Contacts of the helix formed by residues 213 - 249 (chain A) in PDB entry 4NSW
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 213 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 4.0 37.5 - - + +
83A PHE* 4.1 22.2 - - + -
86A SER* 3.4 34.3 - - - +
209A GLU* 3.1 18.8 + - - +
210A LEU* 3.4 22.2 - - + +
211A SER 3.1 0.8 - - - -
212A ARG* 1.3 75.6 - - - +
214A SER* 1.3 61.9 + - - +
215A GLN 3.6 1.1 - - - -
216A TYR* 3.2 13.3 + - + +
217A ARG* 3.1 27.4 + - - +
196B VAL* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU 3.2 2.0 + - - -
211A SER* 2.9 25.7 + - - -
212A ARG 3.2 0.6 - - - -
213A LEU* 1.3 73.6 - - - +
215A GLN* 1.3 66.3 + - - +
217A ARG* 3.5 25.6 + - - +
218A LYS* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER 4.7 0.6 + - - -
212A ARG 4.8 2.6 + - - +
213A LEU 3.6 0.4 - - - -
214A SER* 1.3 79.9 + - - +
216A TYR* 1.3 56.7 + - - +
218A LYS* 2.8 47.9 + - + +
219A GLU* 2.9 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 4.5 1.6 + - - +
78A GLU* 3.5 32.5 + - + +
79A CYS* 3.3 32.3 + - - +
82A LYS* 4.0 33.0 - - + -
83A PHE* 3.7 36.6 - + - -
212A ARG 5.4 0.8 + - - +
213A LEU* 3.2 15.4 + - + +
215A GLN* 1.3 79.0 - - - +
217A ARG* 1.3 54.0 + - - +
219A GLU* 3.8 12.0 + - + +
220A LEU* 2.8 54.6 + - + +
223A GLN* 5.8 5.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 4.0 7.9 - - + -
210A LEU* 2.7 35.1 + - - +
211A SER* 4.6 0.6 - - - +
213A LEU* 3.1 25.3 + - - +
214A SER* 3.6 20.1 - - - +
215A GLN 3.3 0.2 - - - -
216A TYR* 1.3 74.6 - - - +
218A LYS* 1.3 60.1 + - - +
220A LEU* 3.5 2.1 + - - +
221A GLY* 2.9 26.7 + - - -
193B LEU* 3.9 24.0 - - + +
196B VAL* 3.8 23.7 - - + +
197B GLU* 2.6 43.4 + - - +
200B ALA* 3.3 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A SER 3.2 12.0 + - - +
215A GLN* 2.8 40.0 + - + +
217A ARG* 1.3 79.2 - - - +
219A GLU* 1.3 66.0 + - - +
221A GLY* 3.5 1.9 + - - -
222A ALA* 3.1 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLN* 2.9 58.4 + - - +
216A TYR* 3.8 13.4 + - + +
218A LYS* 1.3 79.9 + - - +
220A LEU* 1.3 59.5 + - - +
222A ALA* 3.1 8.5 + - - +
223A GLN* 2.9 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 3.7 27.6 - - + -
79A CYS* 4.0 11.4 - - + -
83A PHE* 3.4 38.6 - - + -
216A TYR* 2.8 43.8 + - + +
217A ARG 3.8 2.7 - - - +
219A GLU* 1.3 71.2 - - - +
221A GLY* 1.3 57.9 + - - +
223A GLN* 3.8 9.5 - - - +
224A LEU* 2.9 47.7 + - + +
189B MET* 4.7 9.2 - - + +
193B LEU* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG 2.9 17.6 + - - -
218A LYS* 3.9 2.2 - - - -
219A GLU 3.2 0.2 - - - -
220A LEU* 1.3 75.8 - - - +
222A ALA* 1.3 60.1 + - - +
224A LEU* 3.6 4.2 - - - +
225A HIS* 3.2 24.1 + - - +
193B LEU* 3.9 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS* 3.1 15.0 + - + +
219A GLU* 3.1 11.6 + - - +
221A GLY* 1.3 73.5 - - - +
223A GLN* 1.3 65.4 + - + +
224A LEU 3.1 1.3 + - - -
225A HIS* 3.4 7.9 + - - +
226A GLN* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 3.7 32.7 - - + +
78A GLU* 5.7 2.3 + - - +
216A TYR* 5.8 5.6 - - - -
219A GLU* 2.9 36.8 + - + +
220A LEU* 3.8 8.2 - - - +
222A ALA* 1.3 72.8 - - + +
224A LEU* 1.3 58.2 + - - +
226A GLN* 3.2 8.2 - - - +
227A LEU* 2.9 40.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 3.4 27.8 - - + -
220A LEU* 2.9 26.1 + - + +
221A GLY* 3.6 5.4 - - - +
222A ALA 3.1 0.2 - - - -
223A GLN* 1.3 73.1 - - - +
225A HIS* 1.3 66.2 + - - +
226A GLN 3.1 1.1 - - - -
227A LEU* 3.1 14.1 + - + +
228A VAL* 3.0 23.7 + - - +
186B PHE* 3.7 23.1 - - + -
189B MET* 4.0 26.9 - - + +
190B GLU* 3.9 37.0 - - + +
193B LEU* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A GLY 3.2 14.0 + - - +
222A ALA* 3.8 6.5 - - - +
224A LEU* 1.3 77.1 - - - +
226A GLN* 1.3 71.2 + - - +
228A VAL* 3.6 8.8 + - - +
229A LEU* 3.3 49.2 + - + +
186B PHE* 5.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA 3.0 15.2 + - - +
223A GLN* 3.2 15.0 - - - +
225A HIS* 1.3 83.8 - - - +
227A LEU* 1.3 68.3 + - + +
229A LEU* 3.1 15.6 + - + +
230A ASN* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU* 6.0 1.1 - - - +
75A MET* 4.3 23.8 - - + -
223A GLN* 2.9 35.5 + - + +
224A LEU* 3.1 10.1 + - + +
226A GLN* 1.3 79.9 - - + +
228A VAL* 1.3 59.6 + - + +
230A ASN* 3.5 18.7 + - + +
231A SER* 3.0 31.1 + - - -
186B PHE* 5.9 3.6 - - + -
189B MET* 6.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU 3.0 18.4 - - - +
225A HIS* 3.9 7.9 - - - +
226A GLN 3.1 1.0 - - - -
227A LEU* 1.3 75.7 - - + +
229A LEU* 1.3 60.5 + - + +
231A SER* 3.9 6.1 - - - -
232A ALA* 3.2 25.6 + - - +
186B PHE* 3.2 50.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A HIS* 3.3 38.2 + - + +
226A GLN* 3.1 18.0 + - + +
228A VAL* 1.3 77.7 - - + +
230A ASN* 1.3 68.3 + - - +
232A ALA* 3.1 8.8 + - + +
233A ARG* 2.9 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 3.0 30.1 + - - +
227A LEU* 3.6 25.8 - - + +
229A LEU* 1.3 73.9 - - - +
231A SER* 1.3 53.7 + - - +
233A ARG* 2.7 42.1 + - - +
234A GLU* 2.8 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LEU 3.0 16.0 + - - -
228A VAL* 3.9 7.4 - - - -
230A ASN* 1.3 80.3 - - - +
232A ALA* 1.3 58.9 + - - +
234A GLU* 4.0 11.5 - - - +
235A LYS* 3.1 28.8 + - - +
178B ASN* 5.9 1.0 + - - -
179B VAL* 5.8 0.9 - - - -
182B ASP* 2.7 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL 3.2 14.8 + - - +
229A LEU* 3.1 12.0 + - + +
231A SER* 1.3 76.8 - - - +
233A ARG* 1.3 60.7 + - - +
235A LYS* 3.3 7.4 + - - +
236A ARG* 2.8 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LEU* 2.9 16.1 + - - +
230A ASN* 2.7 41.0 + - - +
232A ALA* 1.3 76.4 - - - +
234A GLU* 1.3 57.5 + - + +
236A ARG* 3.4 11.6 + - - +
237A ASP* 3.1 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ASN* 2.8 29.6 + - - +
231A SER* 4.0 12.8 + - - +
233A ARG* 1.3 72.8 - - + +
235A LYS* 1.3 60.3 + - - +
237A ASP* 3.1 13.1 + - + +
238A MET* 2.9 34.7 + - + +
178B ASN* 5.4 8.3 + - - +
182B ASP* 4.4 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A SER 3.1 19.4 + - - +
232A ALA* 3.7 8.3 - - - +
233A ARG 3.3 0.2 - - - -
234A GLU* 1.3 76.8 - - - +
236A ARG* 1.3 62.0 + - + +
238A MET* 3.4 7.7 + - - +
239A GLU* 3.1 48.7 + - - +
175B LEU* 4.3 16.2 - - + -
176B GLN* 5.8 1.3 + - - -
178B ASN* 5.9 4.7 - - - +
179B VAL* 3.9 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA* 2.8 38.9 + - - +
233A ARG* 3.6 10.0 - - - +
235A LYS* 1.3 76.7 - - + +
237A ASP* 1.3 61.5 + - - +
239A GLU* 3.5 15.2 + - - +
240A GLN* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ARG* 3.1 25.0 + - - +
234A GLU* 3.1 15.5 + - - +
236A ARG* 1.3 80.0 - - - +
238A MET* 1.3 57.1 + - + +
240A GLN* 3.3 16.4 + - - +
241A ARG* 2.9 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLU* 2.9 19.2 + - + +
235A LYS* 3.8 2.7 - - - +
237A ASP* 1.3 73.9 - - + +
239A GLU* 1.3 61.1 + - - +
241A ARG* 3.3 21.7 + - - +
242A HIS* 2.9 66.3 + - + +
5B LEU 5.4 4.9 - - - +
6B ASP* 6.3 0.9 - - - -
7B PHE* 6.0 3.1 - - + +
174B ALA* 4.7 7.0 - - + +
175B LEU* 3.6 38.1 - - + +
178B ASN* 4.2 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LYS* 3.1 49.4 + - - +
236A ARG* 3.9 14.8 - - - +
238A MET* 1.3 72.3 - - - +
240A GLN* 1.3 65.7 + - - +
242A HIS* 3.8 6.7 - - - +
243A VAL* 2.9 34.1 + - + +
175B LEU* 4.5 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ARG 3.0 18.7 + - - +
237A ASP* 3.4 16.9 - - - +
239A GLU* 1.3 77.9 - - - +
241A ARG* 1.3 61.4 + - - +
243A VAL* 3.4 6.8 + - - +
244A LEU* 3.0 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 2.9 15.9 + - - +
238A MET* 3.4 27.3 - - - +
240A GLN* 1.3 76.5 - - - +
242A HIS* 1.3 62.4 + - + +
244A LEU* 3.0 15.2 + - + +
245A LEU* 2.8 41.7 + - + +
7B PHE* 3.5 52.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A MET* 2.9 58.2 + - + +
239A GLU* 3.3 6.2 + - - +
241A ARG* 1.3 87.3 - - + +
243A VAL* 1.3 62.4 + - + +
245A LEU* 3.2 6.9 + - + +
246A LYS* 2.9 56.1 + - - +
7B PHE* 5.0 2.6 - - - +
171B LEU* 3.3 54.8 + - + +
172B ASP* 4.7 2.4 + - - -
174B ALA* 5.3 0.9 - - + -
175B LEU* 3.7 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A GLU* 2.9 25.3 + - + +
240A GLN* 3.5 7.6 - - - +
242A HIS* 1.3 75.8 - - + +
244A LEU* 1.3 60.1 + - + +
246A LYS* 4.1 6.7 - - - +
247A GLN* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 3.0 37.4 + - + +
241A ARG* 3.0 16.0 + - + +
243A VAL* 1.3 78.7 - - + +
245A LEU* 1.3 61.6 + - - +
247A GLN* 4.5 3.1 - - + -
248A LYS* 2.8 57.8 + - + +
249A GLU* 3.8 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ARG* 2.8 29.1 + - + +
242A HIS* 3.2 10.3 + - + +
244A LEU* 1.3 75.9 - - + +
246A LYS* 1.3 64.6 + - - +
249A GLU* 3.3 39.3 + - + +
250A LEU* 4.0 10.7 - - + +
7B PHE* 3.9 38.6 - - + -
11B LEU* 3.9 24.2 - - + -
167B ARG* 6.3 1.1 - - - -
171B LEU* 4.1 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A HIS* 2.9 47.0 + - - +
243A VAL* 4.1 6.5 - - - +
245A LEU* 1.3 77.1 - - - +
247A GLN* 1.3 64.8 + - - +
249A GLU 4.4 0.3 + - - -
250A LEU* 4.7 16.9 - - + +
164B ALA 6.1 0.4 - - - +
168B GLY* 4.3 16.0 + - - -
171B LEU* 4.2 24.3 - - + +
172B ASP* 3.5 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 3.0 25.3 + - + +
244A LEU* 4.0 3.4 - - + +
246A LYS* 1.3 79.2 - - - +
248A LYS* 1.3 61.0 + - + +
249A GLU 2.8 19.7 + - - +
250A LEU 5.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 2.8 39.0 + - + +
247A GLN* 1.3 79.7 - - + +
249A GLU* 1.3 79.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 4.4 4.7 - - - +
245A LEU* 3.3 38.4 + - + +
246A LYS 4.8 0.4 - - - -
247A GLN 2.8 13.1 + - - +
248A LYS* 1.3 102.1 - - + +
250A LEU* 1.3 74.6 + - + +
----------------------------------------------------------
Back to top of page
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