Contacts of the helix formed by residues 140 - 171 (chain A) in PDB entry 3AG2
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 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU* 4.4 13.0 - - - -
135A ASN* 5.9 0.8 - - - +
138A HIS 3.9 0.7 - - - +
139A ALA* 1.3 76.3 - - - +
141A ALA* 1.3 60.9 + - - -
142A SER 3.4 2.9 + - - -
143A VAL 4.3 0.2 + - - -
213A ARG* 2.7 32.5 + - - +
36C HIS* 3.4 21.9 - - - -
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Residues in contact with ALA 141 (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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118A VAL* 4.1 15.5 - - + -
119A GLU* 4.1 8.6 + - + +
140A GLY* 1.3 72.3 - - - -
142A SER* 1.3 65.4 + - - +
143A VAL 3.4 0.2 - - - -
144A ASP* 3.1 5.5 + - - +
145A LEU* 2.9 24.9 + - + +
32C THR* 3.8 23.6 - - + -
36C HIS* 3.7 19.8 + - + -
37C PHE* 4.2 16.4 - - + -
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Residues in contact with SER 142 (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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115A SER* 2.9 37.7 + - - +
118A VAL* 3.0 22.4 + - - +
119A GLU* 3.8 6.7 - - - +
121A GLY 3.3 28.7 + - - -
122A ALA* 3.7 2.2 - - - -
138A HIS* 5.6 0.9 - - - -
140A GLY 3.4 2.6 + - - -
141A ALA* 1.3 74.6 - - - +
143A VAL* 1.3 65.5 + - - +
145A LEU 3.2 1.2 + - - -
146A THR* 3.0 24.6 + - - -
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Residues in contact with VAL 143 (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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122A ALA* 3.9 17.7 - - + -
124A THR* 3.9 15.3 - - + -
128A VAL* 4.3 16.4 - - + -
133A ALA* 3.5 17.3 - - + +
138A HIS* 3.8 29.1 + - + +
140A GLY 4.3 0.4 + - - -
141A ALA 3.4 0.6 - - - -
142A SER* 1.3 75.3 - - - +
144A ASP* 1.3 58.3 + - - +
146A THR* 3.2 8.1 + - - -
147A ILE* 2.9 36.8 + - + +
209A LEU* 4.6 0.7 - - + -
213A ARG* 3.5 28.0 - - - +
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Residues in contact with ASP 144 (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 ALA 3.1 7.2 + - - +
143A VAL* 1.3 78.6 - - - +
145A LEU* 1.3 56.2 + - - +
147A ILE* 3.3 7.1 + - - +
148A PHE* 3.0 43.5 + - + -
210A LEU* 3.4 16.6 - - + +
213A ARG* 2.7 35.2 + - - +
214A ASN* 3.1 24.2 + - - +
32C THR* 4.9 3.1 - - + +
35C PHE* 5.1 1.8 - - + -
36C HIS* 2.5 35.7 + - + +
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Residues in contact with LEU 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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111A LEU* 3.7 36.4 - - + +
114A ALA* 3.8 13.0 - - + -
115A SER* 3.6 21.8 - - - +
118A VAL* 3.6 34.8 - - + -
141A ALA* 2.9 19.3 + - + +
142A SER 3.6 6.1 - - - +
144A ASP* 1.3 76.9 - - - +
146A THR* 1.3 56.4 + - - +
148A PHE* 3.4 4.4 + - + +
149A SER* 2.9 29.3 + - - -
29C SER* 5.4 2.9 - - - +
32C THR* 3.6 28.0 - - + +
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Residues in contact with THR 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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59A THR* 5.7 0.4 - - + +
63A PHE* 3.5 38.8 - - + -
112A LEU* 4.3 8.0 - - + +
115A SER* 3.4 17.5 + - - -
122A ALA* 3.5 15.3 - - + +
124A THR* 5.8 0.7 - - - +
128A VAL* 4.6 11.7 - - + -
142A SER 3.0 14.8 + - - -
143A VAL* 3.2 12.5 + - - -
145A LEU* 1.3 73.2 - - - +
147A ILE* 1.3 66.1 + - + +
149A SER* 3.2 7.9 + - - -
150A LEU* 3.0 26.1 + - + +
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Residues in contact with ILE 147 (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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128A VAL* 5.3 4.0 - - + -
143A VAL* 2.9 29.2 + - + +
144A ASP* 3.3 16.1 + - - +
146A THR* 1.3 74.9 - - + +
148A PHE* 1.3 60.3 + - + +
150A LEU* 3.1 11.8 + - + +
151A HIS* 2.8 48.3 + - + -
206A ILE* 3.7 29.0 - - + +
209A LEU* 4.0 22.4 - - + -
210A LEU* 3.8 39.3 - - + +
213A ARG* 4.1 0.9 - - - -
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Residues in contact with PHE 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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111A LEU* 3.8 8.3 - - + -
144A ASP* 3.0 30.2 + - + +
145A LEU* 3.8 5.8 - - + +
147A ILE* 1.3 73.8 - - + +
149A SER* 1.3 66.3 + - - +
151A HIS* 3.2 21.4 + + - +
152A LEU* 3.0 27.0 + - - +
210A LEU* 3.8 37.0 - - + -
28C THR* 3.6 37.2 - - + -
31C LEU* 3.6 35.7 - - + -
32C THR* 3.3 33.0 - - - -
35C PHE* 4.4 4.5 - + - -
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Residues in contact with SER 149 (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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68A PHE* 3.7 5.9 - - - -
108A SER* 2.6 52.3 + - - -
111A LEU* 3.8 7.3 - - - +
112A LEU* 3.7 25.7 - - - +
145A LEU 2.9 15.5 + - - -
146A THR* 3.2 11.2 + - - -
148A PHE* 1.3 78.2 - - - +
150A LEU* 1.3 63.1 + - - +
152A LEU 3.3 0.3 + - - -
153A ALA* 3.0 11.5 + - - +
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Residues in contact with LEU 150 (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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63A PHE* 3.9 30.5 - - + -
67A PHE* 3.8 43.0 - - + -
126A TRP 5.5 0.2 - - - +
128A VAL* 4.8 7.0 - - + -
146A THR* 3.0 20.0 + - + +
147A ILE* 3.4 9.9 - - + +
149A SER* 1.3 75.9 - - - +
151A HIS* 1.3 60.2 + - - +
153A ALA* 4.0 3.4 - - + +
154A GLY* 2.8 27.9 + - - -
202A LEU* 4.9 16.4 - - + +
206A ILE* 3.7 31.6 - - + +
231A TYR* 6.1 0.2 - - - +
235A PHE* 5.8 3.4 - - + -
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Residues in contact with HIS 151 (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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147A ILE* 2.8 34.5 + - + -
148A PHE* 3.2 34.9 + + + +
150A LEU* 1.3 72.5 - - - +
152A LEU* 1.3 65.2 + - + +
154A GLY* 3.2 1.8 + - - -
155A VAL* 2.9 36.0 + - + +
203A ALA* 4.5 13.7 - - + -
206A ILE* 3.7 18.4 - - + +
207A THR* 2.9 31.5 + - + -
210A LEU* 4.6 5.8 - - + -
28C THR* 5.2 1.6 - - + -
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Residues in contact with LEU 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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104A LEU* 4.1 16.8 - - + +
107A PRO* 3.9 25.6 - - + -
108A SER* 3.9 11.0 - - - +
111A LEU* 3.8 19.7 - - + -
148A PHE 3.0 16.2 + - - +
149A SER 3.9 4.5 - - - +
151A HIS* 1.3 82.8 - - + +
153A ALA* 1.3 63.1 + - - +
155A VAL* 3.3 8.3 + - + +
156A SER* 3.0 23.9 + - - -
24C ALA* 3.9 29.8 - - + -
25C LEU* 4.2 6.3 - - - +
28C THR* 3.6 26.5 - - + -
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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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67A PHE* 4.4 25.1 - - + +
68A PHE* 4.6 7.4 - - + -
105A LEU* 4.1 20.7 - - + +
108A SER* 3.6 11.3 + - - +
149A SER 3.0 16.3 + - - +
150A LEU* 4.0 5.6 - - - +
152A LEU* 1.3 75.7 - - - +
154A GLY* 1.3 62.8 + - - +
156A SER* 3.4 2.8 + - - -
157A SER* 3.1 26.3 + - - -
199A LEU* 5.1 0.4 - - - +
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Residues in contact with GLY 154 (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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67A PHE* 6.0 0.6 - - - -
150A LEU 2.8 18.1 + - - -
151A HIS* 3.6 1.8 - - - -
153A ALA* 1.3 75.6 - - - +
155A VAL* 1.3 58.6 + - - +
157A SER* 3.3 1.4 + - - -
158A ILE* 2.9 38.4 + - - +
199A LEU* 3.9 25.3 - - - +
202A LEU* 6.2 0.2 - - - -
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Residues in contact with VAL 155 (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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100A MET* 5.6 0.9 - - + -
104A LEU* 3.8 14.1 - - + -
151A HIS* 2.9 26.5 + - + +
152A LEU* 3.8 7.6 - - + +
154A GLY* 1.3 68.7 - - - +
156A SER* 1.3 68.4 + - - +
158A ILE* 3.3 8.0 + - + +
159A LEU* 2.9 48.0 + - + +
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Residues in contact with SER 156 (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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19A TYR* 4.2 3.1 + - - -
101A SER* 2.6 55.8 + - - -
104A LEU* 3.8 16.0 - - - +
105A LEU* 3.7 21.1 - - - +
152A LEU 3.0 14.5 + - - -
153A ALA 3.4 10.1 - - - -
155A VAL* 1.3 77.0 - - - +
157A SER* 1.3 57.7 + - - +
160A GLY* 3.0 12.0 + - - -
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Residues in contact with SER 157 (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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71A MET* 4.1 19.1 - - - +
75A ILE* 5.7 1.0 - - - +
105A LEU* 6.1 0.7 - - - +
153A ALA 3.1 15.4 + - - -
156A SER* 1.3 74.5 + - - +
158A ILE* 1.3 62.0 + - - +
160A GLY* 3.7 2.4 - - - +
161A ALA* 2.8 30.0 + - - +
195A LEU* 4.2 16.2 - - - +
199A LEU* 3.5 25.4 - - - -
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Residues in contact with ILE 158 (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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154A GLY* 2.9 24.5 + - - +
155A VAL* 3.9 8.1 - - + +
157A SER* 1.3 75.4 - - - +
159A LEU* 1.3 68.6 + - + +
161A ALA* 3.2 7.2 + - - +
162A ILE* 3.0 32.0 + - + +
195A LEU 4.2 7.2 - - - +
196A LEU* 4.4 5.3 - - + +
199A LEU* 3.8 30.3 - - + +
200A PRO* 3.9 22.9 - - + -
203A ALA* 5.7 3.6 - - + -
86C PHE* 5.7 1.8 - - + -
89C SER* 4.0 24.5 - - - +
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Residues in contact with LEU 159 (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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97A MET* 3.4 38.6 - - + +
100A MET* 3.6 31.6 - - + -
101A SER* 3.7 12.1 - - - +
104A LEU* 4.8 3.8 - - + -
155A VAL* 2.9 35.6 + - + +
158A ILE* 1.3 80.2 - - + +
160A GLY* 1.3 62.3 + - - +
162A ILE* 3.3 17.3 + - + +
163A ASN* 3.0 18.9 + - - +
86C PHE* 5.0 12.3 - - + -
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Residues in contact with GLY 160 (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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75A ILE* 6.1 1.6 - - - -
98A ASN* 5.8 2.5 - - - -
101A SER* 3.3 10.2 + - - -
156A SER 3.0 17.2 + - - -
157A SER* 3.7 2.7 - - - -
158A ILE 3.2 0.4 - - - -
159A LEU* 1.3 78.1 - - - +
161A ALA* 1.3 56.2 + - - +
163A ASN* 3.1 8.9 + - - +
164A PHE* 2.8 43.6 + - - -
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Residues in contact with ALA 161 (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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157A SER 2.8 18.3 + - - +
158A ILE* 3.2 6.9 + - - +
160A GLY* 1.3 76.4 - - - +
162A ILE* 1.3 57.8 + - - +
164A PHE* 5.0 0.9 - - - -
165A ILE* 2.9 37.7 + - + +
192A ALA* 3.3 40.1 - - - +
195A LEU* 4.0 11.8 - - + +
196A LEU* 4.2 10.5 - - + +
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Residues in contact with ILE 162 (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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94A PHE* 4.0 9.6 - - + -
97A MET* 4.3 7.6 - - + -
158A ILE* 3.0 22.8 + - + +
159A LEU* 3.6 17.3 - - + +
160A GLY 3.3 0.2 - - - -
161A ALA* 1.3 74.4 - - - +
163A ASN* 1.3 63.3 + - - +
165A ILE* 4.9 0.7 - - - -
166A THR* 2.8 32.1 + - - +
196A LEU* 3.6 21.1 - - + -
82C GLY* 3.7 31.2 - - - +
85C LEU* 3.9 15.7 - - + +
86C PHE* 3.7 39.7 - - + -
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Residues in contact with ASN 163 (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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92A MET* 3.7 16.8 - - + +
93A ALA* 3.5 6.9 + - - -
94A PHE* 2.9 61.2 + - - +
97A MET* 4.1 5.0 - - + +
98A ASN* 3.4 25.6 - - - +
101A SER* 5.9 0.2 + - - -
159A LEU 3.0 12.1 + - - +
160A GLY* 3.3 12.3 - - - +
162A ILE* 1.3 78.2 - - - +
164A PHE* 1.3 55.1 + - - +
166A THR* 3.9 1.2 - - - -
167A THR* 2.7 37.4 + - - -
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Residues in contact with PHE 164 (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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75A ILE* 3.5 37.2 - - + -
76A GLY* 5.2 0.4 - - - -
79A GLY* 3.4 41.1 - - - -
80A ASN* 3.5 12.8 - - - -
83A VAL* 4.0 13.9 - - + -
92A MET* 3.6 29.8 - - + -
98A ASN* 5.6 1.3 - - - -
160A GLY* 2.8 34.0 + - - +
161A ALA* 4.0 2.9 - - - +
163A ASN* 1.3 70.2 - - - +
165A ILE* 1.3 68.6 + - - +
167A THR* 3.7 0.6 - - - -
168A ILE* 2.9 31.8 + - + +
188A VAL* 3.5 26.2 - - + -
192A ALA* 4.1 11.9 - - + -
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Residues in contact with ILE 165 (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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161A ALA 2.9 24.1 + - - +
162A ILE* 4.9 0.2 - - - -
164A PHE* 1.3 77.8 - - - +
166A THR* 1.3 61.9 + - - +
168A ILE* 4.0 0.3 - - - +
169A ILE* 3.0 37.7 + - + +
189A MET* 4.3 15.7 - - + +
192A ALA* 3.6 19.3 - - + +
193A VAL* 3.8 37.9 - - + +
196A LEU* 4.2 10.8 - - + -
81C TYR* 6.3 1.3 - - + -
85C LEU* 3.7 38.6 - - + -
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Residues in contact with THR 166 (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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93A ALA* 3.6 19.1 - - + -
94A PHE* 3.6 16.7 - - + -
162A ILE 2.8 23.4 + - - -
163A ASN 3.9 1.3 - - - -
165A ILE* 1.3 76.5 - - - +
167A THR* 1.3 58.5 + - - +
169A ILE* 3.9 1.9 - - - +
170A ASN* 2.8 37.6 + - + +
78C GLY* 3.3 35.0 - - - +
81C TYR* 3.8 11.2 - - + +
82C GLY* 3.7 7.1 + - - -
85C LEU* 3.5 13.5 - - - +
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Residues in contact with THR 167 (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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83A VAL* 4.5 9.0 - - + -
84A PRO* 5.0 2.5 - - + -
87A ILE* 3.8 18.5 - - + +
89A ALA* 5.0 1.1 - - + -
91A ASP 4.1 18.6 - - - +
92A MET* 3.7 18.6 - - - +
93A ALA* 2.9 21.2 + - - -
163A ASN* 2.7 22.7 + - - -
164A PHE* 3.7 4.3 - - - -
166A THR* 1.3 77.3 - - - +
168A ILE* 1.3 59.6 - - - +
171A MET* 2.9 42.8 + - + +
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Residues in contact with ILE 168 (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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83A VAL* 3.6 30.5 - - + -
87A ILE* 4.5 6.1 - - + -
164A PHE* 2.9 23.7 + - + +
165A ILE 4.1 1.1 - - - +
167A THR* 1.3 76.0 - - - +
169A ILE* 1.3 58.7 + - - +
172A LYS* 3.2 29.1 + - + +
178A GLN* 3.4 20.3 + - - +
185A VAL* 3.6 39.0 - - + +
188A VAL* 4.1 11.0 - - + -
189A MET* 3.7 38.8 - - + +
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Residues in contact with ILE 169 (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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165A ILE* 3.0 29.8 + - + +
166A THR* 4.0 2.7 - - - +
168A ILE* 1.3 77.8 - - - +
170A ASN* 1.3 59.5 + - - +
171A MET 3.7 0.2 - - - -
172A LYS* 3.1 16.5 + - - +
178A GLN* 3.5 19.5 - - + +
189A MET* 3.7 24.5 - - + -
81C TYR* 3.5 43.7 + - + +
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Residues in contact with ASN 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 6.0 0.4 - - - +
166A THR* 2.8 24.8 + - + +
169A ILE* 1.3 75.0 - - - +
171A MET* 1.4 65.9 + - + +
172A LYS 3.6 3.5 + - - +
8C TYR* 3.0 26.1 + - - -
74C ALA* 2.9 28.8 + - - +
75C VAL* 5.2 0.2 - - - +
77C LYS* 3.3 26.0 - - - +
78C GLY* 3.4 17.2 - - - +
81C TYR* 3.9 13.1 - - + -
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Residues in contact with MET 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 3.6 9.6 - - - +
88A GLY 5.0 0.2 - - - -
89A ALA* 3.6 25.2 - - + +
90A PRO* 4.2 9.9 - - + -
91A ASP 3.5 20.9 - - - +
92A MET 3.9 8.1 - - - +
93A ALA* 3.5 36.1 - - + -
167A THR* 2.9 21.4 + - + +
170A ASN* 1.4 90.1 - - + +
172A LYS* 1.3 62.9 + - - +
8C TYR* 3.7 58.4 - - + -
10C MET* 5.5 1.3 - - + -
----------------------------------------------------------
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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