Contacts of the helix formed by residues 16 - 52 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 2.8 71.1 + - + +
11B LEU* 5.2 3.1 - - - +
13B SER* 3.1 20.6 + - - +
14B ILE 3.1 0.6 - - - -
15B GLU* 1.3 89.4 + - - +
17B LEU* 1.3 64.2 - - - +
18B PRO* 3.4 2.0 - - - -
19B PHE* 3.0 11.3 + - - +
20B GLU* 3.0 22.1 + - + +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 5.6 0.7 - - - -
13B SER 3.5 3.7 + - - -
14B ILE* 3.2 20.7 + - + +
16B ASN* 1.3 76.1 - - - +
18B PRO* 1.4 60.0 - - + +
20B GLU* 3.1 3.9 + - - -
21B LEU* 2.7 56.0 + - + +
92B MSE 3.8 28.0 - - + -
93B VAL* 4.5 6.5 - - + -
96B HIS* 4.0 27.4 - - + +
49F TYR* 3.8 14.4 - - + +
65F LEU* 3.6 33.4 - - + -
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Residues in contact with PRO 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE 3.8 5.2 - - - +
15B GLU* 3.7 11.7 - - - +
16B ASN 3.4 4.7 - - - -
17B LEU* 1.4 93.9 - - + +
19B PHE* 1.3 66.6 + - + +
21B LEU* 4.3 8.3 - - + -
22B GLN* 3.0 25.5 + - - +
49F TYR* 4.0 18.8 - - + -
50F MSE 3.2 41.1 - - + +
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 5.2 8.3 - - - +
15B GLU 3.8 22.7 - - - -
16B ASN* 3.0 9.3 + - - +
18B PRO* 1.3 87.0 - - + +
20B GLU* 1.3 53.0 + - - +
22B GLN* 3.3 6.1 + - - +
23B ARG* 2.7 36.6 + - - +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B TYR* 4.2 12.1 + - + -
11B LEU* 3.4 29.9 - - + +
16B ASN* 3.0 15.2 + - + +
17B LEU 3.7 6.1 - - - +
19B PHE* 1.3 75.4 - - - +
21B LEU* 1.3 59.6 + - - +
23B ARG* 3.7 23.4 + - - -
24B ASN* 2.8 50.8 + - - +
88B GLN* 4.5 7.8 + - - -
92B MSE 3.4 32.8 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 2.7 46.5 + - + +
18B PRO* 3.7 5.6 - - + +
20B GLU* 1.3 73.5 - - - +
22B GLN* 1.3 61.8 + - - +
24B ASN* 3.4 4.6 + - - +
25B PHE* 3.1 22.9 + - - +
89B THR* 3.7 27.4 - - + -
92B MSE 4.1 3.4 - - + -
93B VAL* 3.9 15.3 - - + -
46F ALA* 4.8 8.2 - - + +
49F TYR* 4.5 13.0 - - + -
50F MSE 3.7 12.6 - - + -
65F LEU* 4.9 2.2 - - + -
68F ILE* 4.1 33.0 - - + -
72F TYR* 4.7 6.3 + - + -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO 3.0 18.6 + - - +
19B PHE* 3.7 5.4 - - - +
21B LEU* 1.3 72.8 - - - +
23B ARG* 1.3 66.4 + - - +
25B PHE* 3.3 11.4 + - - +
26B GLN* 2.9 61.0 + - + +
43F ASP* 4.9 7.8 + - - +
46F ALA* 5.3 2.3 - - - +
47F THR* 5.4 2.8 + - - -
50F MSE 3.5 25.6 - - + +
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Residues in contact with ARG 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE 2.7 21.9 + - - +
20B GLU* 3.3 29.1 + - - +
22B GLN* 1.3 73.7 - - - +
24B ASN* 1.3 63.3 + - - +
26B GLN* 3.2 8.7 + - - +
27B LEU* 3.0 50.7 + - + +
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Residues in contact with ASN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 2.8 43.8 + - - +
21B LEU* 3.8 4.7 - - - +
23B ARG* 1.3 73.0 - - - +
25B PHE* 1.3 57.3 + - - +
27B LEU* 3.3 13.3 + - - +
28B MSE 2.9 29.6 + - - +
85B LEU* 3.5 28.4 - - + +
88B GLN* 4.1 9.4 + - - +
89B THR* 2.8 39.5 + - + +
92B MSE 4.1 7.9 - - - +
72F TYR* 4.6 7.9 - - - +
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Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU 3.1 16.6 + - - +
22B GLN* 3.6 13.0 - - - +
23B ARG 3.2 0.2 - - - -
24B ASN* 1.3 76.5 - - - +
26B GLN* 1.3 80.6 + - - +
28B MSE 3.4 10.0 + - + +
29B ARG* 3.1 52.5 + - + +
39F LYS* 3.6 38.1 - - + -
40F ALA* 5.8 0.2 - - - -
42F ILE* 4.5 15.3 - - + -
43F ASP* 3.6 36.6 - - + -
46F ALA* 6.3 4.5 - - + -
72F TYR* 4.5 8.4 + - - +
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN* 2.9 44.8 + - + +
23B ARG* 3.6 7.9 - - - +
25B PHE* 1.3 98.4 - - - +
27B LEU* 1.3 65.9 + - - +
28B MSE 3.1 1.3 - - - -
29B ARG* 3.2 32.2 + - - +
30B ASP* 3.1 28.4 + - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ARG* 3.0 41.6 + - + +
24B ASN* 3.3 24.9 + - - +
26B GLN* 1.3 76.0 - - - +
28B MSE 1.3 61.2 + - - +
30B ASP* 3.4 14.6 + - + +
31B LEU* 3.1 27.6 + - + +
85B LEU* 3.7 19.7 - - + -
88B GLN* 5.5 2.7 - - - +
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Residues in contact with MSE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN 2.9 17.9 + - - +
25B PHE* 3.5 11.9 - - + +
26B GLN 3.1 0.2 - - - -
27B LEU* 1.3 75.8 - - - +
29B ARG* 1.3 60.3 + - + +
31B LEU* 3.2 3.8 + - - +
32B ASP* 2.8 31.7 + - - +
82B LYS* 3.6 53.6 - - + +
85B LEU* 3.9 19.7 - - + -
86B ALA* 4.2 13.5 - - + +
39F LYS* 3.7 38.1 - - + -
72F TYR* 4.7 14.8 - - + +
75F CYS* 5.2 4.9 - - - -
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 3.1 42.3 + - + +
26B GLN* 3.2 34.5 + - - +
28B MSE 1.3 75.8 - - + +
30B ASP* 1.3 60.3 + - - +
32B ASP* 3.4 10.4 + - - +
33B GLN* 2.9 28.9 + - - +
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Residues in contact with ASP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLN* 3.1 18.6 + - - +
27B LEU* 3.6 16.4 - - + +
28B MSE 3.2 0.2 - - - -
29B ARG* 1.3 73.4 - - - +
31B LEU* 1.3 66.3 + - + +
33B GLN* 3.3 16.1 + - - +
34B ARG* 3.1 29.3 + - + +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.1 18.6 + - + +
28B MSE 3.5 8.7 - - - +
30B ASP* 1.3 77.7 - - + +
32B ASP* 1.3 61.6 + - - +
34B ARG* 3.0 19.0 + - + +
35B THR* 3.0 16.6 + - - +
78B PHE* 4.2 23.6 - - + +
81B ASP* 3.8 47.3 - - + +
82B LYS* 3.9 23.8 - - + -
85B LEU* 4.4 14.1 - - + -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B MSE 2.8 25.8 + - - +
29B ARG* 3.6 10.7 - - - +
31B LEU* 1.3 71.5 - - - +
33B GLN* 1.3 57.5 + - - +
35B THR* 3.0 6.3 + - - -
36B GLU* 2.8 39.3 + - + +
82B LYS* 2.9 20.3 + - - +
39F LYS* 2.7 46.0 + - - +
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Residues in contact with GLN 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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29B ARG 2.9 17.1 + - - +
30B ASP* 3.5 18.2 - - - +
31B LEU 3.2 0.2 - - - -
32B ASP* 1.3 72.7 - - - +
34B ARG* 1.3 78.6 + - - +
36B GLU* 3.3 6.1 + - + +
37B ASP* 3.0 42.8 + - - +
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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
----------------------------------------------------------
30B ASP* 3.1 19.3 + - + +
31B LEU* 3.0 12.8 + - + +
33B GLN* 1.3 92.0 - - - +
35B THR* 1.3 57.4 + - - +
37B ASP* 3.1 37.9 + - - +
38B LEU* 3.0 30.0 + - - +
78B PHE* 3.6 39.2 - - + -
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 3.0 3.1 + - - +
32B ASP 3.0 11.4 + - - -
34B ARG* 1.3 74.1 - - - +
36B GLU* 1.3 67.2 + - - +
38B LEU* 3.7 6.9 - - - +
39B LYS* 2.8 46.3 + - - +
75B CYS* 4.5 14.1 - - - +
78B PHE* 3.5 33.7 - - + -
79B GLY* 4.9 0.7 - - - +
82B LYS* 2.7 37.4 + - - +
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Residues in contact with GLU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ASP* 2.8 29.2 + - + +
33B GLN* 3.7 7.9 - - + +
35B THR* 1.3 78.5 + - - +
37B ASP* 1.3 66.2 + - - +
39B LYS* 3.1 30.8 + - - +
40B ALA* 3.1 22.9 + - - +
82B LYS* 5.4 0.3 + - - -
32F ASP* 4.3 6.7 - - - +
36F GLU* 6.0 1.8 - - - -
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 3.0 31.9 + - - +
34B ARG* 3.1 32.1 + - - +
36B GLU* 1.3 80.5 - - - +
38B LEU* 1.3 61.1 + - - +
40B ALA* 3.3 7.6 + - - +
41B GLU* 3.2 19.9 + - - +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG 3.0 14.1 + - - +
35B THR* 3.7 7.0 - - - +
36B GLU 3.3 0.2 - - - -
37B ASP* 1.3 76.7 - - - +
39B LYS* 1.3 58.9 + - - +
41B GLU* 3.1 11.5 + - + +
42B ILE* 2.8 35.2 + - + +
71B ALA* 3.7 30.5 - - + +
74B LYS* 3.6 35.4 - - + +
75B CYS* 3.7 19.3 - - + +
78B PHE* 3.8 24.0 - - + -
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Residues in contact with LYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 2.8 35.2 + - - +
36B GLU* 3.1 24.9 + - - +
38B LEU* 1.3 77.5 - - - +
40B ALA* 1.3 57.9 + - - +
42B ILE* 4.3 9.4 - - + -
43B ASP* 2.9 29.3 + - - +
75B CYS* 4.1 24.2 - - - -
82B LYS* 4.5 5.7 - - - +
25F PHE* 3.6 22.7 - - + -
28F MSE 3.9 21.8 - - + +
32F ASP* 2.7 41.3 + - - +
82F LYS* 4.6 2.8 - - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLU 3.1 11.3 + - - +
37B ASP* 3.7 10.5 - - - +
38B LEU 3.2 0.2 - - - -
39B LYS* 1.3 74.7 - - - +
41B GLU* 1.3 61.5 + - - +
43B ASP* 3.8 5.7 - - - +
44B LYS* 3.0 30.1 + - - +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP 3.2 12.6 + - - +
38B LEU* 3.1 17.6 + - + +
40B ALA* 1.3 74.5 - - - +
42B ILE* 1.3 64.8 + - + +
44B LYS* 3.5 10.0 + - + +
45B LEU* 2.9 36.4 + - + +
71B ALA* 5.7 1.6 - - + -
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Residues in contact with ILE 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 2.8 25.4 + - + +
39B LYS* 3.7 11.4 - - + +
40B ALA 3.3 0.2 - - - -
41B GLU* 1.3 76.5 - - - +
43B ASP* 1.3 53.8 + - - +
45B LEU* 3.0 9.6 + - - +
46B ALA* 2.6 41.2 + - + +
68B ILE* 4.8 6.5 - - + +
71B ALA* 3.5 42.6 - - + +
72B TYR* 3.5 49.6 - - + +
75B CYS* 4.6 9.2 - - + -
25F PHE* 4.3 9.9 - - + -
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Residues in contact with ASP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS 2.9 18.0 + - - +
40B ALA* 3.8 6.7 - - - +
42B ILE* 1.3 76.3 - - - +
44B LYS* 1.3 51.4 + - - +
46B ALA* 3.8 5.1 - - - +
47B THR* 2.7 52.9 + - - -
50B MSE 5.3 0.7 - - - +
22F GLN* 4.5 11.4 + - - +
25F PHE* 3.6 32.6 - - + -
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Residues in contact with LYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ALA 3.0 18.8 + - - +
41B GLU* 3.6 9.0 - - - +
43B ASP* 1.3 77.2 - - - +
45B LEU* 1.3 68.6 + - + +
47B THR* 3.7 5.3 - - - -
48B GLU* 2.9 33.7 + - + +
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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
----------------------------------------------------------
41B GLU* 2.9 27.9 + - + +
42B ILE* 3.4 5.8 - - - +
44B LYS* 1.3 82.5 - - + +
46B ALA* 1.3 58.0 + - - +
48B GLU* 3.3 13.9 + - - +
49B TYR* 2.9 27.4 + - - +
64B LEU* 3.7 25.4 - - + +
67B GLN* 3.7 51.6 - - + +
68B ILE* 3.7 16.6 - - + +
71B ALA* 4.8 4.3 - - + -
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 2.6 28.0 + - + +
43B ASP* 3.8 6.1 - - - +
45B LEU* 1.3 71.7 - - - +
47B THR* 1.3 59.8 + - - +
49B TYR* 3.2 1.6 + - - +
50B MSE 2.8 49.5 + - + +
68B ILE* 3.9 17.2 - - + +
21F LEU* 4.5 16.4 - - + -
25F PHE* 6.2 1.8 - - + -
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 2.7 41.2 + - - -
44B LYS* 3.7 5.8 - - - -
46B ALA* 1.3 71.8 - - - +
48B GLU* 1.3 58.2 + - - +
50B MSE 3.6 13.7 - - + +
51B SER* 2.8 44.9 + - - +
22F GLN* 5.5 0.9 + - - -
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LYS* 2.9 23.7 + - + +
45B LEU* 3.4 16.6 - - - +
47B THR* 1.3 79.4 - - - +
49B TYR* 1.3 62.2 + - - +
51B SER* 3.3 5.1 + - - -
52B SER* 2.9 28.0 + - - +
64B LEU* 4.0 24.2 - - + +
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU 2.9 14.2 + - - +
46B ALA* 3.2 9.4 + - - +
48B GLU* 1.3 77.2 - - - +
50B MSE 1.3 69.8 + - + +
51B SER 3.2 0.2 + - - -
52B SER* 4.3 1.3 - - - -
53B ALA* 3.0 41.6 + - + +
56B LEU* 4.9 3.6 - - + -
61B LYS* 4.3 27.2 - - + +
64B LEU* 3.6 28.7 - - + +
65B LEU* 3.7 32.4 - - + +
68B ILE* 4.4 4.5 - - + -
14F ILE* 3.8 19.1 + - - +
17F LEU* 3.7 26.9 - - + +
18F PRO* 4.3 19.3 - - + +
21F LEU* 4.5 8.3 - - + -
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Residues in contact with MSE 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 5.3 0.9 - - - +
46B ALA* 2.8 43.4 + - + +
47B THR* 3.6 15.3 - - + +
49B TYR* 1.3 82.6 - - + +
51B SER* 1.3 61.8 + - - +
52B SER 4.9 0.2 - - - +
53B ALA* 4.5 8.1 - - - +
18F PRO* 3.5 49.2 - - + +
21F LEU* 4.5 7.9 - - + -
22F GLN* 4.1 35.9 - - - +
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 2.8 33.6 + - - +
48B GLU* 3.7 6.3 - - - -
49B TYR 3.1 0.2 - - - -
50B MSE 1.3 78.3 - - - +
52B SER* 1.3 66.0 + - - +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 2.9 18.1 + - - +
49B TYR 3.7 0.2 + - - -
51B SER* 1.3 80.2 - - - +
53B ALA* 1.3 61.2 + - - +
54B ARG* 2.5 23.9 + - - +
55B SER* 3.4 24.7 + - - -
56B LEU* 3.2 27.4 - - - +
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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) + - + + + + + -
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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