Contacts of the helix formed by residues 144 - 174 (chain B) in PDB entry 4CZ8
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 LYS 144 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 1.3 79.2 - - + +
145B GLN* 1.3 65.3 + - - +
146B ASP* 4.5 3.8 - - + +
147B ILE* 3.2 38.5 + - + +
148B GLU* 3.2 20.8 + - - +
352B GLU* 4.4 24.1 + - + +
419B LEU 5.3 6.2 + - - -
420B ASP* 4.8 19.2 + - - +
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Residues in contact with GLN 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 5.8 5.8 - - + +
143B VAL 3.3 5.0 + - - +
144B LYS* 1.3 71.9 - - - +
146B ASP* 1.3 53.5 + - - +
148B GLU* 3.4 19.6 + - - +
149B THR* 2.7 40.3 + - - +
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Residues in contact with ASP 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN* 2.5 35.7 + - - +
144B LYS* 3.3 3.5 - - + +
145B GLN* 1.3 76.6 - - - +
147B ILE* 1.3 61.0 + - + +
149B THR* 3.2 8.5 - - - +
150B VAL* 2.9 29.1 + - - +
348B TRP* 4.6 10.7 - - + -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B PHE* 5.9 0.9 - - + -
143B VAL* 4.8 8.5 - - + -
144B LYS* 3.2 45.4 + - + +
146B ASP* 1.3 74.9 - - + +
148B GLU* 1.3 67.3 + - - +
150B VAL* 3.2 7.2 + - - +
151B ILE* 2.9 44.9 + - + +
348B TRP* 5.0 11.2 - - + -
352B GLU* 5.1 15.7 - - + -
355B PHE* 4.2 28.0 - - + -
356B ILE* 4.3 15.9 - - + +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 5.4 6.8 - - + +
138B PHE* 4.4 28.7 - - + +
139B ARG* 4.1 29.5 + - - -
143B VAL* 5.9 1.6 - - + +
144B LYS 3.2 9.4 + - - +
145B GLN* 3.6 24.2 - - - +
147B ILE* 1.3 79.2 - - - +
149B THR* 1.3 67.2 + - - +
151B ILE* 4.6 4.5 - - - -
152B VAL* 2.9 45.6 + - + +
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Residues in contact with THR 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.7 50.3 - - + +
85B ASN* 5.0 4.7 - - + +
145B GLN* 2.7 27.2 + - - +
146B ASP* 3.2 18.8 - - - +
148B GLU* 1.3 80.3 + - - +
150B VAL* 1.3 56.3 + - - +
152B VAL* 4.0 2.7 - - - +
153B THR* 2.6 44.3 + - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN* 3.6 23.3 - - + +
88B THR* 3.7 11.9 - - + -
89B ILE* 3.3 15.6 - - + +
92B LEU* 3.6 26.2 - - + -
146B ASP 2.9 24.2 + - - +
147B ILE* 3.7 4.9 - - - +
149B THR* 1.3 73.4 - - + +
151B ILE* 1.3 59.3 + - - +
153B THR* 4.5 0.4 - - - -
154B GLU* 2.9 29.1 + - - +
348B TRP* 3.5 27.1 - - + -
356B ILE* 4.4 14.6 - - + -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B THR* 5.1 2.1 + - - +
131B PRO* 4.0 24.5 - - + -
134B LEU* 5.2 3.4 - - + -
138B PHE* 4.0 28.0 - - + -
147B ILE* 2.9 38.5 + - + +
148B GLU* 3.8 3.6 - - - +
150B VAL* 1.3 75.7 - - - +
152B VAL* 1.3 65.3 + - + +
154B GLU* 3.1 17.2 + - - +
155B SER* 2.9 20.6 + - - -
337B ARG* 5.7 2.2 - - - +
355B PHE* 4.7 2.5 - - + -
356B ILE* 4.6 24.5 - - + +
359B GLU* 4.7 15.5 - - + -
360B GLY* 5.7 7.2 - - - +
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Residues in contact with VAL 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN* 5.1 6.7 - - + +
131B PRO* 4.3 17.3 - - + -
135B ILE* 4.2 27.6 - - + -
138B PHE* 5.7 2.7 - - + -
148B GLU* 2.9 39.4 + - + +
149B THR* 4.0 2.7 - - - +
151B ILE* 1.3 74.9 - - + +
153B THR* 1.3 65.3 + - - +
155B SER* 3.1 3.8 + - - -
156B ILE* 2.9 46.1 + - + +
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.7 32.7 - - + +
81B LEU* 5.6 1.6 - - - +
82B LEU* 4.1 13.0 + - + -
89B ILE* 3.8 29.8 - - + -
149B THR* 2.6 33.9 + - - +
150B VAL 3.7 3.4 - - - -
152B VAL* 1.3 74.8 - - - +
154B GLU* 1.3 65.2 + - - +
156B ILE* 3.2 6.3 + - - +
157B PHE* 3.0 31.1 + - + +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 4.0 2.6 - - + +
92B LEU* 3.5 45.7 - - + +
93B ASP* 3.2 29.5 - - - +
96B GLY 6.1 0.7 - - - -
129B THR* 4.8 2.5 + - - -
150B VAL 2.9 17.6 + - - +
151B ILE* 3.3 14.6 - - - +
153B THR* 1.3 76.5 - - - +
155B SER* 1.3 57.7 + - - +
157B PHE 3.4 0.2 + - - -
158B ASN* 2.9 39.5 + - - +
337B ARG* 2.9 42.4 + - - -
356B ILE* 5.0 2.3 - - - +
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Residues in contact with SER 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 4.6 4.0 + - - -
129B THR* 2.5 29.5 + - - -
130B ASP* 4.1 0.3 - - - -
131B PRO* 3.1 28.7 - - - +
151B ILE 2.9 8.9 + - - -
152B VAL 3.3 8.5 - - - -
154B GLU* 1.3 72.9 - - - +
156B ILE* 1.3 67.6 + - - +
157B PHE 3.0 1.6 - - - -
158B ASN* 2.8 31.3 + - - +
159B ASP* 2.8 16.2 + - - +
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Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU* 3.7 55.1 - - + +
74B GLY* 4.5 1.3 - - - +
76B ASN* 3.9 13.0 - - + +
77B LEU* 3.9 40.2 - - + -
152B VAL* 2.9 37.3 + - + +
153B THR* 3.5 6.5 - - - +
155B SER* 1.3 75.6 + - - +
157B PHE* 1.3 58.0 + - + +
160B PRO* 3.3 18.9 - - - +
259B THR* 3.9 18.7 - - + +
263B ILE* 5.2 1.8 - - + -
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 3.6 24.7 - - + -
82B LEU* 4.0 29.6 - - + -
89B ILE* 4.4 2.9 - - + -
93B ASP* 3.1 30.5 - - + +
153B THR* 3.0 27.8 + - + +
156B ILE* 1.3 80.7 - - + +
158B ASN* 1.3 57.5 + - - +
159B ASP 3.5 0.2 - - - -
160B PRO* 3.2 12.2 - - - +
161B LEU* 3.1 30.2 - - + +
207B ILE* 4.6 20.2 - - + -
256B LEU* 5.2 9.6 - - + -
259B THR* 6.5 0.4 - - + -
260B VAL* 5.7 0.7 - - + -
263B ILE* 4.1 20.0 - - + -
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Residues in contact with ASN 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU 5.5 0.4 - - - +
93B ASP* 3.9 9.2 - - - +
97B LEU* 4.1 21.2 - - + +
127B GLY 4.8 0.8 + - - -
128B ALA* 3.3 6.7 - - - +
129B THR* 2.5 45.3 + - - +
154B GLU* 2.9 33.4 + - - +
155B SER* 2.8 9.4 + - - +
157B PHE* 1.3 75.7 - - - +
159B ASP* 1.3 82.9 + - - +
160B PRO 3.3 0.2 - - - -
161B LEU* 4.0 6.1 - - - -
162B GLY* 2.5 32.6 + - - -
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Residues in contact with ASP 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 5.6 0.3 - - - +
70B LEU* 3.5 19.7 - - + +
73B GLU* 2.9 29.8 - - - +
128B ALA* 3.6 6.7 - - - +
129B THR 2.8 20.4 + - - +
130B ASP* 4.6 4.7 - - - +
155B SER* 2.8 11.2 + - - +
158B ASN* 1.3 105.9 + - - +
160B PRO* 1.3 67.0 - - + +
162B GLY 3.7 0.2 + - - -
163B ILE* 3.3 21.8 + - - +
364B VAL* 4.9 1.2 - - - +
365B VAL* 3.2 29.7 - - + +
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.8 18.8 - - + -
156B ILE 3.3 16.8 - - - +
157B PHE* 3.2 16.6 - - - +
159B ASP* 1.3 89.7 - - + +
161B LEU* 1.3 64.5 + - - +
163B ILE* 3.2 9.0 + - + +
164B VAL* 3.1 23.0 + - - +
253B SER* 4.3 4.6 + - - -
255B TYR* 4.2 0.4 - - + -
256B LEU* 3.6 49.8 - - + +
259B THR* 4.0 9.4 - - + +
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP* 3.4 40.4 - - + +
97B LEU* 3.7 16.4 - - + -
157B PHE* 3.1 29.4 - - + +
158B ASN* 3.1 4.6 + - - +
160B PRO* 1.3 76.9 - - + +
162B GLY* 1.3 59.6 + - - +
164B VAL* 3.2 15.9 - - + +
165B LEU* 3.0 32.6 + - - +
199B PHE* 4.7 8.7 - - + -
203B VAL* 4.3 16.6 - - + -
256B LEU* 4.1 27.1 - - + -
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Residues in contact with GLY 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 4.2 6.0 - - - +
124B ALA 2.9 16.0 - - - +
125B ILE 5.6 0.2 - - - -
127B GLY 5.1 0.2 - - - -
128B ALA* 4.2 15.7 - - - -
158B ASN 2.5 20.5 + - - -
159B ASP 4.1 1.8 - - - -
161B LEU* 1.3 72.0 - - - +
163B ILE* 1.3 53.4 + - - +
165B LEU* 3.5 4.5 - - - +
166B THR* 2.8 34.4 + - - -
369B LEU* 4.4 5.2 - - - -
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 4.1 16.6 - - + -
70B LEU* 3.7 23.8 - - + -
159B ASP 3.3 17.7 - - - +
160B PRO* 3.2 6.7 + - + +
161B LEU 3.1 0.6 - - - -
162B GLY* 1.3 73.3 - - - +
164B VAL* 1.3 55.3 + - - +
165B LEU 3.1 1.3 - - - -
166B THR* 2.9 6.1 + - - -
167B LEU* 2.8 45.6 + - + +
253B SER* 5.3 0.2 - - - +
255B TYR* 3.9 42.8 - - + -
365B VAL* 3.8 16.2 - - + -
369B LEU* 4.2 22.0 - - + -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PRO 3.1 5.2 + - - +
161B LEU* 3.2 38.6 - - + +
163B ILE* 1.3 79.4 - - - +
165B LEU* 1.3 56.8 + - - +
167B LEU* 3.3 12.9 + - + +
168B ILE* 3.0 39.1 + - + +
198B TYR* 5.0 4.7 - - + -
199B PHE* 4.5 16.4 - - + -
202B ASN* 3.6 38.1 - - + +
203B VAL* 5.7 1.8 - - + -
253B SER* 4.2 14.8 - - - -
256B LEU* 5.8 1.3 - - + -
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.7 35.4 - - + +
98B ILE* 4.2 25.1 - - + -
101B ALA* 4.5 12.3 - - + -
120B PHE* 4.3 20.8 - - + -
124B ALA* 3.4 25.5 - - + +
127B GLY* 5.7 0.4 - - - -
161B LEU 3.0 17.2 + - - +
162B GLY* 3.5 7.6 - - - +
164B VAL* 1.3 78.2 - - - +
166B THR* 1.3 61.2 + - - +
168B ILE* 3.1 25.3 + - + +
169B ALA* 3.2 5.9 + - - +
199B PHE* 4.5 17.5 - - + -
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Residues in contact with THR 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.7 12.4 - - + +
124B ALA* 3.0 24.4 + - - +
125B ILE* 3.2 28.1 + - + -
162B GLY 2.8 17.1 + - - -
163B ILE* 2.9 9.5 + - - -
165B LEU* 1.3 78.1 - - - +
167B LEU* 1.3 62.5 + - - +
169B ALA 3.6 0.9 + - - -
170B ILE* 3.3 33.1 + - + +
369B LEU* 3.6 22.2 - - + +
372B LEU* 4.7 5.4 - - + -
373B PRO* 6.1 0.4 - - + -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 2.8 29.1 + - + +
164B VAL* 3.6 17.5 - - + +
165B LEU 3.2 0.2 - - - -
166B THR* 1.3 77.4 - - - +
168B ILE* 1.3 55.0 + - - +
170B ILE* 4.0 6.4 - - + +
171B SER* 2.3 41.7 + - - +
198B TYR* 6.2 0.2 - - - +
248B GLU* 4.1 18.8 - - - +
253B SER* 6.2 4.3 - - - -
255B TYR* 5.4 8.1 - - + -
369B LEU* 5.7 0.9 - - + -
372B LEU* 4.7 18.8 - - + -
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 4.3 11.0 - - + -
164B VAL* 3.0 25.0 + - + +
165B LEU* 3.1 16.8 + - + +
167B LEU* 1.3 74.7 - - + +
169B ALA* 1.3 60.6 + - - +
171B SER* 3.0 7.1 + - - +
172B MSE 2.8 57.7 + - + +
182B PHE* 3.9 11.0 - - + -
195B GLY* 4.3 13.0 - - - +
198B TYR* 3.4 38.8 - - + -
199B PHE* 5.0 9.6 - - + +
----------------------------------------------------------
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.9 4.7 - - + +
120B PHE* 3.9 23.1 - - + +
121B LEU* 3.6 40.4 - - + +
124B ALA* 4.9 0.4 - - + -
165B LEU 3.2 6.4 + - - +
166B THR 4.0 1.6 - - - +
168B ILE* 1.3 81.1 - - - +
170B ILE* 1.3 56.5 + - - +
172B MSE 3.2 8.2 + - - +
173B LEU* 2.9 34.4 + - - +
----------------------------------------------------------
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.7 25.1 - - + -
166B THR* 3.3 20.5 + - + +
167B LEU* 4.0 7.4 - - + +
168B ILE 3.3 0.4 - - - -
169B ALA* 1.3 76.7 - - - +
171B SER* 1.3 54.5 + - - +
173B LEU* 3.7 6.9 - - + +
174B VAL* 2.6 46.9 + - + +
372B LEU* 4.0 31.0 - - + -
373B PRO* 5.0 8.1 - - + -
376B LEU* 3.5 31.4 - - + -
385B LEU* 5.3 5.8 - - + -
----------------------------------------------------------
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Residues in contact with SER 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 2.3 29.7 + - - +
168B ILE* 3.0 7.3 + - - +
170B ILE* 1.3 77.1 - - - +
172B MSE 1.3 59.9 + - - +
174B VAL 2.9 21.1 - - - +
175B PRO* 3.9 5.9 - - - +
176B GLY 5.6 2.2 - - - -
177B TYR 5.6 0.5 + - - -
178B GLY* 5.6 7.3 - - - -
182B PHE* 3.5 40.8 - - - +
198B TYR* 6.1 0.3 - - - -
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Residues in contact with MSE 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.1 22.5 - - + +
120B PHE* 4.6 12.6 - - + -
168B ILE* 2.8 36.8 + - + +
169B ALA* 3.4 7.6 - - - +
171B SER* 1.3 78.2 - - - +
173B LEU* 1.3 65.8 + - - +
174B VAL* 4.5 0.9 - - - -
175B PRO* 5.0 1.6 - - - +
182B PHE* 3.9 10.1 - - + -
191B ILE* 3.4 44.8 - - + +
192B TYR* 4.0 33.2 - - + +
195B GLY* 3.8 14.8 - - - -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 6.4 0.4 - - - -
117B LEU* 3.6 34.8 - - + -
118B LEU* 4.9 12.8 - - + +
121B LEU* 3.9 29.2 - - + -
169B ALA 2.9 19.5 + - - +
170B ILE* 3.7 4.7 - - - +
172B MSE 1.3 78.2 - - - +
174B VAL* 1.3 62.6 + - - +
175B PRO* 4.0 4.5 - - - +
384B LEU* 3.9 38.7 - - + +
385B LEU* 3.7 35.0 - - + -
----------------------------------------------------------
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 2.6 27.0 + - + +
171B SER* 2.9 21.6 - - - +
173B LEU* 1.3 79.6 - - - +
175B PRO* 1.3 64.8 - - + +
176B GLY* 3.1 27.0 + - - +
376B LEU* 6.2 2.9 - - + -
380B TYR* 4.6 15.7 - - + -
382B SER* 4.2 29.4 - - - +
384B LEU* 5.4 1.8 - - + -
385B LEU* 3.7 26.2 - - + -
----------------------------------------------------------
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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