Contacts of the helix formed by residues 241 - 277 (chain A) in PDB entry 3OAX
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 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A GLN* 2.7 31.1 - - - +
240A SER* 1.3 80.9 - - - +
242A THR* 1.3 52.8 + - - +
243A THR* 2.9 15.3 - - - +
244A GLN* 2.6 26.8 + - - +
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Residues in contact with THR 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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237A GLN* 3.8 22.6 - - + +
238A GLN* 3.4 23.0 + - - +
241A ALA* 1.3 71.6 - - - +
243A THR* 1.3 55.2 + - - +
244A GLN 3.0 0.9 - - - -
245A LYS* 3.3 2.9 + - + +
246A ALA* 3.1 32.1 + - + +
334A SER* 5.7 4.9 - - - +
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Residues in contact with THR 243 (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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241A ALA* 2.9 10.9 - - - +
242A THR* 1.3 76.7 - - - +
244A GLN* 1.3 57.6 + - - +
246A ALA* 4.2 6.6 - - - +
247A GLU* 3.2 30.7 + - - +
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Residues in contact with GLN 244 (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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230A VAL* 6.4 0.7 - - + -
238A GLN 3.6 0.7 - - - +
239A GLU* 2.9 32.4 + - - +
240A SER* 3.1 36.9 + - - +
241A ALA* 2.6 15.5 + - - +
243A THR* 1.3 77.5 - - - +
245A LYS* 1.3 62.4 + - - -
246A ALA 3.2 1.3 - - - -
247A GLU* 3.3 6.6 + - + +
248A LYS* 2.8 52.7 + - - +
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Residues in contact with LYS 245 (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 ALA* 3.3 31.8 - - + +
235A ALA 3.0 15.0 - - - +
236A GLN 2.8 20.9 - - - +
237A GLN* 3.9 9.4 - - + -
238A GLN 3.3 21.5 + - - +
239A GLU* 2.8 20.6 + - - +
242A THR* 3.3 6.6 + - + +
244A GLN* 1.3 98.2 + - - +
246A ALA* 1.3 59.5 + - - +
248A LYS* 3.2 24.7 + - - +
249A GLU* 3.5 7.3 + - - +
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Residues in contact with ALA 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A THR* 3.1 20.5 + - + +
243A THR* 4.6 5.8 - - + +
245A LYS* 1.3 74.4 - - - +
247A GLU* 1.3 64.9 + - - +
248A LYS 3.1 2.0 - - - -
249A GLU* 3.3 24.1 + - - +
250A VAL* 3.6 12.0 + - - +
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Residues in contact with GLU 247 (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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135A ARG* 3.1 53.9 + - - +
138A VAL* 4.1 23.0 - - + +
139A VAL* 5.1 6.7 - - + -
230A VAL* 6.2 0.2 - - - -
243A THR* 3.2 27.4 + - - +
244A GLN* 3.3 9.3 + - - +
246A ALA* 1.3 79.2 - - - +
248A LYS* 1.3 59.4 + - - +
250A VAL* 3.6 8.1 + - - +
251A THR* 3.1 12.0 + - - -
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Residues in contact with LYS 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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230A VAL* 4.0 24.5 - - + -
231A LYS 3.5 16.8 - - - +
232A GLU* 4.9 3.4 - - - +
233A ALA 3.0 28.9 + - - +
234A ALA* 3.3 21.1 - - + +
239A GLU* 3.8 7.7 - - - +
244A GLN* 2.8 43.8 + - - +
245A LYS* 3.2 20.8 - - - +
246A ALA 3.1 0.4 - - - -
247A GLU* 1.3 76.4 - - - +
249A GLU* 1.3 64.2 + - - +
251A THR* 3.2 6.4 + - - +
252A ARG* 2.9 25.3 + - + +
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Residues in contact with GLU 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 LYS 3.5 7.0 + - - +
246A ALA* 3.3 18.1 + - - +
248A LYS* 1.3 78.3 - - - +
250A VAL* 1.3 64.1 + - - +
252A ARG* 3.3 8.2 + - - +
253A MET* 3.1 21.8 + - - +
309A MET 3.3 22.5 - - - +
310A ASN* 3.9 17.2 + - - -
311A LYS* 3.0 32.2 + - - +
312A GLN* 5.4 0.9 + - - +
1508A HTG 4.0 13.9 + - - +
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Residues in contact with VAL 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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72A LEU* 3.8 37.5 - - + -
134A GLU* 5.0 1.3 - - - +
135A ARG* 3.6 35.7 - - - +
246A ALA 4.0 10.8 - - - +
247A GLU* 3.6 8.6 + - - +
248A LYS 3.3 0.4 - - - -
249A GLU* 1.3 79.9 - - - +
251A THR* 1.3 58.1 + - - +
253A MET* 3.4 6.8 + - - +
254A VAL* 3.0 31.7 + - + +
310A ASN* 4.6 9.6 - - - +
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Residues in contact with THR 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ARG* 3.1 36.0 + - + +
139A VAL* 4.1 8.5 - - - +
226A LEU* 4.0 17.3 - - + -
230A VAL* 4.5 13.0 - - + +
231A LYS 6.1 1.6 - - - +
247A GLU 3.1 12.7 + - - -
248A LYS* 3.2 12.7 + - - -
250A VAL* 1.3 74.6 - - - +
252A ARG* 1.3 66.6 + - - +
254A VAL* 3.3 2.6 + - + +
255A ILE* 3.0 45.0 + - + +
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Residues in contact with ARG 252 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLU* 2.7 62.9 + - - +
248A LYS* 2.9 14.2 + - + +
249A GLU* 3.5 12.3 - - - +
251A THR* 1.3 76.6 - - - +
253A MET* 1.3 62.3 + - - +
255A ILE* 3.4 12.0 + - - +
256A ILE* 3.0 44.3 + - - +
309A MET* 4.0 15.0 - - + -
1508A HTG 4.2 33.0 + - - +
35B TRP* 5.6 4.4 - - - +
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Residues in contact with MET 253 (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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72A LEU* 3.5 38.8 - - + -
76A LEU* 3.6 18.6 - - + -
249A GLU 3.1 10.2 + - - +
250A VAL* 3.6 10.5 - - - +
251A THR 3.2 0.2 - - - -
252A ARG* 1.3 77.4 - - - +
254A VAL* 1.3 55.0 + - - +
256A ILE* 3.0 4.0 + - - +
257A MET* 2.7 48.5 + - + +
305A ILE* 3.8 17.5 - - + -
306A TYR* 3.6 33.2 - - + +
309A MET* 3.8 34.7 - - + +
310A ASN* 4.4 4.3 - - - -
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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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72A LEU* 4.7 6.7 - - + -
128A LEU* 5.1 3.8 - - + +
131A LEU* 4.0 48.0 - - + +
132A ALA* 4.7 5.6 - - + +
134A GLU* 5.8 0.2 - - - +
135A ARG* 4.1 18.6 - - + -
250A VAL* 3.0 24.7 + - + +
251A THR* 3.3 6.9 + - + +
253A MET* 1.3 76.1 - - + +
255A ILE* 1.3 63.3 + - + +
257A MET* 3.4 10.5 + - - +
258A VAL* 3.1 28.3 + - + +
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Residues in contact with ILE 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A TYR* 3.6 39.3 - - + -
226A LEU* 6.5 0.7 - - + -
231A LYS 6.2 0.9 - - - -
232A GLU* 4.3 32.8 - - + +
251A THR* 3.0 34.7 + - + +
252A ARG* 3.7 11.4 - - - +
254A VAL* 1.3 76.6 - - + +
256A ILE* 1.3 66.2 + - - +
258A VAL* 3.1 10.8 + - + +
259A ILE* 3.1 35.9 + - + +
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Residues in contact with ILE 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 ARG* 3.0 37.5 + - - +
253A MET 3.0 6.9 + - - +
255A ILE* 1.3 75.9 - - + +
257A MET* 1.3 58.8 + - - +
259A ILE* 2.9 13.3 + - + +
260A ALA* 2.9 27.0 + - - +
305A ILE* 4.0 17.9 - - + -
309A MET* 3.8 10.3 - - + -
1410A 4E6 3.9 33.7 - - + -
1508A HTG 3.8 37.0 - - + -
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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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76A LEU* 4.6 10.8 - - + -
79A LEU* 4.3 18.8 - - + -
127A SER* 6.3 0.2 - - - -
128A LEU* 4.0 17.0 - - + +
131A LEU* 4.0 28.7 - - + -
253A MET* 2.7 43.9 + - - +
254A VAL* 3.5 14.1 - - - +
255A ILE 3.2 0.2 - - - -
256A ILE* 1.3 72.8 - - - +
258A VAL* 1.3 56.1 + - - +
260A ALA* 3.8 1.9 - - - +
261A PHE* 3.1 25.8 + - - +
301A TYR* 4.3 4.3 + - - -
302A ASN* 3.6 28.1 + - + +
305A ILE* 4.1 25.4 - - + -
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Residues in contact with VAL 258 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 4.0 28.3 - - + +
216A LEU* 5.1 4.3 - - + -
219A ILE* 4.2 30.5 - - + -
220A PHE* 4.4 10.1 - - + -
254A VAL* 3.1 22.4 - - + +
255A ILE* 3.1 10.5 + - + +
256A ILE 3.0 0.6 - - - -
257A MET* 1.3 76.5 - - - +
259A ILE* 1.3 67.1 + - + +
260A ALA 3.1 0.2 - - - -
261A PHE* 3.2 1.7 + - + +
262A LEU* 2.9 41.9 + - + +
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Residues in contact with ILE 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A PHE* 6.5 1.1 - - + -
255A ILE* 3.1 26.8 + - + +
256A ILE* 2.9 18.5 + - + +
258A VAL* 1.3 78.3 - - + +
260A ALA* 1.3 57.4 + - - +
262A LEU* 3.4 12.2 + - + +
263A ILE* 2.9 51.9 + - + +
1410A 4E6 4.0 13.7 - - + -
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Residues in contact with ALA 260 (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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256A ILE 2.9 14.4 + - - +
257A MET 3.8 0.9 - - - +
259A ILE* 1.3 75.0 - - - +
261A PHE* 1.3 66.7 + - - +
263A ILE* 3.1 12.4 + - - +
264A CYS* 2.9 24.1 + - - +
301A TYR* 3.5 32.2 - - + -
305A ILE* 3.8 11.7 - - + -
1410A 4E6 4.5 15.2 - - + +
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Residues in contact with PHE 261 (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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121A GLY 3.4 20.9 - - - -
124A ALA* 4.4 8.7 - - + -
125A LEU* 3.7 32.8 - - + -
128A LEU* 3.7 23.3 - - + -
212A PHE* 5.6 2.2 - + - -
216A LEU* 4.9 8.5 - - + -
257A MET 3.1 19.3 + - - +
258A VAL* 3.5 5.2 - - + +
260A ALA* 1.3 74.4 - - - +
262A LEU* 1.3 73.4 + - + +
264A CYS 3.0 2.4 + - - -
265A TRP* 2.9 63.4 + + + -
266A LEU* 6.3 0.4 - - + -
301A TYR* 3.1 21.9 + - - +
1296A RET 3.5 29.4 - - + -
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Residues in contact with LEU 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A LEU* 3.9 25.8 - - + -
220A PHE* 3.5 30.5 - - + -
258A VAL* 2.9 29.3 + - + +
259A ILE* 3.6 11.9 - - + +
261A PHE* 1.3 85.8 - - + +
263A ILE* 1.3 59.5 + - + +
264A CYS 3.1 0.2 + - - -
265A TRP 4.5 0.2 - - - +
266A LEU* 2.7 73.2 + - + +
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Residues in contact with ILE 263 (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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259A ILE* 2.9 46.3 + - + +
260A ALA* 3.1 9.6 + - - +
262A LEU* 1.3 76.0 - - + +
264A CYS* 1.3 58.8 + - - +
266A LEU* 5.3 0.9 - - - -
267A PRO* 3.5 12.5 - - - +
294A PHE* 3.1 27.6 - - + -
1410A 4E6 4.5 13.5 - - + -
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Residues in contact with CYS 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ALA 2.9 15.9 + - - +
261A PHE 3.0 4.9 + - - +
263A ILE* 1.3 80.5 - - - +
265A TRP* 1.3 63.5 + - + +
267A PRO* 4.3 4.4 - - - +
268A TYR* 4.9 0.5 - - - +
294A PHE* 3.7 15.1 - - + -
295A ALA* 3.4 43.0 - - - +
297A THR* 3.3 25.4 - - - -
298A SER* 3.7 16.2 - - - -
301A TYR* 4.1 11.0 - - + -
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Residues in contact with TRP 265 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MET* 5.3 0.9 - - + -
117A ALA* 4.1 14.4 - - + -
121A GLY* 3.7 19.8 - - - -
124A ALA* 5.8 0.6 - - - +
212A PHE* 5.9 0.9 - - + -
261A PHE* 2.9 59.5 + + + +
262A LEU* 5.2 0.2 - - - -
264A CYS* 1.3 84.8 - - + +
266A LEU* 1.3 61.9 + - + +
267A PRO* 3.2 2.9 - - - -
268A TYR* 3.1 15.7 + + - +
269A ALA* 2.8 31.4 + - - +
295A ALA* 3.6 30.1 - - + -
296A LYS* 5.8 0.4 - - - -
298A SER* 3.3 37.5 - - - -
301A TYR* 4.7 1.0 + - - -
1296A RET 3.9 69.3 - - + -
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Residues in contact with LEU 266 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PHE* 4.2 26.2 - - + -
261A PHE* 6.3 0.4 - - + -
262A LEU* 2.7 62.0 + - + +
263A ILE* 5.3 0.7 - - - -
265A TRP* 1.3 73.3 - - + +
267A PRO* 1.3 62.2 - - + +
269A ALA* 3.8 2.1 - - + +
270A GLY* 2.7 28.4 + - - -
1507A HTG 4.1 5.6 - - + +
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Residues in contact with PRO 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ILE* 3.5 24.7 - - - +
264A CYS 4.4 3.1 - - - +
265A TRP 3.5 0.9 - - - -
266A LEU* 1.3 95.9 - - + +
268A TYR* 1.3 58.1 + - - +
270A GLY* 3.8 0.5 - - - -
271A VAL* 3.1 33.5 + - + +
291A PRO* 3.8 15.3 - - + +
294A PHE* 4.3 16.6 - - + -
1507A HTG 3.9 20.4 - - + +
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Residues in contact with TYR 268 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLU* 2.6 24.5 + - - -
188A GLY* 3.9 0.3 - - - -
191A TYR* 2.5 32.5 + + - -
264A CYS 4.9 0.2 - - - +
265A TRP* 3.1 29.2 + + + +
267A PRO* 1.3 78.2 - - - +
269A ALA* 1.3 68.1 + - - +
271A VAL 3.4 0.5 + - - -
272A ALA* 3.0 23.7 + - + +
288A MET* 3.3 35.3 - - + +
291A PRO* 3.8 16.5 - - - +
292A ALA* 3.7 18.6 - - + -
295A ALA* 4.5 2.9 - - + -
1296A RET 3.6 57.6 - - + +
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Residues in contact with ALA 269 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 3.9 7.8 - - + -
212A PHE* 4.0 29.6 - - + -
265A TRP 2.8 17.6 + - - +
266A LEU* 3.8 4.0 - - - +
268A TYR* 1.3 77.2 - - - +
270A GLY* 1.3 58.4 + - - +
272A ALA* 3.2 3.1 + - - +
273A PHE* 2.9 31.1 + - - +
1296A RET 3.9 27.6 - - + -
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Residues in contact with GLY 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU 2.7 19.2 + - - -
269A ALA* 1.3 77.6 - - - +
271A VAL* 1.3 60.8 + - - +
273A PHE* 3.4 5.6 + - - +
274A TYR* 3.1 22.9 + - - +
1507A HTG 3.8 23.0 - - - +
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Residues in contact with VAL 271 (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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267A PRO* 3.1 19.7 + - + +
270A GLY* 1.3 75.9 - - - +
272A ALA* 1.3 57.9 + - - +
274A TYR* 3.7 2.0 - - - +
275A ILE* 3.2 29.4 + - + +
287A PHE* 3.4 48.9 - - + +
288A MET* 4.0 20.2 - - + -
291A PRO* 3.8 17.5 - - + -
1507A HTG 4.0 22.4 - - + -
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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
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191A TYR* 3.8 39.0 - - + +
208A PHE* 4.0 12.8 - - + -
268A TYR* 3.0 22.1 + - + +
269A ALA* 3.5 5.8 - - - +
270A GLY 3.1 0.2 - - - -
271A VAL* 1.3 76.4 - - - +
273A PHE* 1.3 60.5 + - - +
275A ILE* 3.6 2.8 + - - +
276A PHE* 3.0 30.1 + - - +
288A MET* 3.8 8.5 - - + +
1296A RET 5.3 0.7 - - + -
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Residues in contact with PHE 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 3.9 36.5 - + + -
269A ALA 2.9 16.8 + - - +
270A GLY* 3.9 6.3 - - - +
272A ALA* 1.3 73.7 - - - +
274A TYR* 1.3 59.1 + - - +
276A PHE* 3.5 12.7 + + - +
277A THR* 2.8 62.0 + - + +
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Residues in contact with TYR 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A GLY 3.1 16.8 + - - +
271A VAL* 3.7 5.8 - - - +
272A ALA 3.2 0.2 - - - -
273A PHE* 1.3 74.4 - - - +
275A ILE* 1.3 61.8 + - + +
277A THR* 2.7 31.5 + - - -
278A HIS* 2.8 60.3 + + + +
281A SER* 4.3 10.4 + - - -
283A PHE* 5.1 2.5 - + - -
287A PHE* 3.8 22.4 - + - -
1507A HTG 3.6 65.9 + - + -
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Residues in contact with ILE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 3.8 17.7 - - + +
192A TYR* 3.6 53.2 - - + +
271A VAL* 3.2 29.9 + - + +
272A ALA* 3.8 3.8 - - - +
274A TYR* 1.3 81.1 - - - +
276A PHE* 1.3 59.0 + - - +
278A HIS* 2.7 23.5 + - - +
279A GLN* 2.8 16.3 + - - +
283A PHE* 4.1 22.0 - - + -
287A PHE* 4.1 17.0 - - + -
288A MET* 4.2 11.0 - - + -
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP 5.4 0.4 - - - -
191A TYR* 3.4 19.7 - - + -
193A THR 6.1 0.4 - - - -
200A ASN 5.3 0.4 - - - -
201A GLU* 3.7 45.5 - - + -
204A VAL* 3.6 49.1 - - + -
205A ILE* 4.3 16.8 - - + -
208A PHE* 5.3 0.4 - + + -
272A ALA 3.0 18.8 + - - +
273A PHE* 3.6 16.4 - + - +
275A ILE* 1.3 76.1 - - - +
277A THR* 1.3 68.6 + - + +
279A GLN* 3.0 31.1 + - - +
957A ZN 4.1 4.9 - - - -
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PHE* 2.8 46.5 + - + +
274A TYR* 2.7 26.3 + - - -
276A PHE* 1.3 82.2 - - + +
278A HIS* 1.3 82.7 + - - -
279A GLN* 3.8 0.9 - - - -
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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) + - + + + + + -
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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