Contacts of the helix formed by residues 16 - 53 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 2.9 72.2 + - + +
11C LEU 5.1 2.7 - - - +
13C SER* 3.0 19.6 + - - +
15C GLU* 1.3 84.3 - - - +
17C LEU* 1.3 65.4 + - - +
18C PRO* 3.4 0.7 - - - -
19C PHE* 3.4 8.3 + - - +
20C GLU* 2.9 25.9 + - + +
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.3 3.6 - - - +
61A LYS* 4.1 14.8 - - - +
65A LEU* 3.9 27.8 - - + -
11C LEU 5.4 0.9 - - - -
13C SER 3.4 3.6 + - - -
14C ILE 3.2 14.4 + - - +
16C ASN* 1.3 77.8 - - - +
18C PRO* 1.3 69.2 - - + +
20C GLU* 4.0 2.2 - - - +
21C LEU* 2.9 48.8 + - + +
92C MSE 4.1 21.3 - - + -
93C VAL* 4.4 7.2 - - + -
96C HIS* 3.5 44.4 - - + +
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Residues in contact with PRO 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.6 28.7 - - + +
50A MSE 3.3 37.0 - - + +
61A LYS* 5.6 1.1 - - - +
14C ILE 3.9 5.2 - - - +
15C GLU 3.4 16.8 - - - +
16C ASN 3.6 0.2 - - - -
17C LEU* 1.3 93.2 - - + +
19C PHE* 1.3 62.8 + - - +
21C LEU* 3.3 2.4 + - + +
22C GLN* 3.1 18.9 + - - +
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Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MSE 5.3 0.4 - - - -
10C TYR* 3.1 30.1 - + - -
15C GLU 4.9 2.0 + - - +
16C ASN* 3.4 12.5 + - + +
17C LEU 3.4 0.6 - - - -
18C PRO* 1.3 81.7 - - - +
20C GLU* 1.3 72.2 + - - +
22C GLN* 3.5 4.4 + - - +
23C ARG* 3.0 52.3 + - + +
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Residues in contact with GLU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 3.7 14.4 - - - -
11C LEU* 3.4 31.5 - - + +
16C ASN* 2.9 21.7 + - + +
17C LEU 4.0 0.2 - - - +
19C PHE* 1.3 78.6 - - + +
21C LEU* 1.3 61.1 + - - +
23C ARG* 3.4 25.1 + - - +
24C ASN* 2.9 48.9 + - - +
88C GLN* 5.0 4.0 + - - -
92C MSE 3.6 31.0 - - + -
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.2 20.9 - - + -
50A MSE 5.4 1.8 - - + -
65A LEU* 4.6 5.4 - - + -
68A ILE* 4.1 34.8 - - + -
72A TYR* 4.6 5.4 + - + -
17C LEU* 2.9 35.8 + - + +
18C PRO* 3.5 4.5 - - + +
20C GLU* 1.3 78.8 - - - +
22C GLN* 1.3 58.7 + - + +
24C ASN* 3.4 4.6 + - - +
25C PHE* 3.0 26.2 + - - +
89C THR* 3.6 30.3 - - + -
92C MSE 4.1 5.7 - - + +
93C VAL* 4.0 11.2 - - + -
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 5.9 0.6 + - - -
46A ALA* 3.4 28.8 - - + +
50A MSE 3.6 30.9 - - + +
18C PRO 3.1 9.6 + - - +
19C PHE* 4.1 4.3 - - - +
21C LEU* 1.3 78.9 - - + +
23C ARG* 1.3 64.2 + - - +
25C PHE* 3.2 19.9 + - - +
26C GLN* 3.0 54.4 + - + +
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Residues in contact with ARG 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.0 45.8 + - + +
20C GLU* 3.6 28.1 + - - +
22C GLN* 1.3 78.4 - - - +
24C ASN* 1.3 57.2 + - - +
26C GLN* 3.1 9.3 + - - +
27C LEU* 2.9 59.7 + - + +
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Residues in contact with ASN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 4.6 4.3 - - + +
20C GLU* 2.9 39.5 + - - +
21C LEU* 3.6 6.3 - - - +
23C ARG* 1.3 75.0 - - - +
25C PHE* 1.3 58.7 + - - +
27C LEU* 3.2 18.7 + - - +
28C MSE 2.8 28.6 + - - +
85C LEU* 3.5 23.9 - - + +
88C GLN* 3.9 15.6 + - - +
89C THR* 2.8 28.0 + - + +
92C MSE 3.9 12.8 - - - +
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Residues in contact with PHE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 3.6 37.5 - - + -
42A ILE* 3.6 26.0 - - + -
43A ASP* 3.9 26.9 - - + -
46A ALA* 5.9 0.7 - - + -
72A TYR* 3.5 21.5 + + - +
21C LEU 3.0 14.1 + - - +
22C GLN* 3.2 24.4 + - - +
24C ASN* 1.3 75.9 - - - +
26C GLN* 1.3 67.1 + - - +
28C MSE 3.1 13.1 + - + +
29C ARG* 2.9 59.8 + - + +
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Residues in contact with GLN 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 3.0 45.5 + - - +
23C ARG* 3.1 7.8 + - + +
25C PHE* 1.3 83.5 - - - +
27C LEU* 1.3 68.4 + - + +
29C ARG* 3.0 34.2 + - - +
30C ASP* 2.9 31.4 + - - +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG* 2.9 42.8 + - + +
24C ASN* 3.3 28.0 - - - +
26C GLN* 1.3 74.8 - - + +
28C MSE 1.3 63.0 + - - +
30C ASP* 3.2 13.1 + - + +
31C LEU* 3.1 29.0 + - + +
85C LEU* 3.6 19.3 - - + -
88C GLN* 5.3 3.1 - - - +
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Residues in contact with MSE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 3.6 33.0 - - + -
72A TYR* 4.1 23.3 - - + +
75A CYS* 4.6 10.8 - - - -
24C ASN 2.8 12.7 + - - +
25C PHE* 3.2 21.3 - - + +
27C LEU* 1.3 77.2 - - - +
29C ARG* 1.3 55.9 + - + +
31C LEU* 3.4 3.5 + - - +
32C ASP* 3.0 28.9 + - - +
82C LYS* 3.7 50.5 - - + +
85C LEU* 3.5 19.2 - - + +
86C ALA* 4.2 9.2 - - + +
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Residues in contact with ARG 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 2.9 45.9 + - + +
26C GLN* 3.0 36.4 + - - +
28C MSE 1.3 77.2 - - + +
30C ASP* 1.3 65.1 + - - +
32C ASP* 3.3 10.3 + - - +
33C GLN* 3.0 23.0 + - - +
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Residues in contact with ASP 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLN* 2.9 20.7 + - - +
27C LEU* 3.6 15.2 - - + +
29C ARG* 1.3 79.6 - - - +
31C LEU* 1.3 63.7 + - + +
33C GLN* 3.1 10.8 + - - +
34C ARG* 3.0 41.4 + - - +
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Residues in contact with LEU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 3.1 24.0 + - + +
28C MSE 3.7 4.3 - - - +
29C ARG 3.3 0.2 - - - -
30C ASP* 1.3 77.9 - - + +
32C ASP* 1.3 56.5 + - - +
34C ARG* 3.2 10.1 + - - +
35C THR* 3.0 32.2 + - - +
78C PHE* 3.9 25.5 - - + +
81C ASP* 3.6 29.8 - - + +
82C LYS* 3.8 32.5 - - + +
85C LEU* 3.7 24.5 - - + -
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Residues in contact with ASP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LYS* 3.0 44.8 + - - +
82A LYS* 5.5 0.5 + - - -
28C MSE 3.0 23.4 + - - +
29C ARG* 3.6 10.2 - - - +
30C ASP 3.2 0.2 - - - -
31C LEU* 1.3 73.2 - - - +
33C GLN* 1.3 60.8 + - - +
35C THR* 3.4 5.4 + - - -
36C GLU* 2.9 32.3 + - - +
82C LYS* 3.2 20.8 + - - +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ARG 3.0 12.9 + - - +
30C ASP* 3.3 13.7 - - - +
32C ASP* 1.3 76.3 - - - +
34C ARG* 1.3 64.8 + - + +
36C GLU* 3.5 8.4 + - - +
37C ASP* 3.0 59.2 + - - +
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASP* 3.0 34.4 + - - +
31C LEU* 3.5 13.0 - - - +
32C ASP 3.2 0.2 - - - -
33C GLN* 1.3 79.2 - - + +
35C THR* 1.3 57.3 + - - +
37C ASP* 3.3 7.6 + - - +
38C LEU* 3.0 31.9 + - - +
78C PHE* 3.4 46.0 - - + -
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Residues in contact with THR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU 3.0 9.7 + - - +
32C ASP* 3.4 7.6 + - - -
34C ARG* 1.3 73.3 - - - +
36C GLU* 1.3 62.2 + - - +
38C LEU* 3.1 7.6 + - - +
39C LYS* 2.8 46.9 + - - +
75C CYS* 4.1 22.7 - - - +
78C PHE* 3.6 29.2 - - + -
79C GLY* 4.9 0.4 - - - +
82C LYS* 2.9 33.3 + - - +
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ASP 2.9 23.1 + - - +
33C GLN* 3.8 12.8 - - - +
35C THR* 1.3 72.5 + - - +
37C ASP* 1.3 65.2 + - - +
39C LYS* 3.2 9.4 + - - +
40C ALA* 3.0 23.1 + - - +
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Residues in contact with ASP 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN* 3.0 43.1 + - - +
34C ARG* 3.5 7.5 - - - +
36C GLU* 1.3 76.1 - - - +
38C LEU* 1.3 63.7 + - + +
40C ALA* 3.3 9.0 + - - +
41C GLU* 3.0 20.8 + - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ARG* 3.0 14.7 + - + +
35C THR* 3.1 8.5 + - - +
37C ASP* 1.3 76.8 - - + +
39C LYS* 1.3 59.7 + - - +
41C GLU* 3.0 11.1 + - + +
42C ILE* 2.7 34.7 + - + +
71C ALA* 3.9 20.9 - - + +
74C LYS* 3.6 42.2 - - + -
75C CYS* 3.6 22.9 - - + +
78C PHE* 3.9 21.3 - - + -
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Residues in contact with LYS 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.4 24.7 - - + -
28A MSE 3.6 26.6 - - + -
32A ASP* 2.8 42.9 + - - +
82A LYS* 4.4 6.3 - - - +
35C THR* 2.8 34.5 + - - +
36C GLU* 3.7 7.9 - - - +
38C LEU* 1.3 75.8 - - - +
40C ALA* 1.3 56.8 + - - +
42C ILE* 3.3 10.3 + - + -
43C ASP* 2.8 31.0 + - - +
72C TYR* 6.3 1.6 - - + -
75C CYS* 3.8 26.6 - - - -
82C LYS* 4.8 1.6 - - - +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU 3.0 13.1 + - - +
37C ASP* 3.4 12.6 - - - +
38C LEU 3.2 0.2 - - - -
39C LYS* 1.3 77.5 - - - +
41C GLU* 1.3 60.8 + - - +
43C ASP* 3.4 5.9 + - - +
44C LYS* 3.1 24.3 + - - +
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Residues in contact with GLU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP 3.0 11.9 + - - +
38C LEU* 3.0 16.7 + - + +
40C ALA* 1.3 76.7 - - - +
42C ILE* 1.3 56.8 + - - +
44C LYS* 3.2 23.0 + - - +
45C LEU* 3.0 50.8 + - + +
67C GLN* 4.4 9.9 + - - -
71C ALA* 4.7 10.3 - - + -
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Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 4.0 10.8 - - + -
38C LEU* 2.7 29.3 + - + +
39C LYS* 3.6 13.2 - - + +
41C GLU* 1.3 70.8 - - - +
43C ASP* 1.3 58.1 + - - +
45C LEU* 3.3 8.6 + - - +
46C ALA* 2.8 33.0 + - + +
68C ILE* 4.7 8.8 - - + +
71C ALA* 3.5 32.5 - - + +
72C TYR* 3.5 60.3 - - + +
75C CYS* 4.9 4.0 - - + -
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Residues in contact with ASP 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.7 30.2 - - + -
39C LYS 2.8 17.2 + - - +
40C ALA* 3.7 7.6 - - - +
42C ILE* 1.3 76.0 - - - +
44C LYS* 1.3 55.5 + - - +
46C ALA* 3.9 5.3 - - - +
47C THR* 2.7 48.4 + - - -
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA 3.1 17.3 + - - +
41C GLU* 3.5 18.6 - - - +
43C ASP* 1.3 77.8 - - - +
45C LEU* 1.3 59.5 + - + +
47C THR* 3.7 5.8 - - - -
48C GLU* 3.0 43.7 + - - +
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 3.0 45.5 + - + +
42C ILE* 3.8 3.8 - - - +
44C LYS* 1.3 75.5 - - + +
46C ALA* 1.3 55.8 + - - +
48C GLU* 3.1 14.6 - - - +
49C TYR* 2.8 34.0 + - - +
64C LEU* 3.7 24.6 - - + +
67C GLN* 3.6 55.9 - - + +
68C ILE* 3.7 21.5 - - + +
71C ALA* 5.0 0.7 - - + -
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Residues in contact with ALA 46 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 5.5 0.5 - - - +
21A LEU* 5.1 16.6 - - + -
22A GLN* 6.2 4.3 - - + +
25A PHE* 6.3 1.1 - - + -
42C ILE* 2.8 23.3 + - + +
43C ASP* 3.9 7.2 - - - +
45C LEU* 1.3 73.9 - - - +
47C THR* 1.3 57.4 + - - +
49C TYR* 3.6 7.4 - - - +
50C MSE 2.7 37.9 + - - +
68C ILE* 4.3 10.7 - - + +
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Residues in contact with THR 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASP* 2.7 34.8 + - - -
44C LYS* 3.7 7.2 - - - +
46C ALA* 1.3 76.6 - - - +
48C GLU* 1.3 62.7 + - - +
50C MSE 3.8 6.0 - - - +
51C SER* 3.1 27.6 + - - +
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LYS* 3.0 37.3 + - - +
45C LEU* 3.1 18.2 - - - +
47C THR* 1.3 77.8 - - - +
49C TYR* 1.3 63.1 + - - +
51C SER* 3.1 20.5 + - - -
52C SER* 3.1 16.1 + - - +
64C LEU* 3.8 24.2 - - + +
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Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.4 32.6 + - - +
17A LEU* 4.3 7.0 - - + +
18A PRO* 3.3 43.2 - - + +
21A LEU* 5.4 4.7 - - + -
45C LEU 2.8 18.9 + - - +
46C ALA* 3.6 8.3 - - - +
48C GLU* 1.3 73.9 - - - +
50C MSE 1.3 56.4 + - - +
52C SER* 4.3 1.3 - - - -
53C ALA* 2.9 51.7 + - + +
56C LEU* 4.2 4.5 - - + -
61C LYS* 3.5 31.9 + - + +
64C LEU* 3.9 26.8 - - + +
65C LEU* 3.8 21.8 - - + -
68C ILE* 4.6 4.7 - - + -
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Residues in contact with MSE 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 3.6 48.2 - - + +
19A PHE* 4.0 30.3 - - + -
22A GLN* 3.2 36.8 - - + +
46C ALA 2.7 21.7 + - - +
47C THR* 3.8 6.7 - - - +
49C TYR* 1.3 74.6 - - - +
51C SER* 1.3 61.2 + - - +
52C SER 3.4 0.9 + - - -
53C ALA* 4.2 4.6 + - - +
16F ASN* 4.4 2.7 - - - +
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C THR* 3.1 16.8 + - - +
48C GLU* 3.1 15.2 + - - -
50C MSE 1.3 78.7 - - - +
52C SER* 1.3 59.3 + - - +
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLU* 3.1 18.4 + - - +
49C TYR* 3.3 0.9 + - - -
50C MSE 3.3 0.2 - - - -
51C SER* 1.3 80.5 - - - +
53C ALA* 1.3 61.9 + - - +
54C ARG* 2.9 12.0 + - - -
55C SER* 3.1 23.4 + - - -
56C LEU* 3.6 29.8 + - - +
64C LEU* 4.8 2.4 - - - +
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Residues in contact with ALA 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PRO* 5.0 5.4 - - + -
49C TYR* 2.9 49.0 + - + +
50C MSE 4.2 6.2 + - - +
52C SER* 1.3 76.7 - - - +
54C ARG* 1.3 61.5 + - - +
55C SER 3.3 0.6 + - - -
56C LEU* 3.9 14.8 + - - +
61C LYS* 3.6 22.4 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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