Contacts of the helix formed by residues 133 - 157 (chain E) in PDB entry 1O9R
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 ASP 133 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG* 5.6 0.2 + - - -
10E LEU* 3.5 29.4 - - + +
14E ALA* 5.4 0.2 - - + -
18E VAL* 3.5 21.3 - - + +
72E ARG* 3.0 18.2 + - - -
76E LEU* 3.6 2.8 - - - +
128E SER 3.0 18.6 + - - +
129E ASP 3.9 0.6 + - - -
131E ALA 5.1 0.2 - - - -
132E GLY* 1.3 80.8 - - - +
134E PRO* 1.3 57.9 - - - +
135E THR* 3.4 4.3 + - - -
136E THR* 2.5 40.4 + - - -
137E ALA* 3.0 22.3 + - - +
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Residues in contact with PRO 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 6.0 4.5 - - + +
125A ILE* 4.2 24.0 - - + -
126A ASP* 3.6 23.6 - - - +
141A THR* 4.0 5.7 - - - +
129E ASP* 4.0 18.1 - - - +
132E GLY* 3.3 10.8 - - - +
133E ASP* 1.3 87.3 - - - +
135E THR* 1.3 61.0 + - - +
136E THR 3.4 0.2 - - - -
137E ALA* 3.6 10.8 - - + +
138E ASP* 2.9 28.2 + - - +
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Residues in contact with THR 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 4.9 4.5 + - - +
125A ILE* 3.4 11.8 - - - +
141A THR* 4.1 8.0 - - - +
144A SER* 2.7 34.6 + - - +
145A ARG* 3.7 29.0 - - + +
72E ARG* 3.5 34.1 - - - +
133E ASP* 3.2 2.6 - - - -
134E PRO* 1.3 78.7 - - - +
136E THR* 1.3 61.9 + - - +
138E ASP* 3.2 12.3 + - - +
139E ILE* 3.3 14.1 + - + +
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Residues in contact with THR 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E VAL* 3.4 23.5 - - + +
22E LEU* 3.8 14.4 - - + -
72E ARG* 2.8 25.2 + - + +
76E LEU* 4.1 0.2 - - - +
128E SER* 3.6 4.0 - - - +
133E ASP* 2.5 36.4 + - - -
135E THR* 1.3 72.1 - - - +
137E ALA* 1.3 65.3 + - - +
139E ILE* 3.0 17.1 + - + +
140E PHE* 3.1 34.8 + - + -
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Residues in contact with ALA 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ILE* 3.6 31.3 - - + +
128E SER* 3.8 7.1 - - - -
129E ASP* 3.8 15.7 - - + +
133E ASP 3.0 14.8 + - - +
134E PRO* 3.6 13.5 - - + +
135E THR 3.2 0.2 - - - -
136E THR* 1.3 76.0 - - - +
138E ASP* 1.3 55.9 + - - +
140E PHE* 3.3 5.0 + - - +
141E THR* 2.8 31.6 + - - -
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Residues in contact with ASP 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ASP* 4.1 3.5 - - - +
141A THR* 3.5 24.9 - - + +
145A ARG* 2.9 24.9 + - - -
138C ASP* 4.1 3.5 - - - +
134E PRO 2.9 7.2 + - - +
135E THR 3.4 9.9 - - - +
136E THR 3.1 0.2 - - - -
137E ALA* 1.3 73.1 - - - +
139E ILE* 1.3 64.7 + - - +
141E THR* 3.1 7.6 + - - -
142E ALA* 2.9 23.4 + - - +
1164E TRS 2.6 48.3 + - - -
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Residues in contact with ILE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ARG* 3.5 35.2 - - + +
22E LEU* 5.1 4.9 - - + -
65E HIS* 4.7 2.9 + - - +
68E THR* 3.7 27.8 - - + +
69E ILE* 4.1 27.8 - - + +
72E ARG* 3.7 41.1 - - + +
75E GLN* 5.4 2.0 - - - +
135E THR* 3.3 10.7 + - + +
136E THR* 3.0 8.6 + - - +
138E ASP* 1.3 78.5 - - - +
140E PHE* 1.4 62.1 + - + +
142E ALA* 3.4 3.7 + - - +
143E ALA* 3.1 21.8 + - + +
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Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ILE* 3.8 15.5 - - + -
22E LEU* 3.5 24.9 - - + -
25E SER* 3.6 25.4 - - - -
69E ILE* 4.1 17.3 - - + -
121E ILE* 3.3 24.0 - - + +
124E ALA* 3.7 23.8 - - + -
125E ILE* 3.7 20.2 - - + +
128E SER* 3.3 29.4 - - - -
136E THR* 3.1 33.7 + - + -
137E ALA 3.7 4.0 - - - +
139E ILE* 1.4 78.6 - - + +
141E THR* 1.3 56.9 + - - +
143E ALA* 3.3 2.5 + - - -
144E SER* 2.8 29.5 + - - -
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Residues in contact with THR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PRO* 4.0 12.6 - - - +
135C THR* 4.2 9.1 + - - +
138C ASP* 3.4 40.4 - - + +
125E ILE* 3.4 25.8 - - - +
137E ALA 2.8 18.8 + - - -
138E ASP* 3.1 11.0 + - - +
140E PHE* 1.3 72.7 - - - +
142E ALA* 1.3 66.3 + - - +
144E SER* 3.2 2.1 + - - -
145E ARG* 3.0 23.7 + - - +
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Residues in contact with ALA 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ARG* 4.4 15.3 - - - +
65E HIS* 3.5 18.0 + - + -
138E ASP 2.9 15.1 + - - +
139E ILE 3.7 4.7 - - - +
141E THR* 1.3 79.1 - - - +
143E ALA* 1.4 62.4 + - - +
145E ARG* 3.4 15.6 + - - +
146E ASP* 3.4 11.3 + - - +
1164E TRS 4.5 17.2 + - - +
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E HIS* 3.5 37.4 + - + +
69E ILE* 5.0 5.6 - - + -
121E ILE* 4.0 17.9 - - + -
139E ILE* 3.1 12.9 + - + +
140E PHE* 3.6 9.4 - - - +
141E THR 3.2 0.2 - - - -
142E ALA* 1.4 76.3 - - - +
144E SER* 1.3 58.3 + - - +
146E ASP* 3.2 3.5 + - - +
147E LEU* 2.8 38.0 + - + +
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Residues in contact with SER 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C THR* 2.8 27.8 + - - +
118E ALA 5.1 1.6 + - - -
121E ILE* 3.7 14.1 - - - +
122E ARG* 4.2 11.2 + - - -
125E ILE* 3.8 11.7 - - - +
140E PHE 2.8 16.7 + - - -
141E THR 3.2 6.0 + - - -
143E ALA* 1.3 73.8 - - - +
145E ARG* 1.3 60.9 + - - +
147E LEU* 4.4 4.3 - - - +
148E ASP* 2.8 40.7 + - - +
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Residues in contact with ARG 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C THR* 3.6 25.7 + - - +
75C GLN* 4.7 3.5 + - - +
135C THR* 3.6 25.4 - - + +
138C ASP* 2.9 41.7 + - - -
139C ILE* 3.6 24.4 - - + +
142C ALA* 4.3 10.5 - - - +
141E THR 3.0 15.9 + - - +
142E ALA* 3.6 9.9 - - - +
143E ALA 3.2 0.4 - - - -
144E SER* 1.3 76.4 - - - +
146E ASP* 1.3 64.7 + - - +
148E ASP* 4.0 2.1 - - - +
149E LYS* 3.1 24.3 + - - +
1164E TRS 3.7 14.0 + - - -
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Residues in contact with ASP 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E GLN* 3.8 30.2 + - + +
65E HIS* 2.7 38.9 + - + +
142E ALA 3.4 4.5 + - - +
143E ALA 3.2 3.4 + - - +
145E ARG* 1.3 82.2 - - - +
147E LEU* 1.3 58.6 + - + +
149E LYS* 3.3 9.6 + - - +
150E SER* 2.9 33.2 + - - -
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 5.5 2.7 - - + -
32E LEU* 4.1 16.8 - - + -
62E LEU* 4.1 16.6 - - + -
65E HIS* 6.1 2.0 - - + -
114E TYR* 4.3 14.2 - - + +
117E VAL* 3.8 26.5 - - + +
118E ALA* 3.9 19.0 - - + +
121E ILE* 3.5 37.2 - - + -
143E ALA* 2.8 29.1 + - + +
144E SER* 4.0 3.4 - - - +
146E ASP* 1.3 69.7 - - + +
148E ASP* 1.3 62.3 + - - +
150E SER* 3.3 4.4 + - - -
151E LEU* 2.8 31.2 + - - +
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Residues in contact with ASP 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ASN* 3.2 15.4 - - - +
72C ARG* 2.7 34.4 + - - +
75C GLN* 3.7 9.3 - - + +
118E ALA* 3.6 11.3 - - - +
122E ARG* 2.9 40.3 + - - -
144E SER* 2.8 28.9 + - - +
145E ARG 4.2 1.1 - - - +
147E LEU* 1.3 72.1 - - - +
149E LYS* 1.3 62.1 + - - +
151E LEU* 3.8 6.6 - - - +
152E TRP* 3.1 22.7 + - - +
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Residues in contact with LYS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLU* 3.1 36.3 + - - +
75C GLN* 3.8 16.7 + - - +
145E ARG 3.1 19.6 + - - +
146E ASP* 3.8 8.5 - - - +
148E ASP* 1.3 75.2 - - - +
150E SER* 1.3 60.6 + - - +
152E TRP* 3.2 14.1 + - + +
153E PHE* 2.9 61.6 + - + +
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Residues in contact with SER 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E PHE* 3.5 36.4 - - - +
61E GLN* 3.5 11.3 + - - -
114E TYR* 3.9 21.3 - - - -
146E ASP 2.9 18.4 + - - -
147E LEU* 3.7 5.8 - - - -
149E LYS* 1.3 75.1 - - - +
151E LEU* 1.3 63.9 + - - +
153E PHE* 3.2 4.0 + - - +
154E LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C THR* 4.1 5.6 - - - +
7C LYS* 4.2 1.3 - - + -
8C ASN* 3.7 36.8 - - + +
111E ILE* 4.0 14.4 - - + +
114E TYR* 4.2 10.0 - - + -
115E GLY* 3.8 33.4 - - - +
118E ALA* 4.4 11.0 - - + -
147E LEU 2.8 21.9 + - - +
148E ASP* 3.8 7.0 - - - +
150E SER* 1.3 70.2 - - - +
152E TRP* 1.3 56.3 + - - +
154E LEU* 3.2 8.8 + - + +
155E GLU* 2.9 57.4 + - + +
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Residues in contact with TRP 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLU* 3.7 41.7 - - + -
74C VAL* 3.3 38.1 - - + +
75C GLN* 3.7 34.1 - - + +
148E ASP 3.1 14.0 + - - +
149E LYS* 3.4 10.3 - - + +
150E SER 3.2 0.2 - - - -
151E LEU* 1.3 76.8 - - - +
153E PHE* 1.3 92.1 + + - +
155E GLU* 3.2 8.2 + - - +
156E ALA* 2.7 46.2 + - + +
159E GLN* 4.9 8.1 - - - -
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Residues in contact with PHE 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLU* 5.6 0.7 - - - -
54E LEU* 3.9 31.0 - - + -
58E PHE* 4.0 16.2 - + + -
149E LYS* 2.9 40.3 + - + +
150E SER 3.2 8.0 + - - +
152E TRP* 1.3 114.3 - + - +
154E LEU* 1.3 54.7 + - - +
156E ALA* 3.6 10.2 + - + +
157E HIS* 2.7 33.2 + - + -
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Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E VAL* 5.8 1.3 - - + -
54E LEU* 5.3 5.4 - - + -
55E LEU* 4.5 5.2 - - + -
58E PHE* 3.8 20.9 - - + -
107E LEU* 3.7 25.0 - - + +
110E LEU* 4.2 26.5 - - + +
111E ILE* 3.6 22.3 - - + +
114E TYR* 3.6 44.9 - - + -
150E SER 3.0 17.6 + - - +
151E LEU* 3.6 5.6 - - - +
153E PHE* 1.3 73.5 - - - +
155E GLU* 1.3 65.5 + - - +
157E HIS* 3.2 22.8 + - - +
158E VAL* 3.9 1.7 + - - +
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Residues in contact with GLU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LYS 4.3 1.3 - - - -
6C THR* 2.6 33.0 + - - -
7C LYS* 2.8 36.6 + - - +
111E ILE* 3.7 27.5 - - + +
151E LEU* 2.9 35.6 + - + +
152E TRP* 3.9 6.4 - - - +
154E LEU* 1.3 72.1 - - - +
156E ALA* 1.3 59.1 + - - +
158E VAL* 2.9 21.5 + - + +
159E GLN* 3.0 32.4 + - + +
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Residues in contact with ALA 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E TRP* 2.7 39.3 + - + +
153E PHE* 4.0 7.9 - - - +
154E LEU 3.2 0.4 - - - -
155E GLU* 1.3 72.5 - - - +
157E HIS* 1.3 60.7 + - - +
158E VAL 3.5 0.3 + - - -
159E GLN* 3.3 19.8 + - - +
160E GLU* 4.6 5.5 + - - +
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Residues in contact with HIS 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLN* 5.7 7.2 - - + -
50E ALA* 6.0 3.0 - - - +
51E VAL* 4.2 24.4 - - + +
54E LEU* 4.2 23.1 - - + -
107E LEU* 3.8 24.5 - - + +
153E PHE* 2.7 27.6 + - + -
154E LEU* 3.2 12.4 + - - +
155E GLU 3.1 0.8 + - - -
156E ALA* 1.3 78.8 - - + +
158E VAL* 1.3 62.0 + - - +
160E GLU 3.7 10.0 - - - +
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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