Contacts of the helix formed by residues 335 - 367 (chain E) in PDB entry 1R4N
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 335 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E ASP* 3.6 17.2 - - - +
211E HIS* 3.4 31.5 + - + +
334E ALA* 1.3 77.9 - - - +
336E SER* 1.3 84.6 + - - +
337E GLY* 3.2 12.6 + - - -
338E LYS* 3.4 35.8 + - + +
339E TYR* 3.1 17.0 + - - +
221F MET* 4.4 3.6 - - - -
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Residues in contact with SER 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E ALA 3.5 1.4 + - - -
335E ASP* 1.3 82.5 + - - +
337E GLY* 1.3 62.5 + - - -
339E TYR* 3.4 2.4 + - - +
340E ILE* 3.4 24.1 + - - +
220F SER 4.6 2.0 - - - -
221F MET* 3.8 16.1 - - - +
222F PRO 3.2 23.8 + - - +
223F ARG* 5.2 0.6 - - - +
271F TYR* 2.9 43.6 + - - +
273F ILE* 5.2 0.2 - - - +
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Residues in contact with GLY 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335E ASP* 3.2 6.3 + - - -
336E SER* 1.3 79.8 + - - +
338E LYS* 1.3 57.0 + - - +
340E ILE* 3.7 9.6 - - - +
341E LYS* 3.0 30.1 + - - +
271F TYR 6.0 0.4 - - - -
272F ASN* 5.9 1.6 - - - -
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Residues in contact with LYS 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E HIS* 5.0 0.3 + - - -
199E TYR* 4.2 30.9 + - + +
208E ASP* 2.7 34.1 + - - -
211E HIS 3.0 20.6 + - - +
212E THR* 4.0 8.6 + - - -
213E PRO* 4.3 11.1 - - + +
335E ASP* 3.4 27.0 + - + +
336E SER 3.2 1.2 - - - -
337E GLY* 1.3 73.8 - - - +
339E TYR* 1.3 66.1 + - - +
341E LYS* 3.5 6.7 + - - +
342E LEU* 3.2 21.5 + - - +
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Residues in contact with TYR 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213E PRO* 4.3 8.4 - - - +
329E ILE* 2.9 27.9 + - + +
330E PRO 2.8 21.1 + - - -
331E ASP* 3.5 7.4 + - - -
332E MET* 3.2 47.1 - - + -
334E ALA* 4.0 5.2 - - + -
335E ASP 3.1 18.1 + - - +
336E SER 3.8 2.9 - - - +
338E LYS* 1.3 76.5 - - - +
340E ILE* 1.3 63.4 + - + +
342E LEU* 3.2 5.6 + - - +
343E GLN* 2.8 50.9 + - + -
223F ARG* 3.6 43.5 - - + -
224F LEU* 4.5 6.2 - - + +
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Residues in contact with ILE 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336E SER* 3.4 14.5 + - - +
337E GLY* 3.7 10.3 - - - +
338E LYS 3.3 0.2 - - - -
339E TYR* 1.3 82.8 - - + +
341E LYS* 1.3 61.2 + - - +
343E GLN* 2.6 39.6 + - + +
344E ASN* 2.7 28.5 + - - +
222F PRO 5.6 0.2 - - - +
223F ARG* 4.9 4.7 - - - +
271F TYR 3.1 28.3 - - - +
272F ASN* 3.3 29.4 - - - +
273F ILE* 3.8 17.7 - - + -
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Residues in contact with LYS 341 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E HIS* 3.9 25.5 + - + +
198E SER* 4.6 13.3 + - - -
199E TYR* 6.0 1.7 - - + +
337E GLY 3.0 17.8 + - - +
338E LYS* 3.8 7.4 - - - +
339E TYR 3.4 0.2 - - - -
340E ILE* 1.3 79.0 - - - +
342E LEU* 1.3 63.4 + - - +
344E ASN* 3.2 8.6 + - - +
345E VAL* 3.0 26.0 + - + +
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Residues in contact with LEU 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E LEU* 4.4 5.8 - - + -
195E HIS* 3.8 31.8 + - + +
196E PHE* 4.8 3.8 - - + -
213E PRO* 3.7 14.1 - - + -
215E ILE* 3.9 15.3 - - + -
216E VAL* 4.8 2.9 - - + -
329E ILE* 3.7 10.5 - - + -
332E MET* 3.2 35.2 - - + -
338E LYS 3.2 10.0 + - - +
339E TYR* 3.2 9.6 + - - +
340E ILE 3.0 0.6 - - - -
341E LYS* 1.3 75.7 - - - +
343E GLN* 1.3 70.3 + - - +
345E VAL* 3.2 8.6 + - + +
346E TYR* 3.2 42.8 - - + -
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Residues in contact with GLN 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E GLY 4.8 6.9 - - - +
328E THR* 6.0 0.8 - - - +
329E ILE* 3.5 26.7 + - + +
339E TYR* 2.8 40.8 + - + +
340E ILE* 2.6 27.3 + - - +
342E LEU* 1.3 70.6 - - - +
344E ASN* 1.3 65.3 + - - +
346E TYR* 2.9 10.0 + - - +
347E ARG* 2.9 24.4 + - + -
223F ARG 4.8 5.4 + - - +
224F LEU* 5.1 7.1 - - - +
273F ILE* 5.8 1.7 - - - +
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Residues in contact with ASN 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340E ILE* 2.7 32.3 + - - +
341E LYS* 3.5 11.9 - - + +
343E GLN* 1.3 74.5 - - - +
345E VAL* 1.3 58.4 + - - +
347E ARG* 3.8 29.5 + - - +
348E GLU* 2.7 49.0 + - + +
274F ARG* 5.7 4.2 - - - +
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Residues in contact with VAL 345 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E PHE* 4.0 5.9 - - + -
191E GLU* 4.0 12.7 - - + +
192E LEU* 3.6 42.2 - - + +
195E HIS* 3.7 29.2 - - + +
341E LYS* 3.0 19.6 + - + +
342E LEU* 3.3 11.2 - - + +
344E ASN* 1.3 77.1 - - - +
346E TYR* 1.3 63.6 + - + +
348E GLU* 3.9 4.3 - - - +
349E LYS* 3.1 20.6 + - - +
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Residues in contact with TYR 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182E ASP 3.7 9.6 - - - -
183E LEU* 2.9 45.0 + - - +
184E ARG* 4.9 0.2 - - + -
185E LEU* 5.3 0.5 - - - +
189E PHE* 4.3 20.9 - + - -
192E LEU* 3.6 21.7 - - + +
215E ILE* 3.7 18.0 - - + +
325E VAL* 4.4 9.2 - - + +
327E GLY* 3.8 19.4 - - - -
328E THR 5.3 0.2 - - - -
329E ILE* 3.7 27.6 - - + -
342E LEU* 3.2 44.0 - - + -
343E GLN 2.9 7.4 + - - +
345E VAL* 1.3 79.5 - - + +
347E ARG* 1.3 66.2 + - - +
349E LYS* 3.2 2.8 + - - +
350E ALA* 2.8 25.3 + - - +
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Residues in contact with ARG 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E GLY 4.0 12.9 + - - +
343E GLN* 2.9 17.9 + - + +
344E ASN* 3.4 31.8 + - - +
346E TYR* 1.3 77.4 - - - +
348E GLU* 1.3 73.6 + - + +
350E ALA* 3.1 6.4 + - - +
351E LYS* 2.9 23.6 + - + +
274F ARG* 2.7 54.8 - - - +
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Residues in contact with GLU 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E GLU* 6.4 1.6 - - + -
344E ASN* 2.7 34.0 + - + +
345E VAL* 3.9 4.5 - - - +
347E ARG* 1.3 79.7 + - + +
349E LYS* 1.3 67.2 + - - +
351E LYS* 3.0 27.1 + - - +
352E LYS* 3.0 41.3 + - - +
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Residues in contact with LYS 349 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ARG* 5.8 0.7 - - - +
189E PHE* 3.4 54.6 - - + +
190E PRO* 5.3 3.0 - - - +
191E GLU* 4.2 15.8 + - - +
318E GLU 5.4 5.3 + - - -
325E VAL* 3.4 25.8 - - + -
345E VAL 3.1 9.5 + - - +
346E TYR 3.6 4.0 - - - +
348E GLU* 1.3 76.4 - - - +
350E ALA* 1.3 63.8 + - - +
352E LYS* 2.9 24.0 + - + +
353E ASP* 2.9 50.4 + - - +
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Residues in contact with ALA 350 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E PRO* 5.6 0.7 - - - +
325E VAL* 3.2 31.0 - - - +
326E ARG 3.5 15.0 - - - +
327E GLY* 3.8 5.8 - - - +
346E TYR 2.8 12.7 + - - +
347E ARG* 3.3 9.4 - - - +
349E LYS* 1.3 76.3 - - - +
351E LYS* 1.3 58.1 + - - +
353E ASP* 3.5 3.3 + - - +
354E ALA* 2.8 28.6 + - - +
384E CYS* 5.8 1.4 - - - +
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Residues in contact with LYS 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E ARG* 2.9 15.1 + - + +
348E GLU* 3.0 30.7 + - - +
350E ALA* 1.3 76.3 - - - +
352E LYS* 1.3 60.0 + - + +
354E ALA* 2.8 23.2 - - - +
355E ALA* 3.2 8.3 + - - +
381E LYS* 4.3 29.2 - - - +
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Residues in contact with LYS 352 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E GLU* 3.3 34.1 + - - +
348E GLU* 3.0 33.2 + - - +
349E LYS* 2.9 15.7 + - + +
351E LYS* 1.3 73.2 - - + +
353E ASP* 1.3 68.5 + - - +
354E ALA 2.8 4.4 + - - -
355E ALA* 2.8 17.4 + - - +
356E ALA* 3.0 10.8 + - - +
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Residues in contact with ASP 353 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ARG* 5.6 0.3 + - - -
314E PHE* 3.0 33.7 - - + -
318E GLU 5.1 1.5 - - - +
319E GLY* 5.3 0.5 - - - -
323E LEU 4.5 1.2 - - - +
324E PRO* 3.7 14.2 - - + +
325E VAL* 3.6 18.0 + - - +
349E LYS* 2.9 50.1 + - - +
350E ALA 3.9 3.1 - - - +
352E LYS* 1.3 74.8 - - - +
354E ALA* 1.3 63.6 + - - +
356E ALA* 3.2 4.9 - - - +
357E VAL* 3.0 29.6 + - - +
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Residues in contact with ALA 354 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E PRO* 5.1 0.4 - - - +
350E ALA 2.8 16.4 + - - +
351E LYS* 2.8 24.0 - - + +
352E LYS 2.8 0.6 + - - -
353E ASP* 1.3 78.3 - - - +
355E ALA* 1.3 54.9 + - - +
357E VAL* 3.2 5.4 + - - +
358E GLY* 2.9 22.3 + - - -
380E LEU* 3.8 10.5 - - + +
381E LYS* 4.9 20.2 - - + -
384E CYS* 4.2 20.4 - - + -
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Residues in contact with ALA 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E LYS 3.2 5.1 + - - +
352E LYS* 2.8 11.8 + - - +
354E ALA* 1.3 72.8 - - - +
356E ALA* 1.3 55.4 + - - +
358E GLY* 2.5 24.3 + - - +
359E ASN* 2.6 26.8 + - - +
380E LEU* 5.0 2.9 - - - -
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Residues in contact with ALA 356 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E PHE* 3.3 22.7 - - + -
318E GLU* 3.7 20.5 - - + +
352E LYS 3.0 8.3 + - - +
353E ASP* 3.2 14.8 + - - +
355E ALA* 1.3 75.1 - - - +
357E VAL* 1.3 63.0 + - - +
359E ASN* 3.0 21.0 + - - +
360E HIS* 3.2 20.8 + - - -
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Residues in contact with VAL 357 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E ALA* 3.6 16.6 - - + +
311E LEU* 3.3 25.4 - - + -
314E PHE* 3.4 19.0 - - + -
324E PRO* 3.5 23.6 - - + -
353E ASP 3.0 16.0 + - - +
354E ALA 3.4 5.4 - - - +
356E ALA* 1.3 74.5 - - - +
358E GLY* 1.3 62.1 + - - +
360E HIS* 3.5 10.7 + - - +
361E VAL* 3.0 27.3 + - + +
380E LEU* 4.2 12.6 - - + -
383E LEU* 4.9 2.7 - - + -
384E CYS* 4.0 8.7 - - - -
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Residues in contact with GLY 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E ALA 2.9 6.7 + - - -
355E ALA* 2.5 16.2 + - - -
357E VAL* 1.3 74.1 - - - +
359E ASN* 1.3 63.7 + - - +
361E VAL* 3.3 5.7 - - - +
362E ALA* 3.2 17.8 + - - +
380E LEU* 3.3 29.6 - - - +
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Residues in contact with ASN 359 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E GLU* 5.7 2.5 - - - +
355E ALA* 2.6 20.8 + - - +
356E ALA* 3.0 12.7 + - - +
358E GLY* 1.3 70.7 - - - +
360E HIS* 1.3 69.9 + - + +
361E VAL 2.9 1.3 - - - -
362E ALA* 2.8 21.1 + - - +
363E LYS* 2.9 31.8 + - + +
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Residues in contact with HIS 360 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310E ALA* 3.6 22.9 - - - +
313E GLU* 3.9 26.1 + - + +
314E PHE* 3.7 26.7 - - + -
317E LYS* 3.8 17.5 - - + -
318E GLU* 2.7 35.7 + - - -
356E ALA 3.2 20.6 + - - -
357E VAL 3.5 1.8 + - - +
359E ASN* 1.3 76.7 - - + +
361E VAL* 1.3 63.3 + - - +
363E LYS* 3.4 23.9 + - - +
364E LEU* 2.9 30.9 + - + +
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Residues in contact with VAL 361 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ILE* 4.4 2.9 - - + -
307E LEU* 3.8 18.2 - - + -
310E ALA* 3.3 23.1 - - + -
357E VAL* 3.0 24.7 + - + +
358E GLY* 3.3 12.6 - - - +
359E ASN 2.8 0.8 + - - -
360E HIS* 1.3 75.1 - - - +
362E ALA* 1.3 65.8 + - - +
364E LEU* 2.8 8.6 + - - +
365E LEU* 2.8 44.1 + - + +
372E PRO 5.7 0.4 - - - +
375E ILE* 4.0 22.4 - - + -
380E LEU* 4.2 8.1 - - + -
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Residues in contact with ALA 362 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358E GLY 3.2 7.3 + - - +
359E ASN* 2.8 15.5 + - - +
361E VAL* 1.3 75.9 - - - +
363E LYS* 1.3 64.9 + - + +
365E LEU* 2.9 15.4 + - - +
366E GLN* 2.7 31.0 + - + +
372E PRO* 4.0 21.9 - - + +
----------------------------------------------------------
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Residues in contact with LYS 363 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317E LYS* 4.0 21.8 - - - +
359E ASN* 2.9 32.2 + - - +
360E HIS* 3.6 27.5 + - - +
362E ALA* 1.3 72.4 - - + +
364E LEU* 1.3 68.5 + - + +
366E GLN* 3.1 16.5 + - - +
367E SER* 3.0 22.5 + - - -
----------------------------------------------------------
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Residues in contact with LEU 364 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297E ILE* 4.2 14.8 - - + -
306E ILE* 3.7 20.4 - - + +
309E ARG* 3.2 40.8 - - + +
310E ALA* 3.6 23.3 - - + +
313E GLU* 4.9 9.9 - - + -
360E HIS* 2.9 14.6 + - - +
361E VAL* 2.8 13.8 + - - +
363E LYS* 1.3 73.6 - - + +
365E LEU* 1.3 67.3 + - - +
366E GLN 2.9 1.4 + - - -
367E SER* 3.0 25.9 + - - +
368E ILE* 3.5 13.8 + - + +
----------------------------------------------------------
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Residues in contact with LEU 365 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306E ILE* 3.6 27.6 - - + -
361E VAL* 2.8 39.2 + - + +
362E ALA* 3.4 7.0 - - - +
364E LEU* 1.3 73.2 - - - +
366E GLN* 1.3 56.7 + - - +
368E ILE* 3.3 7.5 + - - +
369E GLY 3.0 19.2 + - - -
370E GLN* 2.9 35.7 + - + +
371E ALA 4.1 2.9 - - - +
372E PRO* 3.6 33.9 - - + +
374E SER* 4.6 9.6 - - - +
375E ILE* 4.0 26.5 - - + +
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Residues in contact with GLN 366 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E ALA* 2.7 21.0 + - - +
363E LYS* 3.2 20.9 + - - +
364E LEU 2.9 0.6 + - - -
365E LEU* 1.3 68.9 - - - +
367E SER* 1.3 52.7 + - - +
368E ILE 2.4 19.7 + - - -
369E GLY* 2.9 14.4 + - - +
370E GLN 4.5 2.7 - - - -
372E PRO* 3.7 24.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 367 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E LYS 3.0 11.0 + - - -
364E LEU* 3.0 23.0 + - - +
366E GLN* 1.3 72.3 - - - +
368E ILE* 1.3 63.5 + - - +
----------------------------------------------------------
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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