Contacts of the helix formed by residues 11 - 43 (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 PRO 11 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ASP 3.2 7.2 - - - +
10E LEU* 1.3 99.1 - - + +
12E SER* 1.3 65.7 + - - +
13E ASN* 4.4 6.3 - - + +
14E ALA* 3.0 14.8 + - + +
15E LYS* 2.9 19.2 + - - +
132E GLY 5.5 0.4 - - - +
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Residues in contact with SER 12 (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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10E LEU 3.5 2.3 + - - -
11E PRO* 1.3 69.7 - - - +
13E ASN* 1.4 60.4 + - - +
15E LYS* 3.2 15.6 + - - +
16E SER* 3.0 33.9 + - - -
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Residues in contact with ASN 13 (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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11E PRO* 3.2 5.1 - - + +
12E SER* 1.4 80.5 - - - +
14E ALA* 1.3 61.5 + - - +
16E SER* 3.8 4.8 - - - -
17E THR* 3.1 29.1 + - - +
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Residues in contact with ALA 14 (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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10E LEU* 3.8 24.9 - - + -
11E PRO* 3.0 19.6 + - + +
13E ASN* 1.3 75.3 - - - +
15E LYS* 1.3 67.8 + - - +
17E THR* 3.3 5.1 + - - -
18E VAL* 2.9 29.3 + - + +
131E ALA* 3.2 29.2 - - + +
132E GLY* 5.0 0.7 - - - -
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Residues in contact with LYS 15 (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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6E THR* 4.1 16.7 + - + +
8E ASN* 2.8 37.9 + - - +
9E ASP* 4.2 0.8 - - - +
10E LEU* 2.7 39.8 + - + +
11E PRO 2.9 14.4 + - - +
12E SER* 3.2 16.5 + - - +
14E ALA* 1.3 77.7 - - - +
16E SER* 1.4 64.3 + - - +
18E VAL* 3.4 0.5 + - - +
19E ILE* 2.9 32.5 + - + +
76E LEU* 3.3 38.3 - - + +
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Residues in contact with SER 16 (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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12E SER* 3.0 17.8 + - - -
13E ASN* 3.8 6.5 - - - -
15E LYS* 1.4 77.6 - - - +
17E THR* 1.4 64.6 + - - +
19E ILE* 3.5 9.3 + - - +
20E GLY* 3.3 16.6 + - - -
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Residues in contact with THR 17 (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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13E ASN* 3.1 16.7 + - - +
14E ALA* 3.8 3.4 - - - -
16E SER* 1.4 79.1 - - - +
18E VAL* 1.3 63.5 + - - +
20E GLY* 3.2 4.7 + - - -
21E ILE* 3.1 32.8 + - + +
127E ASP 5.3 0.2 - - - +
131E ALA* 4.1 22.2 - - + -
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Residues in contact with VAL 18 (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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14E ALA 2.9 20.8 + - - +
17E THR* 1.3 74.2 - - - +
19E ILE* 1.3 60.9 + - - +
21E ILE* 3.0 7.4 + - + +
22E LEU* 2.8 36.6 + - + +
76E LEU* 3.9 6.5 - - + -
128E SER* 4.2 11.7 - - - +
131E ALA* 3.8 25.4 - - + -
133E ASP* 3.5 28.5 - - + +
136E THR* 3.4 34.8 - - + +
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Residues in contact with ILE 19 (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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15E LYS* 2.9 26.6 + - + +
16E SER* 3.8 8.3 - - - +
17E THR 3.3 0.2 - - - -
18E VAL* 1.3 77.0 - - - +
20E GLY* 1.4 56.6 + - - +
22E LEU* 3.3 7.3 + - - +
23E ASN* 2.9 39.1 + - - +
73E VAL* 4.0 27.4 - - + +
76E LEU* 3.6 37.5 - - + +
77E GLY 4.4 0.9 - - - -
78E GLY* 3.7 21.3 - - - +
79E THR 5.2 0.7 - - - +
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Residues in contact with GLY 20 (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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16E SER 3.3 7.2 + - - -
17E THR 3.2 7.9 + - - -
19E ILE* 1.4 78.3 - - - +
21E ILE* 1.3 59.2 + - - +
23E ASN* 4.0 3.8 - - - +
24E GLU* 2.9 31.6 + - - +
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Residues in contact with ILE 21 (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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17E THR* 3.1 27.7 + - + +
18E VAL* 3.0 15.8 + - + +
20E GLY* 1.3 78.4 - - - +
22E LEU* 1.3 62.7 + - - +
24E GLU* 3.5 12.0 + - - +
25E SER* 3.0 24.2 + - - +
124E ALA* 3.7 30.7 - - + -
127E ASP* 3.7 39.9 - - + +
128E SER* 4.1 6.1 - - - +
140E PHE* 3.8 12.1 - - + -
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Residues in contact with LEU 22 (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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18E VAL* 2.8 34.0 + - + +
19E ILE* 3.7 1.1 - - - +
21E ILE* 1.3 78.4 - - - +
23E ASN* 1.3 58.4 + - - +
25E SER* 3.2 1.6 + - - -
26E LEU* 2.8 25.1 + - - +
69E ILE* 3.3 37.6 - - + +
72E ARG* 3.7 27.4 - - + -
73E VAL* 3.4 30.3 - - + +
76E LEU* 4.2 4.5 - - + -
136E THR* 3.8 11.4 - - + -
139E ILE* 5.1 2.7 - - + -
140E PHE* 3.5 29.4 - - + -
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Residues in contact with ASN 23 (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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19E ILE* 2.9 26.1 + - - +
20E GLY* 4.2 3.4 - - - +
22E LEU* 1.3 73.3 - - - +
24E GLU* 1.4 63.3 + - - +
26E LEU* 3.6 10.8 - - - +
27E ALA* 3.2 21.5 + - - +
73E VAL* 3.7 17.4 - - - +
79E THR 3.0 22.0 + - - -
80E ALA* 3.6 5.5 - - - -
81E LEU* 2.9 49.4 + - + +
90E THR* 4.1 4.8 - - + +
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Residues in contact with GLU 24 (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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20E GLY 2.9 20.2 + - - +
21E ILE* 3.7 12.0 - - - +
23E ASN* 1.4 76.4 - - - +
25E SER* 1.3 65.4 + - - +
27E ALA* 3.3 12.3 + - - +
28E SER* 3.5 11.8 + - - -
90E THR* 3.9 13.0 - - + +
92E LYS* 3.8 33.1 + - - +
120E MET* 4.3 13.9 - - + +
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Residues in contact with SER 25 (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* 3.0 16.4 + - - +
22E LEU 3.7 3.4 - - - -
24E GLU* 1.3 80.6 + - - +
26E LEU* 1.3 64.3 + - - +
28E SER* 3.2 4.2 + - - -
29E VAL* 2.9 27.9 + - - +
69E ILE* 4.5 3.6 - - - -
120E MET* 4.0 18.1 + - - +
121E ILE* 3.5 23.5 - - - +
124E ALA* 4.2 7.4 - - - +
140E PHE* 3.6 22.0 - - - -
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Residues in contact with LEU 26 (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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22E LEU 2.8 20.7 + - - +
23E ASN* 3.6 18.8 - - - +
24E GLU 3.2 0.2 - - - -
25E SER* 1.3 74.0 - - - +
27E ALA* 1.4 62.7 + - - +
29E VAL* 3.2 3.7 + - + +
30E ILE* 2.9 43.4 + - + +
66E GLY* 3.4 37.9 - - - +
69E ILE* 4.0 8.7 - - + +
70E ALA* 3.8 24.9 - - + +
73E VAL* 5.5 0.2 - - + -
81E LEU 3.7 27.4 - - - +
82E GLY 4.3 2.5 - - - +
41F TRP* 4.3 8.1 - - + -
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Residues in contact with ALA 27 (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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23E ASN 3.2 6.2 + - - +
24E GLU 3.8 2.0 - - - +
25E SER 3.2 0.2 - - - -
26E LEU* 1.4 80.8 - - - +
28E SER* 1.3 58.4 + - - +
30E ILE 3.4 0.2 + - - -
31E ASP* 3.0 28.1 + - - +
81E LEU 5.0 3.8 + - - +
86E ALA 4.3 0.7 - - - +
87E VAL* 3.5 29.1 - - + +
90E THR* 3.6 38.8 - - + -
91E THR* 3.8 11.4 - - - +
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Residues in contact with SER 28 (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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24E GLU 3.5 3.9 + - - -
25E SER 3.2 2.6 + - - -
27E ALA* 1.3 76.7 - - - +
29E VAL* 1.3 62.1 + - - +
31E ASP* 3.7 1.4 - - - +
32E LEU* 2.9 29.5 + - - +
91E THR* 3.8 8.3 - - - -
92E LYS* 2.9 37.2 + - - +
93E LEU* 3.8 6.4 + - - +
117E VAL* 3.9 13.1 - - - +
120E MET* 3.8 30.0 - - - +
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Residues in contact with VAL 29 (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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25E SER 2.9 24.4 + - - +
26E LEU* 3.2 6.5 + - - +
28E SER* 1.3 74.1 - - - +
30E ILE* 1.3 60.6 + - + +
32E LEU* 3.3 8.2 + - - +
33E ALA* 2.9 26.9 + - + +
62E LEU* 3.6 38.2 - - + +
65E HIS* 4.8 3.1 - - + -
66E GLY* 3.8 18.2 - - - +
69E ILE* 4.4 14.8 - - + -
117E VAL* 4.1 19.5 - - + -
120E MET* 6.3 0.2 - - + -
121E ILE* 4.5 8.1 - - + -
147E LEU* 5.5 2.5 - - + -
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Residues in contact with ILE 30 (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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26E LEU* 2.9 41.1 + - + +
27E ALA 3.9 3.6 - - - +
29E VAL* 1.3 78.4 - - + +
31E ASP* 1.4 64.2 + - - +
33E ALA* 3.1 9.5 + - + +
34E LEU* 2.9 27.9 + - + +
66E GLY* 5.7 2.0 - - - -
82E GLY* 3.6 34.8 - - - +
87E VAL* 3.9 19.7 - - + -
34F LEU* 3.8 27.8 - - + -
41F TRP* 4.5 10.3 - - + -
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Residues in contact with ASP 31 (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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27E ALA 3.0 18.1 + - - +
28E SER 3.7 3.6 - - - +
30E ILE* 1.4 77.6 - - - +
32E LEU* 1.4 57.1 + - - +
34E LEU* 3.0 10.4 + - - +
35E VAL* 2.8 39.8 + - - +
87E VAL* 4.0 10.9 - - + +
91E THR* 2.6 33.9 + - - +
93E LEU* 3.5 19.9 - - + +
94E LYS 5.3 1.4 - - - +
84F LEU* 3.7 22.4 + - - +
85F GLN* 5.1 3.1 + - - +
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Residues in contact with LEU 32 (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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28E SER 2.9 18.9 + - - +
29E VAL* 3.5 6.3 - - - +
30E ILE 3.2 0.2 - - - -
31E ASP* 1.4 75.1 - - - +
33E ALA* 1.3 58.3 + - - +
35E VAL* 3.3 9.9 + - + +
36E THR* 2.8 33.6 + - - -
62E LEU* 3.9 18.2 - - + -
93E LEU* 3.9 6.4 - - + +
113E ARG* 3.6 40.8 - - + +
114E TYR* 3.7 43.7 - - + -
117E VAL* 3.9 24.2 - - + -
147E LEU* 4.1 2.7 - - + -
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Residues in contact with ALA 33 (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* 2.9 13.8 + - + +
30E ILE* 3.1 13.2 + - + +
32E LEU* 1.3 78.3 - - - +
34E LEU* 1.4 64.1 + - + +
36E THR* 3.3 8.7 + - - -
37E LYS 3.4 5.7 + - - -
59E ARG* 3.0 46.6 + - - +
62E LEU* 3.8 21.3 - - + +
63E ASP* 4.4 4.0 - - - +
59F ARG* 6.2 0.2 - - - +
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Residues in contact with LEU 34 (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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30E ILE* 2.9 22.5 + - + +
31E ASP* 3.0 8.9 + - - +
33E ALA* 1.4 78.4 - - + +
35E VAL* 1.4 56.7 - - - +
37E LYS* 3.3 4.7 + - - +
38E GLN* 2.9 28.5 + - - +
41E TRP* 5.3 0.2 - - - -
59E ARG* 4.2 17.3 - - - +
84E LEU* 5.6 0.4 - - + -
30F ILE* 3.8 28.3 - - + -
34F LEU* 4.6 23.6 - - + -
82F GLY 4.0 18.3 - - - +
83F SER* 5.2 1.3 - - - -
84F LEU* 4.0 44.0 - - + +
87F VAL* 5.4 1.8 - - + -
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Residues in contact with VAL 35 (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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31E ASP* 2.8 33.2 + - - +
32E LEU* 3.4 20.6 - - + +
34E LEU* 1.4 73.8 - - + +
36E THR* 1.4 64.2 + - - +
38E GLN* 3.2 8.6 + - - +
39E ALA* 3.0 24.1 + - - +
93E LEU* 5.0 0.9 - - + -
94E LYS 5.7 0.4 - - - +
96E TYR* 3.7 39.9 - - + +
110E LEU* 3.6 22.0 - - + -
113E ARG* 4.2 18.6 - - - +
83F SER* 5.7 3.1 - - - +
84F LEU 6.1 0.7 - - - +
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Residues in contact with THR 36 (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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32E LEU 2.8 19.7 + - - -
33E ALA* 3.5 8.7 - - - -
34E LEU 3.2 0.4 - - - -
35E VAL* 1.4 78.5 - - - +
37E LYS* 1.3 57.1 + - - +
39E ALA* 3.5 2.8 + - - +
40E HIS* 3.0 26.7 + - - +
55E LEU* 3.2 40.9 - - + +
58E PHE* 4.1 1.8 - - + -
59E ARG* 4.0 14.1 - - + +
62E LEU* 3.7 2.4 - - - +
110E LEU* 4.3 6.1 - - - -
114E TYR* 2.7 35.9 + - - +
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Residues in contact with LYS 37 (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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33E ALA 3.4 1.4 + - - -
34E LEU* 3.3 5.8 + - - +
36E THR* 1.3 74.5 - - - +
38E GLN* 1.3 67.6 + - - +
40E HIS* 3.4 21.5 + - + +
41E TRP* 2.9 51.8 + - + -
56E ASP* 2.6 32.6 + - - +
59E ARG* 3.3 48.9 - - + +
67F ASP* 2.9 41.2 + - - +
1163F FE 4.3 1.0 - - - -
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Residues in contact with GLN 38 (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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34E LEU 2.9 17.2 + - - +
35E VAL* 3.5 9.6 - - - +
37E LYS* 1.3 78.3 - - - +
39E ALA* 1.4 62.3 + - - +
41E TRP* 3.9 6.8 - - - -
42E ASN* 3.0 39.7 + - - +
96E TYR* 3.7 24.9 - - + -
97E PRO 5.2 0.4 - - - +
98E THR* 4.1 21.5 - - + +
106E HIS* 4.5 1.8 - - + -
79F THR* 4.7 0.9 - - - +
80F ALA 3.0 20.7 + - - +
81F LEU* 4.5 0.6 - - - -
82F GLY* 2.8 35.3 - - - +
83F SER* 3.3 20.1 - - - +
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Residues in contact with ALA 39 (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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35E VAL 3.0 14.9 + - - +
36E THR 3.8 4.0 - - - +
38E GLN* 1.4 76.1 - - - +
40E HIS* 1.3 65.7 + - - +
42E ASN 3.1 0.3 + - - -
43E LEU* 3.0 32.9 + - + +
55E LEU* 4.0 3.4 - - + -
96E TYR* 3.5 22.2 - - - +
106E HIS* 3.5 16.6 - - - +
110E LEU* 3.8 22.4 - - + -
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Residues in contact with HIS 40 (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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36E THR 3.0 19.0 + - - +
37E LYS* 3.1 16.9 + - + +
39E ALA* 1.3 77.0 - - - +
41E TRP* 1.3 83.8 + + - +
43E LEU* 4.1 7.6 + - - +
48E PHE* 4.6 1.7 - - - -
52E HIS* 2.8 74.6 + + - +
55E LEU* 3.7 18.1 - - + +
56E ASP* 3.1 34.5 + - - -
1163F FE 2.9 21.7 - - - -
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Residues in contact with TRP 41 (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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37E LYS* 2.9 50.9 + - + +
38E GLN* 3.9 10.3 - - - -
40E HIS* 1.3 92.3 + + - +
42E ASN* 1.3 62.2 + - - +
43E LEU 3.6 3.2 + - - +
44E LYS* 4.8 2.1 + - - -
48E PHE* 5.2 4.0 - - - -
52E HIS* 4.8 3.6 + + - -
26F LEU* 4.4 12.6 - - + -
30F ILE* 4.4 9.9 - - + -
66F GLY 4.3 1.6 - - - -
67F ASP* 3.4 35.9 + - - +
70F ALA* 3.2 34.1 - - + +
71F GLU* 4.1 17.4 - - + +
74F VAL* 3.5 26.0 - - + +
80F ALA* 3.9 23.3 - - + -
82F GLY* 4.1 24.2 - - - -
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Residues in contact with ASN 42 (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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38E GLN* 3.0 34.5 + - - +
39E ALA 3.1 2.4 + - - -
41E TRP* 1.3 77.3 - - - +
43E LEU* 1.3 65.2 + - - +
44E LYS* 3.6 12.0 + - - +
100E ILE 4.5 4.9 - - - +
101E TYR* 3.6 27.2 - - + +
106E HIS* 3.9 15.3 - - + +
74F VAL* 3.7 7.3 - - - +
78F GLY 4.4 0.5 - - - +
79F THR* 3.5 17.7 + - - +
80F ALA* 3.0 50.1 + - - +
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Residues in contact with LEU 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E ALA* 3.0 30.3 + - + +
40E HIS* 4.4 6.5 - - - +
41E TRP 3.6 2.8 - - - +
42E ASN* 1.3 77.9 - - - +
44E LYS* 1.3 66.8 + - - +
48E PHE* 3.2 31.0 - - + +
51E VAL* 3.3 38.4 - - + -
52E HIS* 3.9 10.8 - - - +
55E LEU* 4.0 13.5 - - + -
101E TYR 3.5 6.5 - - - -
103E ILE* 3.9 20.0 - - + +
106E HIS* 3.5 31.6 - - + -
107E LEU* 6.4 0.4 - - + -
110E LEU* 5.1 0.7 - - + -
----------------------------------------------------------
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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
------------------------------------------------------------
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