Contacts of the helix formed by residues 131 - 158 (chain A) in PDB entry 5J8E
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 GLN 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS 3.8 4.8 + - - +
48A ILE 2.9 25.8 - - - +
50A PRO* 4.9 6.4 - - - +
129A CYS* 3.1 4.6 - - - -
130A GLU* 1.3 81.0 - - + +
132A LYS* 1.3 62.9 + - - +
133A GLN 3.2 2.9 - - - -
134A GLU* 2.9 39.1 + - + +
135A TYR* 3.3 32.1 + - + -
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLN* 5.9 6.5 - - - +
126A ALA 3.4 12.1 - - - +
127A VAL* 3.3 34.3 - - + +
128A ASN* 4.2 12.3 + - - +
129A CYS 3.1 18.4 + - - +
130A GLU* 3.2 5.0 + - - +
131A GLN* 1.3 77.6 - - - +
133A GLN* 1.3 69.5 + - + +
135A TYR* 3.2 1.0 + - - +
136A ILE* 2.8 35.3 + - + +
157B LEU* 5.4 3.5 - - + +
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Residues in contact with GLN 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU 5.0 1.2 + - - +
131A GLN 3.1 1.4 + - - -
132A LYS* 1.3 88.4 - - + +
134A GLU* 1.3 57.9 + - - +
136A ILE* 4.5 11.7 - - - +
137A GLN* 2.9 30.5 + - - +
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Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLN* 2.9 38.6 + - + +
133A GLN* 1.3 79.4 - - - +
135A TYR* 1.3 80.3 + - + +
137A GLN* 3.4 6.2 + - - +
138A ALA* 3.0 28.4 + - + +
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Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 5.1 3.7 + + + +
23A PHE* 3.6 32.5 - + - -
47A LYS* 3.0 29.1 + - - +
48A ILE* 3.5 12.7 - - + -
126A ALA* 3.5 38.4 - - + +
127A VAL* 4.9 3.4 - - + +
129A CYS* 3.9 7.6 - - - -
131A GLN* 3.3 46.5 + - + -
132A LYS 3.2 3.2 + - - +
134A GLU* 1.3 96.5 + - + +
136A ILE* 1.3 61.6 + - - +
138A ALA* 3.3 9.7 + - + +
139A ILE* 3.0 35.7 + - + +
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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
----------------------------------------------------------
127A VAL* 3.6 31.9 - - + +
132A LYS* 2.8 21.9 + - + +
133A GLN* 4.0 15.3 - - - +
135A TYR* 1.3 74.1 - - - +
137A GLN* 1.3 66.2 + - - +
139A ILE* 3.2 8.7 + - + +
140A MET* 3.0 30.9 + - + +
153B ALA* 4.4 11.4 - - + -
157B LEU* 4.0 25.1 - - + -
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Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLN 2.9 19.1 + - - +
134A GLU* 3.6 6.3 - - - +
136A ILE* 1.3 77.7 - - - +
138A ALA* 1.3 59.5 + - - +
140A MET* 3.3 10.2 + - - +
141A MET* 2.9 68.8 + - + +
144A GLU* 4.8 3.6 + - - -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 6.0 2.5 - - - +
22A THR* 5.1 14.3 - - - +
134A GLU* 3.0 19.0 + - + +
135A TYR* 3.7 13.0 - - + +
136A ILE 3.2 0.4 - - - -
137A GLN* 1.3 76.7 - - - +
139A ILE* 1.3 62.9 + - + +
141A MET* 3.4 10.7 + - - +
142A MET* 3.3 22.8 + - - +
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Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TRP* 3.5 36.1 - - + +
123A LEU* 4.2 8.7 - - + -
127A VAL* 4.1 16.6 - - + -
135A TYR* 3.0 19.6 + - + +
136A ILE* 3.2 11.0 + - + +
138A ALA* 1.3 77.4 - - - +
140A MET* 1.3 60.6 + - - +
142A MET* 3.0 30.6 + - - +
143A GLU* 3.6 5.2 + - - +
146B VAL* 4.7 0.7 - - + +
149B VAL* 4.2 12.3 - - + -
150B VAL* 3.9 28.3 - - + -
153B ALA* 4.0 24.2 - - + -
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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
----------------------------------------------------------
136A ILE* 3.0 27.2 + - + +
137A GLN* 3.9 12.8 - - - +
139A ILE* 1.3 79.1 - - + +
141A MET* 1.3 58.6 + - - +
143A GLU* 3.0 44.5 + - + +
144A GLU* 3.3 10.0 + - - +
150B VAL* 4.4 25.6 - - + -
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Residues in contact with MET 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN* 2.9 43.0 + - + +
138A ALA* 3.6 9.9 - - - +
139A ILE 3.2 0.2 - - - -
140A MET* 1.3 73.4 - - - +
142A MET* 1.3 57.7 + - - +
144A GLU* 3.3 44.0 + - + +
145A SER* 2.9 30.6 + - - +
11B GLU* 4.6 13.2 - - + +
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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
----------------------------------------------------------
18A THR* 3.4 42.4 - - - +
19A TRP* 3.7 24.7 - - + +
22A THR* 3.8 22.0 - - + -
138A ALA 3.3 14.0 + - - +
139A ILE* 3.0 15.0 + - - +
141A MET* 1.3 76.7 - - - +
143A GLU* 1.3 60.8 + - - +
145A SER* 3.5 6.0 + - - -
146A VAL* 3.2 29.5 + - - +
146B VAL* 4.0 21.1 - - + -
149B VAL* 4.1 20.2 - - + -
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE 3.6 1.8 + - - +
140A MET* 3.0 29.9 + - + +
142A MET* 1.3 76.5 - - - +
144A GLU* 1.3 66.0 + - + +
146A VAL* 3.4 3.1 + - - +
147A GLN* 3.0 44.7 + - - +
143B GLU* 4.2 1.0 - - - +
146B VAL* 3.6 16.3 - - + +
147B GLN* 2.5 44.3 + - - +
150B VAL* 3.6 20.7 - - + +
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN* 4.8 2.9 + - - -
140A MET 3.3 11.5 + - - +
141A MET* 3.4 39.8 - - + +
143A GLU* 1.3 77.1 - - + +
145A SER* 1.3 64.0 + - - +
147A GLN* 3.3 17.5 + - - +
148A HIS* 3.3 28.2 + - + +
11B GLU* 4.7 5.0 - - - +
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Residues in contact with SER 145 (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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141A MET* 2.9 18.2 + - - +
142A MET* 3.7 8.1 - - - -
143A GLU 3.2 0.2 - - - -
144A GLU* 1.3 78.2 - - - +
146A VAL* 1.3 63.8 + - - +
148A HIS* 3.1 18.0 + - - +
149A VAL* 3.4 9.6 + - - +
14B GLU 4.9 0.2 - - - -
15B SER* 3.0 37.3 + - - -
18B THR* 4.2 13.3 + - - +
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Residues in contact with VAL 146 (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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142A MET 3.2 16.4 + - - +
143A GLU* 3.9 4.9 - - - +
144A GLU 3.4 0.2 - - - -
145A SER* 1.3 78.1 - - - +
147A GLN* 1.3 65.1 + - - +
149A VAL* 3.0 11.7 + - + +
150A VAL* 3.0 23.3 + - + +
18B THR* 5.6 1.8 - - - +
139B ILE 4.8 0.2 - - - +
142B MET* 4.0 24.9 - - + +
143B GLU* 3.6 43.3 - - + +
146B VAL* 3.4 24.0 - - + -
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Residues in contact with GLN 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLU* 3.0 32.2 - - - +
144A GLU* 3.6 9.9 - - - +
145A SER 3.2 0.8 - - - -
146A VAL* 1.3 77.0 - - - +
148A HIS* 1.3 61.3 + - + +
150A VAL* 3.8 7.4 - - - +
151A MET* 2.8 30.7 + - - +
143B GLU* 2.5 42.2 + - - +
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Residues in contact with HIS 148 (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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144A GLU* 3.6 25.6 + - + +
145A SER* 3.1 9.4 + - - +
147A GLN* 1.3 76.5 - - + +
149A VAL* 1.3 56.4 + - - +
151A MET* 3.5 5.6 + - - +
152A THR* 2.8 38.7 + - - -
11B GLU* 3.0 36.9 + - + -
12B LEU* 4.1 16.7 - - + +
15B SER* 3.4 26.9 - - - +
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER 3.8 11.4 - - - +
146A VAL* 3.0 11.1 + - + +
148A HIS* 1.3 77.2 - - - +
150A VAL* 1.3 57.6 + - - +
152A THR* 3.2 8.0 + - - -
153A ALA* 3.0 26.7 + - - +
15B SER* 3.4 30.5 - - - +
16B LEU* 4.3 4.9 - - + -
18B THR* 4.2 7.0 - - - +
19B TRP* 4.0 30.1 - - + -
123B LEU* 4.1 10.1 - - + +
139B ILE* 4.1 12.3 - - + -
142B MET* 4.1 19.7 - - + -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.0 20.5 + - + +
147A GLN* 3.8 8.3 - - - +
149A VAL* 1.3 77.0 - - - +
151A MET* 1.3 57.3 + - - +
153A ALA* 3.2 4.5 + - + +
154A ILE* 2.9 46.6 + - + +
139B ILE* 3.8 24.9 - - + -
140B MET* 4.4 16.4 - - + -
143B GLU* 3.5 32.1 - - + +
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Residues in contact with MET 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A GLN 2.8 17.1 + - - +
148A HIS* 4.0 6.1 - - - +
150A VAL* 1.3 75.8 - - - +
152A THR* 1.3 58.2 + - - +
154A ILE* 3.3 17.8 + - - -
155A GLN* 2.9 61.8 + - + +
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Residues in contact with THR 152 (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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148A HIS 2.8 23.2 + - - -
149A VAL* 3.2 7.2 + - - -
151A MET* 1.3 77.5 - - - +
153A ALA* 1.3 56.3 + - - +
155A GLN* 3.2 7.1 + - + +
156A GLU* 2.9 34.6 + - + +
12B LEU* 3.6 20.4 - - - +
16B LEU* 4.2 6.5 - - + +
120B GLN* 3.9 37.5 + - + +
123B LEU* 4.3 16.8 - - + -
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Residues in contact with ALA 153 (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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149A VAL 3.0 12.7 + - - +
150A VAL* 3.2 11.2 + - - +
152A THR* 1.3 77.2 - - - +
154A ILE* 1.3 63.0 + - + +
156A GLU* 3.1 3.6 + - - +
157A LEU* 3.1 29.5 + - + +
123B LEU* 3.5 23.5 - - + +
127B VAL* 4.2 6.8 - - + +
136B ILE* 4.5 8.3 - - + -
139B ILE* 3.9 20.2 - - + -
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Residues in contact with ILE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 2.9 36.8 + - + +
151A MET* 3.7 22.4 - - - +
153A ALA* 1.3 75.8 - - + +
155A GLN* 1.3 63.8 + - - +
157A LEU* 3.0 22.7 + - + +
158A MET* 3.0 34.6 + - + +
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Residues in contact with GLN 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A MET* 2.9 50.0 + - + +
152A THR* 3.2 6.7 + - - +
154A ILE* 1.3 77.5 - - - +
156A GLU* 1.3 62.9 + - + +
157A LEU 3.3 0.3 + - - -
158A MET* 3.5 36.9 + - - +
96B ASN* 2.9 20.1 + - - +
120B GLN* 6.3 0.7 - - - +
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A THR* 2.9 27.4 + - + +
153A ALA* 3.1 6.0 + - - +
155A GLN* 1.3 77.3 - - - +
157A LEU* 1.3 58.5 + - - +
93B GLN* 3.1 18.5 + - - -
94B GLN 4.8 1.0 - - - +
95B ILE* 3.7 5.2 - - - +
96B ASN* 3.2 49.6 + - - +
120B GLN* 3.8 33.9 + - - +
121B LEU* 5.0 1.8 + - - +
123B LEU* 4.5 1.3 - - + -
124B GLY* 3.4 31.7 - - - +
127B VAL* 3.9 8.1 - - + -
128B ASN* 3.3 8.7 + - - -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ALA* 3.1 20.1 + - + +
154A ILE* 3.0 14.1 + - + +
156A GLU* 1.3 79.1 - - - +
158A MET* 1.3 65.0 + - + +
93B GLN* 3.5 20.7 + - - +
127B VAL* 3.3 36.3 - - + +
128B ASN* 4.3 7.4 - - - +
132B LYS* 5.6 3.6 - - + +
136B ILE* 4.1 22.4 - - + -
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Residues in contact with MET 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 3.0 36.0 + - + +
155A GLN* 3.5 30.9 + - - +
156A GLU 4.3 0.9 - - - +
157A LEU* 1.3 83.3 - - + +
93B GLN* 4.4 5.0 + - - -
94B GLN 5.5 0.9 - - - +
96B ASN* 3.5 24.6 + - - +
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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