B ILE* 3.3 35.4 - - + -
30B LEU* 4.2 19.2 - - + +
344B LEU* 5.1 6.3 - - + -
376B LEU* 2.9 41.5 + - + -
377B LEU* 2.9 14.7 + - + +
379B THR* 1.3 76.0 - - - +
381B ALA* 1.3 57.1 + - - +
383B LEU* 3.8 12.0 - - + +
384B ALA* 2.9 30.3 + - - +
390B ILE* 5.4 1.1 - - + -
398B MET* 3.3 26.9 - - + -
1117B D10 3.2 42.0 - - + -
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Residues in contact with ALA 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 3.7 38.1 - - + +
23B GLY* 3.8 3.1 - - - +
26B ALA* 3.8 10.6 - - - +
377B LEU 3.2 5.6 + - - +
378B GLY* 3.4 12.6 - - - +
379B THR 3.2 0.2 - - - -
380B PHE* 1.3 76.0 - - - +
382B VAL* 1.3 65.1 + - - +
384B ALA* 4.1 1.2 - - - +
385B ALA* 3.3 21.8 + - - +
1118B D10 4.8 14.0 - - + +
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Residues in contact with VAL 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B GLY 3.1 14.1 + - - +
379B THR 3.2 6.0 + - - +
381B ALA* 1.3 72.8 - - - +
383B LEU* 1.3 62.6 + - - +
385B ALA* 3.0 15.9 + - - +
386B PHE* 2.8 46.8 + - + -
476B SER* 3.7 23.3 - - - -
480B LEU* 3.7 16.8 - - + -
1113B D10 4.2 6.1 - - + -
1118B D10 4.4 23.1 - - + -
1119B DD9 5.5 5.4 - - + -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.7 7.2 - - + -
379B THR* 2.8 29.3 + - + +
380B PHE* 3.8 16.8 - - + +
382B VAL* 1.3 75.1 - - - +
384B ALA* 1.3 65.7 + - - +
386B PHE* 3.3 7.4 + - + -
387B GLY 3.1 13.3 + - - -
388B PHE* 3.2 42.3 + - + +
389B SER 4.6 6.1 - - - +
390B ILE* 6.1 1.3 - - + -
394B THR* 4.4 20.6 - - + +
398B MET* 5.7 2.7 - - + -
472B ILE* 4.4 4.9 - - + +
473B THR* 4.1 32.1 - - + +
476B SER* 4.2 9.9 - - - +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.9 13.9 - - + -
29B LYS* 6.2 1.1 - - + -
30B LEU* 3.0 32.3 - - + +
380B PHE 2.9 17.2 + - - +
381B ALA 4.1 2.5 - - - +
383B LEU* 1.3 77.9 - - - +
385B ALA* 1.3 55.1 + - - +
387B GLY* 2.6 26.5 + - - +
388B PHE 4.5 0.2 - - - -
1106B DD9 5.8 0.3 - - - +
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Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ALA 3.3 16.6 + - - +
382B VAL* 3.0 7.6 + - - +
384B ALA* 1.3 77.6 - - - +
386B PHE* 1.3 56.7 + - - +
387B GLY 3.5 0.2 - - - -
1106B DD9 4.4 25.4 - - + +
1118B D10 4.5 5.8 - - + -
1119B DD9 3.0 56.1 - - + +
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B VAL* 2.8 45.8 - - + -
383B LEU* 3.5 11.9 - - + -
385B ALA* 1.3 75.7 - - - +
387B GLY* 1.3 65.5 + - - +
388B PHE* 3.1 24.4 + + + -
472B ILE* 4.5 11.0 - - + -
1112B DD9 3.9 37.2 - - + -
1113B D10 3.5 57.5 - - + +
1119B DD9 4.3 28.3 - - + +
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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