Contacts of the helix formed by residues 139 - 179 (chain A) in PDB entry 1BG1
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 GLU 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 1.3 72.4 - - - +
140A LYS* 1.3 67.3 + - - +
142A GLN* 3.0 20.5 + - + +
143A MET* 3.1 36.9 + - + +
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Residues in contact with LYS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A THR* 3.1 8.3 + - - +
139A GLU* 1.3 79.9 - - - +
141A GLN* 1.3 61.5 + - - +
143A MET* 3.4 8.8 + - + +
144A LEU* 3.1 21.8 + - + +
234A THR* 3.9 18.6 - - + -
238A GLU* 2.7 46.7 + - - +
239A GLU* 3.7 20.1 + - + +
242A ASP* 5.4 3.2 + - - +
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Residues in contact with GLN 141 (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 VAL 3.9 5.2 + - - +
137A VAL* 3.5 23.3 - - + +
138A THR* 3.2 35.4 + - - +
139A GLU 3.2 0.2 - - - -
140A LYS* 1.3 77.3 - - - +
142A GLN* 1.3 58.4 - - - +
144A LEU* 3.3 8.8 + - - +
145A GLU* 2.9 29.6 + - - +
239A GLU* 3.2 33.5 + - - +
246A ARG* 5.1 8.3 - - - +
262A ARG* 4.2 12.7 + - - +
266A TRP* 3.7 24.8 - - + -
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Residues in contact with GLN 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 3.7 22.7 + - - +
138A THR 3.1 24.5 + - - +
139A GLU* 3.0 15.8 + - + +
141A GLN* 1.3 76.9 - - - +
143A MET* 1.3 72.0 + - + +
145A GLU* 3.4 9.2 + - - +
146A GLN* 3.0 26.7 + - - +
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Residues in contact with MET 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.1 32.9 + - + +
140A LYS* 3.7 9.0 - - + +
142A GLN* 1.3 89.3 - - + +
144A LEU* 1.3 58.1 + - - +
146A GLN* 3.1 12.3 + - + +
147A HIS* 2.7 59.3 + - + -
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Residues in contact with LEU 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 3.1 14.1 + - + +
141A GLN* 3.3 9.6 + - - +
143A MET* 1.3 77.6 - - - +
145A GLU* 1.3 63.7 + - - +
147A HIS* 3.2 7.3 + - + +
148A LEU* 2.9 38.1 + - + +
231A VAL* 3.7 33.4 - - + +
234A THR* 4.5 15.7 - - + -
235A LEU* 4.6 12.6 - - + +
239A GLU* 3.9 22.0 - - + -
266A TRP* 3.7 38.4 - - + -
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Residues in contact with GLU 145 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN 2.9 17.1 + - - +
142A GLN* 3.7 9.2 - - - +
144A LEU* 1.3 74.0 - - - +
146A GLN* 1.3 64.0 + - - +
148A LEU* 3.2 8.1 + - - +
149A GLN* 3.0 52.0 + - - +
262A ARG* 5.3 8.4 + - - +
266A TRP* 2.9 34.9 + - + +
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Residues in contact with GLN 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A GLN 3.0 14.8 + - - +
143A MET* 3.1 19.7 - - + +
145A GLU* 1.3 74.9 - - - +
147A HIS* 1.3 59.5 + - + +
149A GLN* 2.8 41.8 + - - +
150A ASP* 2.9 40.1 + - - +
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Residues in contact with HIS 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 2.7 45.3 + - + +
144A LEU* 3.7 7.0 + - - +
146A GLN* 1.3 77.2 - - + +
148A LEU* 1.3 63.5 + - - +
150A ASP* 3.6 19.5 - - - +
151A VAL* 2.9 29.5 + - - +
230A TYR* 5.8 8.8 - + - -
231A VAL* 4.0 29.7 - - + +
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Residues in contact with LEU 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 2.9 30.6 + - + +
145A GLU* 3.6 8.7 - - - +
147A HIS* 1.3 76.6 - - - +
149A GLN* 1.3 56.9 + - - +
151A VAL* 3.4 8.8 + - + +
152A ARG* 3.0 25.3 + - - +
231A VAL* 3.6 27.4 - - + -
235A LEU* 5.0 3.8 - - + -
266A TRP* 3.5 52.7 - - + +
269A SER* 4.5 17.7 + - - +
270A LEU* 4.4 29.2 - - + -
273A SER* 5.1 0.9 + - - -
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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 GLU* 3.0 38.3 + - - +
146A GLN* 2.8 28.6 + - - +
148A LEU* 1.3 74.2 - - - +
150A ASP* 1.3 60.2 + - - +
151A VAL 3.1 1.8 - - - -
152A ARG* 2.9 11.3 + - + +
153A LYS* 2.8 29.5 + - - +
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Residues in contact with ASP 150 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLN* 2.9 35.3 + - - +
147A HIS* 3.2 28.2 + - - +
149A GLN* 1.3 75.3 - - - +
151A VAL* 1.3 59.0 + - + +
153A LYS* 3.2 8.1 + - - +
154A ARG* 2.9 39.3 + - + +
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Residues in contact with VAL 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A HIS 2.9 18.5 + - - +
148A LEU* 3.5 15.3 - - + +
150A ASP* 1.3 74.5 - - + +
152A ARG* 1.3 65.9 - - - +
154A ARG* 3.3 3.8 + - - +
155A VAL* 3.1 23.4 + - - +
224A LEU* 4.1 18.4 - - + -
227A ALA* 5.0 15.9 - - + +
228A MET* 3.7 39.7 - - + -
231A VAL* 5.1 6.3 - - + -
270A LEU* 4.5 7.6 - - + -
273A SER* 3.9 13.0 - - - +
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Residues in contact with ARG 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU 3.0 13.4 + - - +
149A GLN* 2.9 16.1 + - + +
151A VAL* 1.3 78.5 - - - +
153A LYS* 1.3 60.9 - - - +
155A VAL* 3.3 5.4 + - - +
156A GLN* 3.2 43.0 + - - +
269A SER* 3.3 26.9 + - - +
272A GLU* 2.8 37.8 + - - +
273A SER* 3.2 41.2 + - - +
276A GLN* 4.4 12.5 + - - -
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Residues in contact with LYS 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLN 2.8 13.0 + - - +
150A ASP* 3.4 12.6 - - - +
152A ARG* 1.3 76.1 - - - +
154A ARG* 1.3 57.8 + - + +
156A GLN* 2.9 24.4 + - - +
157A ASP* 2.5 69.8 + - - +
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Residues in contact with ARG 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ASP* 2.9 25.5 + - + +
151A VAL* 3.7 5.7 - - - +
153A LYS* 1.3 77.3 - - + +
155A VAL* 1.3 58.5 + - - +
157A ASP* 3.5 11.3 + - - +
158A LEU* 3.0 36.0 + - + +
220A GLU* 4.0 10.9 + - - +
223A GLY* 3.8 8.7 + - - -
224A LEU* 3.5 47.3 - - + +
227A ALA* 3.7 23.8 - - - +
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Residues in contact with VAL 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A VAL 3.1 17.3 + - - +
152A ARG* 3.6 9.0 - - - +
154A ARG* 1.3 78.1 - - - +
156A GLN* 1.3 60.2 + - + +
158A LEU* 4.5 4.3 - - - -
159A GLU* 2.9 24.3 + - - +
224A LEU* 3.5 14.1 - - + -
228A MET* 4.3 1.8 - - + -
273A SER* 4.0 20.0 - - - +
276A GLN* 3.1 45.8 - - + +
277A THR* 3.3 23.6 - - - +
280A GLN* 3.2 14.9 + - - +
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Residues in contact with GLN 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG* 3.2 32.7 + - + +
153A LYS* 2.9 31.8 + - - +
155A VAL* 1.3 79.2 - - + +
157A ASP* 1.3 58.1 + - - +
159A GLU* 3.0 10.3 + - - +
160A GLN* 2.8 28.8 + - - +
276A GLN* 5.0 5.6 - - - +
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Residues in contact with ASP 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LYS* 2.5 50.4 + - - +
154A ARG* 3.7 12.4 - - - +
155A VAL 3.3 0.2 - - - -
156A GLN* 1.3 75.9 - - - +
158A LEU* 1.3 58.0 + - + +
160A GLN* 3.0 11.2 - - - +
161A LYS* 2.9 37.7 + - + +
220A GLU* 5.9 0.4 - - - +
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Residues in contact with LEU 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ARG* 3.0 23.0 + - + +
155A VAL* 3.7 2.5 - - - +
157A ASP* 1.3 72.1 - - + +
159A GLU* 1.3 60.7 + - - +
161A LYS* 3.2 8.6 + - + +
162A MET* 2.8 34.2 + - + +
217A ILE* 4.0 30.3 - - + +
220A GLU* 3.5 42.4 - - + +
221A LEU* 3.8 26.7 - - + -
224A LEU* 3.9 18.6 - - + -
280A GLN* 3.4 16.4 - - - +
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Residues in contact with GLU 159 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL 2.9 15.2 + - - +
156A GLN* 3.2 11.9 - - - +
158A LEU* 1.3 76.4 - - - +
160A GLN* 1.3 62.6 - - - +
162A MET* 3.2 13.0 + - - +
163A LYS* 3.1 44.3 + - - +
166A GLU* 5.6 1.6 - - - +
276A GLN* 3.1 24.1 + - - +
279A GLN* 6.0 0.7 - - - +
280A GLN* 2.9 33.4 + - - +
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Residues in contact with GLN 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLN 2.8 12.6 + - - +
157A ASP* 3.0 14.8 - - - +
159A GLU* 1.3 75.0 - - - +
161A LYS* 1.3 58.8 + - + +
163A LYS* 2.9 48.3 + - - +
164A VAL* 3.1 26.3 + - - +
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Residues in contact with LYS 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASP* 2.9 21.9 + - + +
158A LEU* 3.2 9.4 + - + +
160A GLN* 1.3 75.7 - - + +
162A MET* 1.3 60.2 + - - +
164A VAL* 3.9 9.1 - - - +
165A VAL* 3.2 23.7 + - - +
213A MET* 5.5 2.7 - - - +
216A SER* 2.8 30.9 + - - -
217A ILE* 3.7 22.0 - - + +
220A GLU* 2.7 39.7 + - - +
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Residues in contact with MET 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 2.8 25.8 + - + +
159A GLU* 3.4 15.9 - - - +
160A GLN 3.1 0.4 - - - -
161A LYS* 1.3 73.4 - - - +
163A LYS* 1.3 66.1 + - - +
165A VAL* 3.2 7.2 - - + +
166A GLU* 3.0 31.8 + - - +
217A ILE* 4.0 20.4 - - + -
280A GLN* 4.0 25.6 - - + +
283A LYS* 3.8 34.1 - - + -
284A LEU* 3.7 35.2 - - + -
287A LEU* 3.9 12.3 - - + -
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Residues in contact with LYS 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLU* 3.1 38.4 + - - +
160A GLN* 2.9 29.7 + - - +
162A MET* 1.3 75.7 - - - +
164A VAL* 1.3 63.3 + - + +
166A GLU* 3.3 12.6 + - - +
167A ASN* 3.0 34.0 + - - +
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Residues in contact with VAL 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLN* 3.1 28.8 + - - +
161A LYS* 3.9 9.6 - - - +
163A LYS* 1.3 78.5 - - + +
165A VAL* 1.3 57.8 + - - +
167A ASN* 3.3 5.3 + - - +
168A LEU* 3.0 29.0 + - + +
213A MET* 3.5 29.8 - - + -
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Residues in contact with VAL 165 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LYS 3.2 13.4 + - - +
162A MET* 3.2 20.0 - - + +
164A VAL* 1.3 79.7 - - - +
166A GLU* 1.3 61.8 + - - +
168A LEU* 4.5 0.7 - - - -
169A GLN* 3.0 28.8 + - - +
210A LEU* 3.6 25.7 - - + +
213A MET* 3.7 31.6 - - + -
214A ARG* 4.6 12.3 - - + +
217A ILE* 4.0 13.5 - - + -
284A LEU* 5.4 1.6 - - + -
287A LEU* 4.0 22.2 - - + +
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Residues in contact with GLU 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLU* 5.6 1.4 - - - +
162A MET* 3.0 28.1 + - + +
163A LYS* 3.6 11.0 - - - +
164A VAL 3.2 0.2 - - - -
165A VAL* 1.3 75.4 - - - +
167A ASN* 1.3 62.9 + - - +
169A GLN* 2.9 8.8 + - - +
170A ASP* 2.8 37.0 + - - +
283A LYS* 3.2 39.9 + - + +
287A LEU* 4.1 25.1 - - + +
290A LYS* 5.8 0.5 + - - -
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Residues in contact with ASN 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LYS* 3.0 24.2 + - - +
164A VAL* 3.8 5.0 - - - +
166A GLU* 1.3 77.6 - - - +
168A LEU* 1.3 59.3 + - - +
170A ASP* 3.1 17.9 + - - +
171A ASP* 2.8 39.4 + - - +
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Residues in contact with LEU 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A VAL* 3.0 17.6 + - + +
165A VAL* 4.0 4.7 - - - +
167A ASN* 1.3 76.4 - - - +
169A GLN* 1.3 57.2 + - - +
171A ASP* 3.4 8.0 + - + +
172A PHE* 2.8 31.1 + - - +
206A MET* 4.1 36.6 - - + +
209A ALA* 3.8 21.5 - - + -
210A LEU* 4.0 19.7 - - + +
213A MET* 3.7 32.3 - - + -
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Residues in contact with GLN 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A VAL* 3.0 15.8 + - - +
166A GLU* 2.9 11.5 + - - +
168A LEU* 1.3 77.1 - - - +
170A ASP* 1.3 58.7 + - - +
172A PHE* 3.3 5.5 + - + +
173A ASP* 2.8 33.0 + - - +
210A LEU* 4.1 17.4 - - + +
214A ARG* 2.8 25.2 + - - -
287A LEU* 3.2 43.1 + - + +
290A LYS* 3.6 23.4 - - - +
291A VAL* 3.7 24.1 - - + +
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Residues in contact with ASP 170 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A GLU* 2.8 21.5 + - - +
167A ASN* 3.4 21.1 + - - +
169A GLN* 1.3 76.3 - - - +
171A ASP* 1.3 68.4 + - - +
173A ASP* 3.1 7.6 + - - +
174A PHE* 2.9 26.0 + - - +
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Residues in contact with ASP 171 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASN* 2.8 27.7 + - - +
168A LEU* 3.6 11.1 - - - +
170A ASP* 1.3 78.9 - - - +
172A PHE* 1.3 62.9 + - - +
174A PHE* 4.0 4.3 - - - +
175A ASN* 3.0 32.9 + - - +
206A MET* 3.9 18.2 - - + +
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Residues in contact with PHE 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU 2.8 19.0 + - - +
169A GLN 3.5 6.1 - - - +
171A ASP* 1.3 77.4 - - - +
173A ASP* 1.3 61.0 + - - +
175A ASN* 3.5 0.4 + - - -
176A TYR* 2.9 52.4 + + + +
203A LEU* 3.5 45.6 - - + +
206A MET* 3.9 20.8 - - + -
207A LEU* 4.1 25.4 - - + -
210A LEU* 4.2 17.7 - - + -
291A VAL* 4.4 27.4 - - + -
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Residues in contact with ASP 173 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A GLN* 2.8 17.6 + - - +
170A ASP* 3.3 8.7 - - - +
172A PHE* 1.3 78.7 - - - +
174A PHE* 1.3 60.8 + - - +
176A TYR* 3.4 5.5 + - - +
177A LYS* 2.9 63.1 + - - +
290A LYS* 5.0 7.6 - - - +
291A VAL* 3.8 24.3 - - - +
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Residues in contact with PHE 174 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ASP 2.9 15.4 + - - +
171A ASP* 4.0 5.4 - - - +
173A ASP* 1.3 76.0 - - - +
175A ASN* 1.3 72.8 + - - +
177A LYS* 3.2 10.9 + - + +
178A THR* 2.8 51.4 + - + -
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Residues in contact with ASN 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ASP* 3.0 19.9 + - - +
172A PHE* 4.4 0.2 - - - -
174A PHE* 1.3 88.8 - - - +
176A TYR* 1.3 58.4 + - - +
178A THR* 3.4 6.7 + - - +
179A LEU* 2.8 30.8 + - - +
202A GLN* 3.5 21.9 + - - +
203A LEU* 3.6 18.1 - - + +
206A MET* 3.2 34.2 - - - +
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Residues in contact with TYR 176 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A PHE* 2.9 42.7 + + + +
173A ASP* 3.5 7.4 - - - +
175A ASN* 1.3 73.8 - - - +
177A LYS* 1.3 72.8 + - - +
179A LEU* 3.2 1.7 + - - +
180A LYS* 3.0 57.5 + - + +
203A LEU* 3.6 23.5 - - + +
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Residues in contact with LYS 177 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 2.9 40.7 + - - +
174A PHE* 3.3 14.4 - - + +
176A TYR* 1.3 82.5 - - - +
178A THR* 1.3 58.8 + - - +
180A LYS* 3.2 3.7 + - - +
181A SER* 2.9 39.4 + - - +
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Residues in contact with THR 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PHE* 2.8 49.3 + - + -
175A ASN* 3.5 6.3 - - - +
177A LYS* 1.3 74.6 - - - +
179A LEU* 1.3 64.2 + - + +
181A SER* 3.4 23.8 - - - +
182A GLN* 3.7 16.2 + - - +
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN 2.8 19.3 + - - +
176A TYR 3.8 3.6 - - - +
177A LYS 3.2 0.2 - - - -
178A THR* 1.3 74.3 - - + +
180A LYS* 1.3 66.2 + - - +
182A GLN* 3.3 35.6 - - - +
183A GLY* 3.4 7.3 + - - -
195A VAL* 4.3 18.9 - - + +
196A THR* 4.8 1.1 - - - +
199A LYS* 3.9 26.5 - - + +
200A MET* 3.6 38.1 - - + +
203A LEU* 3.6 25.6 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il