Contacts of the helix formed by residues 2 - 25 (chain F) in PDB entry 6C4Z
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 LYS 2 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D LYS* 5.8 1.6 - - - +
19D GLU* 6.3 2.2 - - + -
20D LEU* 3.4 28.6 - - + +
23D LYS* 3.8 40.1 - - + +
1F SER* 1.3 78.0 - - - +
3F LEU* 1.3 60.6 + - - +
4F LEU 3.3 0.2 - - - -
5F GLU* 3.6 17.5 + - - +
6F LEU* 3.2 25.6 + - - +
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Residues in contact with LEU 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D LEU* 4.1 25.3 - - + +
24D TRP* 4.4 14.8 - - + -
3E LEU* 3.8 28.3 - - + -
4E LEU* 3.5 32.3 - - + -
7E LEU* 3.6 31.2 - - + -
1F SER 3.3 6.1 - - - +
2F LYS* 1.3 78.1 - - - +
4F LEU* 1.3 59.8 + - + +
6F LEU* 3.6 2.7 + - + +
7F LEU* 3.0 28.4 + - + +
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Residues in contact with LEU 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LEU* 3.6 29.4 - - + -
1F SER* 3.7 27.3 + - - +
2F LYS 3.3 0.4 - - - -
3F LEU* 1.3 74.9 - - - +
5F GLU* 1.3 60.2 + - - +
7F LEU* 3.1 13.4 + - + +
8F ARG* 2.9 30.1 + - - +
24G TRP* 4.1 16.6 - - + -
18H ILE* 4.8 3.2 - - + +
21H LEU* 4.7 7.2 - - + -
22H GLU* 3.9 37.7 - - + +
25H GLY* 4.1 30.7 - - - -
26H NH2 4.4 1.1 - - - +
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Residues in contact with GLU 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LYS* 3.4 38.9 - - + +
1F SER 3.3 13.0 + - - +
2F LYS* 3.6 19.5 - - - +
4F LEU* 1.3 77.9 - - - +
6F LEU* 1.3 62.3 + - - +
8F ARG* 3.3 24.9 + - - +
9F LYS* 3.1 27.7 + - + +
22H GLU* 3.8 11.6 + - - +
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Residues in contact with LEU 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 5.2 1.3 - - + -
18C ILE* 5.9 1.8 - - + -
21C LEU* 3.8 23.6 - - + -
13D ALA* 3.6 28.5 - - - +
16D LYS* 4.6 13.1 - - + +
17D ALA* 4.0 15.9 - - + +
20D LEU* 4.3 12.6 - - + -
7E LEU* 3.8 22.9 - - + -
2F LYS 3.2 14.8 + - - +
3F LEU* 3.8 4.0 - - + +
5F GLU* 1.3 75.5 - - - +
7F LEU* 1.3 67.3 + - - +
9F LYS* 3.4 6.1 + - - +
10F LEU* 3.1 42.2 + - + +
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Residues in contact with LEU 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 4.0 29.8 - - + -
6E LEU* 3.9 23.8 - - + -
7E LEU* 3.7 30.3 - - + -
10E LEU* 3.5 31.6 - - + +
3F LEU* 3.0 25.5 + - + +
4F LEU* 3.1 19.3 + - + +
6F LEU* 1.3 75.8 - - - +
8F ARG* 1.3 63.8 + - - +
10F LEU* 3.2 8.2 + - + +
11F GLY* 3.0 17.8 + - - -
18H ILE* 3.8 15.4 - - + +
21H LEU* 5.5 3.1 - - + -
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Residues in contact with ARG 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU 2.9 11.9 + - - +
5F GLU* 3.5 34.6 + - - +
6F LEU 3.3 0.2 - - - -
7F LEU* 1.3 74.3 - - - +
9F LYS* 1.3 80.8 + - - +
11F GLY* 2.7 24.1 + - - -
12F GLU* 2.8 34.4 + - + +
15H HIS* 4.8 2.5 - - + +
18H ILE* 3.5 14.9 - - + +
19H GLU* 4.0 28.9 - - + +
22H GLU* 2.8 41.3 + - + +
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Residues in contact with LYS 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 4.6 6.1 - - + +
12D GLU* 3.4 46.8 + - + +
13D ALA* 4.0 23.2 - - - +
16D LYS* 4.7 19.7 - - + +
5F GLU* 3.1 17.7 + - + +
6F LEU* 3.6 8.7 - - - +
8F ARG* 1.3 97.7 - - - +
10F LEU* 1.3 56.5 + - - +
12F GLU* 3.3 25.1 + - - +
13F ALA* 2.9 29.6 + - - +
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Residues in contact with LEU 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.7 36.3 - - + -
18C ILE* 4.5 13.7 - - + -
13D ALA* 4.0 10.8 - - + -
7E LEU* 4.4 20.9 - - + +
10E LEU* 4.2 27.0 - - + +
11E GLY 5.2 3.1 - - - +
14E LEU* 4.2 14.1 - - + +
6F LEU* 3.1 38.9 + - + +
7F LEU* 3.4 7.2 - - - +
9F LYS* 1.3 74.6 - - - +
11F GLY* 1.3 57.8 + - - +
13F ALA* 3.4 4.5 + - - +
14F LEU* 2.9 31.0 + - - +
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Residues in contact with GLY 11 (chain F).
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* 4.7 3.8 - - - +
7F LEU 3.0 9.8 + - - -
8F ARG 2.7 13.7 + - - -
10F LEU* 1.3 71.2 - - - +
12F GLU* 1.3 54.7 + - - -
14F LEU* 3.5 5.9 + - - +
15F HIS* 2.9 30.0 + - - +
11H GLY 5.2 0.3 - - - +
14H LEU* 5.8 1.1 - - - -
15H HIS* 4.1 17.5 - - - +
18H ILE* 4.2 19.4 - - - +
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Residues in contact with GLU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 2.9 39.1 + - + +
8F ARG* 2.8 46.1 + - + +
9F LYS* 3.6 25.2 + - - +
11F GLY* 1.3 72.5 - - - +
13F ALA* 1.3 61.3 + - - +
15F HIS* 3.5 6.1 + - - +
16F LYS* 3.1 30.8 + - - +
15H HIS* 3.3 27.7 + - + +
19H GLU* 4.5 2.6 - - - +
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Residues in contact with ALA 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.3 13.1 - - + +
9D LYS* 3.9 27.7 - - + +
10D LEU* 4.3 15.9 - - + -
13D ALA* 5.3 1.3 - - + -
14E LEU* 4.1 17.0 - - + -
9F LYS 2.9 16.6 + - - +
10F LEU* 3.7 5.8 - - - +
12F GLU* 1.3 72.9 - - - +
14F LEU* 1.3 60.1 + - - +
16F LYS* 3.3 2.0 + - - +
17F ALA* 2.9 25.5 + - - +
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Residues in contact with LEU 14 (chain F).
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* 4.1 15.5 - - + +
13E ALA* 3.9 18.8 - - + -
14E LEU* 3.9 36.9 - - + +
17E ALA* 4.3 11.4 - - + -
10F LEU 2.9 17.7 + - - +
11F GLY* 3.8 4.5 - - - +
13F ALA* 1.3 73.0 - - - +
15F HIS* 1.3 65.7 + - - +
17F ALA* 3.4 2.1 + - - +
18F ILE* 3.0 46.8 + - + +
6G LEU* 4.8 2.0 - - + -
10G LEU* 3.7 22.9 - - + -
11H GLY* 5.8 1.6 - - - -
14H LEU* 3.8 17.7 - - + -
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Residues in contact with HIS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F GLY 2.9 19.2 + - - +
12F GLU* 3.5 8.7 - - - +
14F LEU* 1.3 77.3 - - - +
16F LYS* 1.3 70.0 + - + +
18F ILE* 3.4 8.6 + - - +
19F GLU* 2.7 54.9 + - + +
8H ARG* 4.7 5.2 + - + +
11H GLY* 4.3 5.3 - - - +
12H GLU* 3.3 46.3 + - + +
15H HIS* 4.5 27.7 + + + -
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Residues in contact with LYS 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS 5.5 1.8 - - - +
5D GLU* 3.1 42.7 + - + +
6D LEU* 4.3 18.6 - - + +
8D ARG* 5.9 0.7 - - - +
9D LYS* 4.4 26.5 - - + +
12F GLU* 3.1 17.8 + - - +
13F ALA 3.3 6.7 + - - +
15F HIS* 1.3 79.7 - - + +
17F ALA* 1.3 67.4 + - - +
19F GLU* 3.0 24.7 + - - +
20F LEU* 2.9 23.9 + - - +
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Residues in contact with ALA 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.9 27.7 - - + +
14E LEU* 4.1 9.0 - - + -
17E ALA* 4.0 22.0 - - + -
18E ILE* 5.5 0.4 - - + -
21E LEU* 4.1 7.0 - - + +
13F ALA 2.9 17.6 + - - +
14F LEU 3.5 5.2 - - - +
16F LYS* 1.3 76.1 - - - +
18F ILE* 1.3 57.0 + - - +
20F LEU* 3.4 4.1 + - - +
21F LEU* 3.0 32.9 + - - +
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Residues in contact with ILE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ALA* 5.1 1.1 - - + -
14F LEU* 3.0 39.4 + - + +
15F HIS* 3.8 4.9 - - - +
17F ALA* 1.3 73.6 - - + +
19F GLU* 1.3 66.5 + - - +
21F LEU* 3.2 17.8 + - + +
22F GLU* 2.9 22.8 + - + +
6G LEU* 4.8 7.2 - - + -
10G LEU* 3.8 33.0 - - + -
4H LEU* 4.7 3.3 - - + +
7H LEU* 3.9 12.3 - - + +
8H ARG* 3.6 35.2 - - + +
11H GLY* 4.1 16.2 - - - -
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Residues in contact with GLU 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F HIS* 2.7 52.6 + - + +
16F LYS* 3.0 28.1 + - - +
18F ILE* 1.3 75.2 - - - +
20F LEU* 1.3 62.0 + - - +
22F GLU* 3.2 11.6 + - - +
23F LYS* 3.1 21.4 + - - +
8H ARG* 4.4 19.6 - - + +
12H GLU* 5.0 1.0 - - - +
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D LYS* 3.9 29.8 - - + +
3D LEU* 4.1 29.6 - - + +
6D LEU* 4.2 6.3 - - + -
21E LEU* 3.5 30.3 - - + -
16F LYS 2.9 12.1 + - - +
17F ALA* 3.5 8.5 - - - +
19F GLU* 1.3 73.4 - - - +
21F LEU* 1.3 65.2 + - - +
23F LYS* 3.0 12.9 + - + +
24F TRP* 2.9 61.3 + - + +
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Residues in contact with LEU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ALA* 4.0 19.5 - - + +
20E LEU* 3.6 28.7 - - + -
21E LEU* 3.7 25.5 - - + +
24E TRP* 3.4 26.3 - - + -
17F ALA 3.0 18.7 + - - +
18F ILE* 3.2 15.2 + - + +
20F LEU* 1.3 74.7 - - - +
22F GLU* 1.3 53.1 + - - +
24F TRP* 4.8 0.9 - - - -
25F GLY* 2.8 33.1 + - - -
3G LEU* 5.5 2.5 - - + -
6G LEU* 4.0 27.1 - - + -
4H LEU* 4.0 12.0 - - + +
7H LEU* 5.8 1.1 - - + -
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Residues in contact with GLU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ILE 2.9 11.8 + - - +
19F GLU* 3.3 11.4 - - - +
20F LEU 3.1 0.4 - - - -
21F LEU* 1.3 75.0 - - - +
23F LYS* 1.3 63.2 + - - +
25F GLY 3.1 2.1 + - - -
26F NH2 3.0 21.5 + - - -
1H SER 5.2 1.8 - - - +
4H LEU* 3.9 32.0 - - + +
5H GLU* 3.9 13.4 + - - +
8H ARG* 3.0 46.9 + - + -
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Residues in contact with LYS 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LYS* 5.0 13.7 - - + +
19F GLU 3.1 8.9 + - - +
20F LEU* 3.0 18.7 + - + +
22F GLU* 1.3 79.7 + - - +
24F TRP* 1.3 73.3 + - + +
26F NH2 3.7 4.5 + - - -
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Residues in contact with TRP 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 4.1 25.1 - - + -
3D LEU* 4.5 11.2 - - + -
21E LEU* 3.5 29.8 - - + -
24E TRP* 4.4 18.7 - + + +
25E GLY* 3.4 37.0 - - - -
20F LEU* 2.9 50.3 + - + +
21F LEU* 4.2 2.5 - - - +
23F LYS* 1.3 87.3 - - + +
25F GLY* 1.3 64.6 + - - +
26F NH2 3.4 1.0 + - - -
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Residues in contact with GLY 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 3.4 22.1 - - - -
21F LEU 2.8 24.7 + - - -
22F GLU 3.6 0.9 - - - -
24F TRP* 1.3 74.1 - - - +
26F NH2 1.3 45.3 + - - -
1H SER* 4.9 7.0 - - - -
4H LEU* 3.8 15.2 - - - +
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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