Contacts of the helix formed by residues 145 - 183 (chain B) in PDB entry 1CUN
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 ALA 145 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B THR* 3.0 7.0 + - - +
144B LEU* 1.3 81.0 - - + +
146B ALA* 1.3 63.1 + - - +
147B ILE 3.3 1.6 - - - -
148B GLN* 3.6 11.6 + - - +
149B GLY* 3.2 16.6 + - - -
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY* 4.7 1.6 - - - -
142B ASP* 3.9 18.2 - - + +
143B THR* 2.9 29.8 + - + +
145B ALA* 1.3 74.9 - - - +
147B ILE* 1.3 65.2 + - - +
149B GLY* 3.1 3.5 + - - -
150B LEU* 3.0 30.9 + - + +
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B TYR 3.0 25.4 - - - +
141B GLY* 4.1 7.7 - - - -
142B ASP 5.1 0.2 - - - +
143B THR 3.2 15.7 + - - +
144B LEU* 4.0 13.5 - - + +
146B ALA* 1.3 79.3 - - - +
148B GLN* 1.3 67.9 + - + +
150B LEU* 3.4 3.3 + - - +
151B LEU* 3.0 52.1 + - + +
214B LEU* 3.5 20.4 - - + +
217B ASN* 3.2 16.4 - - - +
218B SER* 3.5 21.1 - - - -
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Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU 4.0 15.4 + - - +
145B ALA* 3.6 11.8 + - - +
146B ALA 3.2 0.6 - - - -
147B ILE* 1.3 84.9 - - + +
149B GLY* 1.3 57.2 + - - +
151B LEU* 3.4 13.0 + - + +
152B LYS* 3.0 35.5 + - + +
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Residues in contact with GLY 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA 3.2 10.8 + - - -
146B ALA* 3.1 8.9 + - - -
148B GLN* 1.3 75.7 - - - +
150B LEU* 1.3 65.5 + - - +
152B LYS* 3.3 7.4 + - - +
153B LYS* 3.1 29.5 + - - +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ASP* 3.4 31.9 - - - +
140B TYR* 3.6 5.8 - - - +
141B GLY* 3.5 27.4 - - - +
146B ALA* 3.0 16.2 + - + +
147B ILE* 3.7 6.5 - - - +
149B GLY* 1.3 78.8 - - - +
151B LEU* 1.3 56.1 + - - +
153B LYS* 3.3 19.2 + - - +
154B HIS* 2.9 29.5 + - - +
210B ARG* 3.6 20.7 + - - +
214B LEU* 3.9 15.1 - - + +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 3.0 44.0 + - + +
148B GLN* 3.6 16.4 - - + +
149B GLY 3.3 0.2 - - - -
150B LEU* 1.3 72.7 - - - +
152B LYS* 1.3 61.1 + - - +
154B HIS* 3.2 6.8 + - - +
155B GLU* 2.9 49.6 + - + +
211B LYS* 5.6 7.1 - - - +
214B LEU* 3.6 27.4 - - + +
215B ASP* 5.0 9.9 - - - +
218B SER* 4.1 21.3 - - - +
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Residues in contact with LYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLN* 3.0 21.5 + - - +
149B GLY* 3.4 11.4 - - - +
150B LEU 3.3 0.2 - - - -
151B LEU* 1.3 77.4 - - - +
153B LYS* 1.3 64.1 + - + +
155B GLU* 3.4 18.3 + - + +
156B ALA* 3.1 21.7 + - - +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLY 3.1 15.7 + - - +
150B LEU* 3.7 20.9 - - - +
151B LEU 3.2 0.2 - - - -
152B LYS* 1.3 78.2 - - + +
154B HIS* 1.3 63.6 + - - +
156B ALA* 3.3 7.4 + - - +
157B PHE* 3.1 21.8 + - - +
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Residues in contact with HIS 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B VAL* 4.5 5.5 - - + +
150B LEU 2.9 16.7 + - - +
151B LEU* 3.2 5.1 + - - +
153B LYS* 1.3 76.3 - - - +
155B GLU* 1.3 57.9 + - - +
157B PHE* 3.2 26.5 + + + +
158B GLU* 2.8 58.1 + - + +
207B ALA* 3.5 20.9 + - + -
210B ARG* 3.7 27.0 - - + +
211B LYS* 3.7 26.4 - - + +
214B LEU* 3.8 16.2 - - + -
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 2.9 44.6 + - - +
152B LYS* 3.5 20.9 + - + +
154B HIS* 1.3 74.1 - - - +
156B ALA* 1.3 63.8 - - - +
158B GLU* 3.3 19.1 + - - +
159B THR* 3.3 23.7 + - - -
211B LYS* 5.2 9.8 - - - -
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LYS* 3.1 13.6 + - + +
153B LYS* 3.7 10.5 - - - +
154B HIS 3.3 0.2 - - - -
155B GLU* 1.3 75.8 - - - +
157B PHE* 1.3 62.1 + - - +
159B THR* 3.2 8.5 + - - -
160B ASP* 3.1 30.4 + - - +
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TRP* 3.7 25.8 - + - -
131B LYS* 3.8 34.5 - - + +
135B VAL* 4.2 9.6 - - + -
153B LYS 3.1 13.9 + - - +
154B HIS* 3.3 29.6 - + + +
156B ALA* 1.3 77.7 - - - +
158B GLU* 1.3 64.8 + - + +
160B ASP* 3.1 8.0 + - - +
161B PHE* 2.8 53.3 + + + +
203B LEU* 4.1 17.5 - - + -
207B ALA* 3.9 22.0 - - + -
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B HIS* 2.8 49.7 + - + +
155B GLU* 3.7 21.8 - - - +
156B ALA 3.3 0.4 - - - -
157B PHE* 1.3 78.6 - - + +
159B THR* 1.3 60.9 + - - +
161B PHE* 3.5 6.2 + - - +
162B THR* 2.9 27.6 + - - -
207B ALA* 6.4 0.2 - - + -
211B LYS* 3.9 19.3 + - - +
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLU 3.3 10.2 + - - -
156B ALA* 3.2 10.6 + - - -
157B PHE 3.2 0.8 - - - -
158B GLU* 1.3 79.5 - - - +
160B ASP* 1.3 67.6 + - - +
162B THR* 3.2 21.4 + - - -
163B VAL* 3.3 13.9 + - + +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B TRP* 4.0 17.4 + - + +
131B LYS* 5.5 4.6 + - - -
156B ALA* 3.1 17.0 + - - +
157B PHE* 3.1 10.5 + - - +
159B THR* 1.3 82.8 - - - +
161B PHE* 1.3 60.8 + - - +
163B VAL* 3.1 9.2 + - - +
164B HIS* 3.0 32.3 + - + -
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B TRP* 3.6 21.9 - + + -
128B ILE* 5.3 1.6 - - + -
157B PHE* 2.8 47.0 + + + +
158B GLU* 3.8 7.4 - - - +
160B ASP* 1.3 69.2 - - - +
162B THR* 1.3 66.4 + - - +
164B HIS* 4.7 2.9 - - + -
165B LYS* 2.9 49.8 + - + +
200B VAL* 3.7 20.0 - - + -
203B LEU* 3.5 34.3 - - + -
204B GLU* 3.6 39.7 - - + -
207B ALA* 4.8 2.9 - - + -
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.2 19.2 - - + +
158B GLU 2.9 19.7 + - - -
159B THR* 3.3 14.3 - - - -
160B ASP 3.1 0.4 - - - -
161B PHE* 1.3 78.4 - - - +
163B VAL* 1.3 62.8 + - + +
165B LYS* 3.5 15.5 + - - +
166B ASP* 3.4 16.3 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.1 19.7 - - + +
79A GLY* 3.8 26.9 - - - +
82A GLU* 4.9 4.9 - - + +
159B THR* 3.3 15.0 + - + +
160B ASP* 3.1 12.2 + - - +
162B THR* 1.3 75.6 - - + +
164B HIS* 1.3 67.4 + - + +
166B ASP* 3.0 6.9 + - - +
167B ARG* 2.9 59.4 + - + +
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Residues in contact with HIS 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU 5.7 0.9 - - - -
124B GLU* 2.7 33.4 + - - +
127B TRP* 3.3 65.7 + + + -
128B ILE* 6.0 1.1 - - + -
160B ASP* 3.0 30.1 + - + +
161B PHE* 3.9 4.9 - - + +
163B VAL* 1.3 81.0 - - + +
165B LYS* 1.3 57.7 + - - +
167B ARG* 3.6 22.8 + - - +
168B VAL* 2.8 35.2 + - + +
200B VAL* 5.9 0.2 - - - -
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B PHE* 2.9 62.8 + - + +
162B THR* 3.7 12.8 + - + +
163B VAL 3.2 0.2 - - - -
164B HIS* 1.3 76.6 - - - +
166B ASP* 1.3 59.4 + - - +
168B VAL* 3.4 7.9 + - - +
169B ASN* 3.0 35.3 + - - +
200B VAL* 4.2 12.3 - - + -
204B GLU* 3.6 28.6 + - - +
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Residues in contact with ASP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A THR* 4.6 5.0 - - - +
78A ILE* 3.6 53.6 + - + +
162B THR 3.4 4.9 + - - +
163B VAL 3.0 9.3 + - - +
165B LYS* 1.3 80.9 - - - +
167B ARG* 1.3 58.9 + - + +
169B ASN* 3.0 15.0 + - - +
170B ASP* 2.9 41.8 + - - +
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.1 17.9 - - + +
9A HIS* 3.8 17.1 + - + +
12A PHE* 3.1 37.2 - - - -
78A ILE 5.3 5.3 + - - +
79A GLY* 5.5 1.6 - - - -
82A GLU* 3.3 21.8 + - - -
83A ILE* 5.2 3.4 - - - +
124B GLU* 3.6 24.7 + - - +
163B VAL* 2.9 37.6 + - + +
164B HIS* 3.2 26.2 + - - +
166B ASP* 1.3 76.0 - - + +
168B VAL* 1.3 60.2 + - - +
170B ASP* 3.1 11.7 + - - +
171B VAL* 2.9 33.5 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 4.0 28.0 - - + +
128B ILE* 4.6 3.4 - - + -
164B HIS* 2.8 24.9 + - + +
165B LYS 3.7 4.7 - - - +
167B ARG* 1.3 71.4 - - - +
169B ASN* 1.3 67.3 + - - +
171B VAL* 3.2 8.2 + - - +
172B CYS* 2.9 31.6 + - - -
196B LEU* 3.8 29.2 - - + +
197B LYS* 4.9 5.6 - - + +
200B VAL* 3.8 31.2 - - + -
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LYS* 3.0 25.0 + - - +
166B ASP* 3.0 16.8 + - - +
168B VAL* 1.3 82.3 - - - +
170B ASP* 1.3 63.9 + - - +
172B CYS* 3.3 6.7 + - - +
173B ALA* 3.0 22.7 + - - +
197B LYS* 5.4 8.7 - - - +
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 6.4 1.8 - - + -
8A VAL* 4.9 13.0 - - - +
9A HIS* 5.8 3.8 - - + -
77A THR* 5.3 3.3 - - - +
166B ASP* 2.9 33.2 + - - +
167B ARG* 3.1 12.4 + - - +
169B ASN* 1.3 78.2 - - - +
171B VAL* 1.3 58.2 + - + +
173B ALA* 3.2 7.8 + - - +
174B ASN* 2.9 30.0 + - - +
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Residues in contact with VAL 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A HIS* 3.5 27.1 - - + +
117B PHE* 3.5 25.2 - - + -
120B ASN* 3.8 17.5 - - + +
121B VAL* 3.8 21.1 - - + +
124B GLU* 4.6 7.2 - - + -
167B ARG 2.9 18.5 + - - +
168B VAL* 3.6 9.2 - - - +
170B ASP* 1.3 76.1 - - - +
172B CYS* 1.3 58.0 + - - +
174B ASN* 3.3 8.0 + - - +
175B GLY 2.9 22.7 + - - -
193B MET* 6.0 0.2 - - + -
196B LEU* 4.0 11.4 - - + -
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Residues in contact with CYS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 2.9 27.2 + - - +
169B ASN* 3.8 6.7 - - - +
171B VAL* 1.3 74.0 - - - +
173B ALA* 1.3 66.5 + - - +
175B GLY 3.2 0.9 + - - -
176B GLU* 3.0 28.3 + - - +
193B MET* 3.3 38.4 - - - +
196B LEU* 4.9 5.6 - - - -
197B LYS* 3.5 42.4 - - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ASN 3.0 14.4 + - - +
170B ASP* 3.5 12.8 - - - +
172B CYS* 1.3 75.4 - - - +
174B ASN* 1.3 63.5 + - - +
176B GLU* 3.2 18.2 - - - +
177B ASP* 3.1 30.5 + - - +
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Residues in contact with ASN 174 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU* 4.5 7.4 + - - +
116B GLN* 5.6 1.2 - - - +
117B PHE* 3.6 31.9 + - - +
120B ASN* 5.1 3.7 - - - +
170B ASP 2.9 16.1 + - - +
171B VAL* 3.5 7.5 - - - +
173B ALA* 1.3 77.6 - - - +
175B GLY* 1.3 62.5 + - - +
177B ASP* 3.0 14.8 + - - +
178B LEU* 3.0 32.6 + - - +
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PHE* 3.7 25.7 - - - -
171B VAL 2.9 10.9 + - - -
172B CYS 3.2 4.2 + - - -
174B ASN* 1.3 77.2 - - - +
176B GLU* 1.3 61.4 + - - +
178B LEU* 3.3 5.2 + - - +
179B ILE* 3.1 25.8 + - - +
189B ILE* 3.6 11.7 - - - +
193B MET* 3.9 7.0 - - - -
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B CYS* 3.0 15.6 + - - +
173B ALA* 3.2 25.7 - - - +
175B GLY* 1.3 76.0 - - - +
177B ASP* 1.3 65.2 + - - +
179B ILE* 3.4 10.0 + - + +
180B LYS* 3.0 43.9 + - - +
193B MET* 3.8 12.2 - - + +
197B LYS* 5.1 8.7 + - - -
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ALA* 3.1 22.5 + - - +
174B ASN* 3.0 17.3 + - - +
176B GLU* 1.3 79.1 - - - +
178B LEU* 1.3 60.5 + - + +
180B LYS* 3.2 16.6 + - - +
181B LYS* 2.9 41.6 + - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLU 5.1 0.9 - - - +
113B GLU* 3.4 47.6 - - + +
114B TYR* 3.9 13.0 - - + +
117B PHE* 3.8 34.5 - - + -
174B ASN* 3.0 25.4 + - - +
175B GLY* 3.6 7.4 - - - +
177B ASP* 1.3 77.6 - - + +
179B ILE* 1.3 62.1 + - - +
181B LYS* 4.2 3.8 - - + -
182B ASN* 2.8 45.5 + - - +
189B ILE* 4.0 20.2 - - + -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B GLY 3.1 9.6 + - - +
176B GLU* 3.7 9.6 - - + +
178B LEU* 1.3 78.3 - - - +
180B LYS* 1.3 64.4 + - + +
183B ASN* 3.4 27.7 + - - +
184B HIS 5.6 0.2 - - - -
186B VAL* 3.8 29.4 - - + -
189B ILE* 3.7 32.5 - - + -
190B THR* 3.4 24.7 - - - +
193B MET* 3.8 14.1 - - + -
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Residues in contact with LYS 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU* 3.0 40.0 + - - +
177B ASP* 3.2 15.4 + - - +
179B ILE* 1.3 81.2 - - + +
181B LYS* 1.3 60.1 + - + +
183B ASN 5.1 0.3 + - - -
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Residues in contact with LYS 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 6.5 0.2 - - - -
113B GLU* 2.9 39.8 + - - +
177B ASP* 2.9 28.2 + - - +
178B LEU* 3.4 3.8 + - - +
180B LYS* 1.3 78.6 - - - +
182B ASN* 1.3 79.7 + - - +
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Residues in contact with ASN 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 3.4 44.6 - - - +
113B GLU* 4.9 0.2 + - - -
178B LEU* 2.8 31.8 + - - +
180B LYS 3.6 0.4 - - - -
181B LYS* 1.3 103.4 - - - +
183B ASN* 1.3 76.0 + - - +
184B HIS* 3.1 29.5 + - + +
189B ILE* 5.5 0.3 - - - +
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Residues in contact with ASN 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178B LEU 3.7 1.0 + - - -
179B ILE* 3.4 21.9 + - - +
180B LYS 4.9 0.4 - - - +
182B ASN* 1.3 83.5 + - - +
184B HIS* 1.3 59.0 + - + +
185B HIS 4.1 0.3 + - - -
186B VAL* 3.0 34.0 - - - +
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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) + - + + + + + -
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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