Contacts of the helix formed by residues 16 - 51 (chain E) in PDB entry 4AFL
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 ASN 16 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E TYR* 2.9 76.6 + - + +
11E LEU* 5.2 2.7 - - - -
13E SER* 3.0 15.4 + - - +
15E GLU* 1.3 86.5 - - - +
17E LEU* 1.3 65.4 + - - +
18E PRO* 3.4 2.5 - - - -
19E PHE* 3.3 12.9 + - - +
20E GLU* 3.0 24.3 + - + +
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Residues in contact with LEU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D TYR* 4.1 8.1 - - + +
65D LEU* 3.5 31.9 - - + -
11E LEU 5.5 1.6 - - - +
13E SER 3.5 3.4 + - - +
14E ILE* 3.4 28.2 + - + +
16E ASN* 1.3 77.6 - - - +
18E PRO* 1.4 70.2 - - + +
20E GLU* 3.2 3.2 + - - -
21E LEU* 2.8 38.9 + - + +
92E MSE 3.5 42.2 - - + -
93E VAL* 4.0 15.7 - - + -
96E HIS* 4.0 16.4 - - + +
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Residues in contact with PRO 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA* 5.5 2.1 - - - +
49D TYR* 3.4 37.5 - - + +
50D MSE 3.6 34.8 - - + +
14E ILE 3.7 6.1 - - - +
15E GLU* 3.5 14.4 - - - +
16E ASN 3.4 4.3 - - - -
17E LEU* 1.4 94.5 - - + +
19E PHE* 1.3 61.8 + - + +
21E LEU* 3.3 7.3 - - + +
22E GLN* 3.1 24.8 + - - +
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Residues in contact with PHE 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D MSE 3.4 33.7 - - + -
10E TYR* 5.2 8.5 - - - +
15E GLU 2.9 29.6 - - - -
16E ASN* 3.7 17.0 - - - +
18E PRO* 1.3 81.4 - - + +
20E GLU* 1.3 60.2 + - - +
22E GLN* 3.2 5.3 + - - +
23E ARG* 2.8 30.3 + - - +
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Residues in contact with GLU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E TYR* 4.4 8.4 + - + -
11E LEU* 3.3 35.2 - - + +
16E ASN* 3.0 17.5 + - + +
17E LEU 3.9 1.3 - - - +
19E PHE* 1.3 76.4 - - - +
21E LEU* 1.3 54.0 + - - +
23E ARG* 3.9 26.4 + - - -
24E ASN* 2.7 52.3 + - - +
88E GLN* 5.1 4.8 + - - +
92E MSE 3.6 35.2 - - + -
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA* 4.7 18.6 - - + -
49D TYR* 4.6 7.0 - - + -
68D ILE* 4.2 34.1 - - + -
72D TYR* 4.4 8.2 + - + -
17E LEU* 2.8 39.0 + - + +
18E PRO* 3.3 13.5 - - + +
20E GLU* 1.3 78.0 - - - +
22E GLN* 1.3 57.7 + - - +
24E ASN* 3.4 3.4 + - - +
25E PHE* 2.9 29.2 + - - +
89E THR* 3.5 29.4 - - + -
92E MSE 4.1 5.4 - - + -
93E VAL* 3.9 15.5 - - + -
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Residues in contact with GLN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ALA* 4.4 17.3 + - + +
47D THR* 4.6 10.7 + - - +
50D MSE 3.2 45.6 - - - +
18E PRO 3.1 7.9 + - - +
19E PHE* 3.2 8.0 + - - +
21E LEU* 1.3 79.3 - - - +
23E ARG* 1.3 63.5 + - - +
25E PHE* 3.3 7.9 + - - +
26E GLN* 3.1 32.6 + - + +
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Residues in contact with ARG 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE 2.8 17.7 + - - +
20E GLU* 3.6 29.9 + - - +
22E GLN* 1.3 77.1 - - - +
24E ASN* 1.3 63.8 + - - +
26E GLN* 3.1 17.1 + - - +
27E LEU* 3.1 38.9 + - + +
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Residues in contact with ASN 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TYR* 4.9 2.5 - - + +
20E GLU* 2.7 38.2 + - - +
21E LEU* 3.8 5.2 - - - +
23E ARG* 1.3 73.1 - - - +
25E PHE* 1.3 58.0 + - - +
27E LEU* 3.2 16.8 + - - +
28E MSE 2.9 25.7 + - - +
85E LEU* 3.5 21.7 - - + +
88E GLN* 3.4 28.5 + - - +
89E THR* 2.7 35.0 + - + +
92E MSE 4.0 7.3 - - - +
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Residues in contact with PHE 25 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 3.4 46.2 - - + -
42D ILE* 3.9 23.8 - - + -
43D ASP* 3.7 31.4 - - + -
46D ALA* 6.2 2.9 - - + -
72D TYR* 4.1 8.9 + - - +
21E LEU 2.9 17.3 + - - +
22E GLN* 3.4 10.3 - - - +
23E ARG 3.1 0.2 - - - -
24E ASN* 1.3 77.9 - - - +
26E GLN* 1.3 74.7 + - - +
28E MSE 3.2 11.4 + - + +
29E ARG* 3.0 52.9 + - + +
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Residues in contact with GLN 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E GLN* 3.1 17.8 + - + +
23E ARG* 3.1 9.0 + - - +
25E PHE* 1.3 100.9 - - - +
27E LEU* 1.3 64.7 + - - +
29E ARG* 3.0 42.8 + - - +
30E ASP* 3.0 20.1 + - - +
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Residues in contact with LEU 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ARG* 3.1 37.0 + - + +
24E ASN* 3.2 28.9 + - - +
26E GLN* 1.3 74.7 - - - +
28E MSE 1.3 62.6 + - - +
30E ASP* 3.2 15.1 + - + +
31E LEU* 3.1 25.7 + - + +
85E LEU* 3.7 19.5 - - + -
88E GLN* 6.1 0.2 - - - +
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Residues in contact with MSE 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 3.7 29.2 - - + -
72D TYR* 4.7 14.4 - - + +
75D CYS* 5.0 4.9 - - - -
24E ASN 2.9 12.0 + - - +
25E PHE* 3.3 17.7 - - + +
26E GLN 3.1 0.2 - - - -
27E LEU* 1.3 78.1 - - - +
29E ARG* 1.3 57.9 + - + +
31E LEU* 3.3 3.8 + - - +
32E ASP* 2.9 37.3 + - - +
82E LYS* 3.7 50.3 - - - +
85E LEU* 3.5 22.8 - - + +
86E ALA* 4.0 15.3 - - + +
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Residues in contact with ARG 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PHE* 3.0 42.2 + - + +
26E GLN* 3.0 37.3 + - - +
28E MSE 1.3 76.8 - - + +
30E ASP* 1.3 60.3 + - - +
32E ASP* 3.3 9.5 + - - +
33E GLN* 3.0 27.5 + - - +
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Residues in contact with ASP 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E GLN* 3.0 19.4 + - - +
27E LEU* 3.2 16.8 + - + +
29E ARG* 1.3 78.7 - - - +
31E LEU* 1.3 62.6 + - + +
33E GLN* 3.3 4.6 + - - +
34E ARG* 3.0 46.5 + - - +
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Residues in contact with LEU 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 3.1 18.1 + - + +
28E MSE 3.6 7.9 - - - +
30E ASP* 1.3 77.7 - - + +
32E ASP* 1.3 62.1 + - - +
34E ARG* 3.1 17.3 + - + +
35E THR* 3.1 14.2 + - - +
78E PHE* 4.0 29.7 - - + +
81E ASP* 4.0 20.6 - - + +
82E LYS* 3.8 42.7 - - + +
85E LEU* 4.2 15.9 - - + -
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Residues in contact with ASP 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 2.6 41.9 + - - +
82D LYS* 4.8 2.8 + - - -
28E MSE 2.9 23.7 + - - +
29E ARG* 3.7 9.2 - - - +
30E ASP 3.3 0.2 - - - -
31E LEU* 1.3 75.6 - - - +
33E GLN* 1.3 55.9 + - - +
35E THR* 3.0 6.0 + - - -
36E GLU* 2.9 30.5 + - - +
82E LYS* 2.9 22.2 + - - +
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Residues in contact with GLN 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ARG 3.0 13.6 + - - +
30E ASP* 3.4 12.6 - - - +
31E LEU 3.2 0.2 - - - -
32E ASP* 1.3 75.6 - - - +
34E ARG* 1.3 74.7 + - - +
36E GLU* 3.4 10.2 + - - +
37E ASP* 3.1 44.7 + - - +
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Residues in contact with ARG 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASP* 3.0 45.0 + - - +
31E LEU* 3.1 10.4 + - + +
33E GLN* 1.3 88.3 - - - +
35E THR* 1.3 63.8 + - - +
37E ASP* 3.2 11.6 + - - +
38E LEU* 3.0 26.0 + - - +
78E PHE* 3.6 43.1 - - + -
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Residues in contact with THR 35 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E LEU 3.1 1.5 + - - +
32E ASP* 3.0 11.6 + - - -
34E ARG* 1.3 76.5 - - - +
36E GLU* 1.3 56.7 + - - +
38E LEU* 3.4 7.0 + - - +
39E LYS* 2.9 50.4 + - - +
75E CYS* 4.4 15.3 - - - +
78E PHE* 3.4 31.2 - - + -
79E GLY* 4.6 1.1 - - - +
82E LYS* 2.5 41.5 + - + +
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Residues in contact with GLU 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E ASP 2.9 18.9 + - - +
33E GLN* 3.7 15.5 - - - +
34E ARG 3.3 0.2 - - - -
35E THR* 1.3 78.0 + - - +
37E ASP* 1.3 58.4 + - - +
39E LYS* 3.3 8.5 + - - +
40E ALA* 3.0 28.1 + - - +
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Residues in contact with ASP 37 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E GLN* 3.1 41.3 + - - +
34E ARG* 3.6 13.1 - - - +
36E GLU* 1.3 74.6 - - - +
38E LEU* 1.3 67.9 + - + +
40E ALA* 3.3 7.3 + - - +
41E GLU* 3.0 25.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ARG 3.0 14.9 + - - +
35E THR* 3.8 5.8 - - - +
37E ASP* 1.3 76.7 - - + +
39E LYS* 1.3 56.9 + - - +
41E GLU* 3.2 20.7 - - - +
42E ILE* 2.8 34.7 + - - +
71E ALA* 4.1 25.4 - - + +
74E LYS* 3.6 40.8 - - + +
75E CYS* 3.6 18.2 - - + +
78E PHE* 3.6 30.7 - - + -
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Residues in contact with LYS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D PHE* 3.5 21.9 - - + -
28D MSE 3.7 29.6 - - + -
32D ASP* 3.0 39.1 + - - +
82D LYS* 4.2 8.7 - - - +
35E THR* 2.9 34.7 + - - +
36E GLU* 3.8 7.9 - - - +
38E LEU* 1.3 75.4 - - - +
40E ALA* 1.3 60.2 + - - +
42E ILE* 3.3 11.1 + - + +
43E ASP* 2.9 29.8 + - - +
72E TYR* 6.3 0.9 - - + -
75E CYS* 3.8 27.5 - - - -
82E LYS* 4.6 2.0 - - - +
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Residues in contact with ALA 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D PHE* 5.7 0.2 - - - -
36E GLU 3.0 16.8 + - - +
37E ASP* 3.6 7.2 - - - +
39E LYS* 1.3 75.1 - - - +
41E GLU* 1.3 56.3 + - - +
43E ASP* 3.5 7.6 + - - +
44E LYS* 2.9 29.3 + - - +
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Residues in contact with GLU 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ASP* 3.0 14.6 + - - +
38E LEU* 3.2 29.0 - - + +
40E ALA* 1.3 75.1 - - - +
42E ILE* 1.3 64.0 + - - +
44E LYS* 3.3 10.3 + - + +
45E LEU* 3.0 42.4 + - + +
71E ALA* 5.3 5.4 - - + -
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Residues in contact with ILE 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 6.1 0.4 - - + -
25D PHE* 4.6 8.1 - - + -
38E LEU 2.8 28.8 + - - +
39E LYS* 3.6 13.7 - - + +
41E GLU* 1.3 72.0 - - - +
43E ASP* 1.3 53.8 + - - +
45E LEU* 3.2 8.1 + - - +
46E ALA* 2.7 43.3 + - + +
68E ILE* 4.5 9.6 - - + +
71E ALA* 3.6 33.9 - - + +
72E TYR* 3.4 54.7 - - + +
75E CYS* 4.6 7.2 - - + -
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Residues in contact with ASP 43 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLN* 5.2 6.2 + - - +
25D PHE* 3.6 33.9 - - + -
39E LYS 2.9 17.9 + - - +
40E ALA* 3.5 8.1 - - - +
42E ILE* 1.3 77.5 - - - +
44E LYS* 1.3 59.6 + - - +
46E ALA* 4.4 4.9 - - - -
47E THR* 2.9 51.0 + - - +
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Residues in contact with LYS 44 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E ALA 2.9 17.0 + - - +
41E GLU* 3.7 12.8 - - + +
42E ILE 3.3 0.2 - - - -
43E ASP* 1.3 79.4 + - - +
45E LEU* 1.3 78.1 + - + +
47E THR* 3.2 17.1 + - - -
48E GLU* 3.2 19.4 + - - +
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Residues in contact with LEU 45 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E GLU* 3.0 35.1 + - + +
42E ILE* 3.7 4.5 - - - +
44E LYS* 1.3 87.0 - - + +
46E ALA* 1.3 60.9 + - - +
48E GLU* 3.4 10.7 + - - +
49E TYR* 2.9 23.7 + - - +
64E LEU* 3.4 22.9 - - + +
67E GLN* 3.5 59.9 - - + +
68E ILE* 3.8 15.7 - - + +
71E ALA* 5.0 3.1 - - + -
----------------------------------------------------------
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Residues in contact with ALA 46 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 4.6 10.5 - - + -
22D GLN* 5.4 2.9 - - - +
25D PHE* 6.2 1.3 - - + -
42E ILE* 2.7 28.9 + - + +
43E ASP* 4.0 4.7 - - - +
45E LEU* 1.3 71.1 - - - +
47E THR* 1.3 68.0 + - + +
49E TYR* 3.0 3.6 + - - +
50E MSE 3.0 42.3 + - + +
68E ILE* 3.9 18.1 - - + +
----------------------------------------------------------
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Residues in contact with THR 47 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLN* 5.2 8.1 - - - +
43E ASP* 2.9 40.9 + - - +
44E LYS* 3.2 9.4 + - - -
46E ALA* 1.3 76.1 - - + +
48E GLU* 1.3 59.6 + - - +
50E MSE 3.3 16.7 + - - +
51E SER* 2.8 32.0 + - - -
----------------------------------------------------------
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Residues in contact with GLU 48 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E LYS* 3.2 21.0 + - + +
45E LEU* 3.5 18.1 - - - +
46E ALA 3.2 0.2 - - - -
47E THR* 1.3 79.8 + - - +
49E TYR* 1.3 66.5 + - - +
51E SER* 3.2 7.1 + - - -
52E SER* 3.2 26.8 + - - -
64E LEU* 4.0 24.0 - - + +
----------------------------------------------------------
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Residues in contact with TYR 49 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 3.6 21.4 + - - +
17D LEU* 4.1 18.8 - - + -
18D PRO* 4.2 16.6 - - + -
21D LEU* 4.9 4.5 - - + -
45E LEU 2.9 14.2 + - - +
46E ALA* 3.0 12.1 + - - +
48E GLU* 1.3 78.1 - - - +
50E MSE 1.3 63.9 + - + +
52E SER* 3.0 3.9 + - - -
53E ALA* 2.6 55.0 + - + +
61E LYS* 3.3 49.3 - - + -
64E LEU* 4.2 23.3 - - + -
65E LEU* 4.0 23.4 - - + +
68E ILE* 4.5 4.3 - - + -
----------------------------------------------------------
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Residues in contact with MSE 50 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D PRO* 3.6 49.1 - - + +
21D LEU* 4.0 22.0 - - + -
22D GLN* 3.5 26.0 - - - +
46E ALA* 3.0 34.3 + - + +
47E THR* 3.4 15.7 - - - +
49E TYR* 1.3 79.6 - - + +
51E SER* 1.3 57.6 + - - +
52E SER 3.3 0.4 - - - -
53E ALA* 4.3 9.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 51 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E THR 2.8 18.7 + - - -
48E GLU* 3.7 8.1 - - - -
49E TYR 3.1 0.4 - - - -
50E MSE 1.3 78.6 - - - +
52E SER* 1.3 59.7 + - - +
53E ALA 3.9 0.2 - - - -
----------------------------------------------------------
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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