Contacts of the helix formed by residues 160 - 193 (chain K) in PDB entry 3GHG
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 ASN 160 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191J LYS* 5.5 7.6 - - - +
192J ASP* 5.1 18.2 - - + +
155K GLU* 3.0 22.4 + - - +
156K THR* 3.5 19.3 + - + +
159K SER* 1.3 87.3 + - - +
161K ILE* 1.3 56.3 + - + +
162K PRO 3.3 1.6 - - - -
163K THR* 2.5 22.8 + - - -
164K ASN* 2.6 26.5 + - + +
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Residues in contact with ILE 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J LYS* 6.1 2.5 - - + -
130J VAL* 5.7 10.1 - - + +
133J ILE* 4.4 25.8 - - + -
192J ASP* 5.8 3.6 - - - +
156K THR* 3.1 30.0 + - + +
157K VAL* 4.2 8.1 - - + +
160K ASN* 1.3 80.4 - - + +
162K PRO* 1.4 57.8 - - + +
164K ASN* 3.3 11.1 - - + +
165K LEU* 2.7 43.7 + - + +
103L HIS* 4.0 32.1 - - + +
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Residues in contact with PRO 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157K VAL 4.0 11.2 - - - +
158K ASN* 3.8 20.6 - - - +
159K SER 4.5 2.5 - - - +
160K ASN 3.4 9.4 - - - +
161K ILE* 1.4 91.2 - - + +
163K THR* 1.3 63.4 + - + +
164K ASN 3.1 1.6 - - - -
165K LEU* 3.9 5.0 - - + +
166K ARG* 3.2 27.6 + - - +
103L HIS* 4.0 21.8 - - + +
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Residues in contact with THR 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188J VAL* 5.7 0.9 - - - +
159K SER 3.1 24.5 + - - +
160K ASN* 2.5 23.2 + - - -
162K PRO* 1.3 78.1 - - + +
164K ASN* 1.3 58.7 + - - +
166K ARG* 2.7 46.0 + - - +
167K VAL* 3.5 10.4 - - - +
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Residues in contact with ASN 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J ILE* 3.5 27.2 - - - +
137J GLN* 3.7 11.1 + - - +
188J VAL* 3.5 30.3 - - - +
160K ASN* 2.6 16.9 + - + +
161K ILE* 3.3 17.5 - - + +
163K THR* 1.3 71.5 - - - +
165K LEU* 1.3 70.0 + - + +
166K ARG 2.9 5.8 + - - -
167K VAL* 3.3 7.2 - - - +
168K LEU* 2.9 40.2 + - - +
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Residues in contact with LEU 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J ILE* 4.7 17.7 - - + -
161K ILE* 2.7 33.9 + - + +
162K PRO* 3.9 6.3 - - + -
164K ASN* 1.3 84.7 - - - +
166K ARG* 1.3 55.5 + - - +
168K LEU* 4.3 20.2 - - + -
169K ARG* 3.5 47.2 + - + +
103L HIS* 4.6 19.5 - - - +
106L SER* 4.6 14.1 - - - +
107L ILE* 5.8 1.8 - - - -
110L LEU* 5.4 10.8 - - + -
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Residues in contact with ARG 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162K PRO 3.2 17.0 + - - +
163K THR* 2.7 56.6 + - - +
164K ASN 2.9 0.8 + - - -
165K LEU* 1.3 78.7 - - - +
167K VAL* 1.3 68.7 + - - +
168K LEU 3.3 0.2 - - - -
169K ARG* 3.3 3.5 + - - +
170K SER* 2.7 37.2 + - - -
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Residues in contact with VAL 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181J GLN* 4.3 3.8 + - - +
184J GLN* 3.0 43.5 - - + +
185J LEU* 5.0 12.8 - - + +
188J VAL* 4.3 20.2 - - + -
163K THR 3.5 12.8 - - - +
164K ASN* 3.3 15.3 - - - +
166K ARG* 1.3 87.9 - - - +
168K LEU* 1.3 66.3 + - + +
170K SER* 3.6 7.1 - - - -
171K ILE* 3.0 29.7 + - + +
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Residues in contact with LEU 168 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J ILE* 5.3 3.8 - - + +
136J LEU* 5.0 8.1 - - + -
137J GLN* 4.6 26.9 - - + +
140J VAL* 4.4 24.7 - - + -
185J LEU* 3.6 31.4 - - + -
164K ASN* 2.9 33.2 + - - +
165K LEU* 4.3 19.5 - - + -
167K VAL* 1.3 79.4 - - + +
169K ARG* 1.3 56.7 + - - +
171K ILE* 3.3 20.9 - - + +
172K LEU* 3.7 2.3 - - + +
110L LEU* 3.2 25.0 - - + +
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Residues in contact with ARG 169 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165K LEU* 3.5 36.4 + - - +
166K ARG* 3.3 6.0 + - - +
167K VAL 3.2 0.2 - - - -
168K LEU* 1.3 75.3 - - - +
170K SER* 1.3 67.5 + - - +
171K ILE 2.7 4.6 + - - -
172K LEU* 2.8 13.7 + - - -
173K GLU* 3.2 23.4 + - + +
106L SER* 3.0 28.3 + - - -
109L TYR* 3.3 31.5 - - + -
110L LEU* 3.3 30.4 - - + +
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Residues in contact with SER 170 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181J GLN* 2.9 19.9 + - - +
184J GLN* 5.1 2.3 + - - -
166K ARG* 2.7 24.2 + - - -
167K VAL* 3.6 10.3 - - - -
169K ARG* 1.3 71.4 - - - +
171K ILE* 1.3 60.5 + - - +
173K GLU* 4.9 1.9 - - - +
174K ASN* 3.2 23.8 + - - +
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Residues in contact with ILE 171 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J VAL* 4.9 12.8 - - + -
144J LEU* 3.4 33.4 - - + -
181J GLN* 3.3 44.8 + - + +
185J LEU* 4.3 15.0 - - + -
167K VAL* 3.0 13.8 + - + +
168K LEU* 3.3 25.8 - - + +
169K ARG 2.7 5.1 + - - -
170K SER* 1.3 70.3 - - - +
172K LEU* 1.3 75.0 + - + +
173K GLU 3.1 3.8 - - - -
174K ASN* 3.0 19.9 + - - +
175K LEU* 3.1 22.2 + - + +
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Residues in contact with LEU 172 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J VAL* 4.0 26.9 - - + -
143J GLN* 4.9 6.7 - - - +
168K LEU 3.7 12.8 - - - +
169K ARG 2.8 5.8 + - - +
171K ILE* 1.3 79.9 - - + +
173K GLU* 1.3 56.9 + - - +
175K LEU* 4.0 8.2 - - + +
176K ARG* 3.8 5.2 + - - +
110L LEU* 3.7 17.9 - - + +
113L ILE* 3.1 50.2 - - + +
114L TYR* 3.5 35.4 - - + +
117L ASN* 3.8 16.3 - - - +
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Residues in contact with GLU 173 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169K ARG* 3.2 21.1 + - + +
170K SER* 4.9 1.8 - - - +
171K ILE 3.1 0.4 - - - -
172K LEU* 1.3 78.0 - - - +
174K ASN* 1.3 62.5 + - - +
175K LEU 3.2 1.1 - - - -
176K ARG* 3.7 18.1 + - + +
177K SER* 3.5 18.2 + - - -
109L TYR* 2.6 30.6 + - - -
113L ILE* 3.5 20.1 - - + +
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Residues in contact with ASN 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177J ASP* 3.3 29.3 + - - +
181J GLN* 4.4 14.4 + - - +
170K SER 3.2 22.1 + - - +
171K ILE* 3.0 6.2 + - - +
173K GLU* 1.3 73.8 - - - +
175K LEU* 1.3 80.2 + - - +
177K SER* 2.6 25.4 + - - -
178K LYS* 3.1 18.0 + - - +
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Residues in contact with LEU 175 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140J VAL 5.7 0.2 - - - +
143J GLN* 3.1 27.6 - - - +
144J LEU* 4.0 32.3 - - + -
147J MET* 4.1 28.1 - - + +
178J TYR* 5.1 9.6 - - + +
181J GLN* 6.5 0.2 - - + -
171K ILE* 3.1 23.8 + - + +
172K LEU* 4.0 7.6 - - + +
174K ASN* 1.3 92.0 + - - +
176K ARG* 1.3 51.6 + - - +
178K LYS* 2.6 28.7 + - + +
179K ILE* 2.7 19.7 + - - +
117L ASN* 3.9 11.2 - - - +
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Residues in contact with ARG 176 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172K LEU 3.8 8.1 + - - +
173K GLU* 3.7 20.8 + - + +
174K ASN 3.4 0.6 - - - -
175K LEU* 1.3 79.2 - - - +
177K SER* 1.3 55.6 + - - +
179K ILE* 3.4 12.9 - - + +
180K GLN* 3.2 20.4 + - - +
109L TYR* 6.0 3.2 - - - -
113L ILE* 4.2 24.3 - - - +
116L SER* 5.6 3.8 + - - -
117L ASN* 3.6 29.0 + - - +
120L LYS* 6.0 1.8 - - + -
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Residues in contact with SER 177 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173K GLU 3.5 8.3 + - - -
174K ASN* 2.6 26.4 + - - -
175K LEU 3.0 0.2 - - - -
176K ARG* 1.3 75.5 - - - +
178K LYS* 1.3 64.0 + - - +
180K GLN* 3.3 20.0 - - - +
181K LYS* 3.1 23.7 + - - +
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Residues in contact with LYS 178 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J MET* 5.1 3.1 - - + -
151J GLU* 4.4 7.5 + - - +
174J ASP* 4.4 13.9 + - - +
177J ASP* 4.2 19.6 + - - -
178J TYR* 3.3 44.0 - - + +
174K ASN* 3.1 21.9 + - - +
175K LEU* 2.6 17.5 + - + +
177K SER* 1.3 76.3 + - - +
179K ILE* 1.3 58.8 + - - +
180K GLN 3.0 1.3 - - - -
181K LYS* 2.6 36.8 + - + +
182K LEU* 2.9 30.5 + - + +
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Residues in contact with ILE 179 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J MET* 3.7 23.3 - - + +
175K LEU 2.7 16.2 + - - +
176K ARG* 3.4 20.9 - - + +
178K LYS* 1.3 71.6 - - - +
180K GLN* 1.3 63.0 + - - +
182K LEU* 4.3 4.9 - - - +
183K GLU* 3.0 27.1 + - - +
117L ASN* 3.7 12.1 - - + +
120L LYS* 3.4 49.6 - - + +
121L ILE* 3.4 31.9 - - + +
124L LEU* 4.6 13.3 - - + +
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Residues in contact with GLN 180 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176K ARG 3.2 11.0 + - - +
177K SER* 3.3 22.6 - - - +
178K LYS 2.9 0.6 + - - -
179K ILE* 1.3 83.3 - - - +
181K LYS* 1.3 58.9 + - - +
183K GLU* 3.1 10.4 + - - +
184K SER* 2.8 31.8 + - - -
120L LYS* 5.1 2.0 - - - +
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Residues in contact with LYS 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J GLU* 5.8 1.8 - - - +
177K SER 3.1 9.7 + - - +
178K LYS* 2.6 27.6 + - + +
180K GLN* 1.3 79.3 - - - +
182K LEU* 1.3 64.7 + - + +
184K SER* 2.3 30.1 + - - +
185K ASP* 2.4 28.3 - - - +
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Residues in contact with LEU 182 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J MET* 5.0 13.5 - - + +
150J LEU* 4.6 6.1 - - + +
151J GLU* 3.2 58.1 - - + +
154J ILE* 5.2 14.4 - - + -
171J ARG* 6.1 2.5 - - - +
178K LYS* 2.9 31.0 + - + +
179K ILE* 4.3 2.9 - - - +
181K LYS* 1.3 79.6 - - + +
183K GLU* 1.3 58.2 + - - +
184K SER 2.9 3.1 - - - -
185K ASP* 2.6 31.4 + - - +
186K VAL* 2.9 12.9 + - - +
124L LEU* 4.7 22.0 - - + -
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Residues in contact with GLU 183 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179K ILE* 3.0 18.0 + - - +
180K GLN* 3.1 6.1 + - - +
182K LEU* 1.3 77.8 - - - +
184K SER* 1.3 59.5 + - - +
186K VAL* 3.6 18.1 - - + +
187K SER* 3.7 10.2 + - - -
120L LYS* 2.3 56.1 + - - +
123L ASN* 4.5 8.5 - - - +
124L LEU* 3.8 29.5 + - + +
127L LYS* 5.3 13.3 + - - +
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Residues in contact with SER 184 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180K GLN* 2.8 16.5 + - - -
181K LYS* 2.3 30.3 + - - +
182K LEU 2.8 4.0 + - - -
183K GLU* 1.3 72.7 - - - +
185K ASP* 1.3 74.2 + - - -
187K SER* 3.6 7.1 + - - -
188K ALA* 3.4 17.3 + - - +
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Residues in contact with ASP 185 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ILE* 6.3 0.9 - - + -
158J ILE* 4.3 9.5 - - + +
169J LEU* 3.8 11.2 - - + +
171J ARG* 3.2 39.9 + - - +
181K LYS* 2.4 40.1 - - - +
182K LEU* 2.6 16.6 + - - +
184K SER* 1.3 82.1 + - - +
186K VAL* 1.3 58.4 + - - +
188K ALA* 2.9 29.4 + - - +
189K GLN 3.3 4.9 + - - -
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Residues in contact with VAL 186 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J ILE* 4.8 9.4 - - + +
158J ILE* 4.8 9.6 - - + +
182K LEU 2.9 10.9 + - - +
183K GLU* 3.6 18.6 - - + +
185K ASP* 1.3 76.6 - - - +
187K SER* 1.3 71.4 + - - +
189K GLN* 3.1 13.1 + - - +
190K MET* 3.2 24.0 + - + +
124L LEU* 4.8 9.4 - - + +
127L LYS* 5.0 19.5 - - + +
128L VAL* 4.2 26.5 - - + +
131L LEU* 4.2 24.6 - - + +
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Residues in contact with SER 187 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K GLU 3.7 11.1 + - - -
184K SER* 3.6 9.3 + - - -
185K ASP 3.3 0.6 - - - -
186K VAL* 1.3 86.9 - - - +
188K ALA* 1.3 60.8 + - - +
190K MET* 4.0 10.3 - - - +
191K GLU* 3.5 21.7 + - - +
127L LYS* 4.8 10.9 + - - -
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Residues in contact with ALA 188 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169J LEU* 3.3 23.8 - - + -
184K SER 3.4 8.7 + - - +
185K ASP* 2.9 18.5 + - - +
187K SER* 1.3 79.0 - - - +
189K GLN* 1.3 54.9 + - - +
191K GLU* 3.3 8.9 - - - +
192K TYR* 3.2 43.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN 189 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J ILE* 4.0 28.9 - - + +
161J CYS* 4.1 30.4 - - + +
167J ARG 2.8 27.7 - - - +
168J ALA* 3.3 8.2 - - - -
169J LEU* 2.9 40.8 - - - +
185K ASP 3.3 1.7 + - - +
186K VAL 3.1 8.7 + - - +
188K ALA* 1.3 75.3 - - - +
190K MET* 1.3 68.5 + - - +
191K GLU 3.0 1.1 - - - -
192K TYR* 2.9 9.8 + - - +
193K CYS* 2.9 29.0 + - - +
131L LEU* 4.1 8.7 - - + -
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Residues in contact with MET 190 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186K VAL* 3.2 23.3 + - + +
187K SER* 4.0 9.9 - - - +
189K GLN* 1.3 76.8 - - - +
191K GLU* 1.3 61.5 + - - +
193K CYS* 3.4 13.4 + - - +
194K ARG* 3.5 12.1 + - - +
127L LYS* 3.2 50.9 - - + +
130L GLN* 4.6 7.4 - - + +
131L LEU* 4.1 23.2 - - + +
134L GLN* 4.7 20.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 191 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187K SER 3.5 11.7 + - - +
188K ALA* 3.3 11.8 + - - +
189K GLN 3.0 0.4 - - - -
190K MET* 1.3 75.0 - - - +
192K TYR* 1.3 67.5 + - + +
193K CYS 2.8 10.5 + - - -
194K ARG* 2.9 44.6 + - - +
195K THR* 4.3 2.3 + - - +
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Residues in contact with TYR 192 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165J CYS* 3.4 8.0 - - - +
166J SER* 3.7 2.4 + - - -
167J ARG* 3.2 70.8 + - + +
169J LEU* 3.9 20.6 - - + +
188K ALA* 3.2 30.8 + - + +
189K GLN* 2.9 27.4 + - - +
191K GLU* 1.3 80.9 - - + +
193K CYS* 1.3 57.4 + - - +
194K ARG 3.5 0.7 - - - -
195K THR* 3.1 28.4 + - - +
----------------------------------------------------------
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Residues in contact with CYS 193 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161J CYS* 3.9 8.5 - - - -
165J CYS* 2.1 50.0 - - - -
189K GLN* 2.9 21.2 + - - +
190K MET* 3.7 11.0 - - - +
191K GLU 2.8 2.2 + - - -
192K TYR* 1.3 78.4 - - - +
194K ARG* 1.3 61.9 + - - +
195K THR* 3.3 1.2 - - - +
196K PRO* 5.3 0.5 - - - +
131L LEU* 5.1 1.1 - - + -
134L GLN* 4.6 19.4 + - + +
135L CYS* 3.7 17.5 - - - -
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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