Contacts of the helix formed by residues 135 - 170 (chain A) in PDB entry 3W03
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 LEU 135 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A TRP* 3.8 36.1 - - + +
24A LEU* 6.5 0.4 - - + -
37A LEU* 5.4 0.7 - - + -
39A SER* 4.7 6.5 - - - +
44A VAL* 3.6 33.9 - - + -
131A VAL* 2.9 15.0 + - + +
133A GLN 3.5 0.8 - - - -
134A HIS* 1.3 87.5 - - + +
136A ILE* 1.3 65.3 + - - +
138A PRO* 3.3 2.8 - - - +
139A LEU* 3.0 47.6 + - + +
210A PHE* 5.1 2.5 - - + -
218A TYR* 5.3 0.9 - - + -
136B ILE* 4.2 28.5 - - + -
140B MET* 4.7 11.7 - - + -
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO 5.5 0.9 - - - +
131A VAL* 3.1 16.5 + - + +
132A SER* 4.1 17.3 - - - +
135A LEU* 1.3 73.2 - - - +
137A ARG* 1.4 60.7 + - + +
139A LEU* 4.8 0.9 - - - -
140A MET* 3.0 43.7 + - + +
41B LEU* 5.4 10.8 - - + +
44B VAL* 4.4 15.0 - - + -
131B VAL* 3.6 27.8 - - + -
135B LEU* 4.4 15.7 - - + -
136B ILE* 3.9 20.0 - - + -
139B LEU* 3.7 21.7 - - + +
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Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER* 2.9 24.1 + - - +
133A GLN* 4.9 0.9 - - - +
136A ILE* 1.4 72.8 - - + +
138A PRO* 1.4 63.4 - - + +
140A MET* 3.2 6.2 + - - +
141A GLY* 2.8 26.3 + - - -
221A VAL* 4.9 0.4 - - - +
225A GLU* 2.6 49.5 + - - +
41B LEU* 3.6 30.2 + - + +
42B GLN* 3.3 27.8 + - - +
204B ILE* 3.4 49.2 - - + +
205B GLY 4.1 10.7 + - - -
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Residues in contact with PRO 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A SER 3.7 0.4 - - - +
133A GLN 3.3 27.6 - - - +
134A HIS 3.6 16.6 - - - +
135A LEU 3.3 11.9 - - - +
137A ARG* 1.4 92.5 - - + +
139A LEU* 1.3 54.4 + - - +
141A GLY 3.3 0.5 + - - -
142A MET* 2.8 37.2 + - - +
218A TYR* 3.7 20.6 - - + -
221A VAL* 3.6 16.4 - - + +
222A THR* 3.8 20.4 - - + -
225A GLU* 6.4 0.2 - - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.0 41.2 + - + +
136A ILE* 3.9 2.5 - - - +
138A PRO* 1.3 76.0 - - + +
140A MET* 1.3 61.6 + - - +
142A MET* 4.0 11.0 - - + -
143A SER* 3.1 27.7 + - - -
210A PHE* 3.8 31.9 - - + -
218A TYR* 5.6 1.6 - - + -
136B ILE* 3.6 42.4 - - + +
139B LEU* 3.8 15.7 - - + +
140B MET* 4.0 22.7 - - + +
143B SER* 3.6 7.9 + - - +
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 3.0 34.9 + - + +
137A ARG* 3.5 4.5 - - - +
139A LEU* 1.3 76.8 - - - +
141A GLY* 1.3 62.6 + - - +
143A SER* 3.3 5.2 + - - -
144A LEU* 3.1 23.0 + - + +
24B LEU* 4.5 2.7 - - + -
41B LEU* 3.7 34.5 - - + -
135B LEU* 4.5 6.5 - - + -
139B LEU* 4.1 18.5 - - + +
204B ILE* 3.9 26.9 - - + -
207B GLY* 4.9 1.3 - - - -
210B PHE* 4.0 52.7 - - + -
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Residues in contact with GLY 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ARG 2.8 18.0 + - - -
138A PRO 3.6 2.7 - - - -
140A MET* 1.3 71.3 - - - +
142A MET* 1.3 56.6 + - - +
144A LEU* 3.4 1.8 + - - -
145A ALA* 3.0 22.5 + - - +
221A VAL* 4.2 6.1 - - - -
202B CYS* 3.3 44.0 - - - +
204B ILE* 3.7 5.8 - - - +
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Residues in contact with MET 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PRO 2.8 31.0 + - - +
139A LEU* 3.7 16.2 - - + +
141A GLY* 1.3 70.0 - - - +
143A SER* 1.3 60.9 + - - +
145A ALA* 3.3 2.5 + - - +
146A LEU* 2.8 36.2 + - - +
210A PHE* 4.2 7.9 - - + -
214A LEU* 3.5 56.1 - - + +
217A LEU* 4.0 14.8 - - + +
218A TYR* 3.8 31.6 - - - +
221A VAL* 3.7 22.7 - - + -
143B SER* 3.8 10.8 - - - +
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Residues in contact with SER 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU 3.1 12.5 + - - -
140A MET* 3.3 7.4 + - - -
142A MET* 1.3 74.9 - - - +
144A LEU* 1.3 61.5 + - - +
146A LEU* 4.5 0.9 - - - -
147A GLN* 3.0 26.2 + - - +
139B LEU* 3.5 13.6 + - - -
142B MET* 3.9 10.8 - - - +
143B SER* 2.9 23.5 + - - -
146B LEU* 3.3 21.8 - - - +
214B LEU* 3.8 16.9 - - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET* 3.1 17.2 + - + +
141A GLY* 3.7 5.4 - - - +
142A MET 3.2 0.2 - - - -
143A SER* 1.3 76.2 - - - +
145A ALA* 1.3 58.6 + - - +
147A GLN* 3.3 5.7 + - + +
148A CYS* 3.0 31.8 + - - -
201B ALA 3.4 14.1 - - - +
202B CYS 4.7 0.7 - - - +
203B SER 3.9 21.5 - - - +
204B ILE* 3.9 27.1 - - + -
209B PRO* 4.1 20.9 - - + +
210B PHE* 4.0 22.4 - - + +
213B ASN* 4.3 9.2 - - + +
214B LEU* 3.5 22.9 - - + -
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Residues in contact with ALA 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY 3.0 17.3 + - - +
142A MET* 3.3 7.8 + - - +
144A LEU* 1.3 74.9 - - - +
146A LEU* 1.3 60.3 + - - +
148A CYS 3.4 1.0 + - - -
149A GLN* 3.0 25.8 + - - +
217A LEU* 4.4 7.0 - - + -
193B PHE* 3.4 13.3 - - + -
198B LEU* 3.8 28.7 - - + -
201B ALA* 3.4 18.6 + - + +
202B CYS* 4.3 2.5 - - + -
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Residues in contact with LEU 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A MET 2.8 21.1 + - - +
143A SER 4.0 2.2 - - - +
145A ALA* 1.3 74.8 - - - +
147A GLN* 1.3 58.8 + - - +
149A GLN* 3.4 29.7 + - - +
150A VAL* 3.0 33.5 + - - +
214A LEU* 4.0 6.5 - - + -
217A LEU* 3.6 21.5 - - + -
143B SER* 3.4 43.1 - - - +
146B LEU* 3.7 16.4 - - + -
147B GLN* 4.4 21.8 - - + +
150B VAL* 4.1 4.5 - - + +
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Residues in contact with GLN 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A SER 3.0 19.3 + - - +
144A LEU* 3.3 7.2 + - + +
146A LEU* 1.3 73.2 - - - +
148A CYS* 1.3 64.3 + - - +
150A VAL* 3.3 16.6 + - - +
151A ARG* 3.0 54.0 + - + +
190A LEU* 6.3 0.6 - - - +
146B LEU* 3.3 24.6 - - + +
149B GLN* 4.8 1.4 + - - -
213B ASN* 4.7 20.2 + - + +
214B LEU* 3.9 22.1 - - + +
217B LEU* 5.7 0.2 - - - +
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Residues in contact with CYS 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.0 19.3 + - - -
145A ALA 3.6 7.9 - - - +
147A GLN* 1.3 73.1 - - - +
149A GLN* 1.3 64.5 + - - +
151A ARG* 3.2 9.7 + - - +
152A GLU* 2.9 29.4 + - - +
193B PHE* 3.9 8.5 - - + -
201B ALA* 3.6 33.2 - - + -
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Residues in contact with GLN 149 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA 3.0 17.1 + - - +
146A LEU* 3.5 34.2 - - - +
147A GLN 3.3 0.2 - - - -
148A CYS* 1.3 73.9 - - - +
150A VAL* 1.3 56.6 + - - +
152A GLU* 3.1 4.2 + - - +
153A LEU* 2.9 36.0 + - - +
217A LEU* 4.5 15.2 - - - +
150B VAL* 3.8 18.0 - - + +
189B PHE* 4.0 12.9 - - + -
190B LEU* 3.5 29.5 - - - +
193B PHE* 3.7 38.3 - - + -
194B MET* 4.6 4.0 - - - -
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Residues in contact with VAL 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU 3.0 18.3 + - - +
147A GLN* 3.4 23.6 - - - +
149A GLN* 1.3 74.4 - - - +
151A ARG* 1.3 58.9 + - - +
153A LEU* 3.4 3.0 + - - +
154A ALA* 3.0 29.2 + - + +
189A PHE* 5.4 2.2 - - + -
190A LEU* 5.6 4.3 - - + -
146B LEU* 4.0 6.3 - - + +
149B GLN* 3.8 35.7 - - + +
150B VAL* 3.7 20.4 - - + +
153B LEU* 3.9 19.3 - - + +
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Residues in contact with ARG 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLN* 3.0 41.2 + - + +
148A CYS* 3.2 9.4 + - - +
150A VAL* 1.3 76.3 - - - +
152A GLU* 1.3 59.0 + - + +
154A ALA* 3.4 8.7 + - - +
155A THR* 3.0 31.1 + - - -
186A GLU* 4.7 14.6 + - - +
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Residues in contact with GLU 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A CYS* 2.9 15.4 + - + +
149A GLN 3.1 7.6 + - - +
151A ARG* 1.3 76.2 - - + +
153A LEU* 1.3 59.9 + - - +
155A THR* 3.3 9.6 + - - -
156A LEU* 3.0 31.6 + - + +
189B PHE* 3.8 24.6 - - + -
193B PHE* 3.8 20.2 - - - +
197B LYS* 3.3 42.5 + - - +
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Residues in contact with LEU 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLN 2.9 21.8 + - - +
150A VAL 3.4 4.0 + - - +
152A GLU* 1.3 72.6 - - - +
154A ALA* 1.3 58.9 + - - +
156A LEU* 3.3 5.3 + - + +
157A LEU* 3.0 34.9 + - - +
150B VAL* 3.4 50.5 - - + +
153B LEU* 3.9 18.8 - - + -
154B ALA* 4.6 1.8 - - + +
157B LEU* 3.7 12.0 - - + +
184B PHE* 3.6 34.8 - - + -
189B PHE* 3.6 22.7 - - + -
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Residues in contact with ALA 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.0 19.1 + - + +
151A ARG* 3.6 14.4 - - - +
153A LEU* 1.3 75.6 - - - +
155A THR* 1.3 62.8 + - - +
157A LEU* 3.2 5.8 + - - +
158A HIS* 3.1 30.2 + - + -
184A PHE* 3.7 29.4 - - + -
186A GLU* 3.8 16.6 - - + +
153B LEU* 4.7 2.1 - - + +
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Residues in contact with THR 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.0 15.5 + - - -
152A GLU* 3.5 11.7 - - - -
154A ALA* 1.3 77.0 - - - +
156A LEU* 1.3 64.0 + - + +
157A LEU 3.4 0.2 + - - -
158A HIS* 3.5 10.3 + - + +
159A MET* 3.3 28.7 + - + +
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Residues in contact with LEU 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLU 3.0 17.8 + - - +
153A LEU* 3.7 8.5 - - + +
154A ALA 3.3 0.4 - - - -
155A THR* 1.3 77.9 - - + +
157A LEU* 1.3 57.6 + - - +
159A MET* 3.2 12.3 + - + +
160A LYS* 3.1 31.4 + - + +
157B LEU* 3.6 16.4 - - + -
184B PHE* 4.0 30.7 - - + -
189B PHE* 4.2 18.6 - - + -
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Residues in contact with LEU 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU 3.0 22.9 + - - +
154A ALA 3.2 6.9 + - - +
156A LEU* 1.3 73.8 - - - +
158A HIS* 1.3 58.9 + - - +
160A LYS* 3.2 5.2 + - - +
161A ASP* 3.0 33.5 + - - +
184A PHE* 3.9 24.7 - - + -
153B LEU* 3.6 39.9 - - + +
156B LEU* 3.7 26.0 - - + -
157B LEU* 3.6 26.2 - - + +
160B LYS* 3.7 21.6 - - + +
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Residues in contact with HIS 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ALA* 3.1 23.0 + - + -
155A THR* 3.5 10.3 + - + +
157A LEU* 1.3 73.5 - - - +
159A MET* 1.3 61.2 + - + +
161A ASP* 3.5 9.2 + - - +
162A LEU* 2.9 27.5 + - - +
184A PHE* 3.3 31.9 + + - +
186A GLU* 2.9 41.0 + - - -
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Residues in contact with MET 159 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 3.3 21.5 + - + +
156A LEU* 3.2 15.5 + - + +
157A LEU 3.2 0.4 - - - -
158A HIS* 1.3 76.1 - - - +
160A LYS* 1.3 59.9 + - - +
162A LEU* 3.3 27.9 + - + +
163A GLU* 3.0 28.2 + - - +
181B THR* 3.9 24.0 - - + +
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Residues in contact with LYS 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LEU* 3.1 17.9 + - + +
157A LEU* 3.2 10.5 + - - +
159A MET* 1.3 74.1 - - - +
161A ASP* 1.3 58.0 + - - +
163A GLU* 3.3 5.2 + - - +
164A ILE* 2.9 33.9 + - - +
157B LEU* 3.8 23.1 - - + -
160B LYS* 3.8 28.0 - - + -
161B ASP* 2.7 36.1 + - - +
164B ILE* 3.7 17.3 - - + +
181B THR* 3.2 21.1 + - - +
182B GLU 2.8 29.1 + - - -
184B PHE* 3.8 4.9 - - - +
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Residues in contact with ASP 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU 3.0 19.7 + - - +
158A HIS* 3.6 9.7 + - - +
160A LYS* 1.3 73.8 - - - +
162A LEU* 1.3 55.6 + - - +
164A ILE* 3.3 13.9 + - - +
165A GLN* 2.8 34.5 + - - +
183A PRO* 3.6 13.1 - - + +
184A PHE* 2.8 35.3 + - - +
160B LYS* 2.7 28.0 + - - +
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Residues in contact with LEU 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS 2.9 18.2 + - - +
159A MET* 3.3 33.4 + - + +
161A ASP* 1.3 77.0 - - - +
163A GLU* 1.3 56.2 + - - +
165A GLN* 3.4 22.9 + - - +
166A ASP* 2.9 45.4 + - - +
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Residues in contact with GLU 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A MET 3.0 12.4 + - - +
160A LYS 3.6 7.2 - - - +
161A ASP 3.3 0.2 - - - -
162A LEU* 1.3 74.3 - - - +
164A ILE* 1.3 63.1 + - - +
166A ASP* 3.3 11.7 + - + +
167A TYR* 3.2 41.1 + - + -
164B ILE* 3.5 30.4 - - + +
168B GLN* 4.7 2.4 + - - -
179B LEU 3.5 17.0 - - - +
180B LYS* 3.5 19.8 - - + +
181B THR* 2.6 44.6 + - + +
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Residues in contact with ILE 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS 2.9 20.1 + - - +
161A ASP* 3.3 23.3 + - - +
163A GLU* 1.3 73.7 - - - +
165A GLN* 1.3 65.7 + - - +
167A TYR* 3.4 6.4 + - - +
168A GLN* 3.1 43.7 + - - +
160B LYS* 4.1 24.5 - - + +
163B GLU* 4.0 20.9 - - + +
164B ILE* 3.9 15.5 - - + +
167B TYR* 3.9 21.9 - - + +
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Residues in contact with GLN 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ASP 2.8 20.5 + - - +
162A LEU* 3.6 26.5 - - - +
163A GLU 3.3 0.2 - - - -
164A ILE* 1.3 73.4 - - - +
166A ASP* 1.3 59.5 + - - +
168A GLN* 3.1 13.9 + - + +
169A GLU* 2.9 57.1 + - + +
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Residues in contact with ASP 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A LEU* 2.9 33.5 + - - +
163A GLU* 3.4 13.5 - - + +
164A ILE 3.2 0.4 - - - -
165A GLN* 1.3 78.1 - - - +
167A TYR* 1.3 60.1 + - + +
169A GLU* 3.7 6.8 + - - +
170A SER* 3.0 25.6 + - - -
175B ILE* 4.6 11.8 - - + +
179B LEU* 3.9 38.4 - - + +
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Residues in contact with TYR 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLU* 3.2 41.2 + - + -
164A ILE* 3.7 6.3 - - - +
165A GLN 3.3 0.2 - - - -
166A ASP* 1.3 74.4 - - + +
168A GLN* 1.3 65.4 + - - +
170A SER* 3.0 20.3 + - - -
172A ALA* 3.2 26.6 + - + +
164B ILE* 4.6 8.1 - - + -
167B TYR* 3.6 59.2 - + + -
168B GLN* 3.0 36.8 + - + +
174B LEU* 4.9 6.2 - - - -
175B ILE* 4.5 26.4 - - + +
180B LYS* 3.6 15.6 + - + +
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Residues in contact with GLN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ILE* 3.1 25.3 + - - +
165A GLN* 3.1 15.8 + - - +
167A TYR* 1.3 77.9 - - - +
169A GLU* 1.3 63.1 + - + +
171A GLY* 3.3 13.5 + - - -
172A ALA* 4.8 3.4 - - - -
173A THR* 3.9 29.5 - - + +
174A LEU* 6.0 0.2 - - - +
180A LYS* 5.7 2.0 - - - +
167B TYR* 3.3 24.7 + - + +
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Residues in contact with GLU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLN* 2.9 44.8 + - + +
166A ASP* 4.1 7.2 - - - +
168A GLN* 1.3 76.4 - - + +
170A SER* 1.3 58.2 + - - +
171A GLY 3.4 1.7 + - - -
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP 3.0 11.5 + - - -
167A TYR* 3.0 20.1 + - - -
169A GLU* 1.3 77.2 - - - +
171A GLY* 1.3 58.3 + - - +
172A ALA* 3.5 2.1 + - - +
175B ILE* 3.4 34.2 - - - +
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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