Contacts of the helix formed by residues 142 - 171 (chain B) in PDB entry 6BAA
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 CYS 142 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 4.4 18.4 - - + -
97B HIS* 4.1 12.6 - - - -
110B CYS* 2.0 44.4 - - - +
139B THR 4.6 2.3 + - - +
140B GLU 3.4 3.1 - - - -
141B GLU* 1.3 76.5 - - - +
143B PRO* 1.3 66.3 - - - +
144B LEU* 2.8 6.4 + - + +
145B ALA* 2.9 31.9 + - + +
146B ILE* 3.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU 4.7 2.6 - - - +
141B GLU 3.2 11.6 - - - +
142B CYS* 1.3 82.6 - - - +
144B LEU* 1.3 62.8 + - + +
146B ILE* 3.5 17.7 - - + +
147B LEU* 3.3 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ILE* 3.4 29.8 - - + -
142B CYS* 4.7 3.1 - - + -
143B PRO* 1.3 82.4 - - + +
145B ALA* 1.3 59.2 + - - +
146B ILE 3.1 2.0 - - - -
147B LEU* 3.0 23.1 + - + +
148B ILE* 2.8 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TRP* 3.2 31.6 - - + -
93B ILE* 3.5 14.7 - - + +
110B CYS* 4.5 9.0 - - + -
111B VAL* 4.9 0.9 - - + -
138B VAL* 4.4 14.8 - - + -
139B THR 5.4 0.7 - - - +
142B CYS* 2.9 24.5 + - + +
144B LEU* 1.3 78.6 - - - +
146B ILE* 1.3 57.7 + - - +
148B ILE* 3.2 2.0 + - - -
149B LEU* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B VAL* 4.8 1.3 - - + -
139B THR 4.4 13.0 - - - +
140B GLU* 4.7 6.1 - - - +
142B CYS 3.2 13.0 + - - +
143B PRO* 3.5 16.8 - - + +
145B ALA* 1.3 77.6 - - - +
147B LEU* 1.3 61.8 + - - +
149B LEU* 3.3 8.2 + - - +
150B ILE* 3.1 27.8 + - + +
118C SER* 4.4 25.4 - - - +
121C PHE* 4.3 22.4 - - + -
122C LEU* 4.0 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B PRO 3.3 10.5 + - - +
144B LEU* 3.0 26.3 + - + +
146B ILE* 1.3 77.7 - - - +
148B ILE* 1.3 65.5 + - + +
150B ILE* 3.1 19.9 + - + +
151B VAL* 2.9 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 4.8 14.5 - - + -
89B VAL* 3.5 32.3 - - + -
90B TRP* 3.7 26.5 - - + +
93B ILE* 3.5 35.4 - - + -
144B LEU* 2.8 32.8 + - + +
145B ALA* 3.6 6.7 - - - +
147B LEU* 1.3 71.9 - - + +
149B LEU* 1.3 56.7 + - - +
151B VAL* 3.3 7.0 + - - +
152B GLN* 2.8 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TRP* 3.9 14.5 - - + -
127B VAL* 3.6 34.3 - - + -
138B VAL* 4.3 17.9 - - + -
145B ALA 2.9 14.2 + - - +
146B ILE* 3.4 8.5 - - - +
148B ILE* 1.3 76.3 - - - +
150B ILE* 1.3 64.4 + - + +
152B GLN* 3.5 2.0 + - - +
153B ASN* 3.0 41.8 + - - +
122C LEU* 3.7 28.9 - - + +
125C ILE* 4.4 16.4 - - + -
126C GLU* 6.0 0.9 - - + -
131C ILE* 4.6 7.0 - - + -
133C PHE* 4.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.1 20.8 + - + +
147B LEU* 3.1 20.1 + - + +
149B LEU* 1.3 77.4 - - + +
151B VAL* 1.3 65.7 + - + +
153B ASN* 3.7 6.4 - - - +
154B ILE* 3.1 47.5 + - + +
76C THR* 6.1 0.2 - - + -
80C LEU* 4.1 25.1 - - + -
83C TRP* 4.2 7.9 - - + -
121C PHE* 3.8 35.2 - - + -
125C ILE* 4.7 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.8 20.6 - - + -
147B LEU* 2.9 34.9 + - + +
148B ILE* 3.6 9.4 - - - +
150B ILE* 1.3 78.1 - - + +
152B GLN* 1.3 58.3 + - - +
154B ILE* 3.3 6.3 + - - +
155B VAL* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.2 38.7 - - + +
90B TRP* 2.6 30.8 + - - +
124B SER* 2.9 31.5 + - - -
127B VAL* 3.5 24.8 - - + +
128B GLN* 3.3 27.6 + - + +
148B ILE 2.8 20.4 + - - +
149B LEU 4.0 2.9 - - - +
151B VAL* 1.3 73.1 - - - +
153B ASN* 1.3 63.7 + - - +
155B VAL* 3.9 0.3 - - - +
156B GLY* 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 3.1 33.0 - - - +
128B GLN* 5.6 2.4 - - - +
149B LEU* 3.0 32.8 + - - +
150B ILE* 3.7 5.4 - - - +
152B GLN* 1.3 74.8 - - - +
154B ILE* 1.3 58.8 + - - +
156B GLY* 3.7 0.9 - - - -
157B LEU* 2.8 33.0 + - - +
83C TRP* 4.6 13.1 - - + -
125C ILE* 3.4 30.7 - - - +
129C VAL* 4.5 17.1 - - + +
131C ILE* 3.8 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ILE* 3.1 33.7 + - + +
151B VAL* 3.7 5.8 - - - +
153B ASN* 1.3 74.1 - - - +
155B VAL* 1.3 62.3 + - + +
157B LEU* 3.1 8.6 + - - +
158B MET* 2.8 45.4 + - + +
76C THR* 3.6 50.7 - - + +
79C PHE* 4.5 7.4 - - + -
80C LEU* 5.7 0.9 - - + -
83C TRP* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 5.4 3.4 - - - -
86B PHE* 3.9 23.8 - - + -
128B GLN* 5.7 0.2 - - - +
151B VAL* 2.9 39.6 + - + +
154B ILE* 1.3 74.3 - - + +
156B GLY* 1.3 64.7 + - - +
158B MET* 3.2 7.1 + - - +
159B ILE* 3.0 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN* 3.6 35.1 - - - +
152B GLN 2.9 13.9 + - - -
153B ASN 3.9 0.7 - - - -
155B VAL* 1.3 77.8 - - - +
157B LEU* 1.3 62.4 + - - +
159B ILE* 3.3 7.3 + - - +
160B ASN* 3.1 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN 5.5 0.2 + - - -
153B ASN 2.8 19.8 + - - +
154B ILE* 3.2 7.6 - - - +
155B VAL 3.1 0.2 - - - -
156B GLY* 1.3 76.8 - - - +
158B MET* 1.3 71.4 + - + +
160B ASN* 3.2 11.8 + - - +
161B ALA* 3.1 18.4 + - - +
79C PHE* 3.2 37.5 - - + -
83C TRP* 5.0 2.9 - - + -
129C VAL* 4.8 22.0 - - + -
160C ASN* 4.1 13.5 - - - +
163C MET* 3.1 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ILE* 2.8 32.2 + - + +
155B VAL* 3.7 6.1 - - - +
157B LEU* 1.3 90.3 - - + +
159B ILE* 1.3 64.1 + - + +
161B ALA* 3.2 4.0 + - - +
162B ILE* 2.9 36.0 + - + +
68C TRP* 6.1 0.2 - - - -
72C LEU* 4.1 31.2 - - + +
75C PHE* 3.4 41.7 - - + -
76C THR 5.1 1.1 - - - +
79C PHE* 4.2 5.2 - - + -
163C MET* 4.4 6.1 - - + +
167C ILE* 4.4 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 5.9 1.8 - - + -
78B SER* 4.8 13.7 - - - +
79B PHE* 3.3 32.3 - - + -
82B SER* 3.7 31.0 - - - +
128B GLN* 4.6 1.1 - - - +
155B VAL* 3.0 33.3 + - + +
156B GLY* 3.5 11.9 - - - +
157B LEU 3.2 0.2 - - - -
158B MET* 1.3 77.9 - - + +
160B ASN* 1.3 56.9 + - - +
162B ILE* 3.3 8.0 + - - +
163B MET* 2.8 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 4.1 13.9 - - - +
79B PHE* 4.0 21.0 - - - -
128B GLN 4.3 13.7 + - - -
129B VAL* 5.7 1.6 - - - +
156B GLY 3.1 19.5 + - - +
157B LEU* 3.2 10.3 + - - +
159B ILE* 1.3 75.2 - - - +
161B ALA* 1.3 57.7 + - - +
163B MET* 3.7 11.2 - - + +
164B LEU* 2.9 41.0 + - + +
164C LEU* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 3.1 12.6 + - - +
158B MET* 3.2 12.5 + - - +
160B ASN* 1.3 77.8 - - - +
162B ILE* 1.3 60.8 + - - +
164B LEU* 3.4 2.6 + - - +
165B GLY 3.1 18.0 + - - -
163C MET* 3.8 19.5 - - + -
164C LEU* 3.6 29.1 - - + +
167C ILE* 3.9 18.1 - - + +
168C PHE* 3.8 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.3 37.2 - - + -
63B LEU* 5.4 2.7 - - + -
75B PHE* 5.4 3.1 - - + -
158B MET* 2.9 27.8 + - + +
159B ILE* 3.7 6.1 - - + +
161B ALA* 1.3 72.2 - - + +
163B MET* 1.3 67.3 + - - +
165B GLY* 3.2 1.7 + - - -
166B CYS* 3.0 27.9 + - - -
68C TRP* 4.9 13.2 - - + -
72C LEU* 6.3 2.2 - - + -
167C ILE* 4.2 17.7 - - + -
171C THR* 4.9 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 3.1 34.8 - - + +
158A MET* 4.4 3.8 - - + -
161A ALA* 3.8 11.4 - - + -
75B PHE* 3.7 42.6 - - + -
79B PHE* 3.8 15.0 - - + -
159B ILE* 2.8 22.4 + - + +
160B ASN* 3.7 13.9 - - + +
162B ILE* 1.3 75.1 - - - +
164B LEU* 1.3 82.0 + - + +
166B CYS* 3.4 3.3 + - - +
167B ILE* 3.0 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASN* 5.0 0.4 - - + -
161A ALA* 3.6 36.1 - - + -
164A LEU* 4.1 23.6 - - + -
160B ASN* 2.9 28.0 + - + +
161B ALA 3.7 2.2 - - - +
163B MET* 1.3 85.0 - - + +
165B GLY* 1.3 66.3 + - - +
167B ILE* 3.1 3.5 + - - +
168B PHE* 2.8 35.4 + - + -
164C LEU* 4.1 29.8 - - + -
168C PHE* 3.4 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ALA 3.1 11.5 + - - -
162B ILE 3.2 4.2 + - - -
164B LEU* 1.3 80.6 - - - +
166B CYS* 1.3 59.8 + - - +
168B PHE* 3.4 2.9 + - - +
169B MET* 3.3 32.8 + - - +
168C PHE* 3.6 26.4 - - - -
171C THR* 4.3 11.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 3.7 20.2 - - - -
63B LEU* 3.5 39.0 - - + -
64B VAL* 4.2 3.4 - - + +
71B THR* 5.8 0.9 - - + -
75B PHE* 3.5 24.9 - - + -
162B ILE* 3.0 26.6 + - - -
163B MET 3.6 0.9 - - - +
165B GLY* 1.3 77.1 - - - +
167B ILE* 1.3 61.9 + - - +
169B MET* 3.4 13.3 + - - +
170B LYS* 3.1 28.5 + - + +
171C THR* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A MET* 4.4 11.7 - - - -
161A ALA* 3.9 34.1 - - + +
162A ILE* 4.1 13.9 - - + +
68B TRP* 3.9 24.5 - - + -
71B THR* 4.1 7.2 - - + -
72B LEU* 5.7 0.2 - - + -
75B PHE* 3.9 20.6 - - + -
163B MET* 3.0 32.2 + - - +
164B LEU 3.1 6.5 + - - +
166B CYS* 1.3 75.5 - - - +
168B PHE* 1.3 63.9 + - + +
170B LYS* 3.2 5.6 + - + +
171B THR* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA 3.8 11.7 - - - -
164A LEU* 3.4 27.6 - - + -
165A GLY* 3.6 22.2 - - - -
168A PHE* 3.1 46.7 - + + -
169A MET* 5.5 0.3 - - - +
164B LEU* 2.8 38.7 + - + +
165B GLY 3.6 5.6 - - - +
167B ILE* 1.3 77.5 - - + +
169B MET* 1.3 63.0 + - + +
171B THR* 2.5 26.6 + - - -
172B ALA* 3.2 9.0 + - - +
168C PHE* 3.1 35.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B PHE* 4.3 10.1 - - + +
64B VAL* 3.6 34.8 - - + -
165B GLY 3.3 19.1 + - - +
166B CYS* 3.8 5.6 - - - +
167B ILE 3.3 0.2 - - - -
168B PHE* 1.3 78.4 - - + +
170B LYS* 1.3 61.1 + - - +
172B ALA* 3.2 17.5 + - - +
173B GLN* 3.1 20.3 + - - -
171C THR* 3.3 52.0 - - - +
172C ALA* 4.6 6.7 - - + -
293C THR 4.3 5.4 - - - +
294C THR* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 5.2 1.6 - - - -
63B LEU 4.3 4.0 - - - +
64B VAL* 2.9 32.4 + - - -
66B LEU 2.6 28.5 + - - -
67B LYS 4.5 0.6 - - - -
68B TRP* 3.7 49.6 + - + +
71B THR* 3.2 37.3 + - + +
166B CYS* 3.1 19.6 + - + +
167B ILE* 3.5 9.2 - - + +
168B PHE 3.1 0.6 - - - -
169B MET* 1.3 73.5 - - - +
171B THR* 1.3 58.8 + - - +
172B ALA 2.9 9.1 + - - -
173B GLN* 3.1 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.7 49.7 - - + +
162A ILE* 4.9 10.1 - - - +
165A GLY* 4.3 6.0 - - - -
169A MET* 3.3 37.2 - - + +
68B TRP* 4.6 4.0 - - + -
167B ILE* 3.0 25.1 + - + +
168B PHE* 2.5 25.9 + - - -
170B LYS* 1.3 75.0 - - - +
172B ALA* 1.3 58.1 + - - +
173B GLN 3.4 0.8 + - - -
294B THR* 5.2 1.7 - - - +
----------------------------------------------------------
Back to top of page
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