Contacts of the helix formed by residues 54 - 84 (chain G) in PDB entry 2UX1
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 GLY 54 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ARG* 3.9 9.2 - - - -
53G ARG* 1.3 72.8 - - - +
55G PHE* 1.3 65.6 + - - +
56G MET 3.2 2.7 - - - -
57G ILE* 2.9 22.5 - - - +
58G TRP* 3.0 16.1 + - - -
111G ILE* 4.7 2.2 - - - -
57I ILE* 5.3 0.4 - - - -
165I GLU* 2.9 11.6 + - - -
173I EPE 3.3 22.6 + - - -
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Residues in contact with PHE 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G HIS 4.5 2.2 - - - -
48G TRP 5.4 0.2 - - - -
50G MET* 3.4 53.8 - - + -
52G GLY 3.1 18.3 + - - +
53G ARG 3.5 0.2 - - - -
54G GLY* 1.3 76.3 - - - +
56G MET* 1.3 69.3 + - + +
59G HIS* 2.8 71.0 + + + +
111G ILE* 4.3 1.6 - - - +
160I TRP* 4.0 20.6 - + - -
161I MET* 3.7 42.8 - - + -
164I ALA* 3.7 16.2 - - + -
165I GLU* 3.4 11.9 + - - +
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Residues in contact with MET 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G GLY 3.2 0.4 - - - -
55G PHE* 1.3 84.3 - - + +
57G ILE* 1.3 57.8 + - - +
60G PRO* 3.3 26.0 - - - +
57I ILE* 3.8 22.5 - - + +
58I TRP* 3.2 39.9 - - + -
61I LYS* 3.9 29.8 - - - +
65I TYR* 4.3 8.1 - - - +
161I MET* 3.7 44.6 - - + +
165I GLU* 3.0 15.8 + - - +
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Residues in contact with ILE 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D MET* 3.3 40.4 - - + +
57D ILE* 4.5 13.9 - - + +
54G GLY* 2.9 20.4 - - - +
56G MET* 1.3 80.4 - - - +
58G TRP* 1.3 92.0 + - + +
59G HIS 3.5 0.4 - - - -
60G PRO* 3.6 5.4 - - - +
61G LYS* 3.4 18.7 + - + +
57I ILE* 3.8 25.7 - - + +
173I EPE 3.8 11.0 - - - +
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Residues in contact with TRP 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ARG* 4.5 2.2 - - - +
56D MET* 3.3 30.5 - - + -
50G MET* 3.6 21.1 - - + -
54G GLY* 3.0 30.6 + - - +
57G ILE* 1.3 94.0 - - + +
59G HIS* 1.3 63.1 + - - +
61G LYS* 3.6 21.4 - - + +
62G MET* 3.2 32.8 + - + +
65G TYR* 3.7 13.9 - + - -
111G ILE* 4.3 14.1 - - + -
115G LEU* 3.6 23.4 - - + +
162G LEU* 3.7 28.9 - - + -
165G GLU* 3.4 48.2 + - + -
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Residues in contact with HIS 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E GLU* 3.6 10.6 + - - -
1173E ZN 3.8 2.0 - - - -
47G HIS* 2.7 80.7 + + - -
48G TRP* 5.1 0.2 - - - -
50G MET* 3.5 8.9 - - - -
55G PHE* 2.8 43.0 + + + +
56G MET* 6.1 0.7 - - - -
58G TRP* 1.3 74.7 - - - +
60G PRO* 1.4 71.8 - - + +
62G MET* 3.3 6.0 + - - +
63G ASP* 3.8 0.4 + - - -
160I TRP* 3.6 16.1 - + - -
161I MET* 3.4 32.6 - - + +
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Residues in contact with PRO 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G MET* 3.3 31.2 - - - +
57G ILE* 3.6 6.1 - - - +
59G HIS* 1.4 104.2 - - + +
61G LYS* 1.3 60.5 + - - +
63G ASP* 3.1 29.7 + - + +
64G GLU* 3.4 14.6 + - - +
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Residues in contact with LYS 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D MET* 3.9 32.9 - - - -
57G ILE* 3.4 18.3 + - - +
58G TRP* 3.3 20.8 + - + +
59G HIS 3.2 1.2 - - - -
60G PRO* 1.3 78.6 - - - +
62G MET* 1.3 62.4 + - - +
64G GLU* 3.0 48.3 + - + +
65G TYR* 3.0 51.9 + - + +
158G HIS* 6.3 0.4 - - - -
161G MET* 6.2 0.6 - - - -
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Residues in contact with MET 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU* 3.6 30.5 - - + +
46G VAL* 3.9 20.0 - - + -
47G HIS* 3.8 33.9 - - + +
50G MET* 4.3 2.5 - - + -
58G TRP* 3.2 36.8 + - + +
59G HIS 3.7 7.2 - - - +
60G PRO 3.2 0.2 - - - -
61G LYS* 1.3 75.1 - - - +
63G ASP* 1.3 56.5 + - - +
65G TYR* 3.3 30.6 + - + +
66G MET* 2.8 35.6 + - + +
115G LEU* 4.3 9.6 - - + -
118G VAL* 4.1 13.2 - - + -
162G LEU* 5.3 0.2 - - + -
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Residues in contact with ASP 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ASP* 5.1 4.2 - - - +
1173E ZN 4.2 2.9 - - - -
44G HIS* 5.4 0.7 + - - -
47G HIS* 3.2 27.1 + - - -
59G HIS* 3.8 1.1 + - - -
60G PRO* 3.1 18.5 + - + +
62G MET* 1.3 77.5 - - - +
64G GLU* 1.3 63.1 + - + +
66G MET* 3.4 19.9 + - - +
67G GLU* 3.0 24.9 + - - +
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Residues in contact with GLU 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G PRO* 3.8 13.4 - - - +
61G LYS* 3.0 51.5 + - + +
63G ASP* 1.3 75.9 - - + +
65G TYR* 1.3 67.0 + - + +
67G GLU* 3.4 7.4 + - - +
68G GLU* 3.1 22.5 + - - +
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Residues in contact with TYR 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D MET* 4.6 5.9 - - - +
43G LEU* 3.9 19.5 - - + -
58G TRP* 3.7 16.6 - - - -
61G LYS* 3.0 41.1 + - + +
62G MET* 3.6 33.9 - - + +
64G GLU* 1.3 78.2 - - + +
66G MET* 1.3 56.3 + - - +
68G GLU* 3.1 7.1 + - - +
69G ILE* 2.9 32.1 + - - +
118G VAL* 4.4 1.3 - - + -
122G PHE* 3.9 27.6 - + + -
158G HIS* 3.6 41.5 + + + +
161G MET* 5.5 1.2 - - - +
162G LEU* 3.8 21.4 - - + +
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Residues in contact with MET 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G HIS* 4.2 24.5 - - + +
43G LEU* 3.7 24.7 - - + +
44G HIS* 3.5 42.8 - - + +
47G HIS* 3.9 24.7 - - + -
62G MET* 2.8 33.7 + - + +
63G ASP* 3.5 27.6 - - - +
64G GLU 3.3 0.2 - - - -
65G TYR* 1.3 71.1 - - - +
67G GLU* 1.3 57.5 + - - +
69G ILE* 3.2 3.2 + - - -
70G ASP* 2.9 36.5 + - - +
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ASP 3.0 17.6 + - - +
64G GLU* 3.7 6.3 - - - +
66G MET* 1.3 75.6 - - - +
68G GLU* 1.3 62.6 + - - +
70G ASP* 3.4 8.4 + - - +
71G GLY* 3.1 19.6 + - - -
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Residues in contact with GLU 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLU 3.1 13.4 + - - +
65G TYR* 3.5 9.7 - - - +
67G GLU* 1.3 76.3 - - - +
69G ILE* 1.3 66.3 + - + +
71G GLY* 3.2 4.1 + - - -
72G TYR* 2.7 60.2 + - + +
154G SER* 2.8 18.7 + - - -
155G ILE* 4.3 3.6 - - - +
158G HIS* 2.8 34.6 + - - -
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Residues in contact with ILE 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.5 51.4 - - + +
39G ALA* 4.6 2.2 - - + -
40G HIS* 4.3 10.1 - - + +
43G LEU* 4.0 17.3 - - + -
65G TYR 2.9 19.0 + - - +
66G MET* 3.7 5.8 - - - +
68G GLU* 1.3 77.7 - - + +
70G ASP* 1.3 64.6 + - - +
72G TYR* 3.1 19.9 + - + +
73G LEU* 2.9 26.0 + - + +
122G PHE* 4.8 7.0 - - + -
125G LEU* 4.1 8.5 - - + -
155G ILE* 4.0 21.1 - - + -
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Residues in contact with ASP 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E HIS* 5.8 4.9 - - - -
44E HIS* 5.5 3.1 - - + -
70E ASP* 5.4 3.3 - - - +
40G HIS* 2.7 43.1 + - - +
66G MET* 2.9 17.0 + - - +
67G GLU* 3.8 7.2 - - - +
69G ILE* 1.3 76.5 - - - +
71G GLY* 1.3 58.4 + - - +
73G LEU* 3.3 17.0 + - + +
74G ASP* 2.9 30.7 + - - +
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Residues in contact with GLY 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G GLU 3.1 14.3 + - - -
68G GLU* 3.2 5.1 + - - -
70G ASP* 1.3 76.7 - - - +
72G TYR* 1.3 63.6 + - - +
74G ASP* 3.5 4.4 + - - +
75G GLU* 3.1 24.6 + - - +
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Residues in contact with TYR 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.8 16.6 - - + -
68G GLU* 2.7 42.7 + - + +
69G ILE* 3.1 19.9 + - + +
71G GLY* 1.3 72.8 - - - +
73G LEU* 1.3 57.7 + - - +
75G GLU* 3.1 15.8 + - - +
76G MET* 2.8 45.4 + - + +
129G PHE* 4.7 5.8 - + - -
147G ILE 5.5 0.2 - - - -
150G VAL* 4.1 10.4 + - + +
151G ALA* 3.6 35.7 - - + -
154G SER* 2.2 31.6 + - - -
155G ILE* 4.2 13.0 - - + -
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Residues in contact with LEU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E HIS* 4.7 3.1 - - + +
48E TRP* 4.3 14.4 - - + -
1174E ZN 4.5 18.4 - - - -
33G VAL* 3.4 48.5 - - + +
36G LEU* 3.6 17.4 - - + +
37G SER* 3.8 25.1 - - - +
40G HIS* 5.7 1.6 - - + -
69G ILE 2.9 13.8 + - - +
70G ASP* 3.5 23.3 - - - +
72G TYR* 1.3 75.5 - - - +
74G ASP* 1.3 58.2 + - - +
76G MET* 4.0 1.0 - - - +
77G SER* 2.9 33.0 + - - -
94G PHE* 6.0 0.4 - - + -
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Residues in contact with ASP 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E HIS* 2.8 30.7 + - + +
47E HIS* 3.7 0.3 - - - -
48E TRP* 3.2 9.5 + - - -
63E ASP* 5.2 1.6 - - - +
70G ASP 2.9 17.3 + - - +
71G GLY* 4.0 4.7 - - - +
73G LEU* 1.3 76.8 - - - +
75G GLU* 1.3 59.1 + - - +
77G SER* 3.7 0.7 - - - -
78G GLU* 2.7 47.5 + - - +
1174G ZN 2.1 36.5 - - - -
157L LYS* 5.2 0.2 + - - -
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Residues in contact with GLU 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G GLY 3.1 18.1 + - - +
72G TYR* 3.8 15.2 - - - +
74G ASP* 1.3 74.4 - - - +
76G MET* 1.3 66.1 + - - +
78G GLU* 3.5 4.2 + - - +
79G ARG* 3.0 23.2 + - - +
147G ILE* 3.4 41.3 - - + +
150G VAL* 5.9 2.4 - - - +
157L LYS* 4.8 16.4 + - - +
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Residues in contact with MET 76 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G LEU* 3.8 33.3 - - + +
32G ALA* 3.7 25.4 - - + -
33G VAL* 4.4 4.3 - - + -
36G LEU* 3.7 16.6 - - + -
72G TYR* 2.8 24.4 + - + +
73G LEU* 4.2 2.2 - - - +
75G GLU* 1.3 69.8 - - - +
77G SER* 1.3 67.3 + - - +
79G ARG* 3.2 4.4 + - - +
80G LEU* 3.1 21.5 + - - +
129G PHE* 3.7 24.7 - - + -
147G ILE* 3.7 29.2 - - + +
148G PHE* 3.9 15.0 - - + -
151G ALA* 3.9 17.0 - - + -
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Residues in contact with SER 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E TRP* 3.1 35.0 - - - -
33G VAL* 3.8 19.4 - - - +
73G LEU 2.9 19.6 + - - -
74G ASP 3.8 0.7 - - - -
76G MET* 1.3 78.1 - - - +
78G GLU* 1.3 58.2 + - - +
80G LEU* 3.1 8.5 + - - +
81G ILE* 3.0 27.3 + - - +
87G PRO* 3.1 24.5 - - - +
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Residues in contact with GLU 78 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E HIS* 3.0 10.2 + - - -
48E TRP* 3.7 14.3 - - + -
59E HIS* 3.8 2.3 + - - -
74G ASP* 2.7 28.2 + - - +
75G GLU 4.3 0.9 - - - +
77G SER* 1.3 72.8 - - - +
79G ARG* 1.3 52.9 + - - +
81G ILE* 3.5 7.6 + - + +
82G THR* 2.8 36.6 + - - -
1174G ZN 2.0 38.3 - - - -
157L LYS* 2.8 33.9 + - - +
160L TRP* 3.4 31.2 - - + -
161L MET* 4.8 1.4 - - - +
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Residues in contact with ARG 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G LEU* 3.8 11.9 - - + -
75G GLU 3.0 18.8 + - - +
76G MET* 3.5 6.1 - - - +
77G SER 3.2 0.2 - - - -
78G GLU* 1.3 73.8 - - - +
80G LEU* 1.3 59.8 + - - +
82G THR* 3.3 23.4 + - - +
83G LEU* 3.0 51.1 + - + +
141G ASP* 3.1 22.8 + - - -
143G VAL* 3.4 26.1 - - - +
144G THR* 3.0 21.7 + - - +
147G ILE* 3.8 24.0 - - + -
152L LYS* 4.4 4.2 - - - +
153L ALA 5.1 2.2 + - - -
156L GLU* 2.8 34.5 + - - +
157L LYS* 5.5 0.4 - - - +
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Residues in contact with LEU 80 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LYS* 3.5 43.3 - - + +
29G LEU* 3.9 12.9 - - + +
30G ASN* 3.3 45.1 - - + +
33G VAL* 5.1 1.3 - - + -
76G MET 3.1 12.7 + - - +
77G SER 3.3 8.5 - - - +
79G ARG* 1.3 73.4 - - - +
81G ILE* 1.3 62.6 + - - +
83G LEU* 3.2 10.4 + - - +
84G GLY 3.2 0.5 + - - -
85G GLY* 2.8 38.0 + - - -
86G ALA 4.0 2.7 - - - +
87G PRO* 3.6 19.5 - - + -
----------------------------------------------------------
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Residues in contact with ILE 81 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E TRP* 3.5 52.9 - - + +
51E ARG* 5.8 0.2 - - - +
107E TYR* 3.4 36.0 + - + +
77G SER 3.0 19.5 + - - +
78G GLU* 3.6 13.9 - - + +
79G ARG 3.3 0.2 - - - -
80G LEU* 1.3 75.1 - - - +
82G THR* 1.3 57.7 + - - +
84G GLY* 2.9 21.7 + - - -
85G GLY 3.9 2.7 + - - +
87G PRO* 3.6 12.3 - - + -
160L TRP* 3.4 32.1 - - + +
170L PRO* 3.7 11.3 - - + +
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Residues in contact with THR 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G GLU 2.8 22.6 + - - -
79G ARG* 3.3 22.1 + - - +
81G ILE* 1.3 75.4 - - - +
83G LEU* 1.3 59.4 + - - +
84G GLY 3.2 1.1 + - - -
156L GLU 3.5 27.8 - - - +
157L LYS* 4.4 5.3 - - - +
160L TRP* 3.6 22.6 - - + +
170L PRO* 3.5 21.8 - - + +
171L LYS 5.1 0.2 + - - -
172L LEU* 3.5 31.4 + - + +
----------------------------------------------------------
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Residues in contact with LEU 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G SER* 4.8 3.8 - - - -
26G LYS* 3.9 36.3 + - + +
29G LEU* 4.3 11.0 - - + -
79G ARG* 3.0 48.5 + - - +
80G LEU 3.2 6.2 + - - +
82G THR* 1.3 76.1 - - - +
84G GLY* 1.3 57.3 + - - +
85G GLY 3.6 0.2 - - - -
139G GLU* 6.0 0.9 - - - +
141G ASP* 3.4 24.2 - - - +
144G THR* 4.1 5.8 - - - +
172L LEU* 4.6 13.2 - - + -
----------------------------------------------------------
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Residues in contact with GLY 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E TYR* 5.6 1.4 - - - -
26G LYS* 4.2 10.5 + - - -
81G ILE 2.9 11.2 + - - -
82G THR 3.2 1.8 + - - -
83G LEU* 1.3 79.2 - - - +
85G GLY* 1.3 63.1 + - - +
170L PRO* 5.2 7.9 - - - -
171L LYS 6.1 1.1 - - - -
----------------------------------------------------------
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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