Contacts of the helix formed by residues 167 - 191 (chain P) in PDB entry 5D4D
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 PRO 167 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ASP* 4.7 1.6 - - - +
165P SER 4.5 2.2 - - - +
166P LEU* 1.3 93.4 - - + +
168P LYS* 1.3 55.1 + - - +
169P GLU* 3.3 23.8 - - - +
170P HIS* 2.9 23.1 + - + -
171P LYS 2.5 33.3 + - - -
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Residues in contact with LYS 168 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403N PHE* 5.2 6.0 - - - -
404N GLU 4.2 6.5 + - - -
405N ASP* 3.9 31.4 + - - +
406N ASP* 3.5 40.9 + - + +
442N ASN* 5.3 8.4 - - - +
167P PRO* 1.3 71.2 - - - +
169P GLU* 1.3 63.5 + - - +
171P LYS* 3.5 4.1 - - - +
172P ARG* 2.9 28.1 + - - +
175P HIS* 5.9 0.2 - - - -
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Residues in contact with GLU 169 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167P PRO* 3.3 24.3 - - - +
168P LYS* 1.3 81.9 + - - +
170P HIS* 1.3 77.5 + - + +
172P ARG* 3.3 25.2 - - - +
173P TYR* 4.2 12.0 - - - -
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Residues in contact with HIS 170 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P LEU* 3.7 20.4 - - - +
119P ILE* 3.6 46.3 - - + +
166P LEU* 4.3 10.2 - - + +
167P PRO* 2.9 29.2 + - + +
169P GLU* 1.3 92.0 + - + +
171P LYS* 1.3 60.3 + - - +
172P ARG 3.1 6.5 + - - -
173P TYR* 3.5 16.6 + + - +
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Residues in contact with LYS 171 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ASP* 3.5 19.6 + - - +
407N VAL 2.4 32.1 + - - -
408N GLU* 3.5 23.1 + - - +
409N VAL 5.1 1.3 - - - -
163P LEU 4.1 11.9 - - - +
164P LYS* 3.5 37.4 + - - +
166P LEU* 3.3 20.8 + - - +
167P PRO 2.5 19.6 + - - +
168P LYS* 3.5 6.5 - - - +
170P HIS* 1.3 71.3 - - - +
172P ARG* 1.3 57.0 + - - +
173P TYR 3.3 0.4 - - - -
174P LEU* 3.4 18.3 + - + +
175P HIS* 2.7 42.3 + - + -
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Residues in contact with ARG 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354N VAL* 6.2 2.2 - - - +
439N LEU* 3.6 45.4 + - + +
168P LYS 2.9 10.9 + - - +
169P GLU* 3.3 19.1 - - - +
170P HIS 3.1 0.2 - - - -
171P LYS* 1.3 78.4 - - - +
173P TYR* 1.3 67.5 + - + +
175P HIS* 3.1 12.8 + - - +
176P ILE* 3.0 43.3 + - + +
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Residues in contact with TYR 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112P ALA* 3.4 23.9 - - + +
115P LYS* 3.4 44.3 + - + +
116P LEU* 3.6 23.6 - - + +
119P ILE* 4.1 16.4 - - + -
169P GLU 4.2 13.2 - - - -
170P HIS* 3.8 14.4 - + - +
171P LYS 3.3 0.2 - - - -
172P ARG* 1.3 82.6 - - + +
174P LEU* 1.3 59.3 + - - +
176P ILE* 3.8 11.2 - - + -
177P ALA* 2.9 30.5 + - - +
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Residues in contact with LEU 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410N SER* 3.7 17.7 - - - +
116P LEU* 3.9 13.2 - - + +
131P VAL* 4.6 7.4 - - + -
160P ASP* 4.1 4.5 - - - +
163P LEU* 3.8 46.4 - - + +
164P LYS* 3.7 30.5 - - + -
170P HIS 4.2 1.0 + - - +
171P LYS* 3.4 23.3 + - + +
173P TYR* 1.3 78.3 - - - +
175P HIS* 1.3 57.1 + - + +
177P ALA* 3.3 2.9 + - - +
178P ARG* 2.9 53.2 + - + +
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Residues in contact with HIS 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ASP* 5.2 0.9 - - - -
407N VAL* 3.2 30.2 + - + +
409N VAL 3.4 6.5 + - - -
410N SER* 3.4 24.4 + - - -
411N THR* 4.4 6.2 + - - +
437N VAL* 3.4 34.3 - - + +
439N LEU* 3.9 21.7 - - + +
171P LYS* 2.7 47.9 + - + -
172P ARG* 3.1 9.6 + - - +
174P LEU* 1.3 72.9 - - + +
176P ILE* 1.3 67.8 + - - +
178P ARG* 3.4 3.2 + - - +
179P GLU* 3.0 27.6 + - - +
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Residues in contact with ILE 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439N LEU* 3.7 22.4 - - + -
105P LYS 4.7 1.7 - - - +
108P GLU* 3.3 41.7 - - + +
109P GLY* 4.1 1.3 - - - +
112P ALA* 3.6 5.6 - - + -
172P ARG* 3.0 35.3 + - + +
173P TYR* 3.7 16.2 - - + +
175P HIS* 1.3 78.1 - - - +
177P ALA* 1.3 57.5 + - - +
179P GLU* 3.5 3.5 + - - +
180P GLY* 2.9 25.1 + - - -
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Residues in contact with ALA 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P GLY* 4.0 14.3 - - - +
112P ALA* 4.3 1.6 - - + -
113P ILE* 3.9 29.0 - - + +
116P LEU* 4.7 3.8 - - + -
131P VAL* 3.7 20.3 - - + +
173P TYR 2.9 18.5 + - - +
174P LEU* 3.7 4.5 - - - +
176P ILE* 1.3 74.2 - - - +
178P ARG* 1.3 66.7 + - - +
180P GLY* 2.9 2.8 + - - -
181P GLU* 2.9 21.5 + - - +
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Residues in contact with ARG 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410N SER* 3.5 17.7 - - - +
411N THR* 2.5 48.3 + - - +
412N GLY 4.2 0.4 - - - -
413N ASP* 2.5 30.3 + - - +
131P VAL* 3.6 29.9 + - + +
134P LYS* 3.5 19.8 - - - +
135P ILE* 3.4 16.1 - - + +
160P ASP* 2.7 40.0 + - - -
164P LYS* 4.0 6.9 - - - +
174P LEU* 2.9 32.4 + - + +
175P HIS 3.6 4.7 - - - +
177P ALA* 1.3 74.2 - - - +
179P GLU* 1.3 64.0 + - - +
180P GLY 3.0 0.5 + - - -
181P GLU 3.1 2.8 + - - -
182P ALA 3.0 18.5 + - - -
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Residues in contact with GLU 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411N THR* 4.5 17.2 + - + +
437N VAL 4.5 11.9 - - - +
105P LYS* 3.5 38.4 + - + +
175P HIS 3.0 17.5 + - - +
176P ILE* 4.1 3.5 - - - +
178P ARG* 1.3 76.9 - - - +
180P GLY* 1.3 58.2 + - - +
182P ALA* 3.7 10.9 - - + +
183P ALA* 2.9 28.6 + - + +
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Residues in contact with GLY 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P LYS 3.7 22.2 - - - -
106P VAL* 3.9 7.6 - - - +
109P GLY* 4.3 6.3 - - - -
176P ILE 2.9 11.7 + - - -
177P ALA 2.9 10.4 + - - -
179P GLU* 1.3 76.0 - - - +
181P GLU* 1.3 56.9 + - - -
183P ALA* 3.2 3.6 + - - +
184P ARG* 2.9 28.6 + - - +
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Residues in contact with GLU 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113P ILE* 4.3 6.4 - - - +
128P ARG* 3.6 25.6 - - - +
131P VAL* 3.6 25.8 - - + -
132P ARG* 3.7 27.2 + - + +
135P ILE* 3.8 17.5 - - + -
177P ALA 2.9 10.7 + - - +
178P ARG 3.1 6.0 + - - +
180P GLY* 1.3 70.6 - - - +
182P ALA* 1.3 63.3 + - - +
184P ARG* 3.1 40.0 + - - +
185P GLN* 3.0 30.0 + - + +
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Residues in contact with ALA 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411N THR* 5.4 3.8 - - + -
434N ARG* 5.3 4.7 - - - +
135P ILE* 4.0 24.1 - - + +
178P ARG 3.0 12.5 + - - +
179P GLU* 3.7 17.3 - - + +
181P GLU* 1.3 76.5 - - - +
183P ALA* 1.3 61.9 + - - +
185P GLN* 3.2 6.8 + - - +
186P HIS* 3.0 22.9 + - - +
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Residues in contact with ALA 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P LEU* 3.7 34.1 - - + +
105P LYS* 3.6 28.9 - - + -
106P VAL* 4.0 2.2 - - + -
179P GLU 2.9 19.0 + - - +
180P GLY 3.5 4.7 - - - +
182P ALA* 1.3 76.2 - - - +
184P ARG* 1.3 57.8 + - - +
186P HIS* 3.3 1.5 + - - -
187P LEU* 2.9 29.5 + - - +
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Residues in contact with ARG 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560N GLN 2.7 30.5 + - - -
561N GLY 3.6 6.7 + - - -
106P VAL* 3.6 23.7 - - + +
132P ARG* 3.7 19.0 - - - +
180P GLY 2.9 12.8 + - - +
181P GLU* 3.1 36.1 + - - +
183P ALA* 1.3 74.3 - - - +
185P GLN* 1.3 87.6 + - - +
187P LEU* 3.1 4.7 + - - +
188P ILE* 2.9 45.8 + - + +
221P ILE* 4.6 2.4 - - - +
224P VAL* 3.9 16.1 - - + +
225P GLU* 3.4 31.3 + - - +
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Residues in contact with GLN 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561N GLY 3.2 21.5 + - - +
563N PRO* 3.4 33.4 - - - +
564N GLU 4.9 0.3 + - - -
132P ARG* 4.9 2.0 - - - +
135P ILE* 4.5 6.0 - - + +
136P LEU* 3.7 30.7 - - + +
181P GLU* 3.0 23.6 + - - +
182P ALA* 3.2 9.6 + - - +
184P ARG* 1.3 97.7 - - - +
186P HIS* 1.3 59.4 + - - +
188P ILE* 4.0 2.3 - - - +
189P GLU* 3.0 41.4 + - - +
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Residues in contact with HIS 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P VAL* 4.0 25.0 - - + +
92P PRO* 5.3 5.6 - - + -
94P LEU* 4.4 17.4 - - + +
98P GLU* 5.8 0.4 + - - -
102P LEU* 4.1 24.7 - - + -
182P ALA 3.0 13.3 + - - +
183P ALA* 3.8 7.2 - - - +
184P ARG 3.2 0.2 - - - -
185P GLN* 1.3 77.1 - - - +
187P LEU* 1.3 56.9 + - - +
189P GLU* 4.4 9.0 + - - +
190P ALA* 2.9 25.2 + - + +
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Residues in contact with LEU 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94P LEU* 3.8 20.0 - - + -
99P GLU* 4.6 14.6 - - + +
102P LEU* 4.0 15.4 - - + +
103P ALA* 4.3 26.5 - - + +
106P VAL* 4.6 4.7 - - + -
183P ALA 2.9 17.2 + - - +
184P ARG* 3.1 5.6 + - - +
186P HIS* 1.3 74.1 - - - +
188P ILE* 1.3 65.5 + - - +
190P ALA* 3.4 1.6 + - - +
191P ASN* 2.8 48.7 + - - +
224P VAL* 3.8 31.6 - - + +
227P PHE* 5.3 1.6 - - + -
235P PHE* 4.5 13.2 - - + -
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Residues in contact with ILE 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561N GLY 5.0 0.9 - - - +
563N PRO* 3.6 33.9 - - + -
566N ILE* 4.2 11.2 - - + -
184P ARG* 2.9 45.2 + - + +
185P GLN* 4.8 1.3 - - - -
187P LEU* 1.3 74.1 - - - +
189P GLU* 1.3 63.9 + - - +
190P ALA 3.2 0.9 + - - -
191P ASN 3.3 9.2 + - - -
192P LEU* 3.6 11.3 + - + +
220P LEU* 3.6 19.4 - - + +
221P ILE* 3.8 33.2 - - + -
224P VAL* 3.8 23.6 - - + -
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Residues in contact with GLU 189 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563N PRO* 3.5 29.6 - - + +
564N GLU* 3.6 15.6 + - - +
565N ILE* 3.8 29.2 - - + +
88P ILE* 5.5 1.2 - - - +
91P VAL* 3.9 24.9 - - + +
185P GLN* 3.0 24.6 + - - +
186P HIS* 4.0 9.4 + - - +
188P ILE* 1.3 77.2 - - - +
190P ALA* 1.3 61.1 + - - +
191P ASN 3.6 0.3 + - - -
192P LEU* 3.7 24.6 + - + +
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Residues in contact with ALA 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P VAL* 4.0 11.4 - - - +
92P PRO 4.4 7.1 - - - +
93P LEU* 3.4 23.6 - - - +
94P LEU* 3.6 41.7 - - + -
186P HIS* 2.9 24.0 + - - +
187P LEU 3.8 3.1 - - - +
188P ILE 3.2 0.2 - - - -
189P GLU* 1.3 79.5 - - - +
191P ASN* 1.3 60.1 + - - +
192P LEU 3.4 0.7 + - - -
193P ARG* 4.6 5.2 + - - -
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Residues in contact with ASN 191 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P LEU* 5.2 0.7 - - - +
94P LEU* 4.7 4.5 - - - +
99P GLU* 4.9 1.6 - - - +
187P LEU* 2.8 35.9 + - - +
188P ILE 3.3 3.0 + - - -
190P ALA* 1.3 80.9 - - - +
192P LEU* 1.3 61.5 + - - +
193P ARG 3.0 5.6 + - - -
194P LEU* 3.1 20.0 + - + +
195P VAL 3.9 0.3 + - - -
220P LEU* 3.5 28.4 - - + +
235P PHE* 3.2 33.3 - - + +
6S T 2.9 38.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il