Contacts of the helix formed by residues 155 - 184 (chain B) in PDB entry 3OLJ
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 ILE 155 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO 3.5 23.6 - - - +
72B LEU* 3.9 19.1 - - + -
76B ASN* 4.1 8.1 - - + +
87B TYR* 3.7 28.5 - - + +
90B ILE* 3.2 35.7 - - + -
153B VAL* 3.9 6.7 - - + -
154B GLN* 1.3 78.0 - - - +
156B THR* 1.3 66.4 + - - +
157B GLU* 4.0 8.7 - - - +
158B ALA* 3.5 27.4 - - + +
159B ARG* 3.1 22.0 + - - +
276B MET* 4.7 0.2 - - - -
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B NA 2.4 27.9 - - - -
76B ASN* 4.2 3.3 + - - +
78B ARG 3.4 1.6 + - - -
79B ARG* 2.9 25.6 + - - +
80B PHE 5.4 0.9 - - - -
81B VAL 3.6 14.8 - - - +
82B ILE* 3.9 28.0 - - + +
85B ILE* 6.1 0.2 - - + -
91B TRP* 5.6 0.7 - - + -
154B GLN 3.6 3.0 + - - -
155B ILE* 1.3 70.7 - - - +
157B GLU* 1.3 69.0 + - + +
159B ARG* 3.2 7.9 + - + +
160B CYS* 2.9 35.4 + - - -
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Residues in contact with GLU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE 5.3 1.1 - - - +
84B PRO 4.3 2.1 - - - +
85B ILE* 3.6 10.3 - - + +
86B GLU* 2.8 32.4 + - - +
87B TYR* 3.1 37.2 + - + +
90B ILE* 3.6 25.3 - - + +
91B TRP* 3.9 32.3 - - + +
94B TYR* 4.3 5.9 - - - +
155B ILE* 4.0 2.9 - - + +
156B THR* 1.3 89.8 + - - +
158B ALA* 1.3 61.9 + - - +
160B CYS* 3.5 3.8 + - - +
161B PHE* 3.2 18.4 + - - +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 3.6 7.8 - - + +
153B VAL* 3.6 19.1 - - + -
155B ILE* 3.2 25.7 + - + +
157B GLU* 1.3 76.7 - - - +
159B ARG* 1.3 62.3 + - - +
161B PHE* 3.2 2.9 + - - +
162B TYR* 2.8 36.0 + - + +
272B PHE* 3.7 19.9 - - + -
276B MET* 3.7 8.1 - - - -
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Residues in contact with ARG 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ARG* 3.3 45.5 - - - +
80B PHE* 3.4 30.9 - - - -
150B SER* 3.4 23.8 + - - +
151B GLN* 2.9 30.5 + - - +
153B VAL* 2.8 23.5 + - + +
154B GLN* 3.7 11.5 - - - +
155B ILE 3.1 13.7 + - - +
156B THR* 3.4 7.9 - - + +
158B ALA* 1.3 77.6 - - - +
160B CYS* 1.3 58.3 + - - +
162B TYR* 3.9 6.4 - - - +
163B GLY* 2.8 27.4 + - - -
146C VAL* 4.1 14.6 - - - +
147C GLU* 5.3 1.2 + - - +
170C ASN* 4.7 2.9 + - - -
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Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE* 3.9 22.7 - - - -
91B TRP* 4.0 11.0 - - + -
94B TYR* 3.7 27.0 - - + -
156B THR* 2.9 23.8 + - - -
157B GLU 3.6 8.7 - - - +
158B ALA 3.3 0.2 - - - -
159B ARG* 1.3 72.1 - - - +
161B PHE* 1.3 67.1 + - - +
163B GLY* 3.3 1.7 + - - -
164B PHE* 3.0 24.1 + - - +
170C ASN* 3.8 34.9 + - - +
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B MET* 3.4 20.9 - - + -
94B TYR* 3.5 34.0 - - + -
97B ALA* 4.0 9.1 - - + +
157B GLU 3.2 8.4 + - - +
158B ALA 3.2 8.6 + - - +
160B CYS* 1.3 78.8 - - - +
162B TYR* 1.3 57.6 + - - +
164B PHE* 3.2 3.8 + - - +
165B GLN* 2.8 46.0 + - + -
268B LEU* 4.0 18.2 - - + -
269B HIS* 4.0 22.9 - + - -
272B PHE* 3.4 64.2 - + + -
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 3.4 30.2 - - + +
149B PHE* 3.5 43.1 - + + -
150B SER* 4.1 17.3 - - - -
153B VAL* 4.0 16.6 - - + -
158B ALA* 2.8 26.8 + - + +
159B ARG 3.9 4.0 - - - +
161B PHE* 1.3 72.2 - + - +
163B GLY* 1.3 62.3 + - - +
165B GLN* 3.2 16.3 + - - +
166B ILE* 3.0 30.0 + - + +
221B TYR* 2.7 27.7 + - - -
225B VAL* 4.6 4.2 - - - +
272B PHE* 3.6 31.7 - + - -
273B ALA* 5.4 1.0 - - - +
276B MET* 3.9 2.9 - - - +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B SER* 5.2 2.1 - - - -
159B ARG 2.8 17.4 + - - -
160B CYS* 3.7 2.0 - - - -
162B TYR* 1.3 75.9 - - - +
164B PHE* 1.3 60.9 + - - +
166B ILE* 3.5 13.3 + - - +
167B ALA* 3.4 18.4 + - - +
163C GLY 4.4 7.8 - - - +
166C ILE* 4.7 18.1 - - - +
167C ALA* 4.5 7.2 - - - +
170C ASN* 5.2 2.7 - - - -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TYR* 4.0 25.4 - + + -
97B ALA* 3.5 35.7 - - + -
98B GLU* 3.6 20.0 - - + -
101B PHE* 3.8 27.6 - + + -
160B CYS 3.0 16.1 + - - +
161B PHE 3.6 4.3 - - - +
163B GLY* 1.3 74.5 - - - +
165B GLN* 1.3 62.2 + - - +
167B ALA* 3.3 8.5 + - + +
168B MET* 3.0 47.1 + - + +
101C PHE* 3.8 21.1 - + - -
164C PHE* 6.4 0.4 - + - -
167C ALA* 4.3 19.5 - - + +
171C ILE* 4.8 3.8 - - + -
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Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL* 4.0 1.4 - - - +
145B LEU* 3.5 23.1 - - + +
161B PHE* 2.8 28.6 + - + +
162B TYR* 3.2 27.7 + - - +
164B PHE* 1.3 77.0 - - - +
166B ILE* 1.3 51.3 + - - +
168B MET* 3.1 3.6 + - - +
169B GLU* 2.8 46.0 + - - +
232B GLU* 3.1 37.6 + - - -
269B HIS* 3.4 40.0 + - + +
272B PHE* 5.2 0.2 - - - -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASN* 3.3 23.3 + - - +
145B LEU* 3.6 33.7 - - + +
146B VAL* 3.9 34.1 - - + +
150B SER* 4.2 12.3 - - - +
162B TYR 3.0 20.6 + - - +
163B GLY* 3.6 11.4 - - - +
164B PHE 3.3 0.2 - - - -
165B GLN* 1.3 75.7 - - - +
167B ALA* 1.3 62.0 + - - +
169B GLU* 3.2 1.4 + - - -
170B ASN* 3.1 28.8 + - - +
159C ARG 6.0 0.2 - - - +
163C GLY* 4.7 14.8 - - - -
166C ILE* 6.4 2.2 - - + -
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 5.9 0.9 - - + -
163B GLY 3.4 8.9 + - - +
164B PHE* 3.3 13.8 + - + +
165B GLN 3.3 0.4 - - - -
166B ILE* 1.3 79.2 - - - +
168B MET* 1.3 65.3 + - + +
170B ASN* 3.3 11.4 + - - +
171B ILE* 3.1 27.3 + - + +
94C TYR* 4.8 0.9 + - - -
163C GLY 4.5 12.7 + - - +
164C PHE* 4.3 26.4 - - + +
167C ALA* 4.5 9.9 - - + -
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 5.6 1.3 - - + +
100B SER 5.0 0.2 - - - +
101B PHE* 3.7 31.4 - - - -
102B TRP* 3.3 50.7 - - + +
164B PHE* 3.0 40.4 + - + +
165B GLN* 3.1 6.9 + - - +
167B ALA* 1.3 75.4 - - - +
169B GLU* 1.3 59.2 + - - +
171B ILE* 3.2 13.3 + - + +
172B HIS* 2.8 42.9 + - - +
265B ASP* 3.7 10.8 - - - +
269B HIS* 4.6 12.3 - - + +
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ASP* 3.4 28.2 - - - +
141B VAL* 3.7 13.1 - - + +
142B ASN* 3.6 22.4 - - + +
145B LEU* 4.2 14.4 - - + -
165B GLN* 2.8 31.0 + - - +
166B ILE 3.2 0.4 + - - +
168B MET* 1.3 69.3 - - - +
170B ASN* 1.3 61.5 + - - +
172B HIS* 3.3 13.2 + - - +
173B SER* 2.9 33.5 + - - -
232B GLU* 3.1 23.9 - - - +
236B PHE* 5.7 0.2 - - - -
266B GLU* 3.2 11.4 - - - +
269B HIS* 3.3 10.1 + - - -
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Residues in contact with ASN 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B ASN* 3.2 21.1 + - - +
166B ILE* 3.1 24.9 + - - +
167B ALA* 3.6 10.0 - - - +
168B MET 3.3 0.2 - - - -
169B GLU* 1.3 76.2 - - - +
171B ILE* 1.3 58.1 + - - +
173B SER* 3.4 6.1 + - - -
174B GLU* 3.0 24.8 + - - +
82C ILE* 3.4 13.5 - - - +
94C TYR* 4.4 11.2 + - + +
159C ARG 4.7 3.4 + - - -
160C CYS* 3.7 45.6 + - + +
163C GLY* 5.2 2.4 - - - -
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.5 25.6 - - + -
102B TRP* 3.5 40.8 - - + +
103B THR* 4.0 12.6 - - - -
104B ALA* 4.1 7.5 - - + +
167B ALA 3.1 16.0 + - - +
168B MET* 3.2 19.9 + - + +
170B ASN* 1.3 75.0 - - - +
172B HIS* 1.3 59.3 + - - +
174B GLU* 3.4 8.1 + - - +
175B MET* 2.9 27.9 + - - +
94C TYR* 3.7 10.3 - - - +
98C GLU* 3.4 23.1 - - + +
164C PHE* 4.8 4.5 - - + -
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Residues in contact with HIS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 3.6 21.4 - + - -
138B ASP* 3.3 18.2 + - - +
168B MET* 2.8 28.0 + - + +
169B GLU* 3.3 14.6 + - - +
171B ILE* 1.3 76.4 - - - +
173B SER* 1.3 61.6 + - - +
175B MET* 3.2 7.8 + - - +
176B TYR* 2.9 33.4 + - + -
262B ILE* 3.7 22.7 - - + +
265B ASP* 2.7 39.2 + - + +
266B GLU* 3.2 28.1 + - - -
269B HIS* 4.2 7.4 - + - -
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Residues in contact with SER 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 4.1 10.9 + - - +
138B ASP* 3.1 27.7 - - - +
139B GLY* 4.4 1.9 + - - -
169B GLU 2.9 23.1 + - - -
170B ASN* 3.7 8.2 + - - -
172B HIS* 1.3 70.9 - - - +
174B GLU* 1.3 59.7 + - - +
176B TYR* 3.3 6.3 + - - +
177B SER* 2.9 31.9 + - - -
80C PHE 5.3 2.7 + - - -
82C ILE* 3.7 24.7 - - - -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA* 4.3 13.1 - - + +
105B GLU* 3.8 3.6 - - - +
170B ASN 3.0 18.0 + - - +
171B ILE* 3.7 7.2 - - - +
173B SER* 1.3 72.8 - - - +
175B MET* 1.3 60.5 + - - +
177B SER* 3.2 2.7 + - - -
178B LEU* 2.8 45.0 + - + +
82C ILE* 3.9 17.6 - - + +
83C PHE* 4.3 13.4 - - + -
91C TRP* 3.8 15.5 + - + -
94C TYR* 4.5 6.4 + - - -
95C LYS* 2.6 37.2 + - - -
98C GLU* 4.0 10.7 - - - +
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Residues in contact with MET 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 4.0 12.1 - - + -
104B ALA* 3.8 24.9 - - + +
107B VAL* 3.8 40.4 - - + -
109B LEU* 4.0 19.5 - - + -
171B ILE 2.9 15.3 + - - +
172B HIS 3.2 9.4 + - - +
174B GLU* 1.3 75.2 - - - +
176B TYR* 1.3 58.2 + - - +
178B LEU* 3.3 6.2 + - + -
179B LEU* 2.9 50.6 + - + +
258B SER* 3.8 19.3 - - - +
262B ILE* 4.0 12.6 - - + -
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 3.8 27.1 - - + +
134B PHE* 3.3 57.6 - + + -
135B ALA* 3.8 17.0 - - + -
138B ASP* 3.3 23.3 - - - -
172B HIS* 2.9 24.8 + - + +
173B SER 3.7 4.3 - - - +
175B MET* 1.3 76.7 - - - +
177B SER* 1.3 58.5 + - - +
179B LEU* 3.3 11.8 + - + +
180B ILE* 3.0 32.5 + - - +
240B PHE* 3.9 4.9 - - - -
255B LEU* 6.1 0.4 - - + -
259B ASN* 5.0 4.3 + - - -
262B ILE* 3.3 45.6 - - + +
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Residues in contact with SER 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ALA* 4.3 9.0 - - - +
173B SER 2.9 18.1 + - - -
174B GLU 3.7 3.8 - - - -
176B TYR* 1.3 74.7 - - - +
178B LEU* 1.3 57.9 + - - +
180B ILE* 3.4 4.4 + - - +
181B ASP* 2.9 33.6 + - - +
194B PHE* 3.8 19.6 - - - -
82C ILE* 3.3 14.6 - - - +
83C PHE* 3.4 31.9 + - - +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ALA* 3.5 35.0 - - + -
105B GLU* 5.3 3.8 - - + +
109B LEU* 4.2 6.1 - - + -
174B GLU* 2.8 30.9 + - + +
175B MET* 3.5 12.3 - - + +
177B SER* 1.3 74.1 - - - +
179B LEU* 1.3 57.9 + - - +
181B ASP* 3.8 7.2 - - + +
182B THR* 2.6 41.6 + - - +
83C PHE* 4.4 16.4 - - + -
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.4 29.6 - - + -
131B LEU* 3.7 31.9 - - + -
175B MET* 2.9 29.4 + - + +
176B TYR* 3.5 19.3 - - + +
178B LEU* 1.3 75.4 - - - +
180B ILE* 1.3 64.0 + - - +
182B THR* 3.7 1.1 - - - -
183B TYR* 3.0 59.3 + - + +
255B LEU* 3.9 16.2 - - + -
258B SER* 3.7 18.6 - - - +
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B SER* 4.8 1.8 - - - +
131B LEU* 3.9 33.4 - - + +
132B ALA* 4.1 16.8 - - - +
135B ALA* 5.1 4.5 - - + -
176B TYR 3.0 18.8 + - - +
177B SER* 3.5 6.7 - - - +
179B LEU* 1.3 75.0 - - - +
181B ASP* 1.3 56.7 + - - +
183B TYR* 3.2 1.4 + - - -
184B ILE* 2.8 46.0 + - + +
190B ARG* 4.4 11.0 - - + -
193B LEU* 4.1 33.9 - - + -
194B PHE* 3.9 31.6 - - + -
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Residues in contact with ASP 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B SER 2.9 20.3 + - - +
178B LEU* 3.4 11.0 + - + +
179B LEU 3.4 0.2 - - - -
180B ILE* 1.3 72.2 - - - +
182B THR* 1.3 60.4 + - - +
184B ILE 3.2 4.9 - - - +
185B LYS* 3.4 7.3 + - - -
190B ARG* 2.7 55.6 + - - +
194B PHE* 3.2 23.4 - - - -
83C PHE* 3.4 24.6 - - - -
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 3.4 31.9 - - + +
113B ILE* 4.1 29.1 - - + +
178B LEU* 2.6 25.2 + - - +
179B LEU 3.7 3.6 - - - -
181B ASP* 1.3 78.7 - - - +
183B TYR* 1.3 73.1 + - + +
185B LYS* 3.7 19.4 + - - +
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Residues in contact with TYR 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 5.0 1.6 - - + -
112B ASP* 2.5 44.5 + - + -
113B ILE* 5.1 4.9 - - + -
116B TRP* 3.2 57.2 + + + +
127B ILE* 5.0 0.2 - - + -
131B LEU* 4.1 19.1 - - + -
179B LEU* 3.0 39.7 + - + +
180B ILE* 4.2 1.3 - - - +
182B THR* 1.3 95.7 - - + +
184B ILE* 1.3 64.1 + - + +
185B LYS* 4.1 3.5 + - - +
252B MET* 3.3 26.3 - - + +
255B LEU* 3.4 19.7 - - + +
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Residues in contact with ILE 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TRP* 4.1 21.1 - - + +
128B SER* 4.3 18.4 - - - -
180B ILE* 2.8 26.3 + - + +
181B ASP 3.2 8.1 - - - +
183B TYR* 1.3 77.4 - - + +
185B LYS* 1.3 54.6 + - - +
186B ASP* 3.9 11.2 - - + +
189B GLU* 3.6 41.3 - - + -
190B ARG* 2.7 38.6 + - + +
193B LEU* 4.2 11.7 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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