Contacts of the helix formed by residues 11 - 51 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS* 4.5 4.9 - - - +
9B ASN 4.2 0.2 + - - -
10B LEU* 1.3 77.8 - - - +
12B LEU* 1.3 64.1 + - - +
13B GLU* 3.5 9.1 + - - +
14B GLU* 2.9 27.9 + - - +
15B LEU* 3.0 23.2 + - - +
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Residues in contact with LEU 12 (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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48A MET* 3.5 52.7 - - + +
51A LYS* 4.1 26.9 - - + +
10B LEU 3.9 0.4 + - - -
11B SER* 1.3 72.2 - - - +
13B GLU* 1.3 58.5 + - + +
15B LEU* 3.4 5.6 + - + +
16B GLN* 3.0 30.3 + - - +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 3.2 7.2 + - - +
12B LEU* 1.3 78.3 - - + +
14B GLU* 1.3 58.6 + - - +
16B GLN* 3.5 6.3 + - - +
17B MET* 3.1 35.6 + - + +
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Residues in contact with GLU 14 (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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10B LEU* 3.9 26.7 - - + -
11B SER* 2.9 26.2 + - - +
13B GLU* 1.3 76.4 - - - +
15B LEU* 1.3 58.9 + - - +
17B MET* 3.3 22.5 + - - +
18B ARG* 2.8 59.5 + - - +
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.4 21.5 - - + +
47A ALA* 3.8 16.4 - - + +
48A MET* 3.5 35.4 - - + +
51A LYS* 5.2 1.3 - - + -
7B LEU* 3.5 49.1 - - + +
8B LYS* 5.5 0.2 - - - -
10B LEU* 3.8 23.3 - - + +
11B SER 3.0 21.9 + - - +
12B LEU* 3.8 6.1 - - + +
14B GLU* 1.3 75.2 - - - +
16B GLN* 1.3 64.9 + - - +
18B ARG* 3.1 4.3 + - - +
19B LEU* 3.0 19.4 + - - +
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Residues in contact with GLN 16 (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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48A MET* 3.7 23.0 - - + +
12B LEU 3.0 18.1 + - - +
13B GLU* 3.8 7.6 - - - +
15B LEU* 1.3 75.0 - - - +
17B MET* 1.3 64.5 + - + +
19B LEU* 3.2 15.6 + - - +
20B LYS* 3.0 31.8 + - + +
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Residues in contact with MET 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 3.1 21.2 + - - +
14B GLU* 3.5 25.1 - - - +
15B LEU 3.2 0.2 - - - -
16B GLN* 1.3 79.1 - - + +
18B ARG* 1.3 56.8 + - + +
20B LYS* 3.4 7.6 + - + +
21B ALA* 3.0 29.3 + - - +
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Residues in contact with ARG 18 (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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44A ILE* 4.1 16.6 - - + +
2B SER* 4.2 8.1 + - - +
6B PHE* 3.8 29.9 - - - -
7B LEU* 4.0 22.7 - - - +
10B LEU* 3.6 17.3 - - - +
14B GLU* 2.8 42.1 + - - +
15B LEU* 3.1 10.5 + - - +
17B MET* 1.3 74.6 - - + +
19B LEU* 1.3 64.9 + - - +
21B ALA* 3.4 16.6 + - - +
22B LEU* 3.7 13.5 - - - +
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Residues in contact with LEU 19 (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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41A ARG* 3.9 41.2 - - + +
44A ILE* 3.7 28.4 - - + +
45A LEU* 3.6 26.2 - - + -
48A MET* 3.9 19.3 - - - -
15B LEU 3.0 7.7 + - - +
16B GLN* 3.2 17.0 + - - +
18B ARG* 1.3 77.0 - - - +
20B LYS* 1.3 63.0 + - - +
22B LEU* 3.2 21.3 + - + +
23B ASP* 3.9 8.0 - - - +
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Residues in contact with LYS 20 (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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16B GLN* 3.0 23.7 + - + +
17B MET* 3.8 8.1 - - + +
19B LEU* 1.3 76.8 - - - +
21B ALA* 1.3 61.9 + - - +
23B ASP* 3.2 31.8 + - - +
24B PRO* 3.5 5.4 - - - +
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Residues in contact with ALA 21 (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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17B MET 3.0 16.9 + - - +
18B ARG* 3.6 10.1 - - - +
19B LEU 3.2 0.6 - - - -
20B LYS* 1.3 78.5 - - - +
22B LEU* 1.3 62.2 + - + +
23B ASP 3.2 0.6 + - - -
24B PRO* 3.5 13.6 - - - +
25B MET* 3.6 19.5 - - + +
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Residues in contact with LEU 22 (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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37A TYR* 3.7 12.8 - - + +
40A LYS* 3.6 41.5 - - + -
41A ARG* 3.7 29.8 - - + -
44A ILE* 4.2 20.0 - - + -
18B ARG 3.7 10.1 - - - +
19B LEU* 3.2 10.7 + - - +
20B LYS 3.2 1.0 - - - -
21B ALA* 1.3 77.6 - - + +
23B ASP* 1.3 61.8 + - - +
25B MET* 3.4 27.2 + - + +
26B MET* 2.9 32.6 + - + +
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Residues in contact with ASP 23 (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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41A ARG* 5.7 4.7 - - - -
19B LEU 3.9 9.0 - - - +
20B LYS* 3.4 23.0 - - - +
22B LEU* 1.3 78.1 - - - +
24B PRO* 1.4 67.7 - - + +
26B MET* 3.2 18.0 + - - +
27B GLU* 2.9 42.1 + - - +
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Residues in contact with PRO 24 (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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20B LYS 3.5 7.4 - - - +
21B ALA* 3.5 13.9 - - - +
23B ASP* 1.4 94.3 - - + +
25B MET* 1.3 60.5 + - + +
27B GLU* 3.4 19.8 - - - +
28B ARG* 2.8 31.9 + - - +
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Residues in contact with MET 25 (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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37A TYR* 3.5 20.8 + - + +
40A LYS* 5.5 2.9 - - + -
21B ALA* 3.6 14.1 - - + +
22B LEU* 3.4 41.3 + - + +
23B ASP 3.2 0.2 - - - -
24B PRO* 1.3 81.9 - - + +
26B MET* 1.3 62.4 + - - +
28B ARG* 3.4 5.8 + - - +
29B GLU* 3.1 26.0 + - - +
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Residues in contact with MET 26 (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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33A LEU* 4.1 4.2 - - + +
34A ARG* 5.0 14.6 - - - +
37A TYR* 3.6 47.3 + - + -
41A ARG* 3.6 24.2 - - - +
22B LEU* 2.9 16.7 + - + +
23B ASP* 3.6 17.9 - - - +
25B MET* 1.3 76.9 - - - +
27B GLU* 1.3 65.9 + - + +
29B GLU* 3.3 2.4 + - - +
30B ILE* 3.0 43.4 + - + +
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Residues in contact with GLU 27 (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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23B ASP* 2.9 37.1 + - - +
24B PRO* 3.4 18.9 - - - +
26B MET* 1.3 78.9 - - + +
28B ARG* 1.3 61.6 + - - +
30B ILE* 3.4 7.3 + - - +
31B GLU* 3.0 28.2 + - - +
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Residues in contact with ARG 28 (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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24B PRO 2.8 20.8 + - - +
25B MET* 3.7 6.5 - - - +
26B MET 3.3 0.2 - - - -
27B GLU* 1.3 74.0 - - - +
29B GLU* 1.3 59.4 + - + +
31B GLU* 3.2 6.6 + - - +
32B GLU* 3.0 58.3 + - + +
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Residues in contact with GLU 29 (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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33A LEU* 3.8 19.1 - - + +
36A ARG* 3.3 20.6 + - - +
37A TYR* 2.4 39.8 + - - -
25B MET* 3.1 14.7 + - - +
26B MET 4.0 2.0 - - - +
28B ARG* 1.3 81.2 - - + +
30B ILE* 1.3 57.9 + - - +
32B GLU* 3.5 19.1 + - - +
33B LEU* 3.0 28.4 + - - +
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Residues in contact with ILE 30 (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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30A ILE* 4.7 10.8 - - + -
33A LEU* 3.5 20.9 - - + -
34A ARG* 3.8 34.1 - - + +
26B MET* 3.0 36.3 + - + +
27B GLU* 3.8 5.6 - - - +
29B GLU* 1.3 73.6 - - - +
31B GLU* 1.3 71.7 + - + +
33B LEU* 3.0 7.5 + - - +
34B ARG* 2.9 54.4 + - + +
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Residues in contact with GLU 31 (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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27B GLU* 3.0 20.6 + - + +
28B ARG* 3.2 7.2 + - - +
30B ILE* 1.3 80.0 - - - +
32B GLU* 1.3 56.4 + - + +
34B ARG* 3.3 28.9 + - - +
35B GLN* 2.9 46.4 + - - +
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Residues in contact with GLU 32 (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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28B ARG* 3.0 54.5 + - + +
29B GLU* 3.7 20.2 - - - +
31B GLU* 1.3 74.5 - - + +
33B LEU* 1.3 66.2 + - + +
35B GLN* 3.7 13.4 - - - +
36B ARG* 3.0 24.6 + - - +
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Residues in contact with LEU 33 (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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26A MET* 4.3 5.0 - - + +
29A GLU* 3.7 32.2 - - + +
30A ILE* 3.6 28.3 - - + -
33A LEU* 3.6 26.9 - - + -
29B GLU 3.0 9.7 + - - +
30B ILE 3.0 10.6 + - - +
32B GLU* 1.3 77.9 - - + +
34B ARG* 1.3 61.4 + - - +
36B ARG* 3.3 38.0 + - - +
37B TYR* 3.1 21.0 + - - +
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Residues in contact with ARG 34 (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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26A MET* 3.5 23.0 - - + +
30A ILE* 3.5 20.9 - - + +
34A ARG* 3.6 25.1 - - - +
30B ILE* 2.9 36.3 + - - +
31B GLU* 3.8 22.6 + - - +
33B LEU* 1.3 74.5 - - - +
35B GLN* 1.3 58.6 + - - +
37B TYR* 3.1 5.2 + - + +
38B THR* 3.0 32.9 + - - +
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Residues in contact with GLN 35 (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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31B GLU* 2.9 33.4 + - - +
32B GLU* 3.7 18.4 + - - +
34B ARG* 1.3 76.3 - - - +
36B ARG* 1.3 57.4 + - - +
38B THR* 3.9 6.6 - - - +
39B ALA* 2.9 30.0 + - - +
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Residues in contact with ARG 36 (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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25A MET* 6.0 1.0 - - - -
29A GLU* 3.0 42.4 + - - +
32B GLU 3.0 18.3 + - - +
33B LEU* 3.3 24.6 - - - +
34B ARG 3.2 0.4 - - - -
35B GLN* 1.3 78.3 - - - +
37B TYR* 1.3 57.3 + - - +
39B ALA* 3.5 6.3 + - + +
40B LYS* 3.0 51.5 + - + +
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Residues in contact with TYR 37 (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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22A LEU* 3.9 26.4 - - + +
23A ASP* 2.5 32.5 + - - -
26A MET* 3.2 54.7 - - + -
33B LEU 3.1 6.6 + - - +
34B ARG* 3.1 7.0 + - + +
36B ARG* 1.3 74.3 - - - +
38B THR* 1.3 76.7 + - - +
40B LYS* 3.3 9.9 + - - +
41B ARG* 3.1 54.8 + - - +
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Residues in contact with THR 38 (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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34B ARG* 3.0 17.2 + - - +
35B GLN* 4.0 6.7 - - - -
37B TYR* 1.3 88.2 - - - +
39B ALA* 1.3 63.9 + - - +
41B ARG* 3.3 13.5 + - - +
42B GLN* 3.1 40.1 + - + +
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Residues in contact with ALA 39 (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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35B GLN 2.9 19.0 + - - +
36B ARG* 3.6 9.4 - - + +
37B TYR 3.2 0.2 - - - -
38B THR* 1.3 76.4 - - - +
40B LYS* 1.3 62.7 + - + +
42B GLN* 3.1 12.2 + - - +
43B PRO* 3.0 20.4 - - - +
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Residues in contact with LYS 40 (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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1A GLY* 3.7 31.3 - - - +
22A LEU* 3.9 33.2 - - + +
25A MET* 5.0 15.0 - - - +
36B ARG* 3.0 43.8 + - + +
37B TYR* 3.3 8.5 + - - +
39B ALA* 1.3 75.5 - - - +
41B ARG* 1.3 61.1 + - - +
43B PRO* 3.6 14.6 - - - +
44B ILE* 3.7 18.3 - - + +
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Residues in contact with ARG 41 (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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19A LEU* 4.0 27.5 + - + +
22A LEU* 3.5 22.9 - - + -
23A ASP* 5.2 4.8 + - - -
37B TYR* 3.1 52.4 + - + +
38B THR* 3.5 13.0 - - - +
39B ALA 3.1 0.8 + - - -
40B LYS* 1.3 78.3 - - - +
42B GLN* 1.3 66.2 + - - +
44B ILE* 3.2 5.7 + - - +
45B LEU* 2.9 54.5 + - + +
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Residues in contact with GLN 42 (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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38B THR* 3.1 39.8 + - + +
39B ALA* 3.1 7.4 + - - +
41B ARG* 1.3 85.8 - - - +
43B PRO* 1.3 66.0 - - + +
45B LEU* 3.2 19.0 + - - +
46B ASP* 2.8 43.8 + - - +
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Residues in contact with PRO 43 (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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2A SER 4.8 7.0 - - - +
3A ASP* 4.8 0.7 - - - -
4A PHE* 3.7 26.2 - - + +
7A LEU* 3.8 19.7 - - + +
39B ALA 3.0 26.5 - - - +
40B LYS* 3.6 12.3 - - - +
42B GLN* 1.3 82.0 - - + +
44B ILE* 1.3 56.6 + - - +
46B ASP* 4.3 7.4 - - + +
47B ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 44 (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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7A LEU* 3.8 25.1 - - + -
15A LEU* 3.5 35.0 - - + +
18A ARG* 4.0 26.2 - - + +
19A LEU* 3.9 15.0 - - + +
22A LEU* 4.0 22.7 - - + -
40B LYS 3.7 18.4 - - - +
41B ARG 3.2 6.2 + - - +
42B GLN 3.2 0.6 - - - -
43B PRO* 1.3 73.8 - - - +
45B LEU* 1.3 60.8 + - - +
47B ALA* 3.2 4.9 + - - +
48B MET* 2.9 37.4 + - - +
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Residues in contact with LEU 45 (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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19A LEU* 3.8 29.8 - - + -
41B ARG* 2.9 48.4 + - - +
42B GLN* 3.6 26.5 - - - +
44B ILE* 1.3 75.8 - - - +
46B ASP* 1.3 62.6 + - - +
48B MET* 3.3 11.8 + - + +
49B ASP* 3.0 27.7 + - - +
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Residues in contact with ASP 46 (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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4A PHE* 3.6 18.9 - - + -
42B GLN* 2.8 31.3 + - - +
43B PRO* 3.8 4.3 - - - +
45B LEU* 1.3 79.4 - - - +
47B ALA* 1.3 59.7 + - - +
49B ASP* 3.2 7.0 + - - +
50B ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 47 (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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4A PHE* 3.5 11.8 - - + -
7A LEU* 3.8 24.0 - - + -
8A LYS* 3.8 19.3 - - - +
15A LEU* 3.9 14.7 - - + +
43B PRO 3.0 19.0 + - - +
44B ILE 3.5 4.9 - - - +
46B ASP* 1.3 73.8 - - - +
48B MET* 1.3 65.7 + - - +
50B ALA* 3.3 10.5 + - - +
51B LYS* 3.5 13.3 + - - +
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.7 35.2 - - + +
15A LEU* 3.7 22.0 - - + -
16A GLN* 3.1 39.5 - - + +
19A LEU* 4.2 17.3 - - - -
44B ILE* 2.9 23.4 + - - +
45B LEU* 3.6 13.5 - - + +
47B ALA* 1.3 79.0 - - - +
49B ASP* 1.3 61.7 + - - +
50B ALA 3.3 0.9 + - - -
51B LYS* 3.4 11.1 + - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU 3.0 16.3 + - - +
46B ASP* 3.2 7.4 + - - +
48B MET* 1.3 76.5 - - - +
50B ALA* 1.3 59.7 - - - +
51B LYS* 3.3 5.1 + - - +
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Residues in contact with ALA 50 (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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4A PHE* 4.2 20.4 - - + -
8A LYS* 5.2 5.4 - - + -
46B ASP 2.9 16.4 + - - +
47B ALA* 3.8 5.6 - - - +
48B MET 3.2 0.6 - - - -
49B ASP* 1.3 77.7 - - - +
51B LYS* 1.3 65.0 + - - +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS 2.6 31.3 + - - +
9A ASN* 3.9 7.0 + - - +
10A LEU 2.9 24.7 + - - +
11A SER* 4.3 6.1 - - - +
12A LEU* 3.8 34.9 - - + +
15A LEU* 4.9 3.6 - - + -
47B ALA 3.5 5.6 + - - +
48B MET 3.4 13.9 + - - +
49B ASP 3.3 6.7 - - - +
50B ALA* 1.3 84.8 - - - +
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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