Contacts of the helix formed by residues 245 - 285 (chain A) in PDB entry 6JOD
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 GLY 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A TYR* 1.3 73.6 - - - +
246A LYS* 1.3 61.4 + - - -
247A ASN 3.1 2.7 - - - -
248A ARG* 2.8 29.3 + - - +
249A ILE* 3.3 10.7 + - - +
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Residues in contact with LYS 246 (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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245A GLY* 1.3 72.8 - - - -
247A ASN* 1.3 64.8 + - - +
249A ILE* 3.0 27.4 + - + +
250A THR* 3.0 20.8 + - - +
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Residues in contact with ASN 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASN* 3.4 36.6 + - + +
244A TYR* 3.2 17.3 - - - +
246A LYS* 1.3 79.7 + - - +
248A ARG* 1.3 56.8 + - - +
250A THR* 4.2 4.1 - - - -
251A ARG* 2.9 32.4 + - - +
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Residues in contact with ARG 248 (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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242A ASN 3.2 8.1 + - - -
243A SER 3.2 27.0 + - - +
244A TYR 3.7 0.8 + - - -
245A GLY 2.8 16.7 + - - +
247A ASN* 1.3 78.0 - - - +
249A ILE* 1.3 63.6 + - + +
251A ARG* 3.7 16.5 - - - +
252A ASP* 2.9 54.3 + - - +
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Residues in contact with ILE 249 (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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245A GLY 3.3 9.4 + - - +
246A LYS* 3.0 21.4 + - + +
248A ARG* 1.3 80.2 - - + +
250A THR* 1.3 66.6 + - - +
252A ASP* 3.2 8.8 + - - +
253A GLN* 3.0 21.6 + - + +
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Residues in contact with THR 250 (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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246A LYS* 3.0 16.2 + - - +
247A ASN* 4.3 4.0 - - - -
249A ILE* 1.3 76.8 - - - +
251A ARG* 1.3 57.5 + - - +
253A GLN* 3.1 9.9 + - + +
254A VAL* 3.0 37.4 + - + +
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Residues in contact with ARG 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A ARG 5.2 0.4 + - - -
238A LEU* 3.0 45.5 + - + +
239A LEU* 3.3 43.6 - - - +
242A ASN* 3.2 32.6 + - + +
243A SER* 4.3 10.5 + - - +
247A ASN 2.9 20.4 + - - +
248A ARG* 3.7 24.8 - - - +
250A THR* 1.3 77.8 - - - +
252A ASP* 1.3 76.4 + - - +
254A VAL* 3.3 6.9 + - - +
255A LEU* 2.9 39.4 + - + +
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Residues in contact with ASP 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 ARG* 2.9 52.7 + - - +
249A ILE* 3.6 6.1 - - - +
251A ARG* 1.3 97.6 + - - +
253A GLN* 1.3 57.6 + - - +
255A LEU* 3.4 13.5 + - + +
256A LYS* 2.9 37.0 + - + +
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Residues in contact with GLN 253 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ILE* 3.0 13.3 + - + +
250A THR* 3.3 13.7 - - + +
252A ASP* 1.3 77.4 - - - +
254A VAL* 1.3 64.1 + - + +
256A LYS* 3.1 15.5 + - - +
257A MET* 3.0 35.1 + - + +
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Residues in contact with VAL 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 5.7 2.7 - - + -
238A LEU* 4.0 21.5 - - + -
250A THR* 3.0 26.4 + - + +
251A ARG* 3.3 5.8 + - - +
253A GLN* 1.3 76.7 - - + +
255A LEU* 1.3 61.8 + - - +
257A MET* 2.9 20.6 + - + +
258A ALA* 3.0 16.0 + - + +
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Residues in contact with LEU 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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231A TYR* 3.6 23.8 - - + +
234A ILE* 6.4 0.2 - - + -
235A ARG* 3.5 46.4 - - + -
238A LEU* 4.6 9.8 - - + +
251A ARG* 2.9 28.4 + - + +
252A ASP* 3.6 16.2 - - + +
254A VAL* 1.3 77.2 - - - +
256A LYS* 1.3 71.4 + - - +
258A ALA* 3.3 4.6 + - + +
259A ALA* 2.9 27.0 + - - +
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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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231A TYR* 5.5 2.2 + - - -
252A ASP* 2.9 21.1 + - + +
253A GLN* 3.5 18.4 - - - +
255A LEU* 1.3 89.0 - - - +
257A MET* 1.3 58.6 + - - +
259A ALA* 4.1 15.2 - - + +
260A ALA* 2.9 29.6 + - - +
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Residues in contact with MET 257 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 5.0 9.2 - - - +
253A GLN* 3.0 28.1 + - + +
254A VAL* 2.9 18.6 + - + +
256A LYS* 1.3 75.2 - - - +
258A ALA* 1.3 65.4 + - - +
260A ALA* 3.1 7.5 + - - +
261A VAL* 2.9 27.9 + - + +
317A LEU* 3.2 45.1 - - + +
321A VAL* 3.7 34.8 - - + -
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Residues in contact with ALA 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A ARG* 4.6 10.5 - - - +
231A TYR* 3.7 23.8 - - + -
234A ILE* 5.0 20.2 - - + -
254A VAL* 3.0 13.3 + - + +
255A LEU* 3.3 6.7 + - + +
257A MET* 1.3 75.2 - - - +
259A ALA* 1.3 64.0 + - - +
261A VAL* 3.0 20.4 + - - +
262A VAL* 3.1 16.1 + - - +
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Residues in contact with ALA 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A TYR* 3.5 28.5 - - + +
255A LEU* 2.9 17.7 + - + +
256A LYS* 4.1 18.6 - - + +
258A ALA* 1.3 76.3 - - - +
260A ALA* 1.3 58.1 + - - +
262A VAL* 3.4 4.6 + - - +
263A LEU* 2.9 43.2 + - + +
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Residues in contact with ALA 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LYS 2.9 21.2 + - - +
257A MET* 3.1 11.2 + - - +
259A ALA* 1.3 74.4 - - - +
261A VAL* 1.3 60.4 + - - +
263A LEU* 3.9 8.8 - - - +
264A ALA* 2.9 31.7 + - - +
317A LEU* 4.0 15.0 - - + +
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Residues in contact with VAL 261 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 4.5 9.4 - - + -
139A SER* 4.4 13.0 - - - +
142A ARG* 3.8 21.1 - - - +
227A ILE* 4.6 7.0 - - + -
257A MET* 2.9 18.2 + - + +
258A ALA* 3.0 8.7 + - - +
260A ALA* 1.3 76.6 - - - +
262A VAL* 1.3 66.3 + - + +
264A ALA* 3.2 3.8 + - - +
265A PHE* 3.0 21.7 + - - +
317A LEU* 3.5 30.4 - - + +
318A TYR* 3.2 29.8 - - + +
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Residues in contact with VAL 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 5.2 3.6 - - + -
227A ILE* 3.6 31.0 - - + +
228A ALA* 4.9 13.2 - - + +
231A TYR* 3.6 31.6 - - + -
258A ALA 3.1 13.8 + - - +
259A ALA* 3.9 6.1 - - - +
261A VAL* 1.3 76.6 - - + +
263A LEU* 1.3 58.8 + - + +
265A PHE* 3.3 3.6 + - + +
266A ILE* 2.9 54.0 + - + +
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Residues in contact with LEU 263 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ALA* 2.9 32.6 + - + +
260A ALA* 3.9 8.1 - - - +
262A VAL* 1.3 78.1 - - + +
264A ALA* 1.3 57.2 + - - +
266A ILE* 3.5 12.0 + - + +
267A ILE* 2.8 48.2 + - + +
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Residues in contact with ALA 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ALA 2.9 18.7 + - - +
261A VAL 3.7 3.4 - - - +
263A LEU* 1.3 73.8 - - - +
265A PHE* 1.3 66.3 + - - +
267A ILE* 3.2 5.2 + - - -
268A CYS* 3.0 33.0 + - - +
310A ASN* 3.8 12.1 - - - +
313A VAL* 4.8 12.3 - - + -
314A ASN* 5.3 0.7 - - - +
317A LEU* 4.0 17.0 - - + -
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Residues in contact with PHE 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.8 24.0 - - + -
135A ILE* 4.3 16.6 - - + -
219A GLY 4.1 4.0 - - - -
220A PHE* 3.8 32.1 - + - -
223A PRO* 4.1 17.9 - - + -
224A LEU* 4.1 27.8 - - + -
227A ILE* 4.1 23.1 - - + -
261A VAL 3.0 12.7 + - - +
262A VAL* 3.7 9.4 - - + +
264A ALA* 1.3 75.4 - - - +
266A ILE* 1.3 66.3 + - + +
268A CYS 3.7 0.3 - - - -
269A TRP* 3.0 54.9 + + - +
310A ASN* 3.8 14.6 + - - +
314A ASN* 6.1 0.2 - - - +
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Residues in contact with ILE 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 4.7 6.5 - - + -
224A LEU* 3.8 28.3 - - + -
262A VAL* 2.9 38.0 + - + +
263A LEU* 3.9 13.9 - - + +
265A PHE* 1.3 79.4 - - + +
267A ILE* 1.3 67.8 + - + +
270A LEU* 2.9 50.6 + - + +
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Residues in contact with ILE 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 2.8 38.9 + - + +
264A ALA* 3.8 4.7 - - - +
266A ILE* 1.3 79.2 - - + +
268A CYS* 1.3 71.0 + - - +
271A PRO* 3.3 21.1 - - - +
306A LEU* 3.6 11.7 - - + +
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Residues in contact with CYS 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ALA* 3.0 22.6 + - - +
267A ILE* 1.3 89.4 - - - +
269A TRP* 1.3 60.5 + - - +
271A PRO* 4.4 1.3 - - - -
272A PHE* 5.3 1.1 - - - +
303A ALA 4.9 0.3 - - - +
306A LEU* 3.5 24.5 - - + +
307A GLY* 3.3 27.0 + - - -
309A THR* 4.6 5.6 - - - -
310A ASN* 3.3 38.4 - - + -
313A VAL* 5.6 7.0 - - - -
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Residues in contact with TRP 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A MET* 3.4 37.5 - - + -
132A ILE* 3.8 27.5 - - + +
135A ILE* 5.8 0.2 - - - +
220A PHE* 3.6 18.8 - - + -
265A PHE* 3.0 34.2 + + + +
268A CYS* 1.3 80.5 - - - +
270A LEU* 1.3 64.5 + - - +
271A PRO* 3.4 2.4 - - - -
272A PHE* 3.4 38.3 + + + +
273A HIS* 3.1 50.5 + + - +
304A ILE 5.5 0.7 - - - -
307A GLY* 3.8 19.5 + - - -
310A ASN* 3.2 33.6 - - - +
311A SER* 5.5 2.6 + - - -
8B PHE* 3.6 12.3 - + - -
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Residues in contact with LEU 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 3.7 29.0 - - + -
266A ILE* 2.9 32.9 + - + +
267A ILE* 6.4 0.2 - - - -
269A TRP* 1.3 77.1 - - - +
271A PRO* 1.3 66.7 - - + +
273A HIS* 3.3 1.6 + - + -
274A VAL* 2.9 46.6 + - + +
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Residues in contact with PRO 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A ILE* 3.3 19.1 - - - +
268A CYS 4.4 0.2 - - - -
269A TRP 3.6 4.0 - - - +
270A LEU* 1.3 94.4 - - + +
272A PHE* 1.3 62.8 + - - +
274A VAL* 3.3 5.8 + - + +
275A LEU* 2.9 29.6 + - + +
303A ALA* 4.2 9.4 - - + -
306A LEU* 3.6 26.0 - - + -
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Residues in contact with PHE 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A LYS* 4.9 8.5 - - + -
268A CYS 5.3 0.7 - - - +
269A TRP* 3.4 38.7 + + + +
270A LEU 3.4 0.2 - - - -
271A PRO* 1.3 80.0 - - - +
273A HIS* 1.3 71.1 + + - +
275A LEU* 3.2 4.4 + - - +
276A THR* 2.9 56.0 + - + +
300A LEU* 4.3 5.6 - - + -
303A ALA* 3.5 24.9 - - + +
304A ILE* 3.4 44.4 - - + -
306A LEU* 5.7 0.6 - - + +
4B TYR* 4.0 3.1 - - - -
8B PHE* 3.5 40.6 - + - -
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Residues in contact with HIS 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 5.2 1.3 - - + -
215A LYS* 3.0 29.8 + - + +
216A ASN* 3.0 27.6 - - - +
219A GLY* 3.7 12.5 - - - -
220A PHE* 3.5 40.1 + + + +
269A TRP* 3.1 54.1 + + - +
270A LEU* 4.1 2.2 - - + +
272A PHE* 1.3 86.9 - + - +
274A VAL* 1.3 62.1 + - + +
276A THR* 2.8 21.9 + - - -
277A PHE* 2.9 15.2 + - - +
8B PHE* 5.7 3.0 - + - -
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Residues in contact with VAL 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU* 2.9 44.0 + - + +
271A PRO* 3.7 6.3 - - + +
273A HIS* 1.3 76.6 - - - +
275A LEU* 1.3 58.8 + - + +
277A PHE* 3.2 7.7 + - + +
278A LEU* 2.9 52.7 + - + +
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Residues in contact with LEU 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A PRO* 2.9 16.6 + - + +
272A PHE 3.4 7.9 - - - +
274A VAL* 1.3 78.6 - - + +
276A THR* 1.3 56.6 + - - +
278A LEU* 3.4 11.7 + - + +
279A ASP* 2.9 28.6 + - - +
295A VAL* 5.0 4.5 - - + +
296A ILE* 4.2 25.7 - - + +
299A ALA* 3.7 37.7 - - + +
300A LEU* 3.7 17.0 - - + +
303A ALA* 3.7 28.5 - - + -
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Residues in contact with THR 276 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ALA* 3.6 17.4 + - - +
215A LYS* 5.0 7.9 - - + -
216A ASN* 3.2 13.3 + - - -
272A PHE* 2.9 49.3 + - + +
273A HIS* 2.8 28.9 + - - -
275A LEU* 1.3 76.2 - - - +
277A PHE* 1.3 55.7 + - - +
279A ASP* 3.4 8.3 + - - +
280A ALA* 2.9 27.5 + - - +
300A LEU* 4.5 6.1 - - + -
4B TYR* 4.4 12.3 - - + +
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Residues in contact with PHE 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 4.1 18.6 - - + -
216A ASN* 3.4 24.0 - - + +
273A HIS 2.9 14.5 + - - +
274A VAL* 3.2 7.8 + - + +
276A THR* 1.3 75.6 + - - +
278A LEU* 1.3 70.7 + - + +
280A ALA* 3.1 5.9 + - - +
281A LEU* 2.9 66.9 + - + +
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Residues in contact with LEU 278 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A VAL* 2.9 36.0 + - + +
275A LEU* 3.8 9.6 - - + +
277A PHE* 1.3 85.3 - - + +
279A ASP* 1.3 57.3 + - - +
281A LEU* 3.1 23.1 + - + -
282A ALA* 2.9 24.1 + - - +
287A ILE* 3.3 17.3 - - + +
292A VAL* 5.2 8.5 - - + -
296A ILE* 3.7 22.4 - - + -
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Residues in contact with ASP 279 (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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212A ALA* 5.5 1.6 - - + -
275A LEU 2.9 18.5 + - - +
276A THR* 3.5 9.9 - - - +
278A LEU* 1.3 76.3 - - - +
280A ALA* 1.3 57.0 + - - +
282A ALA* 3.0 4.7 + - - +
283A TRP* 2.6 56.7 + - - +
296A ILE* 3.7 26.1 - - + +
297A ASP* 4.6 0.9 - - - +
300A LEU* 4.0 15.2 - - + +
2B ARG* 3.1 23.7 + - - -
4B TYR* 4.3 13.0 - - + -
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Residues in contact with ALA 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ALA* 3.8 9.2 - - + +
212A ALA* 3.6 17.0 - - + -
213A LEU* 3.9 24.7 - - + -
276A THR 2.9 15.0 + - - +
277A PHE* 3.1 10.1 + - + +
279A ASP* 1.3 74.7 - - - +
281A LEU* 1.3 64.0 + - + +
283A TRP* 3.3 13.2 + - - +
284A MET* 3.0 28.0 + - + +
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Residues in contact with LEU 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 6.3 0.7 - - + -
277A PHE* 2.9 53.4 + - + +
278A LEU* 3.1 27.3 + - + +
280A ALA* 1.3 77.8 - - + +
282A ALA* 1.3 60.6 + - - +
284A MET* 3.3 9.3 + - + +
285A GLY 3.1 16.1 + - - -
286A VAL* 3.2 30.6 + - + -
287A ILE* 3.7 19.0 + - + -
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Residues in contact with ALA 282 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LEU 2.9 12.7 + - - +
279A ASP* 3.0 11.6 + - - +
281A LEU* 1.3 74.1 - - - +
283A TRP* 1.3 61.7 + - - +
285A GLY* 2.9 20.4 + - - -
287A ILE* 3.3 25.4 - - + +
293A ILE* 4.0 26.3 - - + +
296A ILE* 4.9 2.5 - - + -
2B ARG* 4.2 11.0 - - - +
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Residues in contact with TRP 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A TYR* 4.1 16.8 - + - -
205A ALA* 3.5 50.6 - - + +
206A GLN* 4.9 0.5 + - - +
208A ALA* 3.4 27.9 - - + +
209A ALA* 3.7 13.2 - - + -
212A ALA* 5.1 3.0 - - + +
279A ASP* 2.6 51.2 + - + -
280A ALA* 3.3 8.7 + - - +
282A ALA* 1.3 75.3 - - - +
284A MET* 1.3 64.2 + - - +
285A GLY* 3.4 0.3 + - - -
2B ARG* 3.2 68.2 - - + -
3B VAL 4.4 9.6 - - - -
4B TYR* 4.8 11.8 - + - -
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Residues in contact with MET 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLN* 4.6 20.2 - - + +
209A ALA* 3.7 22.9 - - + -
213A LEU* 6.0 6.7 - - + -
280A ALA* 3.0 20.5 + - + +
281A LEU* 3.5 13.0 - - + +
282A ALA 3.1 0.2 - - - -
283A TRP* 1.3 78.1 - - - +
285A GLY* 1.3 59.0 + - - +
286A VAL* 3.5 15.4 - - + +
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LEU 3.1 0.4 + - - -
282A ALA 2.9 17.3 + - - -
283A TRP 4.5 0.2 - - - -
284A MET* 1.3 79.0 - - - +
286A VAL* 1.3 65.2 + - - +
287A ILE 3.3 7.8 - - - -
288A ASN* 4.4 13.4 + - - +
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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