Contacts of the helix formed by residues 133 - 160 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H PHE* 1.3 92.9 - - + +
134H LYS* 1.3 93.7 + - + +
136H LEU* 4.1 10.5 + - + +
137H ILE* 3.3 26.7 + - - +
194H ARG* 3.5 28.0 - - + +
195H TYR* 4.5 7.0 - - - +
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Residues in contact with LYS 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132H PHE* 3.4 7.9 - - + +
133H PRO* 1.3 114.6 - - + +
135H LEU* 1.3 71.2 + - + +
136H LEU 3.1 1.8 - - - -
137H ILE* 3.1 18.2 + - + +
138H ALA* 2.9 20.7 + - - +
195H TYR 5.5 2.2 + - - -
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Residues in contact with LEU 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46H ILE* 3.7 39.7 - - + -
123H TYR* 4.1 15.2 - - + -
126H ASN* 4.8 10.8 - - + +
127H ILE* 3.5 36.3 - - + +
132H PHE* 3.6 38.7 - - + +
133H PRO 3.7 0.2 - - - -
134H LYS* 1.3 79.6 - - + +
136H LEU* 1.3 57.0 + - - +
138H ALA* 3.0 12.7 + - + +
139H LEU* 2.9 27.5 + - - +
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Residues in contact with LEU 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H PHE* 4.8 14.1 - - + -
124H TYR* 4.5 15.7 - - + -
127H ILE* 3.6 31.4 - - + -
132H PHE 3.3 24.9 - - - +
133H PRO* 4.2 9.4 - - + +
134H LYS 3.1 0.6 - - - -
135H LEU* 1.3 72.7 - - - +
137H ILE* 1.3 60.7 + - + +
139H LEU* 2.9 24.1 + - + +
140H LEU* 2.9 13.7 + - - +
186H GLU* 4.0 17.0 - - - +
189H VAL* 4.0 26.2 - - + -
190H ILE* 6.5 0.2 - - - -
193H ARG* 5.2 6.5 - - - -
194H ARG 6.5 0.4 - - - -
195H TYR* 6.1 8.3 - - + -
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Residues in contact with ILE 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H PRO 3.3 19.7 - - - +
134H LYS* 3.1 17.6 + - + +
136H LEU* 1.3 75.5 - - + +
138H ALA* 1.3 62.4 + - - +
140H LEU* 3.0 25.8 + - + -
141H ILE* 3.0 17.4 + - + +
195H TYR* 3.8 29.2 - - + +
196H ILE* 4.8 11.2 - - + -
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Residues in contact with ALA 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PHE* 5.7 2.9 - - - -
39H LEU* 4.3 9.4 - - + +
42H ILE* 5.3 10.1 - - + -
46H ILE* 6.3 0.4 - - + -
123H TYR* 4.7 17.3 - - + +
134H LYS 2.9 12.9 + - - +
135H LEU* 3.0 18.4 + - + +
137H ILE* 1.3 76.8 - - - +
139H LEU* 1.3 61.5 + - - +
141H ILE* 3.9 5.8 + - - +
142H TYR* 3.9 14.6 + - - +
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Residues in contact with LEU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU* 4.3 23.3 - - + -
74H ARG* 4.8 2.2 - - - +
120H SER* 3.9 37.9 - - - +
123H TYR* 4.3 24.9 - - + -
124H TYR* 4.5 17.5 - - + -
127H ILE* 4.8 7.9 - - + -
135H LEU 2.9 11.0 + - - +
136H LEU* 2.9 12.4 + - + +
138H ALA* 1.3 75.5 - - - +
140H LEU* 1.3 67.2 + - - +
142H TYR* 3.1 8.4 + - + +
143H TRP* 3.0 31.3 + - - +
186H GLU* 3.6 22.2 - - - +
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Residues in contact with LEU 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H LEU 2.9 11.9 + - - +
137H ILE* 3.0 20.8 + - + +
139H LEU* 1.3 76.0 - - - +
141H ILE* 1.3 64.1 + - - +
143H TRP* 3.2 7.9 + - - +
144H THR* 3.0 30.0 + - + -
183H LEU* 3.7 26.5 - - + +
186H GLU* 4.1 24.7 - - + +
187H VAL* 4.8 10.1 - - + -
190H ILE* 5.5 15.9 - - + -
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Residues in contact with ILE 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H PHE* 5.2 12.3 - - + -
137H ILE* 3.0 16.5 + - + +
138H ALA* 4.2 6.1 - - - +
139H LEU 3.2 0.2 - - - -
140H LEU* 1.3 77.4 - - - +
142H TYR* 1.3 61.0 + - - +
144H THR* 2.5 23.4 + - - -
145H LEU* 3.0 20.4 + - + +
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Residues in contact with TYR 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PRO* 3.5 33.9 - - + -
36H HIS* 2.8 43.1 + + - -
38H PHE* 5.4 8.2 - + + -
39H LEU* 3.5 40.8 - - + -
113H ALA* 4.7 0.7 + - - -
116H ALA* 3.2 17.9 - - + +
117H ALA* 4.9 1.0 + - - -
120H SER* 5.6 0.9 - - - -
138H ALA 3.9 3.0 + - - +
139H LEU* 3.1 10.7 + - + +
141H ILE* 1.3 78.3 - - - +
143H TRP* 1.3 100.2 + + - +
145H LEU* 3.3 7.3 + - - +
146H ALA* 2.9 26.5 + - + +
179H TYR* 3.5 10.0 + + - -
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Residues in contact with TRP 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ARG* 4.1 4.5 - - + +
78H THR* 6.0 1.6 - - - -
81H LEU* 4.3 10.5 - - + -
117H ALA* 5.8 3.1 - - - -
120H SER* 3.8 25.8 - - - -
139H LEU* 3.0 30.3 + - + +
140H LEU* 3.2 3.8 + - - +
142H TYR* 1.3 97.0 - + - +
144H THR* 1.3 62.8 + - - +
146H ALA* 3.3 2.0 + - - +
147H PHE* 3.0 24.1 + - - +
179H TYR* 3.3 47.1 - + - -
182H LEU* 3.6 43.2 - - + +
183H LEU* 3.5 27.0 - - + +
186H GLU* 3.2 41.6 + - + +
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Residues in contact with THR 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LEU* 3.0 24.8 + - + +
141H ILE* 2.5 26.4 + - - -
143H TRP* 1.3 74.8 - - - +
145H LEU* 1.3 68.1 + - - +
147H PHE* 3.3 7.2 + - - +
148H ILE* 3.0 31.6 + - - +
183H LEU* 3.6 20.2 - - + -
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Residues in contact with LEU 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PRO* 4.2 22.2 - - + -
38H PHE* 5.3 14.8 - - + -
141H ILE* 3.0 24.1 + - + +
142H TYR* 3.9 5.6 - - - +
144H THR* 1.3 81.2 - - - +
146H ALA* 1.3 63.2 + - - +
148H ILE* 3.2 21.2 + - + +
149H THR* 3.0 28.4 + - + +
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Residues in contact with ALA 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H PRO* 4.6 5.7 - - + +
36H HIS* 5.0 5.2 - - + -
142H TYR* 2.9 28.6 + - + +
143H TRP 3.8 0.4 - - - +
145H LEU* 1.3 76.9 - - - +
147H PHE* 1.3 61.6 - - - +
149H THR* 2.7 22.9 + - - -
150H LYS* 3.0 17.7 + - + +
179H TYR* 3.3 38.4 - - + +
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Residues in contact with PHE 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143H TRP 3.0 14.3 + - - +
144H THR* 3.5 9.0 - - - +
145H LEU 3.2 0.2 - - - -
146H ALA* 1.3 77.4 - - - +
148H ILE* 1.3 68.4 + - + +
150H LYS* 3.3 5.3 + - - +
151H THR* 2.9 43.7 + - + -
176H VAL* 3.7 37.7 - - + -
179H TYR* 4.7 7.9 - - + -
180H GLY* 4.5 10.3 - - - -
183H LEU* 3.8 22.2 - - + -
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Residues in contact with ILE 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H THR* 3.0 19.7 + - - +
145H LEU* 3.2 26.2 + - + +
147H PHE* 1.3 82.3 - - + +
149H THR* 1.3 68.1 + - + +
151H THR* 3.2 6.6 + - - -
152H ILE* 3.0 37.3 + - + +
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Residues in contact with THR 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H LEU* 3.4 38.4 - - + +
32H ASN* 3.4 35.2 + - - +
35H PRO* 4.1 11.9 - - + +
145H LEU* 3.0 11.8 + - + +
146H ALA* 2.7 26.3 + - - -
148H ILE* 1.3 79.1 - - + +
150H LYS* 1.3 60.9 + - - +
152H ILE* 3.2 9.6 + - - +
153H LYS* 3.0 18.9 + - - +
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Residues in contact with LYS 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ASN* 3.4 23.8 - - - +
36H HIS* 5.6 5.7 + - - -
88H GLU* 3.6 8.7 + - - -
109H PRO* 5.4 7.1 - - - +
146H ALA* 3.0 22.8 + - - +
147H PHE* 3.8 5.8 - - - +
149H THR* 1.3 77.3 + - - +
151H THR* 1.3 58.5 + - - +
153H LYS* 3.2 18.7 + - + +
154H PHE* 2.9 28.6 + - - +
172H THR* 5.3 6.5 - - - +
175H LEU* 2.7 41.1 - - + +
176H VAL* 3.3 26.8 - - + +
179H TYR* 4.4 24.2 - - + -
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Residues in contact with THR 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H PHE* 2.9 39.4 + - + -
148H ILE* 3.5 11.0 - - - -
150H LYS* 1.3 76.6 - - - +
152H ILE* 1.3 70.2 + - + +
154H PHE* 3.2 8.9 + - + +
155H VAL* 3.0 33.7 + - + +
176H VAL* 4.5 6.1 - - - +
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Residues in contact with ILE 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 3.6 26.2 - - + -
31H LEU* 4.9 14.4 - - + -
148H ILE* 3.0 34.1 + - + +
149H THR* 3.2 8.5 + - - +
151H THR* 1.3 81.9 - - + +
153H LYS* 1.3 64.5 + - - +
155H VAL* 3.3 6.2 + - + +
156H LYS* 3.0 37.6 + - + +
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Residues in contact with LYS 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H GLY 4.6 2.0 + - - -
28H VAL* 3.5 21.2 - - + +
29H ASP* 3.5 31.6 - - - +
32H ASN* 3.4 39.5 - - - +
109H PRO* 5.0 7.0 - - - -
149H THR 3.0 8.0 + - - +
150H LYS* 3.2 21.7 + - + +
152H ILE* 1.3 77.8 - - - +
154H PHE* 1.3 61.8 + - - +
156H LYS* 3.4 3.8 + - - +
157H PHE* 2.9 24.7 + - - +
168H ARG* 5.7 9.5 - - - +
172H THR* 5.1 17.0 - - + -
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Residues in contact with PHE 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H LYS 2.9 13.2 + - - +
151H THR* 3.2 12.1 + - + +
153H LYS* 1.3 76.9 - - - +
155H VAL* 1.3 66.7 + - + +
157H PHE* 3.3 5.8 + - + +
158H TYR* 2.9 40.4 + + + +
169H PHE* 3.4 42.1 - + - -
172H THR* 5.1 11.2 - - - -
173H GLY* 5.1 17.3 - - - -
176H VAL* 5.1 8.3 - - + -
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Residues in contact with VAL 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H THR* 3.0 32.3 + - + +
152H ILE* 3.8 6.1 - - + +
154H PHE* 1.3 83.9 - - + +
156H LYS* 1.3 77.2 + - + +
158H TYR* 3.0 16.4 + - - +
159H ASP* 3.0 24.0 + - - +
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Residues in contact with LYS 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H VAL* 5.0 13.2 - - + -
152H ILE* 3.0 30.8 + - + +
153H LYS* 4.0 4.5 - - - +
155H VAL* 1.3 86.4 - - + +
157H PHE* 1.3 59.2 + - - +
159H ASP* 3.7 14.8 + - + +
160H HIS* 2.9 33.5 + - + +
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Residues in contact with PHE 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153H LYS 2.9 17.6 + - - +
154H PHE* 3.6 7.2 - - - +
155H VAL 3.1 0.2 - - - -
156H LYS* 1.3 76.9 - - - +
158H TYR* 1.3 65.2 + - - +
160H HIS* 3.0 36.1 + - + +
167H LEU 5.8 2.0 - - - -
168H ARG* 3.8 28.3 - - + -
169H PHE* 3.7 47.3 - + + -
172H THR* 5.8 4.0 - - + +
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Residues in contact with TYR 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H PHE* 2.9 37.1 + + + +
155H VAL* 3.5 7.4 - - - +
157H PHE* 1.3 78.9 - - - +
159H ASP* 1.3 73.1 + - - +
160H HIS 3.1 6.5 + - - +
169H PHE* 5.2 10.7 - + + -
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Residues in contact with ASP 159 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H VAL* 3.0 26.5 + - - +
156H LYS* 4.0 18.5 + - + +
157H PHE 3.2 0.4 - - - -
158H TYR* 1.3 85.9 - - - +
160H HIS* 1.3 66.4 + - + +
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Residues in contact with HIS 160 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H LYS* 2.9 28.9 + - + +
157H PHE* 3.0 30.7 + - + +
158H TYR 3.9 5.1 - - - +
159H ASP* 1.3 87.5 - - + +
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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