Contacts of the helix formed by residues 56 - 90 (chain A) in PDB entry 5LSJ
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 SER 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 5.1 1.0 - - - +
54A ASP* 4.3 2.0 - - - -
55A ILE* 1.3 82.0 - - - +
57A PRO* 1.3 69.3 - - - +
58A VAL* 4.0 6.9 + - - +
59A GLN* 3.5 31.3 + - - +
60A ILE* 3.8 8.3 + - - +
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Residues in contact with PRO 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.0 28.3 - - + -
47A LEU* 5.1 4.9 - - + -
54A ASP* 5.8 2.7 - - - +
55A ILE 3.9 5.2 - - - +
56A SER* 1.3 83.3 - - - +
58A VAL* 1.3 64.9 + - + +
59A GLN 3.1 2.5 - - - -
60A ILE* 3.0 13.6 + - + +
61A ARG* 2.9 28.8 + - - +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 3.4 6.2 + - - +
57A PRO* 1.3 80.3 - - + +
59A GLN* 1.3 61.2 + - - +
61A ARG* 3.5 9.7 + - + +
62A LYS* 3.4 26.5 + - - +
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Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.2 28.8 - - - +
56A SER* 3.5 18.7 + - - +
57A PRO 3.1 0.6 - - - -
58A VAL* 1.3 76.9 - - - +
60A ILE* 1.3 59.2 + - + +
62A LYS* 3.5 5.3 + - - +
63A CYS* 2.9 24.9 + - - +
64B CYS* 3.8 31.3 - - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU* 4.9 6.7 - - + -
43A ILE* 3.5 37.9 - - + -
44A LEU* 3.6 26.5 - - + -
47A LEU* 3.7 26.2 - - + -
55A ILE* 6.3 1.1 - - + -
56A SER 3.8 5.1 + - - +
57A PRO* 3.0 21.2 + - + +
59A GLN* 1.3 78.8 - - - +
61A ARG* 1.3 61.0 + - + +
63A CYS* 3.2 7.8 + - + +
64A THR* 2.9 32.8 + - - -
62B TYR* 4.2 10.8 - - + -
64B CYS* 5.2 7.4 - - - +
65B PHE* 4.8 12.6 - - + -
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLN* 4.1 8.1 - - - +
40A GLU* 3.1 37.5 + - - +
57A PRO 2.9 12.4 + - - +
58A VAL* 3.6 15.5 - - + +
60A ILE* 1.3 77.6 - - + +
62A LYS* 1.3 57.9 + - - +
64A THR* 3.3 6.6 + - - -
65A GLU* 2.9 47.8 + - - +
6P LEU* 3.2 45.0 + - - +
8P HIS* 4.9 7.3 + - - -
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.4 18.1 + - - +
59A GLN* 4.1 4.0 - - - +
61A ARG* 1.3 77.2 - - - +
63A CYS* 1.3 60.6 + - - +
65A GLU* 3.2 39.7 + - + +
66A LYS* 2.9 26.7 + - - +
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Residues in contact with CYS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 2.9 15.9 + - + +
60A ILE* 3.2 15.5 - - + +
61A ARG 3.2 0.2 - - - -
62A LYS* 1.3 73.6 - - - +
64A THR* 1.3 65.5 + - - +
66A LYS* 3.0 17.6 + - - +
67A PHE* 3.1 13.2 + - - +
61B CYS* 3.0 31.4 - - - -
62B TYR* 3.5 34.7 - - - -
64B CYS* 4.4 12.6 - - - -
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 4.3 33.7 - - + +
39A VAL* 5.2 0.2 - - + -
40A GLU* 3.4 30.8 + - + +
43A ILE* 4.6 0.5 - - - +
60A ILE 2.9 12.3 + - - -
61A ARG 3.5 2.7 - - - -
63A CYS* 1.3 75.2 - - - +
65A GLU* 1.3 57.0 + - - +
67A PHE* 3.5 2.2 + - - +
68A LEU* 2.9 32.7 + - + +
62B TYR* 2.4 35.8 + - - +
6P LEU* 4.3 16.6 - - + -
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Residues in contact with GLU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 2.9 46.0 + - + +
62A LYS* 3.2 42.6 + - + +
63A CYS 3.1 0.4 - - - -
64A THR* 1.3 76.7 - - - +
66A LYS* 1.3 58.1 + - - +
68A LEU* 3.8 6.1 - - - +
69A CYS* 2.9 38.9 + - - -
6P LEU* 5.1 9.4 - - + -
8P HIS* 5.2 14.3 - - + -
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Residues in contact with LYS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 2.9 13.6 + - - +
63A CYS* 3.3 11.0 - - - +
65A GLU* 1.3 72.9 - - - +
67A PHE* 1.3 67.7 + - - +
69A CYS* 3.1 7.3 + - - +
70A PHE* 3.0 21.7 + - + +
60B ASP* 5.3 0.4 + - - -
61B CYS* 3.5 32.3 + - + +
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Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 3.5 35.4 - - + -
63A CYS 3.1 7.2 + - - +
64A THR* 4.0 5.8 - - - +
66A LYS* 1.3 79.9 - - - +
68A LEU* 1.3 57.0 + - - +
70A PHE* 3.5 10.8 - + + +
71A MET* 2.9 46.4 + - + +
53B GLY* 3.8 27.4 - - - -
57B ARG* 3.6 20.9 - - + -
58B PHE* 3.5 46.7 - + + -
61B CYS* 3.8 15.0 - - - -
62B TYR* 4.3 7.4 - - + -
80B PHE* 4.2 13.9 - + - -
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.3 14.8 - - + -
33A PHE* 3.8 40.8 - - + -
36A MET* 3.6 39.3 - - + -
64A THR* 2.9 18.9 + - + +
65A GLU* 3.8 5.8 - - - +
67A PHE* 1.3 76.5 - - - +
69A CYS* 1.3 61.5 + - - +
71A MET* 3.3 11.1 + - + -
72A LYS* 2.8 29.6 + - + +
6P LEU* 3.8 22.7 - - + -
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Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 2.9 26.4 + - - +
66A LYS* 3.1 6.3 + - - +
68A LEU* 1.3 72.4 - - - +
70A PHE* 1.3 66.7 + - - +
72A LYS* 3.2 7.5 + - - +
73A GLY* 3.0 19.9 + - - -
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Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 3.0 12.3 + - + +
67A PHE* 3.5 14.8 - + + +
69A CYS* 1.3 77.1 - - - +
71A MET* 1.3 85.3 + - + +
73A GLY* 3.1 12.1 + - - -
74A HIS* 3.1 47.5 + + - -
52B ALA* 3.6 7.9 - - + -
53B GLY 3.3 25.8 - - - -
57B ARG* 3.5 45.8 - - + -
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.9 29.4 - - + -
36A MET* 5.2 1.3 - - - -
67A PHE* 2.9 40.8 + - + +
68A LEU* 3.3 12.5 + - + +
70A PHE* 1.3 107.8 - - + +
72A LYS* 1.3 51.6 + - - +
74A HIS* 5.1 0.4 - - + -
75A PHE* 2.7 40.6 + - - +
49B LEU* 4.3 19.9 - - + +
52B ALA* 3.6 13.7 - - + +
53B GLY* 3.5 23.6 - - - +
80B PHE* 4.8 9.0 - - + -
84B LEU* 6.1 1.6 - - - -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.6 4.6 + - - -
29A GLN* 3.2 28.3 + - - +
32A LEU* 4.9 3.8 - - + -
33A PHE* 3.7 33.4 - - + -
68A LEU* 2.8 22.9 + - + +
69A CYS* 3.7 8.1 - - - +
70A PHE 3.2 0.4 - - - -
71A MET* 1.3 74.0 - - - +
73A GLY* 1.3 65.3 + - - +
75A PHE* 4.2 8.3 - - - -
76A ASP* 2.9 52.5 + - - +
8P HIS 5.5 1.8 - - - +
9P LEU* 4.8 1.3 - - - -
10P LYS* 4.0 22.0 - - - +
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A CYS 3.0 13.3 + - - -
70A PHE* 3.1 3.1 + - - -
72A LYS* 1.3 80.7 - - - +
74A HIS* 1.3 66.7 + - - +
76A ASP* 3.8 1.9 - - - +
77A ASN* 3.0 22.6 + - - +
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Residues in contact with HIS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PHE* 3.1 49.5 + + - +
71A MET* 4.6 1.3 - - + +
73A GLY* 1.3 77.1 - - - +
75A PHE* 1.3 63.7 + - - +
77A ASN* 4.0 4.2 - - - +
78A LEU* 2.9 43.4 + - + +
48B LYS 5.3 0.6 + - - -
49B LEU* 4.2 3.4 - - + -
52B ALA* 3.4 29.1 - - + +
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.8 31.2 - + - -
28A PHE* 3.6 27.6 - - + -
29A GLN* 3.6 35.0 - - + -
32A LEU* 4.2 17.0 - - + -
71A MET 2.7 23.6 + - - +
72A LYS* 4.2 12.1 - - - +
74A HIS* 1.3 77.6 - - - +
76A ASP* 1.3 61.0 + - - +
79A PHE* 2.9 35.6 + + + +
45B PHE* 3.8 18.6 - + - -
49B LEU* 3.6 36.4 - - + +
88B ILE* 5.1 2.2 - - + -
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Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.1 36.7 + - - -
72A LYS* 2.9 34.1 + - - +
73A GLY* 3.8 2.9 - - - +
75A PHE* 1.3 77.9 - - + +
77A ASN* 1.3 66.4 + - - +
79A PHE* 3.3 3.6 + - - +
80A SER* 3.0 27.9 + - - -
10P LYS* 3.7 22.8 + - - +
13P TYR* 4.0 6.8 - - - -
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Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLY 3.0 16.5 + - - +
74A HIS* 4.0 4.6 - - - +
76A ASP* 1.3 77.8 - - - +
78A LEU* 1.3 68.0 + - - +
80A SER* 3.0 19.5 + - - -
81A LYS* 3.1 42.7 + - - +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A HIS* 2.9 35.9 + - + +
77A ASN* 1.3 80.9 - - - +
79A PHE* 1.3 57.4 + - - +
81A LYS* 3.5 30.0 + - - +
82A MET* 2.9 30.5 + - - +
45B PHE* 3.5 20.2 - - + -
48B LYS* 3.4 57.4 - - + +
49B LEU* 3.8 8.1 - - + +
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Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.6 12.3 - - + -
24A ILE* 3.9 13.5 - - + -
25A TYR* 3.4 53.6 - + + -
28A PHE* 3.8 32.1 - + - -
75A PHE* 2.9 24.1 + + + +
76A ASP* 3.7 5.2 - - - +
78A LEU* 1.3 74.7 - - - +
80A SER* 1.3 58.9 + - - +
82A MET* 3.9 14.8 - - + -
83A GLU* 2.9 42.4 + - + +
45B PHE* 3.3 10.9 - + + -
13P TYR* 3.3 26.7 - + - -
----------------------------------------------------------
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Residues in contact with SER 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 3.0 16.2 + - - -
77A ASN* 3.0 13.2 + - - -
79A PHE* 1.3 76.5 - - - +
81A LYS* 1.3 64.5 + - - +
83A GLU* 3.1 7.0 + - - +
84A GLN* 2.9 24.1 + - - +
13P TYR* 3.6 22.8 + - - -
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASN* 3.1 40.1 + - - +
78A LEU* 3.7 27.5 - - - +
80A SER* 1.3 75.5 - - - +
82A MET* 1.3 63.0 + - - +
84A GLN* 3.2 25.3 + - - +
85A LEU* 3.0 27.9 + - + +
48B LYS* 5.8 2.4 - - - +
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 6.1 0.9 - - - +
24A ILE* 5.7 1.3 - - + -
28A PHE* 4.0 13.2 - - + -
78A LEU 2.9 17.9 + - - +
79A PHE* 3.9 24.2 - - + +
81A LYS* 1.3 76.2 - - - +
83A GLU* 1.3 58.1 + - - +
85A LEU* 3.5 11.0 + - - +
86A PHE* 2.9 61.5 + - - -
41B MET* 3.6 29.6 - - + +
42B VAL* 4.1 8.7 - - + -
45B PHE* 3.5 37.9 - - + -
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.6 36.1 - - + -
79A PHE* 2.9 28.1 + - + +
80A SER* 3.6 5.7 - - - +
82A MET* 1.3 78.3 - - - +
84A GLN* 1.3 65.2 + - - +
86A PHE* 3.1 9.3 + - - +
87A LEU* 2.9 44.5 + - - +
13P TYR* 3.1 26.6 + - + +
15P ARG 5.7 2.1 - - - +
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Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER 2.9 12.0 + - - +
81A LYS* 3.4 27.8 + - - +
83A GLU* 1.3 81.6 + - - +
85A LEU* 1.3 67.8 + - + +
87A LEU* 3.2 6.1 + - - +
88A GLN* 2.9 48.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.0 18.0 + - + +
82A MET* 3.6 13.7 - - + +
84A GLN* 1.3 81.2 - - + +
86A PHE* 1.3 63.4 + - - +
88A GLN* 3.7 15.6 - - - +
89A LEU* 3.0 52.4 + - + +
90A ILE* 4.1 1.7 - - - +
41B MET* 4.2 22.6 - - + +
----------------------------------------------------------
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Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.5 36.8 - - + -
24A ILE* 5.2 9.9 - - + -
82A MET* 2.9 45.4 + - - +
83A GLU 3.1 11.4 + - - +
85A LEU* 1.3 77.2 - - - +
87A LEU* 1.3 52.5 + - - +
90A ILE* 2.5 59.4 + - + +
91A LEU* 4.4 5.2 - - + +
38B LEU* 3.6 42.2 - - + -
41B MET* 3.5 17.5 - - + -
42B VAL* 3.9 12.3 - - + -
92B ILE* 6.0 2.9 - - + -
----------------------------------------------------------
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A MET* 3.7 26.7 - - + +
17A PRO* 3.4 31.4 - - + -
18A GLN* 4.4 18.4 - - + +
21A MET* 4.1 17.9 - - + -
83A GLU* 2.9 34.0 + - - +
84A GLN* 3.2 7.6 + - - +
86A PHE* 1.3 78.0 - - - +
88A GLN* 1.3 61.6 + - + +
90A ILE 3.4 8.3 - - - +
91A LEU* 4.4 6.3 - - + +
92A ARG* 3.4 24.4 + - - +
15P ARG 5.9 0.4 - - - +
----------------------------------------------------------
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLN* 2.9 35.4 + - - +
85A LEU* 3.2 20.2 + - - +
87A LEU* 1.3 80.8 - - - +
89A LEU* 1.3 75.1 + - + +
90A ILE 3.5 0.2 - - - -
92A ARG* 3.6 30.6 - - - +
34B ARG* 5.5 1.0 + - - -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 3.0 32.3 + - + +
88A GLN* 1.3 89.1 - - + +
90A ILE* 1.3 69.8 + - + +
34B ARG* 3.5 27.3 + - - +
37B LEU* 4.4 24.5 - - + +
41B MET* 4.6 9.9 - - + -
----------------------------------------------------------
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Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 4.1 1.1 - - - +
86A PHE* 2.5 45.9 + - + +
87A LEU 3.4 10.0 - - - +
89A LEU* 1.3 85.0 - - + +
91A LEU* 1.3 87.1 + - + +
92A ARG* 2.9 5.5 + - - +
34B ARG* 4.1 24.7 - - + +
37B LEU* 4.6 4.7 - - + -
38B LEU* 4.5 9.0 - - + -
41B MET* 3.4 40.4 - - + -
105B LEU* 3.7 35.0 - - + -
----------------------------------------------------------
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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