Contacts of the helix formed by residues 127 - 157 (chain B) in PDB entry 3A68
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 GLY 127 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP* 5.0 0.7 - - - -
123B HIS* 2.9 21.4 + - - -
125B ASP 3.5 1.6 - - - -
126B LYS* 1.3 83.3 - - - +
128B ASP* 1.3 67.1 + - - -
129B ALA 3.4 2.2 + - - -
130B LEU 3.5 0.8 + - - -
131B HIS* 3.1 18.7 + - - +
193B LYS* 3.8 18.7 - - - +
197B VAL* 6.5 0.2 - - - -
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TYR* 3.8 24.2 + - + +
70B PHE* 3.7 10.0 - - + -
75B VAL* 3.6 15.4 - - - +
77B LEU* 3.9 1.2 - - - +
121B PHE 3.4 22.5 - - - +
122B ASP* 4.1 14.0 + - - +
127B GLY* 1.3 71.4 - - - -
129B ALA* 1.3 77.7 + - - +
131B HIS* 3.3 1.4 + - - +
132B ALA* 2.9 27.2 + - - +
197B VAL* 5.0 0.2 - - - +
190G ARG* 3.2 39.6 + - - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 4.1 5.2 - - - -
77B LEU* 4.2 0.7 - - + -
80B LEU* 3.5 32.3 - - + +
127B GLY 3.4 0.8 - - - -
128B ASP* 1.3 85.0 + - - +
130B LEU* 1.3 62.5 + - - +
132B ALA* 3.5 2.1 + - - +
133B MET* 3.1 26.2 + - - +
188B LEU* 3.7 16.6 - - + +
197B VAL* 3.7 28.3 - - + -
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 3.5 36.1 - - + +
127B GLY 3.5 1.6 + - - -
128B ASP 3.4 0.2 - - - -
129B ALA* 1.3 75.1 - - - +
131B HIS* 1.3 67.6 + - - +
133B MET* 3.3 0.9 + - - -
134B GLU* 2.9 52.1 + - + +
185B VAL* 3.9 32.8 - - + +
188B LEU* 4.0 20.5 - - + +
189B ARG* 3.9 25.1 - - + +
197B VAL* 5.8 2.4 - - + +
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Residues in contact with HIS 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 5.7 2.4 - - - +
120B ASP 5.6 0.6 + - - -
121B PHE* 3.4 25.5 - - - +
122B ASP 3.9 12.4 + - - -
123B HIS* 3.6 32.8 - + + -
126B LYS* 4.1 14.2 - - + +
127B GLY 3.1 19.3 + - - +
128B ASP 3.7 3.4 - - - +
130B LEU* 1.3 77.5 - - - +
132B ALA* 1.3 57.2 + - - +
134B GLU* 3.3 2.9 + - - +
135B LEU* 2.9 53.1 + - + +
25E LEU* 3.8 24.0 - - + +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B MET* 3.6 11.2 - - - +
70B PHE* 3.4 41.5 - - + -
84B PHE* 4.3 10.5 - - + -
121B PHE* 4.5 9.6 - - + -
128B ASP 2.9 8.0 + - - +
129B ALA 3.9 2.0 - - - +
131B HIS* 1.3 76.8 - - - +
133B MET* 1.3 58.6 + - - +
135B LEU* 3.2 11.1 + - - +
136B ALA* 2.8 29.2 + - - +
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Residues in contact with MET 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 3.4 33.4 - - + -
83B PHE* 4.2 16.8 - - + -
84B PHE* 4.3 11.2 - - + -
129B ALA 3.1 16.7 + - - +
130B LEU* 3.9 3.1 - - - +
132B ALA* 1.3 75.8 - - - +
134B GLU* 1.3 58.9 + - - +
136B ALA* 3.3 3.3 + - - -
137B LEU* 2.9 24.6 + - - +
181B ILE* 3.4 23.5 - - + +
184B TYR* 3.6 50.3 - - + -
185B VAL* 3.7 17.0 - - + +
188B LEU* 4.0 11.0 - - + -
200B PHE* 4.7 0.9 - - + -
204B LEU* 4.5 2.5 - - + -
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 3.0 36.6 + - - +
130B LEU* 2.9 39.2 + - + +
131B HIS* 3.7 4.3 - - - +
133B MET* 1.3 73.0 - - - +
135B LEU* 1.3 66.2 + - - +
137B LEU* 3.3 5.7 + - - +
138B SER* 3.0 26.3 + - - -
185B VAL* 4.0 15.9 - - + -
189B ARG* 2.8 35.3 + - - +
25E LEU* 3.7 13.6 - - + +
28E VAL* 4.1 17.1 - - + +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B MET* 3.8 9.6 - - + -
118B LEU* 4.7 12.3 - - + -
121B PHE* 3.8 29.4 - - + -
131B HIS* 2.9 42.8 + - + +
132B ALA 3.5 7.2 - - - +
134B GLU* 1.3 77.1 - - - +
136B ALA* 1.3 56.7 + - - +
138B SER* 3.2 3.7 + - - -
139B LEU* 2.9 29.2 + - - +
18E PHE* 5.2 8.1 - - + -
21E VAL* 3.7 25.6 - - + +
25E LEU* 3.5 31.2 - - + -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 3.9 27.8 + - + +
66B MET* 4.0 5.3 - - - +
83B PHE* 5.6 0.2 - - + -
84B PHE* 4.2 12.6 - - + -
132B ALA 2.8 16.9 + - - +
133B MET* 3.5 9.4 - - - +
135B LEU* 1.3 75.7 - - - +
137B LEU* 1.3 61.6 + - - +
139B LEU* 3.2 7.8 + - - +
140B GLU* 2.9 27.5 + - - +
181B ILE* 4.3 11.9 - - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B MET 2.9 17.3 + - - +
134B GLU* 3.5 6.3 - - - +
136B ALA* 1.3 75.5 - - - +
138B SER* 1.3 63.2 + - - +
140B GLU* 3.2 2.9 + - + -
141B LYS* 3.0 36.0 + - + +
178B ILE* 3.9 26.9 - - + +
181B ILE* 3.6 14.1 - - + +
182B SER* 3.4 30.3 - - - +
185B VAL* 4.4 13.2 - - + -
28E VAL* 4.4 18.6 - - + -
36E LEU* 3.9 23.6 - - + +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU 3.0 12.9 + - - -
135B LEU* 3.6 8.3 - - - -
137B LEU* 1.3 76.5 - - - +
139B LEU* 1.3 59.1 + - - +
141B LYS* 3.4 4.6 + - - -
142B LEU* 3.0 20.3 + - - +
21E VAL* 4.0 19.7 - - - -
24E GLU* 2.8 35.0 + - - +
25E LEU* 3.2 28.3 + - - +
28E VAL* 5.3 3.5 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 4.6 11.2 - - - +
59B VAL* 3.7 39.5 - - + +
62B VAL* 3.7 35.4 - - + -
63B TYR* 4.8 8.3 - - + +
66B MET* 5.7 0.7 - - + -
135B LEU 2.9 16.0 + - - +
136B ALA* 3.6 7.2 - - - +
137B LEU 3.2 0.4 - - - -
138B SER* 1.3 74.5 - - - +
140B GLU* 1.3 59.8 + - + +
142B LEU* 3.3 12.2 + - + +
143B THR* 2.9 30.8 + - - +
18E PHE* 5.8 2.7 - - + -
21E VAL* 4.4 20.6 - - + +
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 4.3 5.3 - - - +
63B TYR* 2.5 31.1 + - - +
91B GLU* 3.9 14.5 - - - +
136B ALA 2.9 21.0 + - - +
137B LEU* 3.8 4.7 - - - +
139B LEU* 1.3 74.1 - - - +
141B LYS* 1.3 62.4 + - - +
143B THR* 3.3 6.8 + - - +
144B ASN* 2.9 17.3 + - - +
174B GLN* 2.7 52.1 + - - +
177B ALA* 4.6 11.6 - - + +
178B ILE* 3.9 15.2 - - + +
181B ILE* 3.3 23.6 - - + +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.0 35.6 + - + +
138B SER* 3.7 6.7 - - - +
140B GLU* 1.3 78.1 - - - +
142B LEU* 1.3 56.8 + - - +
144B ASN* 3.2 1.2 + - - +
145B GLU* 3.0 17.5 + - - +
178B ILE* 4.2 9.0 - - + -
24E GLU* 3.8 16.2 - - - +
27E LEU 5.8 0.8 + - - -
28E VAL* 5.8 1.2 - - - +
29E PRO* 4.9 10.3 - - - +
35E SER 5.5 0.2 + - - -
36E LEU 2.7 29.3 + - - -
37E ALA 3.7 15.9 - - - -
38E ARG 3.6 15.9 + - - -
39E GLN* 3.0 45.9 + - + +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER 3.0 15.6 + - - +
139B LEU* 3.6 11.4 - - + +
140B GLU 3.3 0.2 - - - -
141B LYS* 1.3 73.1 - - - +
143B THR* 1.3 63.9 + - - +
145B GLU* 3.3 19.9 + - - +
146B LYS* 3.0 32.4 + - - +
20E GLU* 4.0 40.8 - - + +
21E VAL* 3.6 33.0 - - + -
24E GLU* 3.1 36.8 - - + +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLN* 4.0 4.7 - - - +
55B VAL* 4.2 8.2 - - + +
56B GLU* 3.8 24.7 - - - +
59B VAL* 3.4 23.6 - - - +
139B LEU* 2.9 15.8 + - - +
140B GLU* 3.5 12.4 + - - +
142B LEU* 1.3 72.7 - - - +
144B ASN* 1.3 60.8 + - - +
146B LYS* 3.1 7.1 + - - +
147B LEU* 2.8 37.0 + - + +
174B GLN* 3.8 16.4 - - - +
214B CA 4.4 7.2 - - - -
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Residues in contact with ASN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU 2.9 14.0 + - - +
141B LYS 3.2 10.1 + - - +
143B THR* 1.3 76.0 - - - +
145B GLU* 1.3 62.9 + - - +
147B LEU* 3.2 3.6 + - - +
148B LEU* 2.9 44.8 + - - +
171B LEU* 4.4 13.3 - - - +
174B GLN* 3.4 29.4 - - + +
175B VAL* 5.2 10.4 + - - +
178B ILE* 3.9 8.3 - - + +
39E GLN* 2.9 31.7 + - - +
40E LYS* 5.5 0.2 - - - +
105E ARG* 6.2 0.2 - - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS 3.0 8.4 + - - +
142B LEU* 3.5 22.5 - - - +
143B THR 3.3 0.2 - - - -
144B ASN* 1.3 74.9 - - - +
146B LYS* 1.3 64.2 + - + +
148B LEU* 3.3 3.7 + - - +
149B ASN* 2.9 37.0 + - - +
20E GLU* 5.4 1.7 - - - +
24E GLU* 3.0 25.3 - - - +
39E GLN* 3.4 20.1 + - - +
40E LYS* 3.7 26.3 + - - +
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 5.2 10.4 + - + +
52B GLN* 3.5 23.4 + - - +
55B VAL* 4.2 25.5 - - + +
142B LEU* 3.0 20.7 + - - +
143B THR 3.1 6.7 + - - +
145B GLU* 1.3 78.2 - - - +
147B LEU* 1.3 59.3 + - - +
149B ASN* 3.3 20.0 + - + +
150B LEU* 2.9 23.6 + - - +
20E GLU* 3.7 28.7 + - - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLN* 3.3 31.6 - - + +
56B GLU* 3.8 7.9 - - - +
98B LEU* 5.5 0.2 - - + -
143B THR* 2.8 30.8 + - + +
144B ASN* 3.7 4.7 - - - +
146B LYS* 1.3 72.9 - - - +
148B LEU* 1.3 58.8 + - - +
150B LEU* 3.2 8.5 + - + +
151B HIS* 2.9 27.2 + - - +
166B VAL* 3.9 11.1 - - + +
170B TYR* 3.8 36.1 - - + +
171B LEU* 3.8 15.0 - - + -
174B GLN* 3.9 34.8 - - + +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 2.9 38.3 + - - +
145B GLU* 3.7 4.7 - - - +
147B LEU* 1.3 75.4 - - - +
149B ASN* 1.3 60.6 + - - +
151B HIS* 3.3 5.1 + - - +
152B SER* 2.9 31.8 + - - +
171B LEU* 3.9 21.3 - - + -
40E LYS* 3.7 33.2 - - + -
160E VAL* 4.0 33.5 - - + +
161E GLN* 5.2 4.9 - - + +
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Residues in contact with ASN 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B GLU* 2.9 26.4 + - - +
146B LYS* 3.4 26.2 - - + +
148B LEU* 1.3 75.4 - - - +
150B LEU* 1.3 64.9 + - - +
152B SER* 3.1 10.0 + - - -
153B VAL* 3.0 28.2 + - + +
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 3.6 36.8 - - + +
49B VAL* 4.0 14.4 - - + +
52B GLN* 3.9 32.1 - - + +
98B LEU* 4.4 11.9 - - + -
146B LYS 2.9 13.5 + - - +
147B LEU* 3.2 10.5 + - + +
149B ASN* 1.3 76.0 - - - +
151B HIS* 1.3 63.6 + - - +
153B VAL* 3.1 6.3 + - + +
154B ALA* 3.0 21.3 + - - +
162B LEU* 4.3 11.2 - - + -
166B VAL* 3.6 29.4 - - + -
170B TYR* 6.5 0.2 - - + -
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Residues in contact with HIS 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU 2.9 13.2 + - - +
148B LEU* 3.5 12.8 - - + +
149B ASN 3.2 0.2 - - - -
150B LEU* 1.3 77.5 - - - +
152B SER* 1.3 58.4 + - - +
154B ALA* 3.3 6.4 + - - +
155B THR* 3.0 49.2 + - + +
163B ALA* 3.2 26.5 + - + +
166B VAL* 4.2 9.4 - - + -
167B GLU* 2.7 34.6 + - + -
171B LEU* 4.1 7.0 - - + -
160E VAL* 3.5 36.1 - - + +
----------------------------------------------------------
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU 2.9 17.1 + - - -
149B ASN* 3.1 14.4 + - - -
151B HIS* 1.3 74.9 + - - +
153B VAL* 1.3 65.5 + - - +
155B THR* 3.1 9.3 + - - -
156B LYS* 2.9 27.5 + - - +
160E VAL* 6.2 0.3 - - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU* 3.8 40.4 - - + +
45B SER* 4.1 7.6 - - - -
48B ALA* 3.9 18.6 - - + -
149B ASN* 3.0 18.9 + - + +
150B LEU* 3.1 8.0 + - + +
152B SER* 1.3 76.2 - - - +
154B ALA* 1.3 64.9 + - - +
156B LYS* 3.7 7.4 - - + +
157B ASN* 2.9 44.8 + - - +
162B LEU* 5.7 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B SER* 4.6 1.3 - - - -
150B LEU 3.0 11.6 + - - +
151B HIS* 3.5 9.6 - - - +
153B VAL* 1.3 78.6 - - - +
155B THR* 1.3 61.4 + - - +
157B ASN 3.2 5.4 + - - -
159B ASP* 2.8 36.7 + - - +
162B LEU* 3.6 36.8 - - + +
163B ALA* 3.7 19.3 - - - +
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Residues in contact with THR 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B HIS* 3.0 42.7 + - + +
152B SER* 3.1 13.3 + - - -
154B ALA* 1.3 74.6 - - - +
156B LYS* 1.3 66.3 + - - +
158B GLY* 2.9 16.1 + - - +
159B ASP 4.8 2.2 - - - +
160B VAL* 6.1 0.4 - - - +
163B ALA* 3.9 11.9 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU* 2.7 43.4 + - - +
152B SER 2.9 18.5 + - - +
153B VAL* 3.7 5.2 - - + +
155B THR* 1.3 78.4 + - - +
157B ASN* 1.3 67.2 + - - +
158B GLY 3.2 3.3 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS 5.8 0.2 - - - +
42B VAL* 3.6 35.9 - - + +
44B GLU* 2.9 28.5 + - - +
45B SER* 3.7 12.2 + - - +
153B VAL* 2.9 31.0 + - - +
154B ALA 3.2 2.9 + - - +
155B THR 3.1 0.6 - - - -
156B LYS* 1.3 88.3 - - - +
158B GLY* 1.3 58.5 + - - +
159B ASP* 3.1 7.3 + - + +
----------------------------------------------------------
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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