Contacts of the helix formed by residues 64 - 87 (chain C) in PDB entry 1Y67
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 64 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C THR* 4.1 34.1 - - + -
48C PHE* 4.6 4.7 - - + -
62C ARG 4.6 1.1 - - - +
63C VAL* 1.4 90.7 - - + +
65C ALA* 1.3 59.3 + - - +
66C ASP* 3.3 16.6 - - - +
67C LYS* 3.0 28.4 + - + +
68C LYS 3.3 7.8 + - - -
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Residues in contact with ALA 65 (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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63C VAL 3.4 4.0 + - - -
64C PRO* 1.3 72.7 - - - +
66C ASP* 1.3 61.4 + - - +
67C LYS 3.1 1.3 + - - -
68C LYS* 3.3 21.8 + - + +
69C GLY 4.7 1.2 + - - -
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Residues in contact with ASP 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C PRO* 3.7 17.5 - - - +
65C ALA* 1.3 78.1 + - - +
67C LYS* 1.3 80.0 + - - +
68C LYS 3.6 0.2 - - - -
69C GLY 5.2 0.8 + - - -
70C ALA* 5.5 3.1 + - - +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LYS 4.7 2.4 + - - -
42C ALA* 2.9 37.4 + - + +
44C GLU 3.1 19.4 + - - -
45C GLY* 5.2 0.8 - - - -
46C THR* 3.9 7.4 - - + +
64C PRO* 3.0 24.2 + - + +
66C ASP* 1.3 102.9 - - - +
68C LYS* 1.3 60.2 + - - +
69C GLY 3.4 2.7 - - - -
70C ALA* 3.4 8.5 + - + +
71C LEU* 2.9 48.7 + - + +
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Residues in contact with LYS 68 (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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60C LEU* 3.7 30.2 + - + +
61C ASP* 4.8 10.0 - - - +
63C VAL* 4.2 7.9 - - + +
64C PRO 3.3 8.8 + - - +
65C ALA* 3.3 18.0 + - - +
67C LYS* 1.3 77.5 - - - +
69C GLY* 1.3 58.6 + - - +
71C LEU* 3.7 1.4 - - - +
72C ARG* 2.8 40.6 + - + +
161C ILE* 3.9 34.9 - - - +
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Residues in contact with GLY 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ALA 4.7 1.8 + - - -
66C ASP 5.2 1.2 + - - -
67C LYS 3.4 0.2 - - - -
68C LYS* 1.3 78.8 - - - +
70C ALA* 1.3 60.2 + - - +
72C ARG* 3.6 7.9 - - - +
73C ASN* 3.1 34.9 + - - -
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASN 5.2 1.1 - - - +
42C ALA* 4.1 17.5 - - + -
66C ASP 5.5 1.9 + - - +
67C LYS* 3.4 11.9 + - + +
69C GLY* 1.3 75.0 - - - +
71C LEU* 1.3 58.6 + - - +
73C ASN* 4.8 2.0 - - - +
74C ASN* 2.8 48.8 + - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA* 4.0 7.0 - - - +
42C ALA* 3.7 21.5 - - + +
43C LEU* 3.7 38.4 - - + -
46C THR* 5.4 2.0 - - + -
56C LEU* 4.0 11.4 - - + -
57C ILE* 4.9 0.3 - - - +
60C LEU* 3.9 14.9 - - + +
63C VAL* 3.9 34.8 - - + -
67C LYS* 2.9 31.3 + - + +
68C LYS* 3.9 2.7 - - - +
70C ALA* 1.3 75.0 - - - +
72C ARG* 1.3 61.5 + - - +
75C ALA* 2.8 39.6 + - + +
76C GLY 3.4 0.7 + - - -
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Residues in contact with ARG 72 (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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60C LEU* 3.9 18.5 - - + +
68C LYS* 2.8 28.9 + - + +
69C GLY* 3.6 8.3 - - - +
71C LEU* 1.3 74.9 - - - +
73C ASN* 1.3 68.2 + - - +
76C GLY* 3.3 18.0 + - - -
152C GLN* 4.0 3.8 - - - +
153C ASP* 2.8 41.5 + - - +
157C MET* 3.4 15.9 - - - +
161C ILE* 3.2 36.6 + - + +
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Residues in contact with ASN 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TYR* 4.0 1.0 - - - -
69C GLY* 3.1 20.0 + - - +
70C ALA* 4.0 2.6 - - - +
72C ARG* 1.3 89.6 + - - +
74C ASN* 1.3 65.4 + - - +
77C GLY* 3.1 18.9 + - - -
151C ASN* 5.3 1.9 - - - +
152C GLN* 3.4 17.1 + - - +
153C ASP* 5.0 2.4 - - - +
130D PHE* 3.5 56.8 - - + +
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Residues in contact with ASN 74 (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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34C THR* 5.2 0.2 - - - +
35C TYR* 3.4 43.3 - - - +
38C ASN* 3.4 34.4 + - - +
39C ALA* 3.6 13.7 - - - +
70C ALA* 2.8 43.1 + - - +
73C ASN* 1.3 78.4 - - - +
75C ALA* 1.3 58.4 + - - +
76C GLY 3.3 0.9 - - - -
77C GLY 3.2 0.5 + - - -
78C HIS* 2.8 27.5 + - - +
130D PHE* 4.8 4.2 - - - -
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Residues in contact with ALA 75 (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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3C TYR* 4.4 3.6 - - + +
39C ALA* 4.0 8.4 - - + +
53C VAL* 3.3 18.0 - - + +
56C LEU* 3.6 31.2 - - + -
57C ILE* 3.7 12.1 - - + -
60C LEU* 5.6 0.4 - - + -
70C ALA 4.1 0.2 + - - -
71C LEU* 2.8 26.2 + - + +
74C ASN* 1.3 71.8 - - - +
76C GLY* 1.3 59.3 + - - +
78C HIS* 3.4 1.3 + - - -
79C ALA* 2.9 26.5 + - - +
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Residues in contact with GLY 76 (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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57C ILE* 3.8 6.2 - - - +
71C LEU 3.4 0.8 + - - -
72C ARG 3.3 21.8 + - - -
74C ASN 3.3 0.2 - - - -
75C ALA* 1.3 76.4 - - - +
77C GLY* 1.3 56.1 + - - +
79C ALA* 3.3 3.1 + - - -
80C ASN* 2.9 36.7 + - - +
152C GLN 3.5 17.3 - - - -
157C MET* 3.7 11.7 - - - -
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Residues in contact with GLY 77 (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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35C TYR* 3.8 17.2 - - - -
73C ASN 3.1 18.4 + - - -
74C ASN 3.2 4.6 + - - -
76C GLY* 1.3 74.1 - - - +
78C HIS* 1.3 60.8 + - - +
81C HIS* 2.7 33.1 + - - +
152C GLN* 3.5 21.6 - - - +
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Residues in contact with HIS 78 (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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3C TYR* 3.5 41.7 - + + +
4C THR 3.5 22.9 + - - -
6C PRO* 4.1 2.9 - - + -
32C HIS* 2.9 30.5 + - - +
35C TYR* 3.8 6.6 - - + +
36C VAL* 3.6 14.6 - - + +
53C VAL* 3.7 24.7 - - + +
74C ASN 2.8 18.2 + - - +
75C ALA* 3.7 6.3 - - - +
76C GLY 3.3 0.2 - - - -
77C GLY* 1.3 72.0 - - - +
79C ALA* 1.3 62.4 + - - +
82C SER* 2.9 47.6 + - - -
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Residues in contact with ALA 79 (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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53C VAL* 4.0 23.5 - - + +
54C GLU* 4.7 12.0 - - + +
57C ILE* 3.9 26.5 - - + -
75C ALA 2.9 17.2 + - - +
76C GLY 3.7 3.4 - - - +
78C HIS* 1.3 77.6 - - - +
80C ASN* 1.3 62.7 + - - +
82C SER* 3.8 2.7 - - - -
83C MET* 3.2 24.1 + - - +
154C ASN* 4.5 7.2 + - - +
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Residues in contact with ASN 80 (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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76C GLY 2.9 17.7 + - - +
77C GLY 3.9 0.4 - - - +
79C ALA* 1.3 75.7 - - - +
81C HIS* 1.3 58.1 + - - +
83C MET* 3.3 5.9 + - - +
84C PHE* 2.9 27.9 + - - +
134C TRP* 3.4 31.7 - - + +
136C TRP* 3.3 17.3 - - + -
152C GLN* 3.0 47.9 + - - +
153C ASP 3.7 5.1 + - - -
154C ASN* 2.8 31.5 + - - +
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Residues in contact with HIS 81 (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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27C HIS* 3.0 27.8 + + - -
31C HIS* 5.1 0.4 - - - +
32C HIS* 3.5 28.7 - + + +
35C TYR* 3.4 27.6 - + - -
77C GLY 2.7 28.7 + - - +
80C ASN* 1.3 72.2 - - - +
82C SER* 1.3 65.6 + - - +
84C PHE* 3.2 6.6 + + - +
85C TRP* 3.0 42.9 + + - +
134C TRP* 3.8 9.1 - + - -
152C GLN* 3.6 18.2 - - - -
173C ASP* 3.4 2.4 + - - -
177C HIS* 4.0 0.4 + - - -
229C FE 2.2 28.2 - - - -
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Residues in contact with SER 82 (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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6C PRO* 3.8 10.3 - - - +
32C HIS* 3.5 9.2 - - - -
53C VAL* 5.5 1.3 - - - -
54C GLU* 4.7 11.0 - - - -
78C HIS* 2.9 45.0 + - - -
79C ALA* 3.8 5.6 - - - -
81C HIS* 1.3 77.1 - - - +
83C MET* 1.3 63.1 + - - +
85C TRP* 3.8 6.6 + - - +
86C GLN* 3.5 27.9 + - - +
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Residues in contact with MET 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 5.8 3.3 + - + -
79C ALA 3.2 15.5 + - - +
80C ASN* 3.6 4.9 - - - +
82C SER* 1.3 77.2 - - - +
84C PHE* 1.3 66.0 + - - +
86C GLN* 3.0 14.2 + - - +
87C ILE* 3.0 21.7 + - + +
136C TRP* 4.0 25.8 - - + -
154C ASN* 5.6 3.6 - - - +
156C LEU* 5.8 3.6 - - + -
168C PRO* 3.1 39.5 - - + +
169C ILE 4.7 0.4 - - - -
170C LEU 4.6 7.9 - - - -
171C GLY 4.8 3.1 - - - +
206C ARG* 2.9 46.7 - - - +
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Residues in contact with PHE 84 (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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19C ILE* 4.9 4.9 - - + -
24C MET* 5.9 0.7 - - - -
27C HIS* 4.0 22.2 - + - -
80C ASN 2.9 18.1 + - - +
81C HIS* 3.2 6.7 + + - +
83C MET* 1.3 78.2 - - - +
85C TRP* 1.3 86.1 + + - +
86C GLN 3.3 0.2 + - - -
87C ILE* 3.3 23.3 + - + +
88C MET* 3.5 30.5 - - + +
134C TRP* 3.8 22.0 - + + -
171C GLY 3.5 17.3 - - - -
172C VAL* 3.9 0.2 - - - -
173C ASP* 3.7 16.8 - - + -
178C ALA* 5.4 0.2 - - + -
190C TYR* 3.7 21.5 - - - -
194C PHE* 3.6 25.1 - + - -
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Residues in contact with TRP 85 (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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6C PRO* 4.4 9.0 - - + -
7C GLN 5.8 0.7 - - - +
8C LEU* 3.5 27.1 - - + -
9C PRO* 3.8 9.8 - - + +
10C TYR* 2.7 34.9 + - - +
24C MET* 3.7 33.4 - - + -
27C HIS* 3.5 39.9 - + + -
28C HIS* 3.7 29.3 - + + -
32C HIS* 2.9 28.4 + + - -
81C HIS* 3.0 35.5 + + - -
82C SER* 4.2 6.3 - - - +
83C MET 3.3 0.4 - - - -
84C PHE* 1.3 93.2 - + - +
86C GLN* 1.3 63.4 + - + +
88C MET* 3.5 9.5 + - + +
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Residues in contact with GLN 86 (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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9C PRO* 4.4 16.4 - - + +
82C SER* 3.5 14.8 - - - +
83C MET 3.0 8.1 + - - +
85C TRP* 1.3 79.2 - - + +
87C ILE* 1.3 58.8 + - - +
88C MET 3.3 7.0 + - - +
199C ASN* 4.2 4.0 + - - +
202C GLU* 3.1 32.9 - - + +
206C ARG* 2.6 35.0 + - - +
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Residues in contact with ILE 87 (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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83C MET* 3.0 23.8 + - + +
84C PHE* 3.3 17.5 + - + +
86C GLN* 1.3 75.3 - - - +
88C MET* 1.3 63.5 + - + +
169C ILE 3.7 22.9 - - - +
170C LEU* 3.7 15.3 - - + -
171C GLY 3.5 27.8 - - - +
194C PHE* 3.9 5.2 - - + -
198C VAL* 3.5 7.1 - - - +
199C ASN* 2.7 29.1 + - - -
202C GLU* 3.9 9.4 - - + -
203C VAL* 4.1 13.0 - - + -
206C ARG* 3.8 23.8 - - - +
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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