Contacts of the helix formed by residues 190 - 220 (chain B) in PDB entry 1I4L
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 190 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.9 27.6 - - + -
117B LEU* 4.3 11.2 - - + -
121B THR* 3.2 40.2 - - + +
122B MET* 4.0 15.3 - - + +
125B THR* 3.4 33.2 - - + +
186B LYS 4.0 1.3 - - - +
187B LEU 2.8 13.6 + - - +
189B PHE 1.3 81.5 - - - +
191B GLU* 1.3 52.9 + - - +
192B GLU 3.1 1.8 - - - -
193B ASN* 2.7 13.0 + - + +
194B LYS* 2.6 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 4.0 9.4 - - - +
187B LEU* 3.8 3.2 + - + -
188B LYS* 3.8 42.7 - - + +
189B PHE 3.7 0.8 - - - +
190B LEU* 1.3 80.4 - - - +
192B GLU* 1.3 61.9 + - + +
194B LYS* 3.2 36.4 + - - -
195B ILE* 3.1 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B LYS* 4.9 8.1 - - - +
189B PHE* 4.5 29.3 - - - +
190B LEU 3.1 0.6 - - - -
191B GLU* 1.3 79.7 - - + +
193B ASN* 1.3 58.2 - - - +
195B ILE* 3.3 8.3 + - - +
196B LYS* 2.9 52.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 193 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.7 3.3 - - + +
121B THR* 4.0 22.5 + - - +
189B PHE 4.2 6.3 + - - +
190B LEU* 2.7 28.7 + - + +
192B GLU* 1.3 78.0 - - - +
194B LYS* 1.3 65.9 + - - +
196B LYS* 3.4 22.6 + - - +
197B VAL* 3.0 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 4.6 6.5 + - - -
81A GLU* 3.4 22.4 + - - -
82A LEU* 4.5 4.5 - - - -
37B LEU* 6.2 2.7 - - + -
40B THR* 4.1 25.2 + - + +
44B TYR* 3.6 40.6 + - + +
117B LEU* 4.2 18.8 - - + +
122B MET* 6.1 3.4 - - + -
190B LEU* 2.6 16.5 + - + +
191B GLU* 3.2 31.4 + - - +
193B ASN* 1.3 74.7 - - - +
195B ILE* 1.3 71.8 + - - +
197B VAL* 3.5 0.5 - - - +
198B MET* 2.8 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 3.2 46.7 - - + +
82A LEU* 4.3 19.9 - - + +
191B GLU* 3.1 28.0 + - + +
192B GLU* 3.4 9.0 - - - +
194B LYS* 1.3 80.1 - - - +
196B LYS* 1.3 65.7 + - + +
199B HIS* 2.9 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 196 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B PHE 5.8 0.8 + - - -
192B GLU* 2.9 55.5 + - - +
193B ASN* 3.7 23.3 + - - +
194B LYS 3.2 0.2 - - - -
195B ILE* 1.3 76.3 - - + +
197B VAL* 1.3 64.8 + - + +
199B HIS* 4.1 4.0 - - - +
200B LYS* 3.6 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B SER* 4.9 10.1 - - - +
114B ILE* 5.4 0.9 - - - +
117B LEU* 4.3 28.5 - - + -
193B ASN* 3.0 31.2 + - - +
194B LYS 3.0 3.7 + - - +
196B LYS* 1.3 75.9 - - + +
198B MET* 1.3 60.0 + - - +
199B HIS 3.1 1.1 - - - -
200B LYS* 3.0 5.8 + - - +
201B GLN* 2.7 58.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 198 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 5.9 0.2 - - + -
82A LEU* 3.5 24.0 - - + -
86A PHE* 3.7 20.2 - - + -
44B TYR* 3.6 39.0 - - + +
47B VAL* 6.2 1.8 - - + -
110B PHE* 4.8 3.4 - - + -
114B ILE* 4.2 25.4 - - + -
117B LEU* 4.4 8.5 - - + -
194B LYS* 2.8 21.9 + - + +
197B VAL* 1.3 75.7 - - - +
199B HIS* 1.3 56.3 + - - +
201B GLN* 4.3 2.5 - - - -
202B LEU* 2.7 69.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 199 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.8 11.3 - - + +
85A GLU* 2.6 35.9 + - + +
195B ILE* 2.9 25.1 + - + +
196B LYS* 4.1 3.8 - - - +
198B MET* 1.3 80.3 - - - +
200B LYS* 1.3 68.3 + - + +
202B LEU* 3.9 1.6 - - - +
203B LEU* 3.2 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 6.0 2.5 - - - -
196B LYS 3.6 12.0 + - - +
197B VAL* 3.0 7.7 + - - +
199B HIS* 1.3 84.9 - - + +
201B GLN* 1.3 73.5 + - - +
203B LEU* 3.1 8.3 + - - +
204B LEU* 2.9 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 201 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PHE* 3.3 37.4 - - - -
110B PHE* 3.6 28.8 - - + -
113B SER* 3.3 28.5 + - - -
114B ILE* 4.1 7.9 - - + -
197B VAL* 2.7 42.0 + - + +
198B MET* 4.1 4.9 - - - +
200B LYS* 1.3 81.9 - - - +
202B LEU* 1.3 63.9 + - - +
203B LEU 3.1 0.3 + - - -
204B LEU* 3.2 8.3 + - - +
205B PHE* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 4.7 3.1 - - + -
82A LEU* 4.7 1.8 - - + -
85A GLU* 3.5 30.7 - - + -
86A PHE* 3.4 39.7 - - + +
89A ASN* 3.3 33.6 + - - +
110B PHE* 3.7 19.5 - - + -
198B MET* 2.7 53.8 + - + +
199B HIS 3.9 2.7 - - - +
201B GLN* 1.3 74.1 - - - +
203B LEU* 1.3 58.9 + - - +
205B PHE* 3.9 0.8 - - - +
206B HIS* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLU* 6.0 2.9 - - + -
88A TYR* 6.4 4.0 - - + -
199B HIS* 3.2 45.2 + - + +
200B LYS* 3.1 7.6 + - - +
202B LEU* 1.3 76.7 - - - +
204B LEU* 1.3 61.3 + - + +
205B PHE 3.3 0.2 - - - -
206B HIS* 3.8 4.5 - - + +
207B ASN* 2.9 68.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA* 5.8 2.0 - - + -
109B PHE* 3.8 34.3 - - + -
200B LYS* 2.9 44.6 + - + +
201B GLN* 3.8 7.9 - - - +
203B LEU* 1.3 76.3 - - + +
205B PHE* 1.3 53.5 + - - +
207B ASN* 3.1 9.8 + - + +
208B ALA* 2.7 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 4.2 10.5 - - + -
72A PHE* 4.1 17.9 - + - -
89A ASN* 3.8 19.1 - - - -
93A GLN* 3.9 18.8 - - - -
54B LEU* 4.0 29.4 - - + -
103B LEU* 6.3 0.2 - - + -
106B ALA* 5.5 2.5 - - - -
107B VAL* 4.4 20.6 - - + -
110B PHE* 3.6 44.8 - + + -
201B GLN 3.0 18.1 + - - +
202B LEU* 3.9 3.1 - - - +
204B LEU* 1.3 75.2 - - - +
206B HIS* 1.3 67.2 + - - +
208B ALA* 3.0 10.0 + - + +
209B VAL* 2.9 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 206 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 3.7 53.9 + + + -
89A ASN* 2.9 25.1 + - - +
92A THR* 3.0 36.2 + - + +
220A LEU 4.1 10.0 + - - -
221A GLU* 4.4 9.1 - - - +
202B LEU 3.3 13.1 + - - +
203B LEU* 4.0 5.2 - - + +
205B PHE* 1.3 81.5 - - - +
207B ASN* 1.3 73.0 + - - +
209B VAL* 3.3 4.8 + - - +
210B SER* 2.9 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 207 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU* 2.9 47.2 + - - +
204B LEU* 3.5 9.4 - - + +
206B HIS* 1.3 85.0 - - - +
208B ALA* 1.3 53.9 + - - +
210B SER* 3.2 6.5 + - - -
211B ALA* 2.7 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 6.5 0.9 - - + -
103B LEU* 4.4 11.6 - - + +
106B ALA* 3.4 32.5 - - + -
204B LEU 2.7 17.0 + - - +
205B PHE* 3.1 11.0 - - + +
207B ASN* 1.3 74.5 - - - +
209B VAL* 1.3 64.3 + - - +
211B ALA* 3.2 7.1 + - - +
212B TYR* 2.8 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 4.0 25.4 - - + -
93A GLN* 4.5 7.2 - - - +
96A LEU* 4.1 9.6 - - + -
54B LEU* 6.3 0.2 - - + -
103B LEU* 4.2 18.1 - - + +
107B VAL* 5.8 0.2 - - + -
205B PHE* 2.9 46.7 + - + +
206B HIS* 3.7 7.6 - - - +
208B ALA* 1.3 71.4 - - - +
210B SER* 1.3 64.4 + - - +
212B TYR* 2.9 23.0 - - - +
213B PHE* 3.0 31.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 3.8 12.1 + - - +
220A LEU* 5.2 8.4 - - - +
221A GLU* 4.6 13.9 - - - +
206B HIS* 2.9 30.3 + - - -
207B ASN* 3.4 7.6 - - - -
209B VAL* 1.3 77.7 - - - +
211B ALA* 1.3 65.4 + - - +
212B TYR 2.9 1.4 + - - -
213B PHE* 2.9 19.2 + - - +
214B ALA* 3.1 10.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ASN 2.7 22.6 + - - +
208B ALA* 3.4 7.6 - - - +
210B SER* 1.3 72.7 + - - +
212B TYR* 1.3 55.8 + - - +
214B ALA* 3.7 7.8 - - - +
215B GLY* 2.7 34.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 5.6 3.6 - + - -
213A PHE* 4.0 15.3 - + - -
58B LEU* 6.0 2.5 - - + +
61B LEU* 5.7 3.5 - - - +
62B LEU* 5.4 0.9 - - - +
65B GLN* 5.0 8.1 + - - -
96B LEU* 4.0 15.5 + - - +
99B ASN* 3.9 13.8 + - + +
100B GLY* 3.6 29.3 - - - -
103B LEU* 3.7 34.3 - - + -
208B ALA 2.8 13.1 + - - +
209B VAL* 2.9 17.7 - - - +
210B SER 2.9 0.6 + - - -
211B ALA* 1.3 76.8 - - - +
213B PHE* 1.3 81.0 + + - -
215B GLY* 3.8 0.7 - - - -
216B ASN* 2.7 60.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.3 23.6 - - + -
212A TYR* 3.9 21.1 - + - -
213A PHE* 3.6 24.0 - + + +
216A ASN* 3.2 40.8 - - + +
217A GLN* 2.5 27.6 - - - +
220A LEU* 5.3 3.4 - - + -
103B LEU* 5.9 0.4 - - + -
209B VAL* 3.0 36.6 - - + -
210B SER* 2.9 9.7 + - - +
212B TYR* 1.3 93.1 - + - +
214B ALA* 1.3 54.9 + - - +
216B ASN* 3.5 4.6 - - - +
217B GLN* 2.7 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLN* 2.9 19.2 + - + +
210B SER* 3.1 12.1 + - - +
211B ALA* 3.7 10.1 - - - +
213B PHE* 1.3 72.7 - - - +
215B GLY* 1.3 68.0 + - - +
217B GLN* 3.2 3.6 + - - +
218B LYS* 2.8 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN* 3.8 4.7 - - - -
211B ALA 2.7 21.3 + - - -
212B TYR 3.8 0.7 - - - -
214B ALA* 1.3 74.3 - - - +
216B ASN* 1.3 62.4 + - - +
218B LYS* 3.8 6.1 - - - +
219B GLN* 2.6 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PHE* 2.9 43.6 - - + -
95B LEU* 4.9 2.6 - - - +
96B LEU* 3.4 21.1 - - + +
99B ASN* 2.7 30.2 + - - +
212B TYR* 2.7 48.1 + - - +
213B PHE 3.5 0.2 - - - +
215B GLY* 1.3 76.2 - - - +
217B GLN* 1.3 64.3 + - - +
218B LYS 3.0 0.3 + - - -
219B GLN* 4.4 0.7 - - - +
220B LEU* 2.8 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PHE* 3.5 8.2 + - + -
214A ALA* 2.9 42.6 + - - +
217A GLN* 2.9 33.5 - - - +
218A LYS* 5.5 1.8 - - - +
213B PHE 2.7 21.7 + - - +
214B ALA* 3.9 3.3 - - - +
216B ASN* 1.3 72.9 - - - +
218B LYS* 1.3 63.8 + - - +
220B LEU* 3.7 13.3 - - + +
221B GLU* 3.1 49.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ALA 2.8 21.2 + - - +
215B GLY* 3.8 7.2 - - - +
216B ASN 3.0 1.4 + - - -
217B GLN* 1.3 69.6 - - - +
219B GLN* 1.3 65.6 + - + +
220B LEU 3.0 3.4 - - - -
221B GLU* 2.7 33.8 + - - +
222B GLN* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 2.9 50.0 - - + +
98B LYS* 4.3 10.7 + - - -
99B ASN* 3.4 17.7 + - - +
215B GLY* 2.6 33.2 + - - +
218B LYS* 1.3 93.8 - - + +
220B LEU* 1.3 56.1 + - - +
221B GLU 3.0 0.2 - - - -
222B GLN* 2.9 36.5 + - + +
223B THR* 4.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A HIS* 4.5 5.8 - - + +
210A SER* 3.5 43.7 - - - +
213A PHE* 4.5 11.2 - - + -
92B THR* 3.8 32.5 - - + +
95B LEU* 4.0 7.3 - - + +
96B LEU* 5.6 5.4 - - + -
216B ASN* 2.8 23.0 + - + +
217B GLN* 3.7 16.4 - - + +
219B GLN* 1.3 76.4 - - - +
221B GLU* 1.3 61.8 + - + +
222B GLN 3.3 1.2 + - - -
223B THR* 4.4 11.1 + - - -
----------------------------------------------------------
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