Contacts of the helix formed by residues 170 - 203 (chain Q) in PDB entry 5IY6
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 LYS 170 (chain Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122Q THR 5.0 2.9 - - - -
123Q ASN* 5.3 6.5 - - - +
124Q ARG* 4.2 16.6 - - - +
166Q SER* 3.0 32.1 - - - +
168Q MET 2.6 8.5 + - - -
169Q PRO* 1.3 72.2 - - - +
171Q LYS* 1.3 56.7 + - - +
172Q ASP* 4.0 17.6 + - + +
173Q ALA* 2.7 28.1 + - + +
174Q ARG* 2.5 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G HIS* 3.7 19.0 + - - +
121Q SER 6.1 3.1 - - - +
122Q THR 4.8 5.7 + - - -
123Q ASN* 3.3 44.2 + - - +
169Q PRO 3.9 0.2 + - - -
170Q LYS* 1.3 73.2 - - - +
172Q ASP* 1.3 60.1 + - + +
174Q ARG* 3.6 24.0 + - - +
175Q THR* 3.2 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170Q LYS* 3.1 19.8 + - + +
171Q LYS* 1.3 77.4 - - - +
173Q ALA* 1.3 63.8 + - - +
175Q THR* 3.5 10.8 + - - -
176Q LEU* 3.4 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166Q SER 5.4 3.4 - - - +
168Q MET 4.5 1.8 - - - +
169Q PRO* 3.7 8.1 - - + -
170Q LYS* 2.7 42.8 + - + +
172Q ASP* 1.3 71.3 + - - +
174Q ARG* 1.3 56.9 + - - +
176Q LEU* 3.1 14.0 + - + +
177Q LEU* 3.0 37.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 174 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Q GLU* 4.2 15.7 + - - +
120Q ASP* 3.2 51.9 + - + +
121Q SER* 3.6 15.2 + - - +
122Q THR 5.7 0.7 - - - -
169Q PRO* 3.8 13.8 - - + +
170Q LYS 2.5 19.6 + - - +
171Q LYS* 3.6 23.5 + - - +
173Q ALA* 1.3 70.6 - - - +
175Q THR* 1.3 70.5 + - - +
177Q LEU* 3.6 4.3 + - - +
178Q ALA* 3.3 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171Q LYS* 3.2 14.5 + - - +
172Q ASP* 3.7 14.9 + - - +
173Q ALA 3.3 0.6 - - - -
174Q ARG* 1.3 86.7 + - - +
176Q LEU* 1.3 56.9 + - - +
178Q ALA* 3.4 7.3 + - + +
179Q ARG* 3.0 60.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172Q ASP 3.4 9.2 + - - +
173Q ALA* 3.1 14.3 + - + +
175Q THR* 1.3 77.1 - - - +
177Q LEU* 1.3 67.2 + - + +
179Q ARG* 3.4 20.1 + - + +
180Q PHE* 3.0 27.7 + - + +
183Q GLN* 5.7 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117Q ASP* 3.8 22.9 - - - +
118Q GLU* 3.6 30.0 - - + +
169Q PRO* 3.7 28.9 - - + -
173Q ALA* 3.0 26.6 + - + +
174Q ARG* 4.2 4.5 - - - +
175Q THR 3.4 0.2 - - - -
176Q LEU* 1.3 83.1 - - + +
178Q ALA* 1.3 60.3 + - - +
180Q PHE* 3.5 10.3 + - + +
181Q ASN* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Q GLU* 3.1 26.3 - - - +
174Q ARG* 3.3 14.8 + - - +
175Q THR* 3.5 10.5 - - + +
177Q LEU* 1.3 79.6 - - - +
179Q ARG* 1.3 56.9 + - + +
181Q ASN* 3.5 4.7 + - - +
182Q GLU* 3.1 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175Q THR* 3.0 40.9 + - + +
176Q LEU* 3.6 23.3 - - + +
177Q LEU 3.3 0.2 - - - -
178Q ALA* 1.3 75.9 - - + +
180Q PHE* 1.3 54.2 + - - +
182Q GLU* 3.1 17.6 + - - +
183Q GLN* 2.7 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114Q ILE* 5.1 9.6 - - + -
176Q LEU* 3.0 19.5 + - + +
177Q LEU* 3.6 11.4 - - + +
179Q ARG* 1.3 73.1 - - - +
181Q ASN* 1.3 57.3 + - - +
183Q GLN* 2.9 27.2 + - + +
184Q ILE* 2.7 62.0 + - + +
214R GLU* 3.5 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 181 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111Q ARG* 4.9 8.0 + - - -
114Q ILE* 3.7 24.1 - - + +
115Q GLU* 2.6 42.9 + - - +
118Q GLU* 4.2 14.6 + - + +
177Q LEU 2.9 17.9 + - - +
178Q ALA* 3.5 9.2 - - - +
179Q ARG 3.3 0.2 - - - -
180Q PHE* 1.3 76.0 - - - +
182Q GLU* 1.3 63.3 + - + +
184Q ILE* 3.2 23.2 + - - +
185Q GLU* 3.6 6.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178Q ALA* 3.1 20.3 + - - +
179Q ARG* 3.2 19.5 - - - +
181Q ASN* 1.3 76.7 - - + +
183Q GLN* 1.3 57.2 + - + +
184Q ILE 3.5 0.2 + - - -
185Q GLU* 3.5 8.4 + - - +
186Q PRO* 2.9 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 183 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176Q LEU* 5.2 3.8 - - - +
179Q ARG* 2.7 21.9 + - + +
180Q PHE* 2.9 40.8 + - + +
182Q GLU* 1.3 70.8 - - + +
184Q ILE* 1.3 59.4 + - - +
186Q PRO* 3.0 21.4 - - - +
187Q ILE* 4.0 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111Q ARG* 3.5 27.5 + - - +
114Q ILE* 3.6 31.6 - - + -
180Q PHE* 2.7 50.3 + - + +
181Q ASN* 3.2 14.1 + - - +
183Q GLN* 1.3 74.2 - - - +
185Q GLU* 1.3 63.0 + - - +
187Q ILE* 3.3 11.4 - - + +
188Q TYR 3.5 1.9 + - - -
212R VAL 3.3 28.5 - - - +
213R ASP* 5.1 2.7 - - - +
214R GLU* 4.7 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 185 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111Q ARG* 2.6 48.6 + - - +
181Q ASN 3.6 4.4 + - - +
182Q GLU* 3.5 9.8 + - - +
184Q ILE* 1.3 80.0 - - - +
186Q PRO* 1.4 58.7 - - + +
188Q TYR 3.1 3.5 + - - -
189Q ALA* 2.5 48.8 + - + +
192Q ARG* 2.9 38.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 186 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182Q GLU 2.9 28.5 - - - +
183Q GLN* 3.0 20.4 - - - +
185Q GLU* 1.4 78.3 - - + +
187Q ILE* 1.3 61.0 + - - +
189Q ALA* 3.2 22.5 + - + +
190Q LEU* 4.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 187 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183Q GLN 4.0 5.0 + - - +
184Q ILE* 3.3 12.9 + - + +
185Q GLU 3.3 0.2 - - - -
186Q PRO* 1.3 78.9 - - - +
188Q TYR* 1.3 53.4 + - - +
190Q LEU 5.4 0.2 - - - -
191Q LEU* 4.1 5.1 - - - +
209R GLN 5.6 0.2 - - - +
210R PHE* 4.6 2.7 - - + +
211R SER* 1.2 109.0 + - - +
212R VAL* 2.1 91.3 + - - +
213R ASP 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 188 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q LEU* 6.4 0.2 - - + -
21Q VAL* 6.0 1.3 - - + -
25Q PHE* 4.9 6.1 - + - -
103Q VAL* 3.6 22.5 + - + +
107Q LEU* 3.4 32.4 - - + +
111Q ARG* 3.6 18.2 - - - +
184Q ILE 3.5 0.6 + - - +
185Q GLU 3.1 2.5 + - - -
186Q PRO 3.1 0.2 - - - -
187Q ILE* 1.3 81.1 - - - +
189Q ALA* 1.3 52.3 + - - +
190Q LEU 3.4 2.7 - - - -
191Q LEU* 2.9 33.0 + - + -
192Q ARG* 2.5 64.7 + - + +
195Q GLU* 3.2 21.9 + - - -
212R VAL* 3.2 19.4 - - + +
213R ASP* 3.8 10.8 - - - +
218R LYS* 3.8 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Q GLU* 2.5 37.4 + - + +
186Q PRO* 3.2 18.4 + - + +
188Q TYR* 1.3 72.6 - - - +
190Q LEU* 1.3 53.4 + - - +
192Q ARG* 3.2 7.3 + - - +
193Q GLU* 2.8 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q TYR* 4.3 25.4 - - + +
186Q PRO 4.3 2.9 + - - +
188Q TYR 3.4 0.2 - - - -
189Q ALA* 1.3 78.3 - - - +
191Q LEU* 1.3 62.1 + - + +
193Q GLU* 3.7 6.2 - - + -
194Q THR* 2.4 51.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 191 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q LEU* 3.4 27.2 - - + +
20Q TYR* 4.6 18.6 - - + -
21Q VAL* 4.8 3.8 - - + -
25Q PHE* 4.4 8.5 - - + -
187Q ILE 4.1 6.7 - - - +
188Q TYR* 2.9 27.7 + - + +
190Q LEU* 1.3 89.3 - - + +
192Q ARG* 1.3 65.3 + - - +
194Q THR* 4.2 0.2 - - - -
195Q GLU* 3.0 22.9 + - - +
210R PHE* 4.3 13.5 - - + -
212R VAL* 2.7 47.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 192 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107Q LEU* 3.9 26.5 - - + -
111Q ARG* 5.2 1.3 - - - +
185Q GLU* 2.9 34.9 + - - -
188Q TYR* 2.5 34.8 + - + +
189Q ALA* 3.8 7.0 + - - +
191Q LEU* 1.3 73.2 - - - +
193Q GLU* 1.3 78.1 + - - +
195Q GLU* 3.4 7.3 + - - +
196Q ASP* 2.7 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189Q ALA 2.8 21.8 + - - +
190Q LEU* 3.8 7.6 - - + +
192Q ARG* 1.3 87.5 + - - +
194Q THR* 1.3 57.4 + - - +
196Q ASP* 3.5 20.6 - - - +
197Q VAL* 2.6 53.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q ALA* 3.9 15.2 - - + +
16Q ARG* 4.8 4.9 - - + -
17Q LEU* 3.5 41.7 - - + +
20Q TYR* 4.6 8.8 - - + -
190Q LEU* 2.4 47.1 + - - +
191Q LEU* 4.2 0.7 - - - -
193Q GLU* 1.3 71.5 - - - +
195Q GLU* 1.3 57.8 + - - +
197Q VAL* 3.6 5.6 + - - +
198Q ASN* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q LEU* 5.8 2.9 - - + -
17Q LEU* 3.7 14.9 - - + +
101Q ASN 3.4 6.9 - - - +
103Q VAL* 3.1 30.5 - - + +
104Q LYS* 2.7 43.2 + - + +
107Q LEU* 5.6 1.0 - - - +
188Q TYR* 3.2 14.0 + - - -
191Q LEU 3.0 15.4 + - - +
192Q ARG* 3.5 5.9 - - + +
194Q THR* 1.3 76.0 - - - +
196Q ASP* 1.3 52.7 + - - +
198Q ASN* 3.1 8.5 + - + +
199Q LEU* 2.5 43.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192Q ARG* 2.7 34.5 + - + +
193Q GLU* 3.4 25.2 - - - +
195Q GLU* 1.3 71.8 - - - +
197Q VAL* 1.3 53.2 + - - +
199Q LEU* 3.2 15.4 + - - +
200Q ALA* 2.7 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13Q ALA* 5.6 6.1 - - + -
193Q GLU* 2.6 40.2 + - + +
194Q THR* 4.0 5.2 - - - +
196Q ASP* 1.3 71.2 - - + +
198Q ASN* 1.3 58.8 + - - +
200Q ALA* 3.4 6.9 + - - +
201Q TYR* 2.9 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 198 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PRO* 4.6 7.4 - - - +
13Q ALA* 3.1 17.9 + - + +
14Q LEU* 2.9 52.2 + - + +
17Q LEU* 5.9 0.4 - - + -
194Q THR 2.9 20.5 + - - +
195Q GLU* 3.3 10.0 + - - +
197Q VAL* 1.3 75.1 - - - +
199Q LEU* 1.3 65.8 + - - +
201Q TYR* 3.2 9.9 + - - +
202Q GLU* 3.2 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q LYS* 4.9 13.2 - - + -
195Q GLU* 2.5 24.6 + - + +
196Q ASP* 3.6 15.5 - - - +
198Q ASN* 1.3 75.7 - - - +
200Q ALA* 1.3 56.5 + - - +
202Q GLU* 3.7 4.0 + - + +
203Q ILE* 2.9 28.9 + - - +
204Q LEU 3.2 26.7 - - - +
238R LYS* 4.8 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 200 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196Q ASP* 2.7 24.0 + - - +
197Q VAL* 3.6 8.7 - - - +
198Q ASN 3.2 0.2 - - - -
199Q LEU* 1.3 70.4 - - - +
201Q TYR* 1.3 67.4 + - - +
203Q ILE* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 201 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PRO* 4.8 14.7 - - + +
197Q VAL* 2.9 19.7 + - + +
198Q ASN* 3.2 11.8 + - - +
200Q ALA* 1.3 78.7 - - - +
202Q GLU* 1.3 88.8 + - + +
203Q ILE* 3.9 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PRO* 3.9 18.2 - - - +
198Q ASN* 3.2 26.1 + - - +
199Q LEU* 4.2 4.9 - - + +
201Q TYR* 1.3 100.1 - - + +
203Q ILE* 1.3 72.0 + - - +
204Q LEU* 3.0 13.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 203 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199Q LEU* 2.9 21.9 + - - +
200Q ALA* 3.0 19.4 + - - +
201Q TYR 3.9 6.7 - - - +
202Q GLU* 1.3 82.5 - - - +
204Q LEU* 1.3 65.4 + - + +
424W ARG* 5.5 12.6 - - + -
----------------------------------------------------------
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