Contacts of the helix formed by residues 176 - 211 (chain A) in PDB entry 2Q1V
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 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 1.3 79.5 - - - +
177A SER* 1.3 63.0 + - - +
178A SER* 2.6 33.9 + - - +
179A GLN* 2.6 37.1 + - - +
180A ASN* 3.0 29.8 + - - -
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN 3.7 1.7 + - - -
176A ASN* 1.3 74.5 - - - +
178A SER* 1.3 61.2 + - - +
180A ASN* 3.2 11.6 + - - +
181A TRP* 2.9 55.9 + - - +
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Residues in contact with SER 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 2.6 19.9 + - - +
177A SER* 1.3 76.3 - - - +
179A GLN* 1.3 54.0 + - - -
181A TRP* 3.3 28.3 + - - +
182A GLN* 2.9 28.4 + - - +
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Residues in contact with GLN 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 2.6 33.4 + - - +
176A ASN* 2.6 47.5 + - - +
177A SER 3.1 0.2 - - - -
178A SER* 1.3 74.3 - - - +
180A ASN* 1.3 57.2 + - - +
182A GLN* 3.3 9.3 + - - +
183A ARG* 3.0 27.6 + - - +
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 4.7 3.9 + - - +
170A ILE* 3.8 31.0 - - + +
171A ALA* 3.9 18.3 - - + +
175A ASN* 2.9 35.9 + - - +
176A ASN 3.0 22.5 + - - -
177A SER* 3.2 11.5 + - - +
179A GLN* 1.3 72.8 - - - +
181A TRP* 1.3 64.6 + - + +
183A ARG* 3.3 3.0 + - - +
184A PHE* 2.9 28.9 + - - +
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Residues in contact with TRP 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ARG* 4.2 16.2 - - - +
177A SER* 2.9 38.1 + - - +
178A SER* 3.4 29.2 - - - +
180A ASN* 1.3 78.0 - - + +
182A GLN* 1.3 59.5 + - - +
184A PHE* 3.2 9.2 + - - +
185A TYR* 2.9 28.1 + - - +
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Residues in contact with GLN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A SER 2.9 16.1 + - - +
179A GLN* 3.6 8.9 + - - +
181A TRP* 1.3 76.4 - - - +
183A ARG* 1.3 58.4 + - - +
185A TYR* 3.1 10.0 + - + +
186A GLN* 2.9 51.6 + - + +
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Residues in contact with ARG 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 2.7 48.1 + - - +
126A GLN 3.3 11.1 + - - -
127A VAL* 3.7 6.1 - - - +
128A THR* 4.7 2.4 - - - +
131A GLU* 2.7 40.4 + - - +
170A ILE* 3.7 25.1 - - + +
179A GLN 3.0 13.9 + - - +
180A ASN 3.4 8.5 - - - +
182A GLN* 1.3 77.8 - - - +
184A PHE* 1.3 55.6 + - - +
186A GLN* 3.3 13.1 + - - +
187A LEU* 2.9 44.3 + - + +
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Residues in contact with PHE 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 4.0 21.1 - - + -
166A LEU* 4.4 10.1 - - + -
167A ARG* 3.3 61.7 - - + +
170A ILE* 3.7 17.0 - - + +
180A ASN 2.9 10.2 + - - +
181A TRP 3.5 8.5 - - - +
183A ARG* 1.3 76.4 - - - +
185A TYR* 1.3 58.9 + - - +
187A LEU* 4.7 1.1 - - - -
188A THR* 2.7 67.8 + - + +
244A PHE* 4.2 14.1 - + + -
245A HIS* 6.1 1.1 - + - -
249A GOL 4.1 9.2 - - - -
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Residues in contact with TYR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TRP 2.9 13.2 + - - +
182A GLN* 3.1 14.3 + - + +
184A PHE* 1.3 80.9 - - - +
186A GLN* 1.3 68.9 + - + +
188A THR* 3.2 4.0 + - - -
189A LYS* 3.1 55.0 + - + +
245A HIS* 3.1 36.3 + + - -
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Residues in contact with GLN 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 4.1 18.4 - - - +
125A LEU* 3.9 38.2 - - + +
182A GLN* 2.9 44.5 + - + +
183A ARG* 3.8 15.8 + - - +
185A TYR* 1.3 80.7 - - + +
187A LEU* 1.3 65.9 + - + +
189A LYS* 3.3 8.9 + - - +
190A LEU* 3.2 19.9 + - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.1 12.1 - - + -
127A VAL* 3.9 23.3 - - + -
131A GLU* 3.6 35.2 - - + +
135A MET* 3.2 38.6 - - + +
166A LEU* 4.2 13.9 - - + -
170A ILE* 3.9 24.7 - - + -
183A ARG* 2.9 31.1 + - + +
184A PHE* 4.2 3.1 - - - +
186A GLN* 1.3 73.8 - - - +
188A THR* 1.3 58.6 + - - +
190A LEU* 3.2 3.6 + - + +
191A LEU* 3.1 20.4 + - - +
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Residues in contact with THR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A LEU* 4.6 6.5 - - + -
184A PHE* 2.7 59.4 + - + +
185A TYR* 3.8 0.2 - - - -
187A LEU* 1.3 74.4 - - - +
189A LYS* 1.3 60.0 + - - +
190A LEU 3.2 0.2 - - - -
191A LEU* 3.5 14.7 - - + +
192A ASP* 2.9 32.4 + - - +
244A PHE* 3.6 30.9 - - + +
245A HIS* 2.7 26.3 + - - -
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TYR* 3.1 53.9 + - + +
186A GLN* 3.4 11.7 - - - +
188A THR* 1.3 76.0 + - - +
190A LEU* 1.3 64.7 + - - +
192A ASP* 3.4 6.4 + - + +
193A SER* 3.0 22.9 + - - -
245A HIS* 3.6 32.8 - - + +
246A LYS 4.0 10.9 + - - -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 4.4 6.1 - - + -
118A ILE* 4.0 22.0 - - + -
121A GLU* 3.9 27.8 - - + +
122A PHE* 3.6 35.0 - - + -
125A LEU* 4.5 18.8 - - + -
127A VAL* 4.7 1.6 - - + -
135A MET* 3.8 15.7 - - + -
186A GLN 3.2 9.7 + - - +
187A LEU 3.4 8.7 - - - +
188A THR 3.2 0.4 - - - -
189A LYS* 1.3 76.7 - - - +
191A LEU* 1.3 64.6 + - - +
193A SER* 2.6 30.7 + - - +
194A MET* 3.5 6.5 + - - +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 4.6 5.2 - - + -
135A MET* 3.7 38.8 - - + +
138A LEU* 3.9 24.7 - - + -
139A LEU* 3.6 29.8 - - + +
142A SER* 5.9 0.9 - - - +
166A LEU* 4.9 1.1 - - + -
187A LEU 3.1 15.1 + - - +
188A THR* 3.5 20.0 - - + +
189A LYS 3.3 0.2 - - - -
190A LEU* 1.3 77.0 - - - +
192A ASP* 1.3 62.7 + - - +
194A MET* 3.1 23.8 + - - +
195A HIS* 4.3 7.2 + - - -
244A PHE* 3.7 30.7 - - + -
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Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A THR 2.9 19.0 + - - +
189A LYS* 3.7 8.5 - - + +
190A LEU 3.3 0.2 - - - -
191A LEU* 1.3 77.2 - - - +
193A SER* 1.3 61.5 + - - +
194A MET 3.1 1.2 + - - -
195A HIS* 3.3 27.6 + - - +
196A ASP* 4.5 1.7 + - - -
242A LEU 4.5 1.0 - - - +
243A LEU* 3.5 22.7 - - + +
244A PHE* 3.0 27.1 + - - -
245A HIS* 2.9 37.7 + - + +
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ILE* 3.9 11.2 - - - +
189A LYS 3.0 13.8 + - - -
190A LEU* 2.6 33.3 + - - +
192A ASP* 1.3 76.0 - - - +
194A MET* 1.3 62.5 + - - +
195A HIS 3.2 0.8 + - - -
196A ASP* 3.6 8.2 + - - +
197A LEU* 3.6 16.8 + - - +
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Residues in contact with MET 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.6 41.1 - - - +
74A ALA* 4.1 13.5 - - + -
75A PHE* 4.0 31.6 - - + +
118A ILE* 3.7 30.1 - - + -
139A LEU* 4.1 16.4 - - + -
190A LEU* 3.8 8.3 - - - +
191A LEU* 3.1 17.3 + - - +
192A ASP 3.1 1.2 - - - -
193A SER* 1.3 79.1 + - - +
195A HIS* 1.3 59.2 + - + +
197A LEU* 3.2 11.1 + - + +
198A VAL* 2.8 39.4 + - + +
----------------------------------------------------------
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Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 6.4 2.0 - - + -
142A SER* 3.5 26.7 + - - -
143A THR* 4.0 12.9 + - - -
191A LEU 4.3 6.0 + - - -
192A ASP* 3.3 27.4 + - - +
193A SER 3.2 1.0 - - - -
194A MET* 1.3 78.4 - - + +
196A ASP* 1.3 65.2 + - - +
198A VAL* 3.9 5.3 - - - +
199A GLY* 3.0 20.3 + - - -
241A PRO* 3.3 30.5 - - + +
242A LEU 4.5 6.5 + - - -
243A LEU* 3.4 25.3 - - + +
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Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASP 4.5 1.5 + - - -
193A SER* 3.6 9.5 + - - +
194A MET 3.4 0.2 - - - -
195A HIS* 1.3 81.4 - - - +
197A LEU* 1.3 63.9 + - - +
199A GLY* 3.3 9.2 + - - -
200A GLY* 3.4 7.8 + - - -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA* 4.7 2.5 - - + -
111A LEU* 4.6 6.5 - - + +
114A GLY* 3.8 30.3 - - - +
115A MET* 4.0 10.1 - - + +
118A ILE* 3.5 34.3 - - + -
193A SER 3.6 10.4 + - - +
194A MET* 3.2 21.7 + - + +
196A ASP* 1.3 78.0 - - - +
198A VAL* 1.3 59.1 + - - +
200A GLY* 2.9 19.1 + - - -
201A LEU* 3.0 39.6 + - + +
----------------------------------------------------------
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Residues in contact with VAL 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR 5.6 4.3 - - - +
70A MET* 4.0 15.7 - - + -
71A SER* 3.6 38.1 - - - +
194A MET* 2.8 34.3 + - + +
195A HIS* 3.9 5.4 - - - +
197A LEU* 1.3 72.6 - - + +
199A GLY* 1.3 58.2 + - - +
201A LEU* 4.1 11.2 - - + -
202A LEU* 2.8 54.3 + - + +
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Residues in contact with GLY 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A HIS 3.0 16.4 + - - -
196A ASP* 3.3 5.4 + - - -
197A LEU 3.1 0.8 - - - -
198A VAL* 1.3 76.8 - - - +
200A GLY* 1.3 57.0 + - - +
202A LEU* 3.7 5.6 + - - +
203A GLN* 3.1 27.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 3.8 23.2 - - - +
196A ASP 3.4 6.4 + - - -
197A LEU 2.9 7.9 + - - -
199A GLY* 1.3 76.9 - - - +
201A LEU* 1.3 63.4 + - - +
203A GLN* 3.3 8.8 + - - +
204A PHE* 3.3 16.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 3.8 30.3 - - + -
74A ALA* 3.8 29.2 - - + -
111A LEU* 4.0 28.5 - - + -
115A MET* 4.0 30.3 - - + -
197A LEU* 3.0 32.5 + - + +
198A VAL* 3.2 9.6 + - + +
200A GLY* 1.3 75.9 - - - +
202A LEU* 1.3 57.9 + - - +
204A PHE* 3.3 5.2 + - - +
205A CYS* 2.9 26.7 + - - +
248A PDN 4.0 13.6 - - + +
----------------------------------------------------------
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR 5.2 5.6 - - - +
69A TRP* 4.5 5.2 - - + -
70A MET* 3.8 30.3 - - + -
198A VAL* 2.8 40.9 + - + +
199A GLY* 4.1 4.7 - - - +
201A LEU* 1.3 73.9 - - - +
203A GLN* 1.3 56.8 + - - +
205A CYS* 3.9 2.9 - - + -
206A PHE* 2.7 62.0 + - + -
230A GLN* 3.9 28.7 - - - +
234A VAL* 5.0 11.2 - - + -
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Residues in contact with GLN 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A GLY 3.1 18.7 + - - +
200A GLY* 3.6 8.9 - - - +
201A LEU 3.2 0.6 - - - -
202A LEU* 1.3 76.7 - - - +
204A PHE* 1.3 58.8 + - - +
206A PHE* 4.0 7.1 - - - +
207A TYR* 3.1 29.8 + - + +
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 5.8 0.2 - - + -
29A LEU* 3.9 25.4 - - + -
106A SER 4.9 1.3 - - - -
107A ALA* 4.7 13.5 - - + -
108A MET* 4.0 22.2 - - + -
111A LEU* 3.7 29.2 - - + -
200A GLY 3.3 2.7 + - - +
201A LEU 3.3 4.1 + - - +
202A LEU 3.3 0.2 - - - -
203A GLN* 1.3 77.9 - - - +
205A CYS* 1.3 59.8 + - - +
207A TYR* 4.2 15.5 - + + -
208A THR* 2.9 53.5 + - + +
248A PDN 3.5 28.7 - - + +
----------------------------------------------------------
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Residues in contact with CYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TRP* 4.1 8.7 - - - -
70A MET* 3.9 18.8 - - + -
201A LEU 2.9 16.9 + - - +
202A LEU* 3.4 10.8 - - - +
204A PHE* 1.3 78.4 - - - +
206A PHE* 1.3 64.2 + - + +
208A THR* 3.2 2.4 + - - -
209A PHE* 2.9 30.8 + - - +
219A PHE* 3.8 5.6 - - - -
227A ILE* 3.6 31.4 - - - -
248A PDN 3.1 23.5 + - + +
----------------------------------------------------------
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Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 2.7 43.2 + - + +
203A GLN* 4.0 5.6 - - - +
205A CYS* 1.3 76.2 - - - +
207A TYR* 1.3 59.2 + - - +
209A PHE* 3.5 3.7 - - - +
210A VAL* 2.8 38.0 + - + +
227A ILE* 3.8 23.3 - - + -
230A GLN* 3.8 41.1 - - + -
231A LEU* 3.9 32.5 - - + -
234A VAL* 4.1 26.9 - - + -
235A MET* 4.5 13.2 - - - -
----------------------------------------------------------
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Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLN* 3.1 21.7 + - + +
204A PHE* 3.7 18.4 - + + +
206A PHE* 1.3 79.1 - - - +
208A THR* 1.3 72.2 + - + +
210A VAL* 3.9 5.7 - - + +
211A GLN* 3.2 51.8 + - - +
215A LEU* 4.4 13.9 - - + +
----------------------------------------------------------
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.6 7.2 - - + -
204A PHE* 2.9 50.3 + - + +
205A CYS 3.2 4.3 + - - -
207A TYR* 1.3 74.9 - - + +
209A PHE* 1.3 57.9 + - - +
211A GLN 3.3 1.4 - - - -
212A SER* 2.8 35.3 + - - -
215A LEU* 4.2 19.5 - - + -
217A VAL* 4.2 13.0 - - + +
219A PHE* 3.4 6.5 - - - -
248A PDN 3.0 26.8 + - - +
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Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A CYS 2.9 20.9 + - - +
206A PHE* 3.5 3.8 - - - +
207A TYR 3.3 0.2 - - - -
208A THR* 1.3 79.0 + - - +
210A VAL* 1.3 69.9 + - + +
212A SER* 3.1 18.7 + - - -
219A PHE* 3.5 32.3 - + + -
224A VAL* 4.0 32.8 - - + -
227A ILE* 3.6 27.8 - - + -
228A SER* 3.5 33.9 - - - -
231A LEU* 4.0 17.0 - - + -
----------------------------------------------------------
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Residues in contact with VAL 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PHE* 2.8 22.6 + - + +
207A TYR* 3.9 6.7 - - + +
209A PHE* 1.3 83.9 - - + +
211A GLN* 1.3 67.5 + - + +
212A SER 3.7 0.9 + - - -
231A LEU* 3.8 23.8 - - + -
----------------------------------------------------------
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Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A TYR* 3.2 50.8 + - - +
208A THR 3.3 3.8 - - - -
209A PHE 3.2 0.6 - - - -
210A VAL* 1.3 86.4 - - + +
212A SER* 1.3 64.7 + - - +
213A GLN 3.4 2.0 - - - -
214A ALA* 3.2 18.3 + - + +
215A LEU* 2.8 45.4 + - + +
----------------------------------------------------------
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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