Contacts of the helix formed by residues 249 - 280 (chain E) in PDB entry 3X0X
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 LEU 249 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E LEU* 4.4 7.0 - - + -
246E ARG* 3.1 28.2 + - + +
248E SER* 1.3 76.0 + - - +
250E PHE* 1.3 66.6 + - - +
252E PRO* 3.2 6.6 - - + +
253E ILE* 3.2 33.8 + - + +
323E LEU* 5.0 4.5 - - + -
326E VAL* 4.0 24.2 - - + +
327E TRP* 4.3 30.5 - - + +
333E LEU* 4.2 9.4 - - + -
338E ARG* 4.0 21.3 - - + -
341E LEU* 3.8 26.7 - - + -
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Residues in contact with PHE 250 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E TYR* 5.6 9.6 - + - -
99E THR* 4.3 20.4 - - - -
103E MET* 3.7 45.1 - - + -
106E LEU* 4.1 12.8 - - + +
129E ASN* 6.2 1.1 - - - -
131E SER* 4.8 6.7 - - - -
132E SER* 4.9 4.9 - - - -
174E PHE* 4.6 7.4 - + - -
237E PHE* 4.4 10.8 - + + -
241E PHE* 4.6 6.7 - - + -
247E GLY 3.4 14.8 + - - +
248E SER 3.1 0.8 - - - -
249E LEU* 1.3 80.4 - - - +
251E ALA* 1.3 62.6 + - - +
253E ILE* 3.6 4.8 - - + +
254E ALA* 3.1 29.4 + - + +
415E PHE* 3.7 47.8 - + + -
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Residues in contact with ALA 251 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E SER 4.2 1.2 + - - -
250E PHE* 1.3 78.8 - - - +
252E PRO* 1.4 69.9 - - + +
254E ALA* 4.7 1.6 - - - -
255E GLN* 2.9 30.9 + - - +
338E ARG* 3.8 0.7 - - - +
342E MET* 3.9 3.4 - - - -
414E GLY 3.4 13.6 + - - +
415E PHE 3.7 14.4 - - - +
416E THR 3.7 3.6 - - - -
417E SER* 3.2 41.1 - - - +
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Residues in contact with PRO 252 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E SER 3.4 10.3 - - - +
249E LEU* 3.2 28.0 - - + +
251E ALA* 1.4 93.9 - - + +
253E ILE* 1.3 60.2 + - - +
256E LEU* 3.1 26.7 + - - +
323E LEU* 5.0 3.7 - - + +
338E ARG* 3.8 9.4 - - - +
341E LEU* 3.8 35.4 - - + -
342E MET* 3.8 20.6 - - + +
345E VAL* 3.8 14.3 - - + +
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Residues in contact with ILE 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E TRP* 3.6 44.2 - - + -
99E THR* 4.2 16.4 - - + +
102E PRO* 4.9 4.5 - - + -
106E LEU* 4.6 8.7 - - + -
249E LEU* 3.2 25.7 + - + +
250E PHE* 3.6 5.6 - - + +
252E PRO* 1.3 77.1 - - - +
254E ALA* 1.3 65.6 + - - +
256E LEU* 3.8 1.4 - - - +
257E ILE* 3.0 30.6 + - + +
323E LEU* 3.9 25.7 - - + +
327E TRP* 3.9 20.9 - - + -
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Residues in contact with ALA 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E TYR* 5.2 5.4 - - + +
99E THR* 4.0 21.5 - - + -
250E PHE* 3.1 22.6 + - + +
251E ALA* 4.0 5.2 - - - +
253E ILE* 1.3 77.9 - - - +
255E GLN* 1.3 60.8 + - + +
257E ILE* 3.2 4.2 + - - +
258E PHE* 2.9 51.7 + - + -
415E PHE 5.3 4.9 - - - +
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Residues in contact with GLN 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251E ALA* 2.9 21.7 + - - +
254E ALA* 1.3 77.4 - - + +
256E LEU* 1.3 60.3 + - - +
258E PHE* 3.4 18.6 + - - +
259E ALA* 3.1 27.0 + - - +
342E MET* 4.1 7.4 - - + -
345E VAL* 3.7 18.1 - - + +
349E LYS* 2.7 36.0 + - + +
391E HIS* 4.2 0.8 + - - -
392E ASP* 2.6 28.4 + - - -
397E LYS* 3.4 16.6 - - - -
415E PHE 5.1 0.8 + - - -
416E THR* 3.7 30.3 - - - +
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Residues in contact with LEU 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ILE* 3.6 21.8 - - + -
252E PRO 3.1 19.8 + - - +
253E ILE* 3.9 2.5 - - - +
255E GLN* 1.3 72.7 - - - +
257E ILE* 1.3 67.8 + - - +
259E ALA* 3.4 1.2 + - - -
260E ASN* 2.8 47.1 + - - +
316E ALA 4.3 4.3 - - - +
319E ALA* 4.0 21.3 - - + +
320E ALA* 3.8 24.9 - - + +
323E LEU* 4.1 13.5 - - + -
345E VAL* 3.7 15.4 - - + +
348E VAL* 3.9 25.1 - - + -
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Residues in contact with ILE 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E TRP* 4.0 24.2 - - + -
77E ILE* 4.5 18.2 - - + -
80E VAL* 4.4 9.4 - - + +
95E GLY* 3.6 38.8 - - - +
96E TYR 4.3 1.1 - - - +
98E LEU* 4.4 9.9 - - + -
99E THR* 3.4 27.1 - - + +
253E ILE* 3.0 15.3 + - + +
254E ALA 3.2 8.7 + - - +
256E LEU* 1.3 76.6 - - - +
258E PHE* 1.4 71.5 + - + +
260E ASN* 3.1 8.7 + - - +
261E VAL* 2.9 24.8 + - + +
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Residues in contact with PHE 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E HIS* 4.1 8.5 - + - -
96E TYR* 3.7 48.7 - + + -
99E THR* 5.8 0.2 - - + -
254E ALA* 2.9 37.3 + - + -
255E GLN* 3.7 26.2 - - - +
256E LEU 3.3 0.2 - - - -
257E ILE* 1.4 82.3 - - + +
259E ALA* 1.3 64.4 + - - +
261E VAL* 3.1 8.3 + - + +
262E TYR* 3.0 35.9 + - + +
349E LYS* 4.0 14.6 - - - -
388E HIS* 3.4 27.8 - + + -
391E HIS* 3.8 25.1 - + - -
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Residues in contact with ALA 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E GLN 3.1 17.1 + - - +
256E LEU* 3.8 5.4 - - - +
257E ILE 3.3 0.2 - - - -
258E PHE* 1.3 76.2 - - - +
260E ASN* 1.3 58.2 + - - +
262E TYR* 3.3 7.1 + - - -
263E LEU* 3.0 25.6 + - - +
348E VAL* 3.7 31.9 - - + +
349E LYS* 4.0 11.1 - - - +
352E ALA* 3.3 25.9 - - + +
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Residues in contact with ASN 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ILE* 3.2 37.0 - - + +
80E VAL* 4.6 6.1 - - + -
81E ARG* 3.2 38.7 + - + +
256E LEU* 2.8 42.0 + - - +
257E ILE* 3.1 10.5 + - - +
259E ALA* 1.3 74.7 - - - +
261E VAL* 1.3 59.8 + - - +
263E LEU* 3.3 2.8 + - - +
264E GLY* 2.9 26.3 + - - -
316E ALA* 3.9 17.6 + - - +
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Residues in contact with VAL 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E VAL* 3.7 12.7 - - + +
84E ALA* 3.7 11.0 - - + +
88E GLY 4.0 16.2 - - - +
91E GLY 3.7 24.0 - - - +
92E HIS* 3.9 13.7 - - + +
210E MET* 4.1 9.9 - - + -
257E ILE* 2.9 23.6 + - + +
258E PHE* 3.1 14.1 + - + +
260E ASN* 1.3 74.5 - - - +
262E TYR* 1.3 67.8 + - + +
264E GLY* 3.2 1.9 + - - -
265E ILE* 2.9 39.4 + - + +
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Residues in contact with TYR 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E MET* 5.2 0.2 - - + -
258E PHE* 3.0 18.0 + - + -
259E ALA* 3.3 9.4 + - - +
261E VAL* 1.3 81.9 - - + +
263E LEU* 1.3 58.5 + - - +
265E ILE* 3.1 13.4 + - + +
266E ALA* 2.7 29.1 + - - +
349E LYS* 3.5 29.2 + - + -
352E ALA* 4.1 5.6 - - + +
353E THR* 3.4 35.9 - - - -
356E ALA* 3.6 21.7 - - + +
385E VAL* 4.3 12.8 - - + -
388E HIS* 2.9 54.1 + + + -
389E SER* 3.3 18.5 - - - -
391E HIS* 4.9 0.2 - - - +
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Residues in contact with LEU 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E ARG* 3.5 28.5 - - - +
259E ALA* 3.0 22.3 + - + +
260E ASN* 3.9 4.5 - - - +
261E VAL 3.1 0.2 - - - -
262E TYR* 1.3 74.1 - - - +
264E GLY* 1.3 66.7 + - - +
266E ALA* 3.8 4.2 - - + +
267E HIS* 2.9 32.2 + - + -
309E LEU* 3.7 18.8 - - + -
312E ALA* 3.6 31.2 - - + +
313E ASP* 3.5 11.2 - - - +
316E ALA* 3.9 20.9 - - + -
348E VAL* 5.2 1.1 - - + -
352E ALA* 3.9 22.7 - - + +
355E ALA* 4.8 2.7 - - + -
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Residues in contact with GLY 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E ARG* 3.6 28.1 - - - +
84E ALA* 4.1 1.3 - - - -
85E ALA* 3.2 19.3 - - - +
260E ASN 2.9 14.4 + - - -
261E VAL 3.6 3.6 - - - -
263E LEU* 1.3 75.3 - - - +
265E ILE* 1.3 61.6 + - - +
267E HIS* 3.2 5.5 + - - +
268E GLY 2.9 17.8 + - - -
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Residues in contact with ILE 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E ALA 3.8 8.7 - - - +
85E ALA* 4.6 0.7 - - - +
88E GLY* 3.7 25.4 - - - +
210E MET* 3.8 30.5 - - + -
261E VAL* 2.9 25.0 + - + +
262E TYR* 3.1 10.7 + - + +
264E GLY* 1.3 76.0 - - - +
266E ALA* 1.3 57.4 + - - +
268E GLY* 3.0 3.1 + - - +
269E ALA* 2.8 27.9 + - - +
381E PHE* 3.6 42.0 - - + +
384E ASN* 4.0 9.6 - - + +
385E VAL* 3.7 15.5 - - + +
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Residues in contact with ALA 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E TYR 2.7 20.1 + - - +
263E LEU* 3.3 2.7 + - + +
265E ILE* 1.3 72.6 - - - +
267E HIS* 1.3 57.6 + - - +
269E ALA* 3.2 8.3 + - - +
270E LEU* 3.0 28.4 + - - +
309E LEU* 3.8 26.2 - - + -
356E ALA* 3.8 27.8 - - + +
359E ILE* 3.9 14.8 - - + +
360E SER* 5.8 0.4 - - - -
385E VAL* 6.0 0.2 - - - -
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Residues in contact with HIS 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E ARG* 3.3 18.7 + - - -
85E ALA* 4.6 8.1 - - + -
263E LEU 2.9 27.6 + - - +
264E GLY* 3.6 9.0 - - - +
266E ALA* 1.3 75.4 - - - +
268E GLY* 1.3 57.7 + - - +
270E LEU* 3.9 8.2 - - + +
271E ASP* 3.1 42.7 + - - +
309E LEU* 3.9 24.7 - - + +
313E ASP* 2.6 29.1 + - - -
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Residues in contact with GLY 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ARG* 5.6 1.8 - - - -
85E ALA* 3.7 28.0 - - - +
264E GLY 2.9 11.3 + - - -
265E ILE 3.0 3.8 + - - -
267E HIS* 1.3 73.1 - - - +
269E ALA* 1.3 63.5 + - - +
271E ASP* 3.9 5.5 - - - +
272E ALA* 3.1 24.4 + - - +
381E PHE* 3.6 11.2 - - - -
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Residues in contact with ALA 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E ILE 2.8 12.0 + - - +
266E ALA* 3.6 8.5 - - - +
268E GLY* 1.3 71.4 - - - +
270E LEU* 1.3 57.8 + - - +
272E ALA* 3.3 2.3 + - - +
273E ALA* 2.9 30.5 + - - +
359E ILE* 4.3 5.6 - - + -
360E SER* 4.0 21.8 - - - -
363E VAL* 4.1 9.5 - - + +
381E PHE* 3.6 38.2 - - + -
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Residues in contact with LEU 270 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E ALA 3.0 16.4 + - - +
267E HIS* 3.9 7.4 - - - +
268E GLY 3.2 0.2 - - - -
269E ALA* 1.3 78.4 - - - +
271E ASP* 1.3 53.5 + - - +
273E ALA* 3.4 2.4 + - - +
274E ARG* 2.8 51.8 + - - +
302E TYR* 3.7 27.4 - - + -
305E PHE* 3.7 34.5 - - + -
306E THR* 4.1 21.1 - - + +
309E LEU* 3.9 23.6 - - + -
359E ILE* 4.3 5.2 - - + -
363E VAL* 4.3 7.4 - - + -
405F THR* 4.8 2.2 - - + -
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Residues in contact with ASP 271 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ARG* 5.4 7.3 + - - +
85E ALA* 5.8 1.6 - - - +
267E HIS* 3.1 30.4 + - - +
268E GLY* 3.9 5.9 - - - +
270E LEU* 1.3 74.2 - - - +
272E ALA* 1.3 63.8 + - - +
274E ARG* 2.6 44.2 + - - +
275E GLU* 3.2 23.7 + - - +
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Residues in contact with ALA 272 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268E GLY 3.1 17.8 + - - +
269E ALA 3.7 3.6 - - - +
271E ASP* 1.3 71.7 - - - +
273E ALA* 1.3 67.9 + - - +
275E GLU* 2.8 29.2 + - - +
276E TYR* 3.0 13.7 + - - +
378E PHE* 4.0 24.2 - - + -
380E ARG* 5.6 2.0 - - - +
381E PHE* 4.0 17.9 - - + -
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Residues in contact with ALA 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E ALA 2.9 17.4 + - - +
270E LEU 3.6 3.4 - - - +
272E ALA* 1.3 76.7 - - - +
274E ARG* 1.3 64.3 + - - +
276E TYR* 3.1 3.6 + - - +
277E THR* 2.8 21.8 + - - -
302E TYR* 3.0 17.5 + - + +
363E VAL* 3.5 32.1 - - + -
366E VAL* 4.4 0.4 - - + -
367E ILE* 4.0 21.8 - - + +
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Residues in contact with ARG 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270E LEU* 2.8 31.9 + - - +
271E ASP* 2.6 34.7 + - - +
272E ALA 3.3 0.2 - - - -
273E ALA* 1.3 74.8 - - - +
275E GLU* 1.3 63.7 + - - +
277E THR* 3.3 2.3 + - - -
278E ARG* 3.0 65.5 + - - +
302E TYR* 3.2 18.8 + - + -
405F THR* 3.6 32.6 + - - +
406F LEU* 4.4 8.2 - - + +
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Residues in contact with GLU 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B ARG* 5.7 6.7 - - - +
271E ASP 3.2 13.7 + - - +
272E ALA* 2.8 31.2 - - - +
273E ALA 3.3 0.2 - - - -
274E ARG* 1.3 76.9 - - - +
276E TYR* 1.3 64.0 + - - +
278E ARG* 3.4 11.7 + - - +
279E THR* 2.8 36.5 + - + +
378E PHE* 4.2 13.5 - - - -
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Residues in contact with TYR 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ALA 3.0 14.2 + - - +
273E ALA* 3.6 8.3 - - - +
275E GLU* 1.3 78.4 - - - +
277E THR* 1.3 63.9 + - - +
279E THR* 3.7 4.7 - - - -
280E GLN* 2.8 59.3 + - + +
281E ALA* 3.0 23.5 + - + -
367E ILE* 3.3 38.0 + - + -
370E ARG* 3.4 28.9 + - - +
371E GLY* 3.6 10.8 + - - -
376E TYR* 3.8 31.8 + + - -
378E PHE* 3.8 25.8 - + + -
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Residues in contact with THR 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273E ALA 2.8 11.6 + - - -
274E ARG 3.7 3.6 - - - -
276E TYR* 1.3 74.8 - - - +
278E ARG* 1.3 61.2 + - - +
279E THR 3.4 0.2 + - - -
281E ALA* 3.6 26.3 + - + +
292E ALA* 4.1 14.6 - - + +
293E THR* 4.0 13.7 - - + +
298E THR* 4.2 18.2 - - + -
302E TYR* 2.6 29.6 + - - -
366E VAL* 3.5 16.9 + - - +
367E ILE* 4.8 0.5 + - - -
406F LEU* 3.6 23.1 - - + -
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Residues in contact with ARG 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLU* 3.5 23.6 + - - +
278B ARG* 3.8 48.2 - - + +
279B THR* 3.3 20.7 - - + +
293B THR* 3.9 16.1 + - - +
274E ARG* 3.0 51.4 + - - +
275E GLU* 3.7 9.9 - - - +
276E TYR 3.1 0.2 - - - -
277E THR* 1.3 77.9 - - - +
279E THR* 1.3 58.7 + - - +
293E THR* 4.1 10.7 - - + +
404F HIS 5.3 0.2 + - - -
405F THR 3.7 6.5 + - - -
406F LEU* 2.8 31.6 + - + +
408F GLY* 4.6 6.5 - - - +
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Residues in contact with THR 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 3.3 42.0 - - + +
291B GLN* 5.9 1.1 + - - -
293B THR* 4.2 6.9 + - - -
406C LEU 3.7 7.0 - - - +
407C ASN* 3.3 45.9 + - - +
275E GLU* 2.8 27.9 + - + +
276E TYR* 3.0 4.4 + - - -
278E ARG* 1.3 81.2 - - + +
280E GLN* 1.3 74.2 + - - +
281E ALA 5.2 1.1 - - - -
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Residues in contact with GLN 280 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291B GLN* 5.4 0.7 - - - -
407C ASN* 3.1 20.6 - - - +
408C GLY 5.8 0.2 - - - -
409C GLN* 2.9 40.1 + - - +
276E TYR* 2.8 44.0 + - + -
279E THR* 1.3 94.5 - - - +
281E ALA* 1.3 67.6 + - - +
282E ARG* 3.6 10.6 + - - +
375E ARG* 5.4 1.2 - - - +
376E TYR* 4.2 16.8 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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