Contacts of the helix formed by residues 243 - 278 (chain A) in PDB entry 2NN6
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 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A MET* 3.9 14.4 - - + +
242A LEU* 1.3 68.7 - - - +
244A LYS* 1.3 53.2 + - + +
245A ASP* 2.6 9.6 + - + +
246A GLN* 2.5 52.0 + - + +
247A VAL* 2.6 14.4 + - - -
192B SER 6.0 0.7 - - - +
193B GLY 4.9 2.5 - - - +
194B GLN* 4.2 29.2 - - + +
195B ILE* 3.7 3.8 - - + -
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Residues in contact with LYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU 3.1 4.4 + - - -
243A LEU* 1.3 69.1 - - + +
245A ASP* 1.3 89.2 + - + +
247A VAL* 2.5 36.5 - - - +
248A LEU* 3.3 9.2 + - + +
193B GLY 5.8 0.4 - - - +
195B ILE* 3.2 16.0 - - + +
210B GLU* 4.5 13.7 + - - +
213B LEU* 3.7 32.5 - - + -
214B GLU* 4.5 18.1 + - - +
217B ALA* 5.6 3.6 - - + -
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Residues in contact with ASP 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 2.6 11.6 + - + +
244A LYS* 1.3 99.4 + - + +
246A GLN* 1.3 65.7 + - - +
248A LEU* 2.3 32.9 + - - +
249A ARG* 2.4 32.5 + - - +
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Residues in contact with GLN 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PHE* 4.9 16.2 - - + -
202A GLY* 5.2 6.8 - - - +
205A LEU* 5.5 4.5 - - + -
241A MET 3.3 12.5 - - - +
242A LEU* 2.7 16.8 - - - +
243A LEU* 2.5 63.0 + - + +
245A ASP* 1.3 76.5 + - - +
247A VAL* 1.3 67.8 + - - +
248A LEU 2.4 16.7 + - - -
249A ARG* 2.8 30.1 + - + +
250A CYS* 2.7 19.8 - - - -
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 5.7 1.2 - - - +
223A ILE* 5.5 0.5 - - - +
242A LEU* 2.9 28.0 - - + +
243A LEU 2.6 27.7 + - - +
244A LYS* 2.5 33.9 - - - +
246A GLN* 1.3 81.2 - - - +
248A LEU* 1.3 63.0 + - + +
250A CYS* 2.7 17.6 - - - -
251A SER* 2.3 26.5 + - - -
195B ILE* 4.8 4.5 - - + -
198B LEU* 6.2 5.6 - - + -
209B LEU* 4.5 5.6 - - + -
213B LEU* 4.1 11.4 - - + -
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LYS* 3.4 15.7 - - + +
245A ASP* 2.3 34.3 + - - +
246A GLN 2.4 2.2 + - - -
247A VAL* 1.3 69.5 - - + +
249A ARG* 1.3 67.4 + - - +
251A SER* 2.4 22.7 + - - +
252A LYS* 3.1 10.8 + - + +
206B GLU* 5.0 8.5 - - - +
209B LEU* 3.2 47.3 - - + -
210B GLU* 4.6 15.7 - - + +
213B LEU* 3.8 13.9 - - + -
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU* 5.9 4.3 - - + -
245A ASP* 2.4 49.4 + - - -
246A GLN* 2.8 34.4 + - + +
248A LEU* 1.3 79.8 - - - +
250A CYS* 1.3 59.6 + - - +
252A LYS* 2.5 20.2 + - + +
253A ILE* 2.4 53.2 + - + +
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Residues in contact with CYS 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.2 37.4 - - + -
198A PHE* 5.8 2.7 - - - -
205A LEU* 4.7 11.4 - - + -
221A LEU* 4.3 13.2 - - + -
223A ILE* 4.0 0.2 - - - -
246A GLN* 2.7 31.9 - - - -
247A VAL* 2.7 24.5 - - - -
249A ARG* 1.3 76.6 - - - +
251A SER* 1.3 53.7 + - - +
253A ILE* 2.9 5.8 + - - +
254A ALA* 2.4 37.9 + - - +
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Residues in contact with SER 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 3.2 22.7 - - - +
225A MET* 3.4 7.9 - - - +
231A ILE* 6.2 4.5 - - - -
234A ILE* 6.3 0.7 - - - -
247A VAL 2.3 29.7 + - - -
248A LEU* 2.4 25.4 + - - +
250A CYS* 1.3 76.5 - - - +
252A LYS* 1.3 66.5 + - - +
254A ALA* 3.3 4.0 + - - +
255A GLY 3.2 10.0 + - - -
206B GLU* 3.3 13.8 - - - +
209B LEU* 4.1 12.2 - - - +
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG* 4.2 9.6 + - - +
248A LEU* 3.1 7.3 + - + +
249A ARG* 2.5 25.8 + - + +
251A SER* 1.3 74.2 - - - +
253A ILE* 1.3 62.9 - - + +
255A GLY* 2.5 34.0 + - - -
256A VAL* 3.1 15.7 + - + +
206B GLU* 2.9 19.3 + - - +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.9 43.1 - - + +
194A VAL* 6.0 0.4 - - + -
196A PHE* 3.6 17.7 - - + -
205A LEU* 6.4 1.8 - - + -
207A VAL* 5.2 2.7 - - + -
249A ARG* 2.4 40.6 + - + +
250A CYS* 3.4 7.2 - - - +
252A LYS* 1.3 79.8 - - + +
254A ALA* 1.3 67.2 + - - +
256A VAL* 3.0 28.1 - - + +
257A LYS* 3.1 12.2 + - + +
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A VAL* 3.8 11.1 - - + +
196A PHE* 3.2 22.2 - - + -
223A ILE* 3.3 33.4 - - + -
250A CYS 2.4 20.6 + - - +
251A SER 3.3 5.2 - - - +
253A ILE* 1.3 72.9 - - - +
255A GLY* 1.3 64.8 + - - +
257A LYS* 2.9 5.5 + - - +
258A VAL* 2.7 26.9 + - - +
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Residues in contact with GLY 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A MET* 2.9 38.5 - - - -
229A ARG* 4.2 12.3 + - - -
252A LYS 2.5 15.7 + - - -
254A ALA* 1.3 70.0 - - - +
256A VAL* 1.3 62.7 + - - +
258A VAL* 2.8 18.2 - - - +
259A ALA* 3.0 11.8 + - - +
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG* 4.6 8.8 - - - +
252A LYS* 3.1 18.8 + - + +
253A ILE* 3.0 37.0 - - + +
255A GLY* 1.3 75.2 - - - +
257A LYS* 1.3 62.2 + - + +
259A ALA* 2.8 26.0 - - - +
260A GLU* 3.9 10.6 + - - +
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Residues in contact with LYS 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.0 38.0 + - + +
31A ASP* 4.0 15.1 - - - +
32A TYR* 4.4 28.7 - - + +
194A VAL* 4.8 9.9 - - + -
207A VAL* 5.4 3.1 - - + -
253A ILE* 3.1 11.0 + - + +
254A ALA* 2.9 10.9 + - - +
256A VAL* 1.3 82.1 - - + +
258A VAL* 1.3 67.0 + - - +
259A ALA 2.5 6.7 + - - -
260A GLU* 2.8 46.4 + - + +
261A ILE* 3.1 16.1 + - + +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A MET 5.8 0.7 - - - +
192A ILE* 3.6 28.5 - - + -
194A VAL* 4.7 4.6 - - + +
225A MET* 3.3 35.7 - - + +
226A ASN 4.9 1.1 - - - +
227A LYS* 4.9 10.5 - - - +
229A ARG* 6.6 0.2 - - - -
254A ALA 2.7 22.1 + - - +
255A GLY* 2.8 24.0 - - - +
257A LYS* 1.3 71.3 - - - +
259A ALA* 1.3 71.2 + - - +
261A ILE* 3.3 5.4 + - - +
262A THR* 2.5 29.6 + - - +
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ARG* 6.4 0.4 - - - +
255A GLY 3.0 11.0 + - - +
256A VAL* 2.8 18.6 - - - +
257A LYS 2.5 3.6 + - - -
258A VAL* 1.3 84.3 - - - +
260A GLU* 1.3 62.3 + - + +
262A THR* 2.6 18.6 + - - -
263A GLU* 3.5 2.4 + - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A VAL* 3.9 11.9 - - - +
257A LYS* 2.8 50.4 + - + +
259A ALA* 1.3 75.1 - - + +
261A ILE* 1.3 48.6 + - + +
263A GLU* 2.7 24.9 + - + +
264A LEU* 2.7 30.6 - - + +
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Residues in contact with ILE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 3.5 38.4 - - + +
35A ILE* 5.9 6.5 - - + -
151A ILE* 4.8 16.8 - - + -
192A ILE* 4.0 42.8 - - + -
193A CYS 5.0 0.4 - - - +
194A VAL* 5.8 1.3 - - + -
257A LYS* 3.1 17.0 + - + +
258A VAL* 3.5 11.4 - - - +
259A ALA 3.1 0.2 + - - -
260A GLU* 1.3 78.6 - - + +
262A THR* 1.3 71.7 + - - +
264A LEU* 3.2 21.3 + - + +
265A ILE* 3.5 11.3 - - + +
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Residues in contact with THR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A MET* 5.1 14.6 - - + +
227A LYS* 5.0 24.5 - - + +
258A VAL* 2.5 33.1 + - - +
259A ALA* 2.6 8.4 + - - -
261A ILE* 1.3 75.2 - - - +
263A GLU* 1.3 57.1 + - - +
265A ILE* 2.5 57.5 + - + +
266A LEU* 3.0 25.1 - - + +
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA 3.5 2.6 + - - +
260A GLU* 2.7 27.9 + - + +
262A THR* 1.3 74.2 - - - +
264A LEU* 1.3 60.1 + - + +
266A LEU* 3.4 12.9 + - - +
267A LYS* 2.5 48.1 + - + +
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 4.9 23.3 - - + +
37A ILE* 4.9 9.2 - - + -
260A GLU* 2.7 28.7 - - + +
261A ILE* 3.3 13.5 - - + +
262A THR 2.6 3.6 + - - -
263A GLU* 1.3 79.3 - - + +
265A ILE* 1.3 73.1 + - - +
267A LYS* 2.7 16.9 + - + -
268A ALA* 2.7 24.7 + - + +
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Residues in contact with ILE 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 6.4 1.8 - - - -
151A ILE* 5.6 2.5 - - + -
154A ILE* 4.1 21.8 - - + +
155A VAL* 3.6 45.3 - - + +
158A CYS* 5.1 2.0 - - - -
190A MET* 5.3 4.0 - - + -
192A ILE* 6.3 1.6 - - + -
261A ILE* 3.5 13.0 - - + +
262A THR* 2.5 48.9 + - + +
264A LEU* 1.3 71.4 - - - +
266A LEU* 1.3 56.0 + - + +
268A ALA* 4.1 1.5 - - - +
269A LEU* 2.3 61.7 + - + +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A CYS* 6.1 2.0 - - - -
190A MET* 5.9 5.2 - - + -
227A LYS* 5.4 13.7 - - - +
262A THR* 3.0 43.5 - - + +
263A GLU* 3.4 15.0 - - - +
265A ILE* 1.3 81.1 - - + +
267A LYS* 1.3 65.8 + - - +
269A LEU* 3.7 14.8 - - + -
270A GLU* 2.7 39.4 + - + +
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Residues in contact with LYS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLU* 2.5 34.3 + - + +
264A LEU* 2.7 23.5 + - + +
266A LEU* 1.3 75.0 - - - +
268A ALA* 1.3 61.7 + - + +
270A GLU* 3.1 7.4 + - - +
271A ASN* 3.0 28.6 + - + +
274A LYS* 4.3 1.8 + - - +
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Residues in contact with ALA 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 5.1 22.7 - - + +
39A PHE* 4.9 9.8 - - + -
264A LEU* 2.7 17.9 + - + +
265A ILE* 4.1 1.6 - - - +
267A LYS* 1.3 74.3 - - + +
269A LEU* 1.3 64.0 + - - +
270A GLU 2.7 6.9 + - - -
271A ASN* 2.7 26.2 + - + +
272A ASP* 2.8 15.6 + - - +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL 5.1 3.8 - - - +
158A CYS* 3.4 48.2 - - + +
159A HIS* 4.8 13.2 - - + +
265A ILE* 2.3 50.1 + - + +
266A LEU* 3.2 16.4 - - + +
268A ALA* 1.3 68.2 - - - +
270A GLU* 1.3 66.6 + - - +
272A ASP* 3.8 7.4 - - + +
273A GLN* 3.4 20.1 + - + +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 2.7 34.4 + - + +
267A LYS* 3.2 8.1 - - - +
268A ALA 2.7 0.6 + - - -
269A LEU* 1.3 83.3 - - - +
271A ASN* 1.3 67.1 + - - +
272A ASP 3.0 1.6 - - - -
273A GLN* 2.9 14.5 + - - +
274A LYS* 2.9 36.6 + - + +
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Residues in contact with ASN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.0 24.7 - - - -
267A LYS* 3.0 20.2 + - - +
268A ALA* 2.7 18.9 + - - +
270A GLU* 1.3 70.8 - - - +
272A ASP* 1.3 60.9 + - - +
274A LYS* 2.7 33.7 - - - +
275A VAL* 3.0 25.6 - - - +
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 3.3 47.8 - - + +
159A HIS* 3.5 24.7 + - - -
268A ALA 2.8 20.0 + - - +
269A LEU* 3.8 9.0 - - - +
271A ASN* 1.3 68.7 - - - +
273A GLN* 1.3 76.1 + - - +
274A LYS 2.9 2.6 + - - -
275A VAL* 3.0 19.3 + - - +
276A ARG* 3.4 33.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 5.2 1.4 - - - -
159A HIS* 6.1 0.2 - - - -
161A ARG* 3.7 25.2 + - - +
269A LEU* 3.4 11.2 + - + +
270A GLU* 2.9 18.5 + - - +
272A ASP* 1.3 85.7 + - - +
274A LYS* 1.3 65.5 + - + +
276A ARG* 3.5 14.8 + - - +
277A LYS* 3.3 41.6 + - + +
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS* 4.3 2.4 + - - +
270A GLU* 2.9 22.8 + - + +
271A ASN* 2.7 52.8 - - - +
272A ASP 2.9 0.2 + - - -
273A GLN* 1.3 78.1 - - + +
275A VAL* 1.3 65.2 + - + +
277A LYS* 3.0 9.6 + - - +
278A GLU* 3.0 41.3 + - - +
----------------------------------------------------------
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 5.8 5.8 - - + -
271A ASN* 3.0 29.4 - - - +
272A ASP* 3.0 8.7 + - - +
274A LYS* 1.3 76.5 - - + +
276A ARG* 1.3 66.9 + - - +
278A GLU* 3.0 13.3 + - - +
279A GLY* 5.6 0.9 - - - +
280A GLY* 3.0 28.8 + - - +
281A LYS* 3.9 35.9 - - + +
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Residues in contact with ARG 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PHE* 4.9 5.3 - - - +
40A GLY 3.3 25.1 + - - -
41A THR 4.1 0.6 + - - -
42A ASP 4.5 1.0 + - - -
43A TYR* 2.8 48.2 - - - +
159A HIS* 3.4 16.3 + - - -
272A ASP* 3.4 41.8 + - - +
273A GLN* 3.9 12.3 - - - +
274A LYS 3.3 0.8 - - - -
275A VAL* 1.3 81.2 - - - +
277A LYS* 1.3 72.7 + - + +
278A GLU 3.4 6.2 + - - +
280A GLY* 4.5 7.7 - - - -
281A LYS 4.7 5.6 + - - +
282A PHE* 3.5 45.7 - - + +
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Residues in contact with LYS 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TYR* 4.9 10.5 + - - -
161A ARG* 5.5 3.2 - - - +
273A GLN* 3.3 44.9 + - + +
274A LYS* 3.0 8.4 + - - +
276A ARG* 1.3 81.7 - - + +
278A GLU* 1.3 62.3 + - + +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A LYS* 3.0 35.0 + - - +
275A VAL* 3.0 10.7 + - + +
276A ARG 3.5 3.8 - - - +
277A LYS* 1.3 85.3 - - + +
279A GLY* 1.3 73.3 + - - +
280A GLY* 2.7 7.1 + - - -
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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