Contacts of the helix formed by residues 16 - 51 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TYR* 2.7 51.3 + - - +
11A LEU* 4.6 8.5 - - + -
13A SER* 2.9 21.4 + - - +
15A GLU* 1.3 83.3 - - - +
17A LEU* 1.3 64.6 + - - +
18A PRO* 3.5 0.7 - - - -
19A PHE* 3.1 11.6 + - - +
20A GLU* 3.0 22.3 + - - +
19F PHE* 3.6 28.6 - - + +
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Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 5.6 1.1 - - - -
13A SER 3.7 2.6 + - - -
14A ILE* 2.9 18.7 + - + +
16A ASN* 1.3 76.3 - - - +
18A PRO* 1.4 65.5 - - + +
20A GLU* 3.1 4.4 + - - +
21A LEU* 2.8 39.4 + - + +
92A MSE 3.8 24.0 - - + -
93A VAL* 4.4 15.3 - - + -
96A HIS* 3.6 37.9 - - + +
49C TYR* 4.3 7.9 - - + +
65C LEU* 3.6 37.0 - - + -
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Residues in contact with PRO 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE 3.5 7.6 - - - +
15A GLU* 3.5 12.8 - - - +
17A LEU* 1.4 89.7 - - + +
19A PHE* 1.3 62.6 + - + +
21A LEU* 3.6 8.9 - - + +
22A GLN* 3.1 28.2 + - - +
46C ALA 5.5 0.7 - - - +
49C TYR* 3.3 41.3 - - + +
50C MSE 3.6 33.6 - - + +
53C ALA* 5.0 6.3 - - + -
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Residues in contact with PHE 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU 3.4 24.7 - - - -
16A ASN* 3.1 11.6 + - - +
17A LEU 3.1 0.6 - - - -
18A PRO* 1.3 81.9 - - + +
20A GLU* 1.3 65.8 + - - +
22A GLN* 3.5 5.6 + - - +
23A ARG* 3.2 19.9 + - - +
50C MSE 4.0 20.6 - - + -
11F LEU* 4.9 3.6 - - - +
15F GLU* 4.0 14.6 - - + -
16F ASN* 3.4 30.7 - - - +
19F PHE* 3.6 45.9 - + + -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.5 20.3 - - + +
16A ASN 3.0 15.0 + - - +
17A LEU* 3.8 2.9 - - - +
19A PHE* 1.3 74.4 - - - +
21A LEU* 1.3 67.8 + - - +
23A ARG* 3.0 12.8 + - - +
24A ASN* 2.9 31.3 + - - +
92A MSE 3.6 34.1 - - + -
19F PHE* 3.4 12.0 - - + -
23F ARG* 2.6 45.9 + - - -
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Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 2.8 36.6 + - + +
18A PRO* 3.6 10.3 - - + +
20A GLU* 1.3 76.6 - - - +
22A GLN* 1.3 53.6 + - - +
24A ASN* 3.0 5.8 + - - +
25A PHE* 2.8 35.2 + - - +
89A THR* 3.5 31.4 - - + -
92A MSE 3.9 14.4 - - + -
93A VAL* 4.0 18.6 - - + -
46C ALA* 5.1 14.6 - - + -
49C TYR* 5.4 3.4 - - + -
68C ILE* 4.3 25.4 - - + -
72C TYR* 4.9 6.5 + - + +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO 3.1 12.2 + - - +
19A PHE* 3.7 5.7 - - - +
20A GLU 3.3 0.2 - - - -
21A LEU* 1.3 78.9 - - - +
23A ARG* 1.3 61.7 + - - +
25A PHE* 3.3 9.1 + - + +
26A GLN* 3.1 22.2 + - - +
46C ALA* 6.2 4.2 - - + +
50C MSE 3.2 31.6 - - + +
11F LEU* 4.3 19.0 - - + +
16F ASN* 3.6 21.4 + - - +
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE 3.2 9.1 + - - +
20A GLU* 3.0 32.2 + - - +
22A GLN* 1.3 78.5 - - - +
24A ASN* 1.3 66.0 + - - +
26A GLN* 3.1 15.6 + - - +
27A LEU* 3.3 30.3 + - + +
11F LEU* 4.1 17.2 - - + +
19F PHE* 4.4 3.4 - - - -
20F GLU* 2.8 36.5 + - - +
23F ARG* 3.5 34.4 - - - +
24F ASN* 5.0 2.2 + - - -
27F LEU* 5.8 0.8 - - - +
88F GLN* 4.8 11.1 + - - -
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Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 2.9 25.8 + - - +
21A LEU* 3.5 9.0 - - - +
23A ARG* 1.3 76.9 + - - +
25A PHE* 1.3 66.5 + - - +
27A LEU* 3.3 16.2 + - - +
28A MSE 3.1 22.3 + - - +
85A LEU* 3.6 21.5 - - + +
88A GLN* 4.8 5.5 + - - +
89A THR* 3.0 34.1 + - + +
92A MSE 3.8 20.2 - - - +
72C TYR* 5.0 3.1 - - - +
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Residues in contact with PHE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU 2.8 19.3 + - - +
22A GLN* 3.6 11.2 - - + +
23A ARG 3.3 0.2 - - - -
24A ASN* 1.3 71.6 - - - +
26A GLN* 1.3 58.1 + - - +
28A MSE 3.3 10.9 - - + +
29A ARG* 3.0 31.2 + - + +
39C LYS* 3.4 47.3 - - + -
42C ILE* 4.0 16.8 - - + -
43C ASP* 3.7 29.6 - - + -
72C TYR* 3.7 19.2 + - - +
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 3.1 10.9 + - - +
23A ARG* 3.1 12.7 + - - +
25A PHE* 1.3 75.3 - - - +
27A LEU* 1.3 69.9 + - + +
29A ARG* 3.3 12.3 + - - +
30A ASP* 3.0 38.1 + - - +
10F TYR* 3.5 32.9 - - - +
11F LEU* 4.1 13.5 + - + +
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 3.3 26.2 + - + +
24A ASN* 3.3 25.1 + - - +
26A GLN* 1.3 79.4 - - + +
28A MSE 1.3 57.5 + - - +
30A ASP* 3.1 14.6 + - + +
31A LEU* 2.9 33.5 + - + +
85A LEU* 3.8 21.1 - - + -
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Residues in contact with MSE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ASN 3.1 12.7 + - - +
25A PHE* 3.3 17.3 - - + +
27A LEU* 1.3 75.0 - - - +
29A ARG* 1.3 54.6 + - - +
31A LEU* 3.0 5.6 + - - +
32A ASP* 2.7 40.3 + - - +
82A LYS* 3.6 50.0 - - + +
85A LEU* 3.5 18.8 - - + +
86A ALA* 4.2 17.7 - - + +
39C LYS* 3.6 38.8 - - + -
72C TYR* 4.6 16.8 - - + +
75C CYS* 5.1 4.3 - - - -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.0 25.9 + - + +
26A GLN* 3.7 14.8 - - - +
28A MSE 1.3 75.4 - - - +
30A ASP* 1.3 57.7 + - - +
32A ASP* 3.3 12.0 + - - +
33A GLN* 3.0 27.4 + - - +
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN* 3.0 40.2 + - - +
27A LEU* 3.2 16.7 - - + +
29A ARG* 1.3 74.5 - - - +
31A LEU* 1.3 65.9 + - + +
33A GLN* 3.3 15.7 + - - +
34A ARG* 3.4 21.5 + - - +
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 2.9 20.3 + - + +
28A MSE 3.6 4.9 - - - +
30A ASP* 1.3 76.4 - - + +
32A ASP* 1.3 62.6 + - - +
34A ARG* 3.3 12.1 + - - +
35A THR* 3.2 22.3 + - - +
78A PHE* 4.1 23.4 - - + +
81A ASP* 4.0 38.4 - - + +
82A LYS* 3.6 31.4 - - + -
85A LEU* 4.1 18.2 - - + -
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A MSE 2.7 22.4 + - - +
29A ARG* 3.4 11.4 - - - +
30A ASP 3.1 0.2 - - - -
31A LEU* 1.3 76.1 - - - +
33A GLN* 1.3 59.8 + - - +
35A THR* 3.0 6.7 + - - -
36A GLU* 2.9 30.2 + - - +
82A LYS* 2.8 23.3 + - - +
39C LYS* 2.8 39.5 + - - +
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG 3.0 13.4 + - - +
30A ASP* 3.3 10.9 + - - +
32A ASP* 1.3 76.2 - - - +
34A ARG* 1.3 61.4 + - + +
36A GLU* 3.4 11.6 + - - +
37A ASP* 2.9 42.9 + - - +
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Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.4 16.7 + - - +
31A LEU* 3.3 16.5 + - - +
32A ASP 3.1 0.6 - - - -
33A GLN* 1.3 80.3 - - + +
35A THR* 1.3 58.6 + - - +
37A ASP* 3.2 10.9 + - - +
38A LEU* 3.0 31.0 + - - +
78A PHE* 3.4 49.0 - - + -
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 3.2 4.3 + - - +
32A ASP* 3.0 9.5 + - - -
34A ARG* 1.3 74.5 - - - +
36A GLU* 1.3 60.8 + - - +
38A LEU* 4.0 6.0 - - - +
39A LYS* 2.9 52.7 + - - +
75A CYS* 4.4 15.5 - - - +
78A PHE* 3.6 33.7 - - + -
79A GLY* 4.9 1.1 - - - +
82A LYS* 2.8 33.9 + - - +
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ASP 2.9 17.2 + - - +
33A GLN* 3.7 18.2 - - - +
34A ARG 3.3 0.2 - - - -
35A THR* 1.3 77.8 + - - +
37A ASP* 1.3 59.5 + - - +
39A LYS* 3.9 7.6 - - - +
40A ALA* 3.1 26.5 + - - +
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 2.9 39.6 + - - +
34A ARG* 3.5 11.6 - - - +
35A THR 3.1 0.2 - - - -
36A GLU* 1.3 76.7 - - - +
38A LEU* 1.3 66.1 + - + +
40A ALA* 3.2 9.5 + - - +
41A GLU* 3.0 20.3 + - - +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG 3.0 15.6 + - - +
35A THR* 4.0 6.3 - - - +
37A ASP* 1.3 77.3 - - + +
39A LYS* 1.3 59.0 + - + +
41A GLU* 3.1 10.3 + - + +
42A ILE* 2.9 33.7 + - + +
71A ALA* 3.9 18.0 - - + +
74A LYS* 3.5 35.2 - - + +
75A CYS* 3.5 37.7 - - + +
78A PHE* 3.7 22.2 - - + -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 2.9 38.1 + - - +
36A GLU* 3.9 6.7 - - - +
37A ASP 3.2 0.2 - - - -
38A LEU* 1.3 76.2 - - - +
40A ALA* 1.3 58.4 + - - +
42A ILE* 3.7 9.8 - - + +
43A ASP* 2.9 29.6 + - - +
75A CYS* 3.6 29.2 - - - -
82A LYS* 4.7 3.0 - - - +
25C PHE* 3.6 22.3 - - + -
28C MSE 3.6 23.0 - - + -
32C ASP* 3.0 41.2 + - - +
82C LYS* 4.5 6.5 - - - +
----------------------------------------------------------
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU 3.1 14.9 + - - +
37A ASP* 3.2 11.9 + - - +
39A LYS* 1.3 73.9 - - - +
41A GLU* 1.3 64.7 + - - +
43A ASP* 3.3 7.4 + - - +
44A LYS* 3.0 23.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ASP 3.0 12.4 + - - +
38A LEU* 3.1 14.3 + - + +
40A ALA* 1.3 77.2 - - - +
42A ILE* 1.3 61.2 + - - +
44A LYS* 3.3 7.0 + - - +
45A LEU* 3.0 33.8 + - + +
71A ALA* 5.1 6.7 - - + -
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Residues in contact with ILE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 2.9 21.5 + - + +
39A LYS* 3.7 20.4 - - + +
41A GLU* 1.3 75.2 - - - +
43A ASP* 1.3 53.0 + - - +
45A LEU* 3.0 11.2 + - + +
46A ALA* 2.7 36.6 + - + +
68A ILE* 4.7 7.3 - - + +
71A ALA* 3.6 26.9 - - + +
72A TYR* 3.8 46.9 - - + +
75A CYS* 5.1 4.0 - - + -
25C PHE* 3.6 26.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS 2.9 17.9 + - - +
40A ALA* 3.6 8.0 - - - +
42A ILE* 1.3 78.2 - - - +
44A LYS* 1.3 58.2 + - - +
46A ALA* 3.3 8.1 + - - +
47A THR* 2.9 41.0 + - - -
22C GLN* 5.9 0.9 + - - -
25C PHE* 3.9 25.4 - - + -
29C ARG* 6.2 0.2 - - - -
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Residues in contact with LYS 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA 3.0 14.5 + - - +
41A GLU* 3.7 9.4 - - - +
43A ASP* 1.3 79.4 + - - +
45A LEU* 1.3 58.5 + - + +
47A THR* 3.4 7.5 + - - -
48A GLU* 2.9 28.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 3.0 30.1 + - + +
42A ILE* 3.0 9.4 + - - +
44A LYS* 1.3 75.0 - - + +
46A ALA* 1.3 59.3 + - - +
48A GLU* 3.1 12.0 + - - +
49A TYR* 2.8 30.6 + - - +
64A LEU* 4.1 17.2 - - + +
67A GLN* 3.6 60.1 - - + +
68A ILE* 3.8 20.6 - - + +
71A ALA* 4.9 4.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 2.7 24.2 + - + +
43A ASP* 3.6 10.5 - - - +
45A LEU* 1.3 71.7 - - - +
47A THR* 1.3 52.6 + - - +
49A TYR* 3.3 8.6 + - - +
50A MSE 2.7 42.8 + - + +
68A ILE* 4.9 6.0 - - + +
22C GLN* 3.4 30.3 - - + +
25C PHE* 5.9 1.6 - - + -
----------------------------------------------------------
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Residues in contact with THR 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 2.9 28.0 + - - -
44A LYS* 3.6 7.8 - - - -
46A ALA* 1.3 73.3 - - - +
48A GLU* 1.3 60.1 + - - +
50A MSE 3.6 5.2 - - - +
51A SER* 2.9 35.5 + - - -
----------------------------------------------------------
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LYS 2.9 13.4 + - - +
45A LEU* 3.1 17.7 + - - +
47A THR* 1.3 76.7 - - - +
49A TYR* 1.3 65.5 + - - +
51A SER* 2.6 29.2 + - - +
52A SER 4.5 0.2 + - - -
64A LEU* 3.8 28.4 - - + +
67A GLN* 5.6 1.1 + - - -
----------------------------------------------------------
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Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 2.8 18.9 + - - +
46A ALA* 3.5 7.6 - - - +
48A GLU* 1.3 74.0 - - - +
50A MSE 1.3 72.9 + - + +
51A SER 3.5 0.2 + - - -
52A SER 3.9 10.0 + - - +
56A LEU* 3.8 30.2 - - + +
61A LYS* 3.1 34.7 + - + -
64A LEU* 3.9 20.8 - - + +
65A LEU* 4.5 8.5 - - + -
68A ILE* 4.5 8.3 - - + -
17C LEU* 4.3 2.7 - - + +
18C PRO* 3.6 34.0 - - + +
21C LEU* 4.2 27.6 - - + -
----------------------------------------------------------
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Residues in contact with MSE 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ALA* 2.7 26.7 + - + +
47A THR* 3.6 5.2 - - - +
49A TYR* 1.3 88.4 - - + +
51A SER* 1.3 56.7 + - - +
52A SER* 3.0 15.5 + - - +
18C PRO* 3.3 49.8 - - + +
19C PHE* 5.3 0.2 - - - -
21C LEU* 5.4 2.0 - - + -
22C GLN* 3.6 28.5 - - + +
----------------------------------------------------------
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 2.9 20.2 + - - -
48A GLU* 2.6 25.4 + - - +
50A MSE 1.3 76.9 - - - +
52A SER* 1.3 62.8 + - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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