Contacts of the helix formed by residues 11 - 51 (chain A) in PDB entry 4OH9
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 SER 11 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 1.3 75.9 - - - +
12A LEU* 1.3 65.2 + - - +
13A GLU* 3.5 7.7 + - - +
14A GLU* 3.0 42.0 + - - +
15A LEU* 3.0 21.1 + - - +
51B LYS* 4.3 5.6 - - - +
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Residues in contact with LEU 12 (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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10A LEU 3.9 1.0 + - - -
11A SER* 1.3 72.7 - - - +
13A GLU* 1.3 59.5 + - + +
15A LEU* 3.4 7.7 + - + +
16A GLN* 3.0 27.7 + - - +
48B MET* 3.7 50.6 - - + +
51B LYS* 3.8 29.8 - - + +
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.1 7.2 + - - +
12A LEU* 1.3 78.4 - - + +
14A GLU* 1.3 63.4 + - - +
16A GLN* 3.5 5.9 + - - +
17A MET* 3.1 40.1 + - + +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.6 25.3 - - + +
11A SER* 3.0 41.8 + - - +
13A GLU* 1.3 75.6 - - - +
15A LEU* 1.3 58.7 + - - +
17A MET* 3.3 20.7 + - + +
18A ARG* 3.0 34.6 + - - +
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.4 44.0 - - + +
8A LYS* 5.2 0.9 - - - -
10A LEU* 4.0 21.1 - - + +
11A SER 3.0 18.3 + - - +
12A LEU* 3.6 15.0 - - + +
13A GLU 3.3 0.2 - - - -
14A GLU* 1.3 72.9 - - - +
16A GLN* 1.3 60.8 + - - +
18A ARG* 3.2 4.3 + - - +
19A LEU* 2.8 24.9 + - - +
44B ILE* 3.5 18.1 - - + +
47B ALA* 3.9 26.2 - - + +
48B MET* 3.7 28.7 - - + +
51B LYS* 4.9 2.5 - - + -
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Residues in contact with GLN 16 (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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12A LEU 3.0 16.7 + - - +
13A GLU* 4.0 6.3 - - - +
14A GLU 3.3 0.2 - - - -
15A LEU* 1.3 75.4 - - - +
17A MET* 1.3 63.6 + - - +
19A LEU* 3.3 15.9 + - - +
20A LYS* 2.9 58.2 + - - +
48B MET* 3.1 28.9 - - + +
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Residues in contact with MET 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU* 3.1 43.2 + - + +
14A GLU* 3.4 25.8 - - + +
16A GLN* 1.3 77.1 - - + +
18A ARG* 1.3 62.1 + - + +
20A LYS* 3.3 9.0 + - + +
21A ALA* 3.0 23.9 + - - +
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Residues in contact with ARG 18 (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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1A GLY* 4.4 8.3 - - - -
2A SER* 3.5 33.3 + - - +
6A PHE* 4.3 11.5 - - - -
7A LEU* 3.8 15.5 - - - +
10A LEU* 3.4 27.6 - - - +
14A GLU* 3.0 19.0 + - - +
15A LEU* 3.6 9.4 - - - +
17A MET* 1.3 72.9 - - + +
19A LEU* 1.3 67.2 + - - +
21A ALA* 3.4 13.9 + - - +
22A LEU* 3.6 16.8 + - - +
44B ILE* 4.0 17.3 - - + +
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Residues in contact with LEU 19 (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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15A LEU 2.8 16.1 + - - +
16A GLN* 3.6 26.5 - - - +
18A ARG* 1.3 76.0 - - - +
20A LYS* 1.3 64.7 + - + +
22A LEU* 3.3 20.5 + - + +
23A ASP* 4.2 6.8 - - - +
41B ARG* 4.0 53.2 + - + +
44B ILE* 3.9 21.2 - - + +
45B LEU* 3.8 25.1 - - + -
48B MET* 4.2 6.5 - - - -
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Residues in contact with LYS 20 (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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16A GLN* 2.9 52.7 + - + +
17A MET* 3.8 7.2 - - - +
18A ARG 3.3 0.2 - - - -
19A LEU* 1.3 80.7 - - + +
21A ALA* 1.3 60.4 + - - +
22A LEU 3.2 0.9 + - - -
23A ASP* 3.3 13.1 + - - +
24A PRO* 3.3 16.8 - - - +
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Residues in contact with ALA 21 (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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17A MET 3.0 16.6 + - - +
18A ARG* 3.8 9.0 - - - +
19A LEU 3.3 0.8 - - - -
20A LYS* 1.3 78.3 - - - +
22A LEU* 1.3 63.0 + - + +
24A PRO* 3.2 14.9 - - - +
25A MET* 3.4 25.3 + - + +
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Residues in contact with LEU 22 (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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18A ARG 3.6 11.7 - - - +
19A LEU* 3.5 12.3 - - - +
20A LYS 3.1 0.8 - - - -
21A ALA* 1.3 79.3 - - + +
23A ASP* 1.3 56.4 + - - +
25A MET* 3.4 14.6 + - + +
26A MET* 2.9 31.7 + - - +
37B TYR* 3.9 16.8 - - + +
40B LYS* 3.9 42.2 - - + +
41B ARG* 3.5 44.4 - - + +
44B ILE* 4.0 14.8 - - + -
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Residues in contact with ASP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU 4.2 7.2 - - - +
20A LYS* 3.3 11.4 + - - +
22A LEU* 1.3 75.1 - - - +
24A PRO* 1.3 72.5 - - + +
26A MET* 3.4 3.2 + - - +
27A GLU* 3.0 35.7 + - - +
37B TYR* 2.5 36.5 + - - -
41B ARG* 5.2 4.5 + - - -
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Residues in contact with PRO 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS 3.3 12.8 - - - +
21A ALA* 3.2 15.3 - - - +
23A ASP* 1.3 93.4 - - + +
25A MET* 1.3 55.0 + - - +
27A GLU* 3.8 9.4 - - + +
28A ARG* 2.9 30.5 + - - +
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Residues in contact with MET 25 (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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21A ALA* 3.4 30.5 + - + +
22A LEU* 3.7 15.9 - - + +
23A ASP 3.2 0.4 - - - -
24A PRO* 1.3 77.4 - - - +
26A MET* 1.3 64.4 + - - +
28A ARG* 3.3 9.7 + - + +
29A GLU* 3.0 45.1 + - + +
36B ARG* 6.0 1.3 - - - -
40B LYS* 5.0 18.2 - - - +
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Residues in contact with MET 26 (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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22A LEU 2.9 18.8 + - - +
23A ASP* 3.7 4.9 - - - +
25A MET* 1.3 78.8 - - - +
27A GLU* 1.3 66.0 + - - +
29A GLU* 3.2 13.9 + - - +
30A ILE* 3.0 47.0 + - + +
33B LEU* 4.7 3.6 - - + +
34B ARG* 3.5 45.1 - - + +
37B TYR* 3.2 49.8 - - + -
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Residues in contact with GLU 27 (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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23A ASP* 3.0 28.4 + - - +
24A PRO* 3.8 7.5 - - + +
25A MET 3.3 0.2 - - - -
26A MET* 1.3 78.9 - - + +
28A ARG* 1.3 62.4 + - - +
30A ILE* 3.6 4.7 + - - +
31A GLU* 3.0 25.5 + - - +
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Residues in contact with ARG 28 (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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24A PRO 2.9 17.4 + - - +
25A MET* 3.6 8.5 - - - +
27A GLU* 1.3 76.7 - - - +
29A GLU* 1.3 63.8 + - + +
31A GLU* 3.3 14.3 + - - +
32A GLU* 3.0 46.6 + - + +
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Residues in contact with GLU 29 (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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25A MET* 3.0 39.6 + - + +
26A MET* 3.2 13.3 + - - +
28A ARG* 1.3 78.4 - - + +
30A ILE* 1.3 62.2 + - - +
32A GLU* 3.3 15.9 + - - +
33A LEU* 3.0 22.0 + - - +
33B LEU* 3.7 22.4 - - + +
36B ARG* 3.0 39.3 + - - -
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Residues in contact with ILE 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 3.0 39.3 + - + +
27A GLU* 4.3 4.0 - - - +
29A GLU* 1.3 72.4 - - - +
31A GLU* 1.3 61.9 + - - +
33A LEU* 3.2 3.1 + - - +
34A ARG* 2.8 58.6 + - + +
30B ILE* 4.7 13.2 - - + -
33B LEU* 3.6 26.9 - - + -
34B ARG* 3.5 35.4 - - + +
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Residues in contact with GLU 31 (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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27A GLU 3.0 19.7 + - - +
28A ARG* 3.5 14.9 - - - +
30A ILE* 1.3 76.5 - - - +
32A GLU* 1.3 59.9 + - - +
34A ARG* 3.2 10.3 + - - +
35A GLN* 2.5 68.8 + - + +
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Residues in contact with GLU 32 (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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28A ARG* 3.0 48.9 + - + +
29A GLU* 3.6 18.4 + - - +
30A ILE 3.3 0.2 - - - -
31A GLU* 1.3 78.3 - - - +
33A LEU* 1.3 58.4 + - - +
35A GLN* 3.3 14.5 + - - +
36A ARG* 2.8 30.5 + - - +
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Residues in contact with LEU 33 (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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29A GLU 3.0 12.1 + - - +
30A ILE* 3.4 9.9 - - - +
32A GLU* 1.3 77.2 - - - +
34A ARG* 1.3 63.1 + - - +
36A ARG* 3.3 29.4 + - - +
37A TYR* 3.1 46.1 + - + -
26B MET* 4.1 6.5 - - + +
29B GLU* 3.8 30.7 - - + +
30B ILE* 3.5 29.6 - - + +
33B LEU* 3.6 24.7 - - + -
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Residues in contact with ARG 34 (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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30A ILE* 2.8 37.2 + - + +
31A GLU* 3.2 7.8 + - + +
33A LEU* 1.3 74.5 - - + +
35A GLN* 1.3 58.7 + - + +
37A TYR* 3.2 5.9 + - - +
38A THR* 2.9 32.6 + - - +
41A ARG* 4.8 1.2 + - - -
26B MET* 5.0 11.1 - - - -
30B ILE* 3.8 28.1 - - + +
34B ARG* 3.6 25.3 - - - +
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Residues in contact with GLN 35 (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 GLU* 2.5 52.3 + - + +
32A GLU* 3.5 15.1 - - - +
34A ARG* 1.3 78.5 - - + +
36A ARG* 1.3 55.8 + - - +
38A THR* 3.2 8.5 + - - -
39A ALA* 2.9 31.5 + - - +
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Residues in contact with ARG 36 (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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32A GLU 2.8 20.7 + - - +
33A LEU* 3.3 33.4 + - - +
35A GLN* 1.3 73.7 - - - +
37A TYR* 1.3 71.0 + - + +
39A ALA* 3.5 7.4 + - - +
40A LYS* 3.1 30.7 + - + +
29B GLU* 3.3 36.5 + - - +
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Residues in contact with TYR 37 (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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33A LEU* 3.1 37.8 + - + -
34A ARG 3.9 3.6 - - - +
36A ARG* 1.3 92.4 + - + +
38A THR* 1.3 61.1 + - - +
40A LYS* 3.1 10.2 + - + +
41A ARG* 2.9 40.2 + - - +
22B LEU* 3.7 36.8 - - + -
25B MET* 3.5 30.3 - - + +
26B MET* 3.6 41.1 - - + -
29B GLU* 2.4 35.3 + - - -
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Residues in contact with THR 38 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 2.9 18.3 + - - +
35A GLN* 3.2 11.7 + - - -
37A TYR* 1.3 75.0 - - - +
39A ALA* 1.3 58.3 + - - +
41A ARG* 2.9 31.6 + - - +
42A GLN* 3.0 36.2 + - + +
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Residues in contact with ALA 39 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLN 2.9 16.4 + - - +
36A ARG* 3.7 7.4 - - - +
38A THR* 1.3 78.7 - - - +
40A LYS* 1.3 61.6 + - - +
42A GLN* 3.9 4.7 - - - +
43A PRO* 3.1 20.8 - - - +
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Residues in contact with LYS 40 (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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36A ARG* 3.1 21.4 + - + +
37A TYR* 3.1 18.1 + - + +
39A ALA* 1.3 78.8 - - - +
41A ARG* 1.3 61.4 + - - +
42A GLN 3.4 0.3 + - - -
43A PRO* 3.5 14.0 - - - +
44A ILE* 3.8 16.7 - - - +
2B SER* 5.4 11.1 + - - +
22B LEU* 3.6 37.5 - - + -
25B MET* 5.5 2.0 - - + -
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Residues in contact with ARG 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG 4.8 0.8 + - - -
37A TYR* 2.9 27.9 + - + +
38A THR* 2.9 38.8 + - - +
40A LYS* 1.3 76.5 - - - +
42A GLN* 1.3 64.8 + - - +
44A ILE* 3.1 6.2 + - - +
45A LEU* 2.9 37.1 + - + +
19B LEU* 3.9 21.5 - - + -
22B LEU* 3.7 23.1 - - + -
23B ASP* 5.7 5.2 - - - -
26B MET* 3.6 30.6 - - - +
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Residues in contact with GLN 42 (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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38A THR* 3.0 22.8 + - + +
39A ALA* 3.9 5.6 - - - +
41A ARG* 1.3 76.9 - - - +
43A PRO* 1.3 66.9 - - + +
45A LEU* 3.3 16.8 + - - +
46A ASP* 2.9 66.3 + - - +
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Residues in contact with PRO 43 (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 ALA 3.1 17.7 - - - +
40A LYS* 3.5 10.8 - - - +
42A GLN* 1.3 93.4 - - + +
44A ILE* 1.3 57.0 + - - +
46A ASP* 4.4 6.5 - - + +
47A ALA* 2.9 28.9 + - - +
2B SER 4.3 8.7 - - - +
3B ASP* 5.3 0.4 - - - -
4B PHE* 3.6 27.0 - - + +
7B LEU* 3.8 18.9 - - + +
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Residues in contact with ILE 44 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS* 3.8 23.1 - - - +
41A ARG 3.1 5.1 + - - +
43A PRO* 1.3 73.6 - - - +
45A LEU* 1.3 66.4 + - - +
47A ALA* 3.2 5.6 + - - +
48A MET* 3.0 24.7 + - - +
7B LEU* 3.8 23.8 - - + -
15B LEU* 3.4 39.7 - - + +
18B ARG* 4.1 22.7 - - + +
19B LEU* 3.7 16.4 - - + -
22B LEU* 4.2 20.2 - - + -
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Residues in contact with LEU 45 (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 ARG* 2.9 40.6 + - + +
42A GLN* 3.7 17.9 - - - +
44A ILE* 1.3 76.6 - - - +
46A ASP* 1.3 65.2 + - - +
48A MET* 3.3 9.5 + - + +
49A ASP* 3.2 24.9 + - - +
19B LEU* 3.6 28.7 - - + -
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Residues in contact with ASP 46 (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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42A GLN* 2.9 48.9 + - - +
43A PRO* 3.8 4.1 - - - +
45A LEU* 1.3 78.0 - - - +
47A ALA* 1.3 63.0 + - - +
49A ASP* 3.1 7.8 + - - +
50A ALA* 3.0 24.8 + - - +
4B PHE* 3.7 18.6 - - + -
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Residues in contact with ALA 47 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO 2.9 19.8 + - - +
44A ILE 3.2 4.9 + - - +
46A ASP* 1.3 77.4 - - - +
48A MET* 1.3 61.6 + - - +
50A ALA* 3.3 12.8 + - - +
51A LYS* 3.6 13.9 + - - +
4B PHE* 3.5 10.5 - - + -
7B LEU* 3.6 37.7 - - + +
8B LYS* 3.8 7.8 - - - +
15B LEU* 3.8 12.7 - - + +
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Residues in contact with MET 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.0 14.1 + - - +
45A LEU* 3.7 10.8 - - + +
46A ASP 3.2 0.4 - - - -
47A ALA* 1.3 76.2 - - - +
49A ASP* 1.3 65.8 + - - +
50A ALA 3.5 0.5 + - - -
51A LYS* 3.7 7.3 + - - +
12B LEU* 3.5 38.5 - - + +
15B LEU* 3.5 27.8 - - + +
16B GLN* 3.7 31.6 - - + +
19B LEU* 3.9 27.4 - - + -
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Residues in contact with ASP 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 3.2 13.8 + - - +
46A ASP* 3.1 8.8 + - - +
48A MET* 1.3 81.7 - - - +
50A ALA* 1.3 59.6 + - - +
51A LYS 3.4 3.9 + - - +
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Residues in contact with ALA 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASP 3.0 15.1 + - - +
47A ALA* 3.6 7.2 - - - +
48A MET 3.2 0.8 - - - -
49A ASP* 1.3 78.3 - - - +
51A LYS* 1.3 67.9 + - - +
4B PHE* 4.1 21.1 - - + -
8B LYS* 5.2 5.2 - - + +
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Residues in contact with LYS 51 (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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47A ALA 3.6 10.2 + - - +
48A MET 3.8 12.6 - - - +
49A ASP 3.4 5.4 - - - +
50A ALA* 1.3 83.5 - - - +
8B LYS 2.8 25.6 + - - +
9B ASN* 3.5 7.9 + - - +
10B LEU 2.6 34.3 + - - +
11B SER* 4.5 6.7 - - - +
12B LEU* 4.1 27.6 - - + +
15B LEU* 5.2 0.9 - - + -
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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
------------------------------------------------------------
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