Contacts of the helix formed by residues 133 - 160 (chain B) in PDB entry 5YWB
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 PRO 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 1.3 91.3 - - + +
134B LYS* 1.3 93.9 + - + +
136B LEU* 4.1 10.0 + - + +
137B ILE* 3.3 26.5 + - - +
194B ARG* 3.5 29.4 - - + +
195B TYR* 4.5 6.9 - - - +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 3.4 8.2 - - + +
133B PRO* 1.3 115.0 - - + +
135B LEU* 1.3 72.3 + - + +
136B LEU 3.1 2.0 - - - -
137B ILE* 3.1 17.9 + - + +
138B ALA* 2.9 20.3 + - - +
195B TYR 5.5 2.6 + - - -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 3.7 38.8 - - + -
123B TYR* 4.1 14.9 - - + -
126B ASN* 4.8 10.8 - - + +
127B ILE* 3.5 35.8 - - + +
130B SER* 5.8 0.2 - - - +
132B PHE* 3.6 37.8 - - + +
134B LYS* 1.3 78.5 - - + +
136B LEU* 1.3 58.1 + - - +
138B ALA* 3.0 12.5 + - + +
139B LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PHE* 4.8 13.5 - - + -
124B TYR* 4.5 15.9 - - + -
127B ILE* 3.6 32.3 - - + -
132B PHE 3.3 23.8 - - - +
133B PRO* 4.2 9.9 - - + +
134B LYS 3.1 0.4 - - - -
135B LEU* 1.3 73.0 - - - +
137B ILE* 1.3 61.2 + - + +
139B LEU* 2.9 23.9 + - + +
140B LEU* 2.9 14.7 + - - +
186B GLU* 4.0 16.1 - - - +
189B VAL* 4.0 27.4 - - + -
190B ILE* 6.5 0.2 - - - -
193B ARG* 5.2 6.3 - - - -
194B ARG 6.5 0.4 - - - -
195B TYR* 6.1 7.9 - - + -
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PRO 3.3 21.1 - - - +
134B LYS* 3.1 19.0 + - + +
136B LEU* 1.3 75.6 - - + +
138B ALA* 1.3 62.8 + - - +
140B LEU* 3.0 26.4 + - + -
141B ILE* 3.0 16.5 + - + +
195B TYR* 3.8 29.8 - - + +
196B ILE* 4.8 11.0 - - + -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 5.7 3.1 - - - -
39B LEU* 4.3 9.5 - - + +
42B ILE* 5.3 9.6 - - + -
46B ILE* 6.3 0.7 - - + -
123B TYR* 4.7 16.2 - - + +
134B LYS 2.9 12.6 + - - +
135B LEU* 3.0 19.0 + - + +
137B ILE* 1.3 76.7 - - - +
139B LEU* 1.3 60.9 + - - +
141B ILE* 3.9 5.6 + - - +
142B TYR* 3.9 13.7 + - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.3 22.4 - - + -
74B ARG* 4.8 2.2 - - - +
120B SER* 3.9 38.1 - - - +
123B TYR* 4.3 24.9 - - + -
124B TYR* 4.5 17.5 - - + -
127B ILE* 4.8 8.3 - - + -
135B LEU 2.9 9.5 + - - +
136B LEU* 2.9 12.2 + - + +
138B ALA* 1.3 75.1 - - - +
140B LEU* 1.3 65.8 + - - +
142B TYR* 3.1 9.0 + - + +
143B TRP* 3.0 31.1 + - - +
186B GLU* 3.6 22.9 - - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU 2.9 13.0 + - - +
137B ILE* 3.0 20.1 + - + +
139B LEU* 1.3 76.4 - - - +
141B ILE* 1.3 64.3 + - - +
143B TRP* 3.2 7.0 + - - +
144B THR* 3.0 29.5 + - + -
183B LEU* 3.7 27.4 - - + +
186B GLU* 4.1 23.1 - - + -
187B VAL* 4.8 11.4 - - + -
190B ILE* 5.5 15.9 - - + -
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B PHE* 5.2 12.3 - - + -
137B ILE* 3.0 16.5 + - + +
138B ALA* 4.2 6.7 - - - +
139B LEU 3.2 0.2 - - - -
140B LEU* 1.3 77.5 - - - +
142B TYR* 1.3 61.9 + - - +
144B THR* 2.5 23.4 + - - -
145B LEU* 3.0 20.8 + - + +
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO* 3.5 33.2 - - + -
36B HIS* 2.8 41.9 + + - -
38B PHE* 5.4 8.4 - + + -
39B LEU* 3.5 41.1 - - + -
113B ALA* 4.7 0.7 + - - -
116B ALA* 3.2 17.4 - - + +
117B ALA* 4.9 1.0 + - - -
120B SER* 5.6 0.9 - - - -
138B ALA 3.9 3.0 + - - +
139B LEU* 3.1 11.2 + - + +
141B ILE* 1.3 79.0 - - - +
143B TRP* 1.3 101.4 + + - +
145B LEU* 3.3 6.7 + - - -
146B ALA* 2.9 25.6 + - + +
179B TYR* 3.5 10.6 + + - -
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Residues in contact with TRP 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 4.1 4.3 - - - +
78B THR* 6.0 1.6 - - - -
81B LEU* 4.3 9.6 - - + -
117B ALA* 5.8 3.6 - - - -
120B SER* 3.8 26.2 - - - -
139B LEU* 3.0 29.7 + - + +
140B LEU* 3.2 3.8 + - - +
142B TYR* 1.3 95.7 - + - +
144B THR* 1.3 63.6 + - - +
146B ALA* 3.8 1.6 - - - +
147B PHE* 3.0 24.3 + - - +
179B TYR* 3.3 47.6 - + - -
182B LEU* 3.6 43.9 - - + +
183B LEU* 3.5 27.1 - - + +
186B GLU* 3.2 42.4 + - + +
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.0 25.2 + - + +
141B ILE* 2.5 26.3 + - - -
143B TRP* 1.3 74.2 - - - +
145B LEU* 1.3 67.9 + - - +
147B PHE* 3.3 7.4 + - - +
148B ILE* 3.0 31.8 + - - +
183B LEU* 3.6 20.0 - - + -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PRO* 4.2 21.8 - - + -
38B PHE* 5.3 15.0 - - + -
141B ILE* 3.0 22.4 + - + +
142B TYR* 3.9 5.8 - - - +
144B THR* 1.3 81.0 - - - +
146B ALA* 1.3 63.1 + - - +
148B ILE* 3.2 21.2 + - + +
149B THR* 3.0 28.5 + - + +
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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
----------------------------------------------------------
35B PRO* 4.6 5.3 - - + +
36B HIS* 5.0 5.2 - - + -
142B TYR* 2.9 28.6 + - + +
143B TRP 3.8 0.4 - - - +
145B LEU* 1.3 76.5 - - - +
147B PHE* 1.3 63.2 + - - +
149B THR* 2.7 22.3 + - - -
150B LYS* 3.0 18.2 + - + +
179B TYR* 3.3 37.9 - - + +
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Residues in contact with PHE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TRP 3.0 14.0 + - - +
144B THR* 3.5 9.6 - - - +
146B ALA* 1.3 77.2 - - - +
148B ILE* 1.3 69.2 + - + +
150B LYS* 3.3 5.8 + - - +
151B THR* 2.9 42.1 + - + -
176B VAL* 3.7 38.6 - - + -
179B TYR* 4.7 8.2 - - + -
180B GLY* 4.5 10.1 - - - -
183B LEU* 3.8 23.1 - - + -
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B THR* 3.0 20.4 + - - +
145B LEU* 3.2 27.1 + - + +
147B PHE* 1.3 83.3 - - + +
149B THR* 1.3 65.9 + - + +
151B THR* 3.2 6.8 + - - -
152B ILE* 3.0 37.2 + - + +
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 6.2 0.2 - - - -
31B LEU* 3.4 38.6 - - + +
32B ASN* 3.4 35.7 + - - +
35B PRO* 4.1 11.9 - - + +
145B LEU* 3.0 12.5 + - + +
146B ALA* 2.7 26.7 + - - -
148B ILE* 1.3 79.5 - - + +
150B LYS* 1.3 60.8 + - - +
152B ILE* 3.2 9.5 + - - +
153B LYS* 3.0 18.0 + - - +
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASN* 3.4 25.3 - - - +
36B HIS* 5.6 5.9 + - - -
88B GLU* 3.6 8.7 + - - -
109B PRO* 5.4 6.9 - - - +
146B ALA* 3.0 22.7 + - - +
147B PHE* 3.8 4.9 - - - +
149B THR* 1.3 77.1 + - - +
151B THR* 1.3 58.3 + - - +
153B LYS* 3.2 18.3 + - + +
154B PHE* 2.9 27.9 + - - +
172B THR* 5.3 6.9 - - - +
175B LEU* 2.7 41.8 - - + +
176B VAL* 3.3 27.8 - - + +
179B TYR* 4.4 25.1 - - + -
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 2.9 38.6 + - + -
148B ILE* 3.5 10.5 - - - -
150B LYS* 1.3 77.0 - - - +
152B ILE* 1.3 69.1 + - + +
154B PHE* 3.2 8.3 + - + +
155B VAL* 3.0 34.4 + - + +
176B VAL* 4.5 6.2 - - - +
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Residues in contact with ILE 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.6 24.5 - - + -
31B LEU* 4.9 15.5 - - + -
148B ILE* 3.0 34.1 + - + +
149B THR* 3.6 7.6 - - - +
151B THR* 1.3 82.9 - - + +
153B LYS* 1.3 65.4 + - - +
155B VAL* 3.3 6.6 + - + +
156B LYS* 3.0 38.7 + - + +
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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
----------------------------------------------------------
25B GLY 4.6 1.8 + - - -
28B VAL* 3.5 21.0 - - + +
29B ASP* 3.5 31.4 - - - +
32B ASN* 3.4 39.0 - - - +
109B PRO* 5.0 6.7 - - - +
149B THR 3.0 7.7 + - - +
150B LYS* 3.2 22.0 + - + +
152B ILE* 1.3 77.4 - - - +
154B PHE* 1.3 62.3 + - - +
156B LYS* 3.4 3.7 + - - +
157B PHE* 2.9 24.9 + - - +
168B ARG* 5.7 8.2 - - - +
172B THR* 5.1 17.9 - - + -
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Residues in contact with PHE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LYS 2.9 14.0 + - - +
151B THR* 3.2 12.5 + - + +
153B LYS* 1.3 75.0 - - - +
155B VAL* 1.3 65.9 + - + +
157B PHE* 3.3 5.8 + - - +
158B TYR* 2.9 41.4 + + + +
169B PHE* 3.4 43.7 - + - -
172B THR* 5.1 11.8 - - - +
173B GLY* 5.1 18.4 - - - -
176B VAL* 5.1 8.3 - - + -
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B THR* 3.0 31.8 + - + +
152B ILE* 3.8 6.7 - - + +
154B PHE* 1.3 83.9 - - + +
156B LYS* 1.3 77.6 + - + +
158B TYR* 3.0 16.4 + - - +
159B ASP* 3.0 24.1 + - - +
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 5.0 13.9 - - + -
152B ILE* 3.0 31.0 + - + +
153B LYS* 4.0 4.5 - - - +
155B VAL* 1.3 87.4 - - + +
157B PHE* 1.3 58.7 + - - +
159B ASP* 3.7 15.4 + - + +
160B HIS* 2.9 34.0 + - + -
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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
----------------------------------------------------------
153B LYS 2.9 17.8 + - - +
154B PHE* 3.6 7.0 - - - +
155B VAL 3.1 0.2 - - - -
156B LYS* 1.3 75.9 - - - +
158B TYR* 1.3 66.9 + - - +
160B HIS* 3.0 34.7 + - + +
167B LEU 5.8 1.8 - - - -
168B ARG* 3.8 29.2 - - + -
169B PHE* 3.7 48.0 - + + -
172B THR* 5.8 4.5 - - + +
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PHE* 2.9 37.7 + + + +
155B VAL* 3.0 7.6 + - - +
157B PHE* 1.3 79.3 - - - +
159B ASP* 1.3 72.6 + - - +
160B HIS 3.1 5.9 + - - -
169B PHE* 5.2 11.2 - + + -
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B VAL* 3.0 26.5 + - - +
156B LYS* 4.0 17.6 + - + +
157B PHE 3.2 0.4 - - - -
158B TYR* 1.3 86.6 - - - +
160B HIS* 1.3 66.3 + - + +
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LYS* 2.9 29.9 + - + +
157B PHE* 3.0 30.2 + - + +
158B TYR 3.9 5.2 - - - -
159B ASP* 1.3 87.6 - - + +
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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