Contacts of the helix formed by residues 158 - 184 (chain A) in PDB entry 3NJ0
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 THR 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 4.0 2.2 - - - -
156A GLY 5.0 2.9 - - - +
157A ASN* 1.3 76.7 - - - +
159A GLU* 1.3 61.8 + - - +
160A GLU* 3.4 14.5 + - - +
161A ASP* 3.0 40.5 + - - +
162A THR* 2.8 28.2 + - - -
68B LYS* 5.7 1.8 - - - +
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Residues in contact with GLU 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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31A ASP 5.2 0.7 - - - +
32A PRO* 5.8 1.7 - - - +
34A THR 3.7 13.4 - - - +
35A CYS* 3.6 21.7 - - + +
36A THR 5.1 0.3 + - - -
153A ILE* 3.6 26.6 - - + +
158A THR* 1.3 73.9 - - - +
160A GLU* 1.3 76.2 + - - +
162A THR* 3.7 1.5 - - - -
163A LYS* 2.9 34.6 + - + +
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 3.4 13.6 + - - +
159A GLU* 1.3 102.2 + - + +
161A ASP* 1.3 60.6 + - - +
163A LYS* 3.7 6.2 - - - +
164A MET* 3.0 32.7 + - + +
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Residues in contact with ASP 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ASN* 5.5 4.0 - - - +
158A THR* 3.0 30.9 + - - +
160A GLU* 1.3 78.4 - - - +
162A THR* 1.3 65.8 + - - +
164A MET* 3.5 10.6 + - - +
165A PHE* 3.0 23.9 + - - +
68B LYS* 2.9 43.9 + - - +
88B ILE* 4.0 21.6 - - + +
89B SER 4.9 2.7 - - - +
92B PRO* 6.4 0.7 - - + -
93B ALA* 3.6 18.1 + - + +
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Residues in contact with THR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 3.8 18.6 - - - -
121A LEU* 4.1 24.5 - - + -
151A VAL* 4.2 11.0 - - + -
153A ILE* 3.8 10.3 - - - +
154A PRO* 4.0 4.3 - - + +
157A ASN* 3.4 25.8 + - - +
158A THR 2.8 22.9 + - - -
159A GLU* 3.7 4.5 - - - -
161A ASP* 1.3 77.6 - - - +
163A LYS* 1.3 57.5 + - - +
165A PHE* 3.2 6.6 + - + +
166A VAL* 2.9 31.6 + - + +
89B SER 5.4 0.9 - - - -
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A CYS* 3.9 13.0 - - + -
36A THR 3.8 11.9 - - - +
37A SER* 3.2 21.9 + - - +
149A TYR* 3.7 11.0 - - - +
159A GLU* 2.9 23.3 + - + +
160A GLU* 3.7 6.5 - - - +
162A THR* 1.3 77.3 - - - +
164A MET* 1.3 58.9 + - - +
167A ASP* 2.8 60.4 + - - +
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Residues in contact with MET 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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160A GLU* 3.0 21.4 + - + +
161A ASP* 3.7 11.2 - - - +
163A LYS* 1.3 75.3 - - - +
165A PHE* 1.3 57.3 + - - +
167A ASP* 3.9 5.2 - - - +
168A THR* 2.7 38.3 + - - +
67B VAL 4.9 4.7 - - - +
68B LYS* 4.6 28.0 - - + +
88B ILE* 3.3 26.2 - - + -
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.9 20.6 - - + -
161A ASP 3.0 18.7 + - - +
162A THR* 3.2 5.1 + - + +
164A MET* 1.3 77.4 - - - +
166A VAL* 1.3 65.4 + - + +
168A THR* 3.2 14.3 + - - -
169A VAL* 3.2 16.6 + - + +
191A PEG 3.9 32.8 - - - -
300A PYV 3.5 27.8 - + + -
66B PHE* 3.7 27.8 - + - -
88B ILE* 3.7 9.6 - - + +
89B SER* 3.5 36.8 - - - +
90B GLY* 3.7 15.3 - - - -
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.1 17.5 - - + -
124A TYR* 4.0 16.2 - - + -
149A TYR* 3.3 40.6 - - + +
151A VAL* 4.4 8.7 - - + -
162A THR* 2.9 22.8 + - + +
165A PHE* 1.3 84.7 - - + +
167A ASP* 1.3 65.7 + - - +
168A THR 3.2 0.3 + - - -
169A VAL* 3.2 1.7 + - - +
170A VAL* 2.9 27.5 + - + +
300A PYV 4.1 15.5 - - + -
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 2.8 17.7 + - - -
39A ILE* 3.4 22.6 - - + +
149A TYR* 2.6 27.7 + - - -
163A LYS* 2.8 51.7 + - - +
164A MET* 3.9 5.0 - - - +
166A VAL* 1.3 71.2 - - - +
168A THR* 1.3 58.0 + - - +
170A VAL* 4.0 0.3 - - - +
171A LYS* 3.0 32.6 + - - +
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Residues in contact with THR 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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164A MET* 2.7 26.3 + - - +
165A PHE 3.4 5.6 - - - -
166A VAL 3.1 0.6 - - - -
167A ASP* 1.3 79.8 - - - +
169A VAL* 1.3 57.8 + - - +
171A LYS* 3.8 3.5 - - - +
172A LEU* 2.9 50.8 + - + +
65B HIS* 3.9 18.8 - - + +
66B PHE* 3.5 32.5 + - + +
88B ILE* 5.3 1.4 - - - +
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Residues in contact with VAL 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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65A HIS* 5.6 0.9 - - + +
66A PHE* 4.8 19.7 - - + -
165A PHE* 3.5 22.4 - - + +
166A VAL 3.2 3.7 + - - +
168A THR* 1.3 74.5 - - - +
170A VAL* 1.3 60.3 + - - +
172A LEU* 3.3 7.9 + - - +
173A ASN* 3.0 42.5 + - - +
191A PEG 5.1 0.7 - - - -
300A PYV 3.7 48.9 - - + -
66B PHE* 4.0 21.8 - - + -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 3.7 28.3 - - + -
124A TYR* 3.6 24.0 - - - +
147A GLU* 3.7 32.3 - - + +
149A TYR* 4.3 7.6 - - + -
166A VAL* 2.9 30.0 + - + +
167A ASP 4.0 2.9 - - - +
169A VAL* 1.3 77.0 - - - +
171A LYS* 1.3 63.0 + - - +
173A ASN* 3.2 10.1 + - - +
174A LEU* 2.9 23.8 + - + +
300A PYV 4.4 8.5 - - + -
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Residues in contact with LYS 171 (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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39A ILE* 3.9 17.7 - - + +
40A THR* 2.9 29.0 + - - +
41A GLN* 2.9 26.6 + - + +
42A ARG 5.3 0.6 - - - +
167A ASP 3.0 19.8 + - - +
168A THR* 3.8 4.7 - - - +
170A VAL* 1.3 75.7 - - - +
172A LEU* 1.3 60.3 + - + +
174A LEU* 3.1 3.4 + - + +
175A GLN* 2.9 49.8 + - - +
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Residues in contact with LEU 172 (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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65A HIS* 3.4 24.3 + - + -
66A PHE* 6.0 1.3 - - + -
168A THR* 2.9 40.3 + - + +
169A VAL* 3.6 8.1 - - + +
170A VAL 3.3 0.2 - - - -
171A LYS* 1.3 77.6 - - + +
173A ASN* 1.3 56.7 + - - +
175A GLN* 3.1 27.1 + - - +
176A LYS 3.0 22.5 + - - -
65B HIS* 3.6 38.8 - - + +
66B PHE* 4.7 4.0 - - + -
172B LEU* 4.0 26.7 - - + -
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Residues in contact with ASN 173 (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 TYR* 3.0 23.4 - - + +
64A LYS* 3.7 33.4 - - + +
65A HIS* 2.9 34.9 + - - +
147A GLU* 5.7 2.0 - - - +
169A VAL* 3.0 32.6 + - - +
170A VAL* 3.2 11.0 + - - +
172A LEU* 1.3 73.4 - - - +
174A LEU* 1.3 61.8 + - + +
176A LYS 3.2 0.7 + - - -
177A LEU* 2.9 27.2 + - - +
300A PYV 4.5 11.5 + - - -
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Residues in contact with LEU 174 (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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39A ILE* 4.1 35.2 - - + +
40A THR 4.4 0.4 - - - -
41A GLN* 3.6 38.0 - - + +
43A ILE* 4.3 1.0 - - - +
63A TYR* 4.8 8.1 - - + -
128A THR* 5.4 2.0 - - + -
145A VAL* 3.9 27.6 - - + +
147A GLU* 3.7 30.7 - - + +
170A VAL* 2.9 16.4 + - + +
171A LYS* 3.1 6.9 + - - +
173A ASN* 1.3 76.7 - - + +
175A GLN* 1.3 57.4 + - - +
177A LEU* 3.3 15.7 - - + +
178A GLY 2.9 22.9 + - - -
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Residues in contact with GLN 175 (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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41A GLN* 3.3 24.8 - - - +
171A LYS* 2.9 39.4 + - - +
172A LEU* 3.1 32.5 - - - +
173A ASN 3.2 0.2 - - - -
174A LEU* 1.3 76.4 - - - +
176A LYS* 1.3 56.5 + - - +
178A GLY* 3.1 3.2 + - - -
179A VAL* 3.0 32.2 + - + +
65B HIS* 6.3 0.4 - - - -
179B VAL* 6.1 3.9 - - - +
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Residues in contact with LYS 176 (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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61A GLU 2.9 28.4 + - - -
62A ARG 3.7 10.1 - - - +
63A TYR* 3.4 26.0 - - - +
64A LYS 2.9 14.8 + - - +
65A HIS* 3.7 38.9 + - + +
172A LEU 3.0 6.8 + - - +
173A ASN 3.2 1.8 + - - +
175A GLN* 1.3 72.8 - - - +
177A LEU* 1.3 65.5 + - - +
179A VAL* 3.2 10.8 + - + +
180A ALA* 3.0 22.1 + - + +
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Residues in contact with LEU 177 (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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43A ILE* 3.9 19.7 - - + -
50A VAL* 4.0 9.9 - - + +
53A LEU* 3.6 36.6 - - + -
54A ILE* 3.9 26.0 - - + -
63A TYR* 3.7 27.4 - - + +
145A VAL* 4.0 9.9 - - + -
173A ASN 2.9 12.9 + - - +
174A LEU* 3.3 24.9 - - + +
176A LYS* 1.3 76.5 - - - +
178A GLY* 1.3 57.2 + - - +
180A ALA* 3.2 3.7 + - - +
181A ALA* 2.9 28.6 + - - +
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Residues in contact with GLY 178 (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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41A GLN* 5.5 2.0 - - - -
43A ILE* 3.7 30.3 - - - -
174A LEU 2.9 13.3 + - - -
175A GLN* 3.1 4.8 + - - -
177A LEU* 1.3 75.4 - - - +
179A VAL* 1.3 60.4 + - - +
181A ALA* 3.3 0.5 + - - -
182A THR* 2.9 34.2 + - - +
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLN* 3.0 20.6 + - + +
176A LYS* 3.2 12.3 + - + +
178A GLY* 1.3 76.4 - - - +
180A ALA* 1.3 63.4 + - - +
182A THR* 3.8 5.4 - - - -
183A SER* 2.7 42.9 + - - +
184A ALA* 6.0 1.1 - - + -
175B GLN* 6.2 1.8 - - - +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 5.5 0.3 - - - +
53A LEU* 4.0 20.6 - - + +
62A ARG* 4.3 22.0 + - - +
63A TYR* 5.4 0.2 - - + -
176A LYS* 3.0 13.0 + - + +
177A LEU* 3.2 9.6 + - - +
179A VAL* 1.3 78.6 - - - +
181A ALA* 1.3 60.2 + - - +
184A ALA* 3.1 44.0 + - + +
185A PRO 5.3 0.2 - - - +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 4.2 3.6 - - + -
45A ALA* 3.6 11.4 - - + +
49A VAL* 3.5 28.5 - - + +
50A VAL* 3.8 29.4 - - + -
53A LEU* 3.9 14.8 - - + +
177A LEU 2.9 17.0 + - - +
178A GLY 4.0 3.1 - - - +
180A ALA* 1.3 77.7 - - - +
182A THR* 1.3 60.3 + - - +
183A SER 3.5 0.2 - - - -
184A ALA 5.1 1.9 - - - +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.9 12.3 - - + -
44A HIS* 3.4 38.4 - - + +
45A ALA* 4.5 2.2 - - - -
178A GLY* 2.9 21.5 + - - +
179A VAL* 3.4 8.0 + - - -
181A ALA* 1.3 77.7 - - - +
183A SER* 1.3 65.3 + - - +
184A ALA 5.5 0.2 - - - -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A VAL* 2.7 35.0 + - - +
181A ALA 3.5 0.6 - - - -
182A THR* 1.3 86.1 + - - +
184A ALA* 1.3 63.8 + - - +
185A PRO* 4.2 2.6 - - - +
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Residues in contact with ALA 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 6.0 0.9 - - - +
62A ARG* 4.6 5.4 - - - +
179A VAL* 4.6 1.6 - - + +
180A ALA* 3.1 34.0 + - + +
181A ALA 5.1 2.1 - - - +
183A SER* 1.3 82.5 + - - +
185A PRO* 1.3 78.2 - - + +
186A MET* 3.7 4.0 + - - +
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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