Contacts of the helix formed by residues 229 - 276 (chain A) in PDB entry 2DGC
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 ALA 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A LEU* 1.3 71.3 + - - +
231A LYS* 4.6 11.2 - - + +
232A ARG* 3.8 47.1 + - + +
233A ALA* 3.4 19.9 + - - +
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Residues in contact with LEU 230 (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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229A ALA* 1.3 76.8 - - - +
231A LYS* 1.3 66.1 + - - +
232A ARG 3.1 1.8 - - - -
233A ALA* 3.2 8.6 + - + +
234A ARG* 3.1 29.6 + - + +
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Residues in contact with LYS 231 (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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229A ALA* 4.7 9.6 - - + +
230A LEU* 1.3 77.0 - - - +
232A ARG* 1.3 90.0 + - + +
234A ARG* 3.5 9.0 + - - +
235A ASN* 3.1 23.6 + - - +
3B C 4.3 7.5 + - - -
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Residues in contact with ARG 232 (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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229A ALA* 3.8 36.0 - - + +
230A LEU 3.1 0.6 - - - -
231A LYS* 1.3 97.8 - - - +
233A ALA* 1.3 58.6 + - - +
235A ASN* 3.1 7.4 + - - +
236A THR* 2.8 35.3 + - - -
2B T 2.6 56.1 + - - +
3B C 3.6 26.8 + - - +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ALA 3.4 12.2 + - - +
230A LEU* 3.2 13.6 + - + +
232A ARG* 1.3 79.7 - - - +
234A ARG* 1.3 62.6 + - + +
236A THR* 3.4 14.1 + - - -
237A GLU* 3.4 17.0 + - - +
2B T 4.9 0.9 + - - -
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Residues in contact with ARG 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.1 17.8 + - + +
231A LYS* 3.9 7.6 - - - +
233A ALA* 1.3 79.7 - - + +
235A ASN* 1.3 57.2 + - - +
237A GLU* 3.1 8.3 + - - +
238A ALA* 2.9 27.5 + - - +
241A ARG* 5.0 13.3 + - - +
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Residues in contact with ASN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LYS 3.1 18.8 + - - +
232A ARG* 3.6 6.5 - - - +
234A ARG* 1.3 76.6 - - - +
236A THR* 1.3 58.1 + - - +
238A ALA* 4.1 11.1 - - - +
239A ALA* 2.9 31.6 + - - +
2B T 3.5 10.6 - - - +
3B C 3.0 34.3 + - - +
4B A 3.9 17.3 - - - +
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Residues in contact with THR 236 (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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232A ARG 2.8 16.6 + - - -
233A ALA* 3.6 8.9 - - - -
234A ARG 3.2 0.2 - - - -
235A ASN* 1.3 77.6 + - - +
237A GLU* 1.3 60.7 + - - +
239A ALA* 3.7 3.1 + - - +
240A ARG* 3.3 30.7 + - - +
243A ARG* 4.8 1.7 + - - -
1B G 3.3 51.2 + - + +
2B T 3.3 27.6 + - + +
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Residues in contact with GLU 237 (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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233A ALA 3.4 10.0 + - - +
234A ARG* 3.1 10.3 + - - +
236A THR* 1.3 77.1 - - - +
238A ALA* 1.3 66.8 + - - +
239A ALA 3.1 1.6 - - - -
240A ARG* 2.8 51.3 + - - +
241A ARG* 3.0 47.2 + - - +
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Residues in contact with ALA 238 (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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234A ARG 2.9 17.3 + - - +
235A ASN* 3.7 15.9 - - - +
237A GLU* 1.3 76.2 - - - +
239A ALA* 1.3 56.1 + - - +
241A ARG* 3.6 24.2 + - - +
242A SER* 3.0 29.3 + - - -
245A ARG* 5.0 1.7 + - - -
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Residues in contact with ALA 239 (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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235A ASN* 2.9 18.8 + - - +
236A THR 3.8 3.8 - - - +
238A ALA* 1.3 74.7 - - - +
240A ARG* 1.3 59.6 + - - +
242A SER* 3.2 6.9 + - - -
243A ARG* 2.9 48.3 + - + +
2B T 3.7 31.0 - - + +
3B C 5.7 0.9 - - - +
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Residues in contact with ARG 240 (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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236A THR* 3.3 14.4 + - - +
237A GLU* 2.8 49.5 + - - +
239A ALA* 1.3 79.4 - - - +
241A ARG* 1.3 62.5 + - + +
243A ARG* 3.5 13.8 + - - +
244A ALA* 3.2 22.7 + - - +
-1B C 3.1 42.4 + - - +
1B G 2.9 35.6 + - - -
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Residues in contact with ARG 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ARG* 5.0 12.1 + - - +
237A GLU* 3.0 33.0 + - + +
238A ALA* 3.8 27.4 - - - +
240A ARG* 1.3 76.3 - - + +
242A SER* 1.3 62.3 + - - +
244A ALA* 3.4 8.2 + - - +
245A ARG* 3.1 51.2 + - - +
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Residues in contact with SER 242 (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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238A ALA 3.0 18.7 + - - -
239A ALA* 3.2 7.8 + - - -
241A ARG* 1.3 74.5 - - - +
243A ARG* 1.3 64.6 + - - +
245A ARG* 3.2 22.6 + - - +
246A LYS* 3.0 47.5 + - - +
249A ARG* 3.9 4.2 + - - -
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Residues in contact with ARG 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR 4.8 1.2 + - - -
239A ALA* 2.9 28.4 + - + +
240A ARG* 3.5 30.3 - - - +
241A ARG 3.4 0.2 - - - -
242A SER* 1.3 75.4 - - - +
244A ALA* 1.3 63.4 + - - +
246A LYS* 3.2 21.0 + - - +
247A LEU* 3.0 23.8 + - - +
-2B A 4.7 5.4 - - - -
-1B C 2.6 66.9 + - - +
1B G 2.5 46.3 + - - -
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Residues in contact with ALA 244 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG 3.2 11.8 + - - +
241A ARG* 3.4 12.1 - - - +
243A ARG* 1.3 81.2 - - - +
245A ARG* 1.3 61.5 + - + +
247A LEU* 3.3 9.1 + - - +
248A GLN* 3.2 25.5 + - - +
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Residues in contact with ARG 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ALA 5.0 1.6 + - - -
241A ARG* 3.1 45.8 + - - +
242A SER* 3.2 29.8 + - - +
244A ALA* 1.3 76.3 - - + +
246A LYS* 1.3 58.4 + - - +
248A GLN* 3.0 20.2 - - + +
249A ARG* 2.9 50.5 + - + +
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Residues in contact with LYS 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A SER* 3.0 40.2 + - - +
243A ARG* 3.2 19.3 + - - +
245A ARG* 1.3 76.1 - - - +
247A LEU* 1.3 61.4 + - - +
249A ARG* 3.2 34.8 - - - +
250A MET* 3.2 22.3 + - - +
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Residues in contact with LEU 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A ARG 3.0 12.8 + - - +
244A ALA* 3.7 11.9 - - - +
245A ARG 3.2 0.2 - - - -
246A LYS* 1.3 75.9 - - - +
248A GLN* 1.3 62.4 + - - +
250A MET* 3.6 6.9 + - + +
251A LYS* 3.3 45.4 + - + +
-2B A 3.6 28.3 - - - +
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Residues in contact with GLN 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ALA 3.2 9.9 + - - +
245A ARG* 3.0 36.3 - - - +
247A LEU* 1.3 76.9 - - - +
249A ARG* 1.3 66.0 + - + +
251A LYS* 3.3 14.7 + - - +
252A GLN* 2.9 35.8 + - - +
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Residues in contact with ARG 249 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A SER* 3.9 6.9 + - - -
245A ARG* 2.9 39.9 + - + +
246A LYS* 3.2 45.5 - - - +
247A LEU 3.4 0.2 - - - -
248A GLN* 1.3 85.5 - - + +
250A MET* 1.3 56.6 + - - +
252A GLN* 3.4 20.0 + - - +
253A LEU* 2.9 31.6 + - - +
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Residues in contact with MET 250 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A LYS 3.2 16.2 + - - +
247A LEU* 3.7 9.2 - - + +
248A GLN 3.2 0.4 - - - -
249A ARG* 1.3 78.9 - - - +
251A LYS* 1.3 58.7 + - + +
253A LEU* 3.2 18.4 + - - +
254A GLU* 2.8 58.4 + - + +
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Residues in contact with LYS 251 (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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247A LEU* 3.3 39.7 + - + +
248A GLN* 3.8 13.8 - - - +
250A MET* 1.3 76.3 - - + +
252A GLN* 1.3 66.3 + - - +
254A GLU* 3.2 17.5 + - - +
255A ASP* 2.9 32.8 + - - +
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Residues in contact with GLN 252 (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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248A GLN* 2.9 21.2 + - - +
249A ARG* 3.4 21.4 - - - +
251A LYS* 1.3 76.0 - - - +
253A LEU* 1.3 69.7 + - - +
255A ASP* 3.2 9.5 + - - +
256A LYS* 3.1 21.9 + - + +
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Residues in contact with LEU 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ARG 2.9 14.6 + - - +
250A MET* 3.4 22.2 - - - +
252A GLN* 1.3 84.0 - - - +
254A GLU* 1.3 63.5 + - + +
256A LYS* 3.2 21.6 + - + +
257A VAL* 3.2 25.1 + - + +
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Residues in contact with GLU 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A MET* 2.8 53.9 + - + +
251A LYS* 3.2 20.2 + - - +
253A LEU* 1.3 72.8 - - + +
255A ASP* 1.3 63.1 + - - +
257A VAL* 3.5 9.7 + - - +
258A GLU* 3.3 20.0 + - - +
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Residues in contact with ASP 255 (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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251A LYS* 2.9 21.2 + - - +
252A GLN* 3.2 12.1 + - - +
254A GLU* 1.3 74.0 - - - +
256A LYS* 1.3 60.5 + - - +
258A GLU* 3.1 17.4 + - - +
259A GLU* 2.8 28.9 + - - +
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Residues in contact with LYS 256 (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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252A GLN* 3.1 13.2 + - + +
253A LEU* 3.4 19.1 - - + +
255A ASP* 1.3 74.6 - - - +
257A VAL* 1.3 59.6 + - + +
259A GLU* 3.2 22.1 + - + +
260A LEU* 2.8 56.8 + - + +
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Residues in contact with VAL 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A LEU* 3.2 22.3 + - + +
254A GLU* 3.7 9.6 - - - +
255A ASP 3.3 0.2 - - - -
256A LYS* 1.3 77.3 - - + +
258A GLU* 1.3 59.5 + - - +
260A LEU* 3.9 6.9 - - + +
261A LEU* 3.0 49.0 + - + +
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Residues in contact with GLU 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLU 3.3 10.3 + - - +
255A ASP* 3.1 21.4 + - - +
257A VAL* 1.3 81.0 - - - +
259A GLU* 1.3 60.6 + - - +
261A LEU* 3.5 8.8 + - - +
262A SER* 3.3 22.0 + - - -
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Residues in contact with GLU 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ASP 2.8 15.8 + - - +
256A LYS* 3.5 27.8 - - + +
258A GLU* 1.3 77.8 - - - +
260A LEU* 1.3 63.6 + - - +
262A SER* 2.9 23.7 + - - +
263A LYS* 3.0 47.4 + - - +
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Residues in contact with LEU 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS* 2.8 52.5 + - + +
257A VAL* 4.1 5.4 - - + +
259A GLU* 1.3 83.9 - - - +
261A LEU* 1.3 61.2 + - + +
263A LYS* 3.9 12.2 - - + +
264A ASN* 2.8 33.6 + - - +
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Residues in contact with LEU 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 3.0 39.3 + - + +
258A GLU* 3.7 9.0 - - - +
260A LEU* 1.3 77.2 - - + +
262A SER* 1.3 58.3 + - - +
264A ASN* 3.4 10.9 - - + +
265A TYR* 3.1 26.2 + - - +
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Residues in contact with SER 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A GLU 3.3 10.3 + - - -
259A GLU* 2.9 15.6 + - - +
260A LEU 3.2 0.4 - - - -
261A LEU* 1.3 75.6 - - - +
263A LYS* 1.3 67.7 + - - +
264A ASN 3.1 1.3 - - - -
265A TYR* 3.2 7.5 + - - +
266A HIS* 3.1 39.3 + - - -
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Residues in contact with LYS 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A GLU* 3.0 44.9 + - - +
260A LEU* 3.9 14.3 - - + +
262A SER* 1.3 81.8 + - - +
264A ASN* 1.3 63.4 + - - +
266A HIS* 3.3 8.4 + - + +
267A LEU* 3.1 37.1 + - + +
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Residues in contact with ASN 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A LEU 2.8 18.9 + - - +
261A LEU* 3.4 14.4 - - + +
263A LYS* 1.3 76.7 - - - +
265A TYR* 1.3 57.3 + - - +
267A LEU* 3.2 11.4 + - - +
268A GLU* 2.9 43.6 + - - +
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Residues in contact with TYR 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A LEU 3.1 14.0 + - - +
262A SER* 3.2 11.0 + - - +
264A ASN* 1.3 77.0 + - - +
266A HIS* 1.3 74.9 + + + +
268A GLU* 3.4 6.3 + - + +
269A ASN* 3.0 51.2 + - + +
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Residues in contact with HIS 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A SER* 3.1 26.3 + - - -
263A LYS* 3.3 9.8 + - - +
265A TYR* 1.3 91.3 - + + +
267A LEU* 1.3 59.5 + - + +
269A ASN* 3.5 5.1 + - - +
270A GLU* 2.9 29.2 + - - +
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Residues in contact with LEU 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LYS* 3.1 32.2 + - + +
264A ASN* 3.7 11.7 - - - +
266A HIS* 1.3 76.3 - - + +
268A GLU* 1.3 60.1 + - - +
270A GLU* 3.1 18.5 + - + +
271A VAL* 2.8 37.3 + - + +
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Residues in contact with GLU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ASN* 2.9 31.8 + - - +
265A TYR* 3.7 9.0 - - + +
267A LEU* 1.3 76.3 - - - +
269A ASN* 1.3 62.0 + - - +
271A VAL* 3.4 16.1 + - - +
272A ALA* 3.3 20.4 + - - +
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A TYR* 3.0 44.8 + - + +
266A HIS* 3.7 6.7 - - - +
268A GLU* 1.3 73.8 - - - +
270A GLU* 1.3 65.3 + - - +
272A ALA* 3.3 9.7 + - - +
273A ARG* 3.1 21.5 + - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A HIS 2.9 20.2 + - - +
267A LEU* 3.4 20.9 - - + +
269A ASN* 1.3 76.8 - - - +
271A VAL* 1.3 65.3 + - + +
273A ARG* 3.2 24.6 + - - +
274A LEU* 3.0 49.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 2.8 24.8 + - + +
268A GLU* 3.7 17.3 - - - +
270A GLU* 1.3 78.6 - - + +
272A ALA* 1.3 58.3 + - - +
274A LEU* 3.8 6.4 - - + +
275A LYS* 2.8 53.7 + - + +
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Residues in contact with ALA 272 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU 3.3 9.1 + - - +
269A ASN* 3.3 13.2 + - - +
271A VAL* 1.3 80.7 - - - +
273A ARG* 1.3 62.4 + - - +
275A LYS* 3.3 8.4 - - - +
276A LYS* 3.1 21.8 + - - +
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Residues in contact with ARG 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ASN 3.1 13.1 + - - +
270A GLU* 3.2 28.2 + - - +
272A ALA* 1.3 73.6 - - - +
274A LEU* 1.3 77.7 + - - +
276A LYS* 3.1 8.4 + - - +
277A LEU* 3.0 25.6 + - + +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLU* 3.0 45.2 + - + +
271A VAL* 4.0 5.8 - - + +
273A ARG* 1.3 87.6 - - - +
275A LYS* 1.3 67.7 + - - +
277A LEU* 3.3 24.1 - - + +
----------------------------------------------------------
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 2.8 35.8 + - + +
272A ALA* 3.3 10.1 - - - +
274A LEU* 1.3 79.8 - - - +
276A LYS* 1.3 63.8 + - - +
277A LEU 3.6 4.3 - - - +
----------------------------------------------------------
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Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ALA 3.1 8.5 + - - +
273A ARG* 3.1 11.5 + - - +
275A LYS* 1.3 80.4 - - - +
277A LEU* 1.3 64.1 + - - +
----------------------------------------------------------
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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