Contacts of the helix formed by residues 66 - 88 (chain F) in PDB entry 3DOY
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 PRO 66 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E MET* 3.8 17.0 - - + -
72E GLU* 5.1 0.7 - - - +
54F VAL* 3.4 35.2 - - + -
55F PHE* 5.0 1.1 - - + -
58F HIS* 3.7 28.3 - - + +
64F ILE 3.1 4.2 - - - +
65F PHE* 1.3 93.3 - - + +
67F GLY* 1.3 61.3 + - - +
68F VAL* 4.3 4.7 - - + -
69F LEU* 2.9 39.9 + - + +
70F ILE* 3.1 11.3 + - - +
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Residues in contact with GLY 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E GLU* 5.5 0.6 + - - -
101E PHE* 5.2 1.5 - - - -
65F PHE 3.3 2.6 + - - -
66F PRO* 1.3 73.0 - - - +
68F VAL* 1.3 61.5 + - - +
70F ILE* 3.1 19.2 + - - +
71F VAL* 3.3 6.4 + - - +
109F PHE* 3.2 41.4 - - - -
1006F CL 3.3 21.3 - - - +
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Residues in contact with VAL 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 4.8 0.4 - - + -
68E VAL* 3.5 45.3 - - + +
69E LEU* 4.4 9.4 - - + -
71E VAL* 4.4 3.8 - - + -
72E GLU* 3.5 35.4 + - + +
101E PHE* 3.7 22.4 - - + -
104E ILE* 4.3 10.3 - - + -
66F PRO* 4.3 10.5 - - + -
67F GLY* 1.3 75.8 - - - +
69F LEU* 1.3 66.8 + - + +
70F ILE 3.3 0.2 - - - -
71F VAL* 3.5 8.8 + - - +
72F GLU* 3.1 19.4 + - - +
109F PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E MET* 5.2 3.6 - - + -
68E VAL* 4.5 10.5 - - + -
69E LEU* 4.7 9.0 - - + -
27F MET* 4.6 15.5 - - + -
29F LEU* 3.6 27.1 - - + +
54F VAL* 3.8 23.3 - - + -
65F PHE* 3.7 22.9 - - + -
66F PRO* 2.9 40.8 + - + +
68F VAL* 1.3 84.5 - - + +
70F ILE* 1.3 60.1 + - - +
71F VAL 3.2 0.2 - - - -
72F GLU* 3.6 7.2 - - + -
73F GLY* 2.9 23.2 + - - -
121F TYR* 4.4 0.7 + - - -
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Residues in contact with ILE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F PHE* 3.9 20.6 - - + +
66F PRO 3.1 10.7 + - - +
67F GLY* 3.1 21.5 + - - +
69F LEU* 1.3 78.4 - - - +
71F VAL* 1.3 63.3 + - - +
73F GLY* 3.2 3.6 + - - -
74F MET* 3.1 24.8 + - - +
109F PHE* 4.3 13.0 - - + -
111F ILE 5.4 2.2 - - - +
113F VAL* 3.8 28.7 - - + +
119F LEU* 4.1 13.9 - - + -
121F TYR* 3.6 2.1 - - + -
139F ALA* 3.6 30.5 - - + -
146F VAL* 4.8 5.2 - - + +
147F ALA* 4.2 9.6 - - + -
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Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E VAL* 4.7 2.0 - - + -
104E ILE* 4.9 5.4 - - + -
67F GLY 3.3 13.4 + - - +
68F VAL* 3.6 11.0 - - - +
70F ILE* 1.3 75.3 - - + +
72F GLU* 1.3 59.5 + - - +
74F MET* 3.0 11.5 + - - +
75F ALA* 2.9 26.5 + - - +
101F PHE* 4.2 17.0 - - + -
104F ILE* 4.3 24.7 - - + -
107F VAL* 4.8 13.5 - - + -
109F PHE* 4.0 19.7 - - + -
148F GLU 5.8 0.2 - - - +
149F ALA* 4.9 11.0 - - + -
151F LEU* 4.4 9.6 - - + -
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Residues in contact with GLU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58E HIS* 4.5 7.9 + - - -
66E PRO* 5.1 1.0 - - - +
67E GLY 5.6 0.3 + - - -
68E VAL* 3.5 19.6 + - + +
23F HIS* 3.8 16.8 + - - -
27F MET* 3.6 26.0 - - + +
29F LEU* 3.9 6.5 - - + -
68F VAL 3.1 17.2 + - - +
69F LEU* 3.7 10.5 - - + +
70F ILE 3.3 0.2 - - - -
71F VAL* 1.3 75.2 - - - +
73F GLY* 1.3 57.2 + - - +
75F ALA* 3.2 5.7 + - - +
76F GLN* 2.9 60.2 + - - +
101F PHE* 3.2 27.8 - - - -
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Residues in contact with GLY 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F LEU* 4.1 13.7 - - - +
30F VAL* 3.7 2.6 - - - +
69F LEU 2.9 12.5 + - - -
70F ILE 3.2 1.1 + - - -
71F VAL 3.2 0.2 - - - -
72F GLU* 1.3 78.2 - - - +
74F MET* 1.3 54.7 + - - +
76F GLN* 3.7 2.9 + - - -
77F SER* 3.0 29.5 + - - -
121F TYR* 3.3 34.7 - - - -
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Residues in contact with MET 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ILE* 3.1 20.1 + - - +
71F VAL* 3.0 12.8 + - - +
73F GLY* 1.3 75.2 - - - +
75F ALA* 1.3 60.6 + - - +
77F SER* 3.3 3.3 + - - -
78F GLY* 2.9 23.6 + - - -
121F TYR* 3.4 20.0 - - + -
123F LEU* 3.5 32.3 - - + +
135F VAL* 5.1 0.2 - - - +
137F GLY 3.7 32.3 - - - +
138F THR* 3.8 11.0 - - - +
139F ALA* 4.1 16.8 - - + -
147F ALA* 5.3 2.2 - - - -
148F GLU 4.6 1.8 - - - -
149F ALA* 3.8 27.6 - - + +
151F LEU* 4.2 7.2 - - + -
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Residues in contact with ALA 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F VAL 2.9 5.8 + - - +
72F GLU* 3.2 7.2 + - - +
74F MET* 1.3 73.6 - - - +
76F GLN* 1.3 53.4 + - - +
78F GLY* 3.0 2.6 + - - -
79F GLY* 2.6 33.6 + - - -
99F VAL* 6.0 1.3 - - - +
101F PHE* 3.3 42.4 - - + -
151F LEU* 3.7 22.9 - - + +
153F ALA* 5.6 4.3 - - + -
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Residues in contact with GLN 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F LEU* 3.9 13.1 - - + +
23F HIS* 3.6 34.0 - - + +
27F MET 2.8 24.8 + - - -
28F LEU* 3.6 7.1 - - - +
29F LEU* 2.7 32.8 + - - +
30F VAL* 3.6 19.8 + - + +
72F GLU* 2.9 44.6 + - - +
73F GLY 3.9 0.2 - - - +
75F ALA* 1.3 76.8 - - + +
77F SER* 1.3 61.8 + - - +
79F GLY* 3.0 3.6 + - - +
80F PHE* 2.9 23.4 + - - +
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Residues in contact with SER 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F VAL* 3.9 9.2 - - - +
33F ILE* 5.5 0.7 - - - -
42F ILE* 3.4 24.2 - - - +
44F ALA* 3.9 12.6 - - - +
73F GLY 3.0 16.6 + - - -
74F MET 3.4 8.7 - - - -
76F GLN* 1.3 79.0 - - - +
78F GLY* 1.3 63.4 + - - +
80F PHE* 3.4 4.1 + - - +
81F LEU 3.3 15.6 + - - -
121F TYR* 3.1 23.8 - - - +
123F LEU* 4.0 16.4 - - - -
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Residues in contact with GLY 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ILE* 4.7 1.3 - - - -
74F MET 2.9 14.7 + - - -
75F ALA 3.0 3.8 + - - -
77F SER* 1.3 74.0 - - - +
79F GLY* 1.3 66.8 + - - +
81F LEU* 3.1 9.8 + - - +
82F ALA* 2.9 22.6 + - - +
123F LEU* 4.4 6.7 - - - +
133F TRP* 5.5 1.0 - - - +
135F VAL* 4.5 24.8 - - - +
151F LEU* 6.0 0.4 - - - -
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 4.1 4.5 - - - -
23F HIS* 6.5 0.4 - - - -
75F ALA 2.6 19.1 + - - -
76F GLN* 3.0 5.1 + - - -
78F GLY* 1.3 72.4 - - - +
80F PHE* 1.3 57.1 + - - +
82F ALA* 3.0 8.8 + - - +
83F PHE* 2.9 41.7 + - - -
99F VAL* 5.4 13.0 - - - -
153F ALA* 6.2 2.7 - - - -
155F ILE* 5.9 1.3 - - - -
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Residues in contact with PHE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F PHE* 3.8 42.4 - + + -
16F HIS 4.5 1.6 - - - -
17F ILE* 4.2 19.7 - - + -
20F ILE* 3.9 34.8 - - + -
21F LEU* 3.7 20.5 - - + +
33F ILE* 4.1 18.8 - - + -
36F LEU* 4.1 12.3 - - + -
42F ILE* 3.8 18.2 - - + -
76F GLN 2.9 12.0 + - - +
77F SER* 3.6 9.0 - - - +
78F GLY 3.2 0.2 - - - -
79F GLY* 1.3 76.3 - - - +
81F LEU* 1.3 59.1 + - - +
83F PHE* 3.6 3.9 + - - +
84F THR* 3.0 48.1 + - + +
89F PHE* 4.5 0.7 - + - -
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Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 3.7 22.9 - - + -
37F GLN 3.8 20.0 - - - +
38F ALA* 4.5 0.7 - - - -
39F ASN 4.3 1.3 - - - +
41F LYS* 3.8 17.7 - - - +
42F ILE* 3.7 23.6 - - + -
77F SER 3.3 9.4 + - - +
78F GLY* 3.1 10.6 + - - +
80F PHE* 1.3 80.9 - - - +
82F ALA* 1.3 55.5 + - - +
84F THR* 3.4 3.2 + - - +
85F SER* 2.5 49.1 + - - +
123F LEU* 4.4 4.5 - - + +
124F GLU 5.0 0.4 - - - -
125F VAL* 3.7 30.1 - - + +
133F TRP* 4.8 2.2 - - + -
135F VAL* 5.2 6.5 - - + -
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Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F GLY 2.9 12.7 + - - +
79F GLY* 3.0 10.7 + - - +
81F LEU* 1.3 74.3 - - - +
83F PHE* 1.3 66.0 + - - +
85F SER* 3.9 0.9 - - - -
86F LEU* 3.0 28.4 + - - +
133F TRP* 3.7 39.5 - - + -
155F ILE* 3.6 20.9 - - + -
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Residues in contact with PHE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ILE* 3.5 43.3 - - + -
21F LEU* 4.2 5.8 - - + -
22F PRO* 4.3 11.7 - - + -
79F GLY 2.9 31.1 + - - +
80F PHE 3.9 1.8 - - - +
82F ALA* 1.3 74.5 - - - +
84F THR* 1.3 58.5 + - - +
86F LEU* 3.5 1.7 - - - +
87F TRP* 2.8 58.4 + + - -
88F GLY 3.9 3.4 - - - +
94F ALA* 4.3 15.9 - - + -
97F LYS* 3.7 34.5 - - + -
98F ILE 4.6 0.2 - - - -
99F VAL* 3.6 31.6 - - + -
155F ILE* 4.0 12.5 - - + +
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Residues in contact with THR 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F PHE* 5.7 1.1 - - + -
20F ILE* 4.7 5.6 - - + -
36F LEU* 3.8 26.2 - - + +
38F ALA* 5.7 1.1 - - - +
80F PHE* 3.0 46.0 + - + +
81F LEU* 3.4 4.3 + - - +
83F PHE* 1.3 76.1 - - + +
85F SER* 1.3 65.9 + - - +
86F LEU 3.1 1.6 - - - -
88F GLY* 2.6 45.6 + - - +
89F PHE* 4.7 8.7 - - + -
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Residues in contact with SER 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ALA* 3.7 12.9 - - - +
39F ASN* 3.1 36.5 + - - +
81F LEU* 2.5 32.3 + - - +
84F THR* 1.3 78.0 + - - +
86F LEU* 1.3 63.3 + - - +
88F GLY 4.9 0.2 + - - -
133F TRP* 3.4 25.6 - - - -
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Residues in contact with LEU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F ALA 3.0 19.7 + - - +
83F PHE 3.5 3.4 - - - +
85F SER* 1.3 81.9 - - - +
87F TRP* 1.3 85.0 + - + +
128F HIS* 5.7 2.9 - - + +
130F GLY* 3.7 13.7 - - - +
131F MET* 3.5 31.2 - - + -
133F TRP* 3.7 27.8 - - + +
155F ILE* 3.9 17.9 - - + -
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Residues in contact with TRP 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PHE* 2.8 56.6 + + - +
86F LEU* 1.3 97.4 + - + +
88F GLY* 1.3 65.4 + - - +
89F PHE 4.6 0.2 - - - -
90F ASP* 3.7 16.5 - - + +
93F ILE* 3.8 42.0 - - + +
94F ALA 5.6 0.7 - - - -
97F LYS* 3.9 23.8 - - + -
131F MET* 3.6 40.5 - - + +
155F ILE* 3.8 11.0 - - + -
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Residues in contact with GLY 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F ILE* 4.9 1.7 - - - +
83F PHE 3.9 2.9 - - - +
84F THR* 2.6 42.7 + - - +
86F LEU 3.8 0.6 - - - -
87F TRP* 1.3 78.9 - - - +
89F PHE* 1.3 58.2 + - - -
90F ASP* 3.0 7.1 + - - +
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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