Contacts of the helix formed by residues 133 - 160 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F PHE* 1.3 91.4 - - + +
134F LYS* 1.3 94.1 + - + +
136F LEU* 4.1 10.7 + - + +
137F ILE* 3.3 26.7 + - - +
194F ARG* 3.5 28.0 - - + +
195F TYR* 4.5 7.2 - - - +
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Residues in contact with LYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F PHE* 3.4 7.7 - - + +
133F PRO* 1.3 113.8 - - + +
135F LEU* 1.3 71.8 + - + +
136F LEU 3.1 1.3 - - - -
137F ILE* 3.1 18.9 + - + +
138F ALA* 2.9 20.5 + - - +
195F TYR 5.5 2.6 + - - -
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F ILE* 3.7 38.8 - - + -
123F TYR* 4.1 15.6 - - + -
126F ASN* 4.8 10.1 - - + +
127F ILE* 3.5 35.2 - - + +
132F PHE* 3.6 40.2 - - + +
134F LYS* 1.3 79.0 - - + +
136F LEU* 1.3 57.9 + - - +
138F ALA* 3.0 12.6 + - + +
139F LEU* 2.9 27.9 + - - +
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PHE* 4.8 12.8 - - + -
74F ARG* 6.0 0.2 - - - +
124F TYR* 4.5 15.9 - - + +
127F ILE* 3.6 32.3 - - + -
132F PHE 3.3 24.0 - - - +
133F PRO* 4.2 10.1 - - + +
134F LYS 3.1 0.2 - - - -
135F LEU* 1.3 73.8 - - - +
137F ILE* 1.3 61.3 + - + +
139F LEU* 2.9 24.1 + - + +
140F LEU* 2.9 14.0 + - - +
186F GLU* 4.0 15.4 - - - +
189F VAL* 4.0 27.6 - - + -
193F ARG* 5.2 6.5 - - - -
194F ARG 6.5 0.4 - - - -
195F TYR* 6.1 7.9 - - + +
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Residues in contact with ILE 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F PRO 3.3 21.1 - - - +
134F LYS* 3.1 19.2 + - + +
136F LEU* 1.3 75.7 - - + +
138F ALA* 1.3 63.4 + - - +
140F LEU* 3.0 26.6 + - + -
141F ILE* 3.0 17.1 + - + +
195F TYR* 3.8 29.8 - - + +
196F ILE* 4.8 11.2 - - + -
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F PHE* 5.7 3.1 - - - -
39F LEU* 4.3 8.6 - - + +
42F ILE* 5.3 9.9 - - + -
46F ILE* 6.3 0.4 - - + -
123F TYR* 4.7 16.6 - - + +
134F LYS 2.9 12.0 + - - +
135F LEU* 3.1 18.6 - - + +
137F ILE* 1.3 77.6 - - - +
139F LEU* 1.3 61.1 + - - +
141F ILE* 3.9 5.0 + - - +
142F TYR* 3.9 14.2 + - - +
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Residues in contact with LEU 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F LEU* 4.3 22.4 - - + -
74F ARG* 4.8 2.7 - - - +
120F SER* 3.9 39.0 - - - +
123F TYR* 4.3 24.7 - - + -
124F TYR* 4.5 18.4 - - + -
127F ILE* 4.8 7.6 - - + -
135F LEU 2.9 10.1 + - - +
136F LEU* 2.9 12.2 + - + +
138F ALA* 1.3 74.9 - - - +
140F LEU* 1.3 66.3 + - - +
142F TYR* 3.1 8.0 + - + +
143F TRP* 3.0 31.2 + - - +
186F GLU* 3.6 22.4 - - - +
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F LEU 2.9 12.8 + - - +
137F ILE* 3.0 19.9 + - + +
139F LEU* 1.3 76.6 - - - +
141F ILE* 1.3 63.5 + - - +
143F TRP* 3.2 6.9 + - - +
144F THR* 3.0 29.3 + - + -
183F LEU* 3.7 27.1 - - + +
186F GLU* 4.1 23.5 - - + -
187F VAL* 4.8 11.0 - - + -
190F ILE* 5.5 16.4 - - + -
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F PHE* 5.2 12.3 - - + -
137F ILE* 3.0 16.7 + - + +
138F ALA* 4.2 7.2 - - - +
139F LEU 3.2 0.2 - - - -
140F LEU* 1.3 77.1 - - - +
142F TYR* 1.3 62.6 + - - +
144F THR* 2.5 23.6 + - - -
145F LEU* 3.0 20.7 + - + +
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Residues in contact with TYR 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F PRO* 3.5 33.2 - - + -
36F HIS* 2.8 42.4 + + - -
38F PHE* 5.4 8.4 - + + -
39F LEU* 3.5 40.2 - - + -
113F ALA* 4.7 0.5 + - - -
116F ALA* 3.2 18.2 - - + +
117F ALA* 4.9 0.9 + - - -
120F SER* 5.6 0.9 - - - -
138F ALA 3.9 2.8 + - - +
139F LEU* 3.1 11.6 + - + +
141F ILE* 1.3 79.2 - - - +
143F TRP* 1.3 101.8 + + - +
145F LEU* 3.3 7.3 + - - +
146F ALA* 2.9 25.6 + - + +
179F TYR* 3.5 9.8 + - - -
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Residues in contact with TRP 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ARG* 4.1 4.6 - - + +
78F THR* 6.0 2.0 - - - -
81F LEU* 4.3 10.1 - - + -
117F ALA* 5.8 4.5 - - + -
120F SER* 3.8 25.8 - - - -
139F LEU* 3.0 32.3 + - + +
140F LEU* 3.2 4.2 + - - +
142F TYR* 1.3 96.9 - + - +
144F THR* 1.3 63.0 + - - +
146F ALA* 3.3 2.0 + - - +
147F PHE* 3.0 24.1 + - - +
179F TYR* 3.3 46.4 - + - -
182F LEU* 3.6 43.9 - - + +
183F LEU* 3.5 27.0 - - + +
186F GLU* 3.2 41.2 + - + +
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Residues in contact with THR 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F LEU* 3.0 24.7 + - + +
141F ILE* 2.5 26.5 + - - -
143F TRP* 1.3 74.6 - - - +
145F LEU* 1.3 68.2 + - - +
147F PHE* 3.3 7.5 + - - +
148F ILE* 3.0 31.7 + - - +
183F LEU* 3.6 20.0 - - + -
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Residues in contact with LEU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F PRO* 4.2 22.2 - - + -
38F PHE* 5.3 14.8 - - + -
141F ILE* 3.0 23.5 + - + +
142F TYR* 3.9 4.9 - - - +
144F THR* 1.3 81.0 - - - +
146F ALA* 1.3 62.6 + - - +
148F ILE* 3.2 22.4 + - + +
149F THR* 3.0 27.3 + - - +
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Residues in contact with ALA 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F PRO* 4.6 6.1 - - + +
36F HIS* 5.0 5.8 - - + -
142F TYR* 2.9 28.4 + - + +
145F LEU* 1.3 76.9 - - - +
147F PHE* 1.3 63.1 + - - +
149F THR* 2.7 22.5 + - - -
150F LYS* 3.0 17.4 + - + +
179F TYR* 3.3 36.8 - - + +
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Residues in contact with PHE 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F TRP 3.0 14.6 + - - +
144F THR* 3.5 9.4 - - - +
145F LEU 3.2 0.2 - - - -
146F ALA* 1.3 76.8 - - - +
148F ILE* 1.3 69.2 + - + +
150F LYS* 3.3 4.8 + - - +
151F THR* 2.9 42.9 + - + -
176F VAL* 3.7 38.4 - - + -
179F TYR* 4.7 8.2 - - + -
180F GLY* 4.5 10.1 - - - -
183F LEU* 3.8 22.7 - - + -
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Residues in contact with ILE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F THR* 3.0 20.2 + - - +
145F LEU* 3.5 26.5 - - + +
147F PHE* 1.3 83.8 - - + +
149F THR* 1.3 66.3 + - + +
151F THR* 3.2 6.7 + - - -
152F ILE* 3.0 36.8 + - + +
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Residues in contact with THR 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F LEU* 3.4 39.7 - - + +
32F ASN* 3.4 35.0 + - - +
35F PRO* 4.1 12.5 - - + +
145F LEU 3.0 11.5 + - - +
146F ALA* 2.7 27.0 + - - -
148F ILE* 1.3 78.5 - - + +
150F LYS* 1.3 60.9 + - - +
152F ILE* 3.2 8.4 + - - +
153F LYS* 3.0 19.4 + - - +
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Residues in contact with LYS 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F ASN* 3.4 25.0 - - - +
36F HIS* 5.6 5.7 + - - -
88F GLU* 3.6 8.5 + - - -
109F PRO* 5.4 6.9 - - - +
146F ALA* 3.0 23.0 + - - +
147F PHE* 3.8 5.8 - - - +
149F THR* 1.3 77.1 + - - +
151F THR* 1.3 56.6 + - - +
153F LYS* 3.2 18.1 + - + +
154F PHE* 2.9 28.4 + - - +
172F THR* 5.3 6.8 - - - +
175F LEU* 2.7 41.8 - - + +
176F VAL* 3.3 27.7 - - + +
179F TYR* 4.4 24.2 - - + -
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Residues in contact with THR 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F PHE* 2.9 38.5 + - + -
148F ILE* 3.5 10.8 - - - -
150F LYS* 1.3 76.6 - - - +
152F ILE* 1.3 68.3 + - + +
154F PHE* 3.2 8.4 + - + +
155F VAL* 3.0 33.8 + - + +
176F VAL* 4.5 5.0 - - - +
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Residues in contact with ILE 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 3.6 24.9 - - + -
31F LEU* 4.9 14.8 - - + -
148F ILE* 3.0 32.9 + - + +
149F THR* 3.6 8.5 - - - +
151F THR* 1.3 84.2 - - + +
153F LYS* 1.3 65.8 + - - +
155F VAL* 3.3 6.9 + - + +
156F LYS* 3.0 36.4 + - + +
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Residues in contact with LYS 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F GLY 4.6 1.8 + - - -
28F VAL* 3.5 21.2 - - + +
29F ASP* 3.5 31.4 - - - +
32F ASN* 3.4 39.3 - - - +
109F PRO* 5.0 7.2 - - - +
149F THR 3.0 8.4 + - - +
150F LYS* 3.2 22.9 + - + +
152F ILE* 1.3 77.4 - - - +
154F PHE* 1.3 61.5 + - - +
156F LYS* 3.4 3.8 + - - +
157F PHE* 2.9 25.3 + - - +
168F ARG* 5.7 8.9 - - - +
172F THR* 5.1 17.7 - - + -
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Residues in contact with PHE 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F LYS 2.9 14.0 + - - +
151F THR* 3.2 12.1 + - + +
153F LYS* 1.3 76.2 - - - +
155F VAL* 1.3 66.1 + - + +
157F PHE* 3.3 6.2 + - + +
158F TYR* 2.9 41.5 + + + +
169F PHE* 3.4 42.1 - + - -
172F THR* 5.1 11.2 - - - +
173F GLY* 5.1 17.3 - - - -
176F VAL* 5.1 7.9 - - + -
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Residues in contact with VAL 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F THR* 3.0 31.0 + - + +
152F ILE* 3.8 7.2 - - + +
154F PHE* 1.3 83.6 - - + +
156F LYS* 1.3 78.0 + - + +
158F TYR* 3.0 17.4 + - + +
159F ASP* 3.0 23.0 + - - +
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Residues in contact with LYS 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F VAL* 5.0 12.8 - - + -
152F ILE* 3.0 32.4 + - + +
153F LYS* 4.0 4.3 - - - +
155F VAL* 1.3 86.2 - - + +
157F PHE* 1.3 59.2 + - - +
159F ASP* 3.7 15.5 + - + +
160F HIS* 2.9 33.7 + - + +
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Residues in contact with PHE 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F LYS 2.9 17.2 + - - +
154F PHE* 3.6 7.4 - - + +
155F VAL 3.1 0.2 - - - -
156F LYS* 1.3 76.3 - - - +
158F TYR* 1.3 65.7 + - - +
160F HIS* 3.0 36.0 + - + +
167F LEU 5.8 2.0 - - - -
168F ARG* 3.8 28.5 - - + -
169F PHE* 3.7 46.9 - + + -
172F THR* 5.8 4.3 - - + +
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Residues in contact with TYR 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F PHE* 2.9 37.3 + + + +
155F VAL* 3.0 7.8 + - + +
157F PHE* 1.3 78.8 - - - +
159F ASP* 1.3 72.6 + - - +
160F HIS 3.1 5.4 + - - -
169F PHE* 5.2 11.4 - + + -
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Residues in contact with ASP 159 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155F VAL* 3.0 27.0 + - - +
156F LYS* 4.0 18.6 + - + +
157F PHE 3.2 0.4 - - - -
158F TYR* 1.3 86.4 - - - +
160F HIS* 1.3 67.7 + - + +
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Residues in contact with HIS 160 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F LYS* 2.9 28.6 + - + +
157F PHE* 3.0 31.6 + - + +
158F TYR 3.9 4.7 - - - -
159F ASP* 1.3 87.8 - - + +
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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