Contacts of the helix formed by residues 329 - 359 (chain A) in PDB entry 2JIF
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 PHE 329 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN 3.5 25.1 - - - -
322A PHE* 3.8 12.8 - + + -
324A LYS* 3.6 30.7 - - + +
325A ARG 3.8 9.4 - - - -
326A LEU* 3.1 30.9 + - + +
327A PHE 4.0 1.1 - - - +
328A ASP* 1.3 76.9 - - - +
330A GLN* 1.3 65.6 + - - +
331A GLY 3.2 1.1 - - - -
332A LEU* 3.0 7.9 + - + +
333A GLN* 2.9 19.1 + - - +
1433C FAD 3.3 59.7 - + + +
330D GLN* 3.4 17.0 - - - +
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A LYS* 5.2 0.6 - - - +
328A ASP 3.4 5.9 + - - +
329A PHE* 1.3 72.1 - - - +
331A GLY* 1.3 56.9 + - - +
333A GLN* 3.9 12.8 + - - +
334A HIS* 2.9 52.3 + - + +
422B ASN* 3.4 17.1 + - - +
1433B FAD 2.9 40.2 + - - -
329D PHE* 3.4 9.2 - - - +
330D GLN* 3.4 19.9 + - + +
331D GLY* 2.9 26.4 + - - +
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Residues in contact with GLY 331 (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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330A GLN* 1.3 73.3 - - - +
332A LEU* 1.3 60.6 + - - +
334A HIS* 3.5 3.5 + - - +
335A GLN* 3.2 34.6 + - - +
418C ASN* 4.4 0.7 - - - -
330D GLN* 2.9 24.0 + - - +
331D GLY* 4.1 9.6 - - - +
334D HIS* 3.7 21.1 - - - -
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Residues in contact with LEU 332 (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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316A ILE* 3.5 32.3 - - + -
326A LEU* 3.6 31.6 - - + +
327A PHE* 4.4 2.7 - - - -
329A PHE* 3.0 12.6 + - + +
331A GLY* 1.3 73.6 - - - +
333A GLN* 1.3 65.5 + - - +
335A GLN* 3.3 7.5 + - - +
336A VAL* 3.0 33.6 + - + +
388A TRP* 4.0 23.8 - - + +
418C ASN* 4.0 15.0 - - - +
1433C FAD 3.6 38.1 - - - +
330D GLN* 4.2 0.6 + - - -
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Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A PHE* 3.0 39.1 + - + +
328A ASP* 3.8 22.0 + - - +
329A PHE 2.9 8.0 + - - +
330A GLN* 3.2 16.3 + - - +
332A LEU* 1.3 79.3 - - - +
334A HIS* 1.3 60.7 + - + +
336A VAL* 3.4 7.7 + - - +
337A ALA* 2.9 29.3 + - - +
422B ASN* 4.0 19.6 - - - +
425B ALA* 3.6 29.8 - - + +
426B LYS* 5.2 4.9 + - - +
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Residues in contact with HIS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN* 2.9 44.0 + - + +
331A GLY* 3.9 5.4 - - - +
333A GLN* 1.3 76.8 - - + +
335A GLN* 1.3 58.2 + - + +
337A ALA* 3.4 1.0 + - - +
338A HIS* 2.9 31.1 + - - +
418B ASN* 3.5 40.8 + - + -
421B LEU* 3.7 33.0 - - + +
422B ASN* 2.7 29.5 + - - -
331D GLY* 3.7 15.8 - - - -
335D GLN* 4.8 2.6 + - - -
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLY 3.2 19.4 + - - +
332A LEU* 3.3 8.5 + - - +
334A HIS* 1.3 77.0 - - - +
336A VAL* 1.3 56.8 + - - +
338A HIS* 3.4 6.3 + - - +
339A VAL* 3.0 34.5 + - - +
384A LYS* 3.7 28.8 + - + +
387A GLU* 4.6 2.4 - - - +
388A TRP* 3.0 31.9 + - + +
418C ASN* 3.0 31.3 + - - +
421C LEU* 6.0 1.0 - - - +
334D HIS* 4.7 4.0 + - - -
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PHE* 3.9 9.6 - - + -
313A ILE* 3.8 21.3 - - + -
316A ILE* 3.7 26.5 - - + -
327A PHE* 4.3 10.1 - - + -
332A LEU* 3.0 27.5 + - + +
333A GLN* 3.6 7.0 - - - +
335A GLN* 1.3 73.9 - - - +
337A ALA* 1.3 61.7 + - - +
339A VAL* 3.4 2.3 + - - +
340A ALA* 2.8 28.2 + - - +
388A TRP* 3.7 24.0 - - + -
425B ALA* 5.8 1.6 - - - -
428B ILE* 4.3 14.4 - - + -
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Residues in contact with ALA 337 (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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333A GLN 2.9 16.0 + - - +
334A HIS 3.9 1.1 - - - +
336A VAL* 1.3 79.0 - - - +
338A HIS* 1.3 56.3 + - - +
340A ALA* 3.4 4.0 + - - +
341A THR* 2.9 33.5 + - - -
421B LEU* 3.4 42.2 - - + +
424B ILE* 3.8 20.5 - - + +
425B ALA* 4.1 5.2 - - + +
428B ILE* 5.4 0.4 - - - -
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Residues in contact with HIS 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A HIS 2.9 18.3 + - - +
335A GLN* 3.7 7.0 - - - +
337A ALA* 1.3 76.3 - - - +
339A VAL* 1.3 66.0 + - + +
341A THR* 3.2 7.5 + - - -
342A GLN* 3.1 58.3 + - + +
380A GLN* 5.0 1.7 + - - -
372B TYR* 2.9 33.9 + + - +
373B TYR* 6.2 4.3 - + - -
421B LEU* 3.8 8.6 - - + +
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PHE* 3.7 25.4 - - + -
335A GLN 3.0 21.8 + - - +
336A VAL 3.7 2.9 - - - +
338A HIS* 1.3 78.9 - - + +
340A ALA* 1.3 63.0 + - - +
342A GLN* 3.2 20.1 + - - +
343A LEU* 2.9 22.8 + - + +
380A GLN* 5.0 1.8 - - + +
381A THR* 3.6 32.9 + - + +
384A LYS* 4.4 17.0 - - + -
388A TRP* 3.8 18.2 - - + -
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Residues in contact with ALA 340 (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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309A PHE* 4.0 12.5 - - + -
336A VAL 2.8 20.7 + - - +
337A ALA* 3.6 6.7 - - - +
339A VAL* 1.3 73.0 - - - +
341A THR* 1.3 56.7 + - - +
343A LEU* 3.4 8.7 + - - +
344A GLU* 3.0 29.1 + - - +
369B MET* 3.6 12.4 - - + +
424B ILE* 4.4 0.4 - - + -
428B ILE* 3.8 32.3 - - + -
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Residues in contact with THR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA 2.9 15.7 + - - -
338A HIS* 3.2 9.6 + - - -
340A ALA* 1.3 75.6 - - - +
342A GLN* 1.3 57.9 + - + +
344A GLU* 3.3 3.5 + - - +
345A ALA* 2.9 27.7 + - - +
349B LEU* 4.4 3.8 - - + +
369B MET* 3.5 49.2 - - + +
372B TYR* 4.2 14.1 - - + -
373B TYR* 3.9 26.0 - - + -
424B ILE* 3.8 9.5 - - - +
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Residues in contact with GLN 342 (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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338A HIS* 3.1 39.7 + - + +
339A VAL* 3.5 25.6 - - - +
341A THR* 1.3 73.9 - - - +
343A LEU* 1.3 59.3 + - - +
345A ALA 3.4 0.2 + - - -
346A ALA* 2.8 26.9 + - - +
373A TYR* 3.4 28.8 - - - +
377A ILE* 4.0 27.4 - - + +
380A GLN* 3.1 30.9 + - - +
381A THR* 5.1 1.6 + - - +
373B TYR* 5.3 5.2 - - + -
1438B CL 4.1 13.3 - - - +
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Residues in contact with LEU 343 (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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302A LEU* 3.6 13.6 - - + +
305A ALA* 3.6 31.9 - - + +
306A GLN* 4.0 27.4 - - - +
309A PHE* 3.6 47.6 - - + -
339A VAL* 2.9 19.3 + - + +
340A ALA* 3.6 9.4 - - - +
342A GLN* 1.3 75.8 - - - +
344A GLU* 1.3 57.5 + - - +
346A ALA* 3.3 0.7 + - - -
347A ARG* 2.9 32.1 + - - +
377A ILE* 3.8 13.5 - - + -
381A THR* 4.2 6.1 - - + +
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Residues in contact with GLU 344 (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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55A GLN* 3.7 22.3 + - - -
340A ALA 3.0 13.5 + - - +
341A THR 3.4 8.5 - - - +
343A LEU* 1.3 77.5 - - - +
345A ALA* 1.3 57.1 + - - +
347A ARG* 3.3 18.1 + - - +
348A LEU* 3.0 36.6 + - + +
349B LEU* 3.6 19.5 - - + -
352B ASN* 4.4 6.2 + - - -
365B LYS* 4.5 11.4 + - - -
366B GLU* 4.2 20.4 - - + +
369B MET* 3.7 24.0 - - - +
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A THR 2.9 16.6 + - - +
342A GLN 3.7 4.3 - - - +
344A GLU* 1.3 75.8 - - - +
346A ALA* 1.3 57.2 + - - +
348A LEU* 3.4 4.5 + - - +
349A LEU* 3.0 32.7 + - - +
373A TYR* 3.9 20.2 - - + +
345B ALA* 3.9 21.8 - - + +
349B LEU* 4.1 21.3 - - + +
373B TYR* 4.9 2.5 - - + -
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Residues in contact with ALA 346 (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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302A LEU* 4.2 9.2 - - + -
342A GLN 2.8 19.9 + - - +
343A LEU 3.7 4.3 - - - +
345A ALA* 1.3 71.2 - - - +
347A ARG* 1.3 60.4 + - - +
349A LEU* 3.5 4.2 + - - +
350A THR* 2.8 34.1 + - - -
370A ALA 5.5 0.2 - - - +
373A TYR* 3.7 20.7 - - + -
374A ALA* 4.0 16.9 - - + +
377A ILE* 4.0 17.3 - - + -
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Residues in contact with ARG 347 (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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55A GLN* 4.8 16.2 - - - +
126A GLU* 2.9 28.7 + - - -
130A LYS* 4.8 1.2 - - - +
302A LEU* 3.6 25.7 - - + +
306A GLN* 2.9 45.6 + - - +
343A LEU* 2.9 20.4 + - - +
344A GLU* 3.5 20.6 + - - +
346A ALA* 1.3 75.1 - - - +
348A LEU* 1.3 59.6 + - + +
350A THR* 3.2 1.7 + - - -
351A TYR* 2.9 71.3 + - + -
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Residues in contact with LEU 348 (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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54A LEU* 3.3 35.8 - - + +
55A GLN* 4.1 12.3 - - - +
344A GLU* 3.0 20.9 + - + +
345A ALA* 3.9 4.5 - - - +
346A ALA 3.3 0.2 - - - -
347A ARG* 1.3 74.7 - - + +
349A LEU* 1.3 60.8 + - - +
351A TYR* 4.8 0.7 - - + -
352A ASN* 2.9 33.4 + - - +
348B LEU* 3.5 41.7 - - + +
349B LEU* 3.7 26.5 - - + +
352B ASN* 3.8 26.7 - - + +
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA 3.0 16.9 + - - +
346A ALA* 3.8 3.4 - - - +
348A LEU* 1.3 75.1 - - - +
350A THR* 1.3 62.5 + - - +
352A ASN* 4.0 0.9 - - - +
353A ALA* 3.1 25.8 + - - +
366A GLU* 4.6 3.9 - - + +
369A MET* 4.1 16.2 - - + +
370A ALA* 3.7 15.2 - - + +
373A TYR* 3.6 43.3 - - + -
341B THR* 4.3 7.0 - - + +
344B GLU* 3.4 37.7 - - + -
345B ALA* 4.0 17.3 - - + +
348B LEU* 3.7 12.5 - - + +
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Residues in contact with THR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A VAL* 3.9 25.1 - - + -
295A ILE* 3.7 14.4 - - + +
298A ALA* 3.6 21.5 + - + +
299A ALA* 3.9 21.8 - - - +
302A LEU* 4.3 7.8 - - + +
346A ALA 2.8 23.1 + - - -
347A ARG 3.6 4.3 - - - -
349A LEU* 1.3 77.8 - - - +
351A TYR* 1.3 64.3 + - + +
353A ALA* 3.4 3.1 + - - +
354A ALA* 3.2 18.4 + - - +
370A ALA* 3.9 9.6 - - - +
374A ALA* 4.5 3.3 - - - +
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Residues in contact with TYR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.5 39.3 - - + +
55A GLN* 4.5 5.8 - - + -
57A PHE* 3.7 21.2 - + - -
65A LYS* 5.4 3.5 + - - -
119A LEU* 4.1 21.7 - - + +
122A VAL* 4.3 10.8 - - + -
123A LEU* 3.5 19.4 - - + +
126A GLU* 2.5 37.2 + - - -
302A LEU* 4.3 6.5 - - + -
347A ARG* 2.9 47.6 + - + +
348A LEU* 4.2 2.5 - - + +
350A THR* 1.3 78.2 - - + +
352A ASN* 1.3 58.4 + - - +
354A ALA* 3.3 3.1 + - - +
355A ARG* 2.9 33.4 + - - +
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Residues in contact with ASN 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU* 3.8 21.0 - - + +
348A LEU 2.9 20.4 + - - +
349A LEU 4.0 1.1 - - - +
351A TYR* 1.3 75.0 - - - +
353A ALA* 1.3 60.4 + - - +
355A ARG* 3.2 5.2 + - - +
356A LEU* 2.8 61.0 + - - +
366A GLU* 4.9 1.8 - - - +
344B GLU* 4.1 13.1 + - - -
348B LEU* 3.7 29.7 - - + +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 3.8 25.8 - - + +
349A LEU 3.1 19.8 + - - +
350A THR 3.7 4.5 - - - +
352A ASN* 1.3 75.1 - - - +
354A ALA* 1.3 62.4 + - - +
356A LEU* 3.3 4.9 + - - +
357A LEU* 3.1 23.2 + - - +
363A PHE* 4.0 3.5 - - - +
366A GLU* 3.8 36.5 - - + +
367A ALA* 4.0 1.6 - - - +
370A ALA* 4.5 2.2 - - + -
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 3.8 31.8 - - + -
119A LEU* 3.8 24.9 - - + -
122A VAL* 4.1 7.2 - - + -
295A ILE* 4.0 2.3 - - + +
350A THR 3.2 13.1 + - - +
351A TYR 3.5 8.7 - - - +
352A ASN 3.2 0.2 - - - -
353A ALA* 1.3 77.0 - - - +
355A ARG* 1.3 57.6 + - - +
357A LEU* 3.4 3.9 + - - +
358A GLU* 3.1 33.6 + - - +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 5.0 7.5 + - - +
53A PRO 4.2 6.9 + - - -
54A LEU* 2.5 57.4 + - + +
56A THR 3.2 26.7 + - - -
57A PHE* 4.0 2.0 - - - +
61A GLU* 5.2 0.2 + - - -
119A LEU* 3.6 29.1 - - + +
351A TYR* 2.9 15.4 + - - +
352A ASN* 3.2 7.8 + - - +
354A ALA* 1.3 74.6 - - - +
356A LEU* 1.3 65.7 + - - +
358A GLU* 3.4 17.7 + - - +
359A ALA* 3.1 24.3 + - - +
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Residues in contact with LEU 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ASN* 2.8 38.0 + - - +
353A ALA* 3.6 4.9 - - - +
355A ARG* 1.3 77.6 - - - +
357A LEU* 1.3 62.5 + - - +
359A ALA* 3.2 8.1 + - + -
361A LYS* 3.0 48.8 + - + +
362A PRO 3.9 7.6 - - - +
363A PHE* 3.9 9.0 - - + -
366A GLU* 3.4 45.8 - - + +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 3.9 39.5 - - + -
292A GLU* 3.5 40.4 - - + +
295A ILE* 4.2 2.2 - - + -
353A ALA 3.1 13.6 + - - +
354A ALA* 3.6 7.9 - - - +
355A ARG 3.4 0.2 - - - -
356A LEU* 1.3 77.0 - - - +
358A GLU* 1.3 67.2 + - - +
360A GLY* 3.2 13.7 + - - -
361A LYS 4.5 0.7 - - - -
363A PHE* 3.9 37.1 - - + +
----------------------------------------------------------
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Residues in contact with GLU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLU* 4.7 3.0 - - - +
117A SER* 3.2 15.4 + - - -
118A PHE* 3.1 24.5 + - + +
119A LEU* 2.9 37.9 + - - +
354A ALA 3.1 16.2 + - - +
355A ARG* 3.8 16.7 - - - +
357A LEU* 1.3 80.0 - - + +
359A ALA* 1.3 58.9 + - - +
360A GLY 3.2 1.5 + - - -
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A ARG 3.1 17.8 + - - +
356A LEU* 3.2 6.4 + - + +
358A GLU* 1.3 74.7 - - - +
360A GLY* 1.3 61.9 + - - +
361A LYS* 3.4 27.2 + - + +
----------------------------------------------------------
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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