Contacts of the helix formed by residues 69 - 97 (chain E) 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 GLN 69 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LYS 5.5 2.1 - - - +
47C LEU* 5.9 0.2 - - - +
50C ILE* 4.9 15.8 - - - +
65E PHE* 4.7 8.9 - - + -
67E GLN 4.0 0.2 + - - -
68E LEU* 1.3 99.7 - - - +
70E PRO* 1.3 70.2 - - - +
71E ALA* 3.1 8.7 + - + +
72E MET* 3.4 25.1 + - + +
73E THR* 3.5 11.1 + - - -
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Residues in contact with PRO 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E TYR* 3.3 19.9 + - - -
66E TYR* 3.3 45.3 - - + +
67E GLN* 4.1 9.4 - - - +
68E LEU 3.8 0.4 - - - -
69E GLN* 1.3 88.9 - - - +
71E ALA* 1.3 59.9 + - - +
72E MET 3.5 0.2 - - - -
73E THR* 4.0 2.5 - - - +
74E GLN* 3.7 4.7 + - - +
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Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E GLN* 3.1 3.6 - - + -
70E PRO* 1.3 78.7 - - - +
72E MET* 1.3 65.1 + - - +
73E THR 3.3 0.2 - - - -
74E GLN* 3.4 6.9 + - - +
75E GLN* 3.1 20.2 + - - +
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Residues in contact with MET 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 5.3 1.1 - - + -
46C LYS* 3.6 49.1 - - + -
65E PHE* 4.8 11.2 - - + -
69E GLN* 3.4 20.9 + - + +
71E ALA* 1.3 76.1 - - - +
73E THR* 1.3 66.2 + - - +
75E GLN* 3.0 25.5 + - - +
76E ILE* 2.9 52.9 + - + +
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Residues in contact with THR 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E TYR* 3.6 24.0 - - + +
58E PHE* 4.0 16.2 - - + -
59E THR* 4.1 6.5 - - + -
62E TYR* 5.6 4.3 - - + -
65E PHE* 3.2 38.3 + - + -
66E TYR* 3.9 22.5 - - + -
69E GLN 3.5 9.7 + - - -
70E PRO 4.0 5.4 - - - -
71E ALA 3.3 0.6 - - - -
72E MET* 1.3 76.8 - - - +
74E GLN* 1.3 56.1 + - - +
76E ILE* 3.4 2.9 + - - +
77E TYR* 2.9 28.1 + - - +
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Residues in contact with GLN 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55E TYR* 3.1 48.4 + - + +
70E PRO 3.7 4.2 + - - +
71E ALA* 3.4 9.0 + - - +
72E MET 3.2 0.6 - - - -
73E THR* 1.3 73.9 - - - +
75E GLN* 1.3 63.6 + - - +
77E TYR* 4.3 3.4 - - - -
78E ASP* 2.8 72.8 + - - +
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Residues in contact with GLN 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ALA 3.1 13.5 + - - +
72E MET* 3.0 32.9 + - - +
74E GLN* 1.3 80.8 + - - +
76E ILE* 1.3 72.3 + - + +
78E ASP* 3.2 6.3 + - - +
79E LYS* 2.9 39.4 + - + +
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Residues in contact with ILE 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 3.5 33.7 - - + +
42C VAL* 3.6 35.4 - - + -
43C ILE* 4.5 10.8 - - + -
58E PHE* 5.7 0.9 - - + -
65E PHE* 5.6 2.9 - - + -
72E MET* 2.9 37.1 + - + +
73E THR* 4.1 3.8 - - - +
75E GLN* 1.3 88.3 - - + +
77E TYR* 1.3 61.1 + - - +
79E LYS* 3.9 12.2 - - + +
80E PHE* 2.9 28.4 + - - +
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Residues in contact with TYR 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E VAL* 4.5 2.9 + - - +
53E GLY 2.7 29.5 + - - -
54E SER* 3.5 3.3 - - - -
55E TYR* 3.4 36.5 + + + -
58E PHE* 3.5 45.4 - + + -
73E THR 2.9 19.4 + - - +
74E GLN* 3.8 4.0 - - - +
76E ILE* 1.3 78.1 - - - +
78E ASP* 1.3 70.8 + - - +
80E PHE* 3.2 19.3 + + - +
81E ILE* 2.9 56.4 + - + +
----------------------------------------------------------
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Residues in contact with ASP 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E GLN* 2.8 60.0 + - - +
75E GLN* 3.5 6.7 - - - +
77E TYR* 1.3 87.0 - - - +
79E LYS* 1.3 64.0 + - + +
81E ILE* 3.3 10.6 - - - +
82E ALA* 2.9 27.2 + - - +
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Residues in contact with LYS 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C VAL* 6.1 3.4 - - - +
75E GLN* 2.9 32.1 + - + +
76E ILE* 3.9 15.3 - - + +
78E ASP* 1.3 75.6 - - + +
80E PHE* 1.3 63.3 + - - +
82E ALA* 4.0 4.4 - - - +
83E GLN* 2.9 42.2 + - - +
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Residues in contact with PHE 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 5.3 4.7 - - + -
35C VAL* 3.3 38.4 - - + +
36C MET* 3.4 36.6 - - + -
39C VAL* 4.6 11.7 - - + -
67C PHE* 4.1 19.5 - + - -
71C MET* 4.9 11.9 - - + -
53E GLY 5.2 0.9 - - - -
58E PHE* 5.5 1.8 - + + -
76E ILE 2.9 20.1 + - - +
77E TYR* 3.2 27.8 + + - +
79E LYS* 1.3 76.5 - - - +
81E ILE* 1.3 84.0 + - + +
84E LEU* 2.9 50.4 + - + +
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Residues in contact with ILE 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E VAL* 3.4 51.4 - - + +
52E ALA 5.2 0.2 - - - +
53E GLY 4.5 2.7 - - - +
77E TYR* 2.9 47.7 + - + +
78E ASP* 3.3 16.2 - - - +
80E PHE* 1.3 89.9 - - + +
82E ALA* 1.3 68.9 + - + +
84E LEU* 3.4 9.3 + - + +
85E GLN* 3.0 34.0 + - - +
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Residues in contact with ALA 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ASP 2.9 19.1 + - - +
79E LYS* 4.0 3.6 - - - +
81E ILE* 1.3 79.3 - - + +
83E GLN* 1.3 59.1 + - - +
84E LEU 3.2 0.3 + - - -
85E GLN* 3.3 16.1 + - - +
86E THR* 2.9 36.8 + - + +
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Residues in contact with GLN 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLU* 5.9 1.2 + - - -
35C VAL* 4.5 16.1 - - + +
38C ALA* 5.7 7.9 - - - +
79E LYS* 2.9 31.9 + - - +
80E PHE 4.3 0.9 - - - +
82E ALA* 1.3 77.5 - - - +
84E LEU* 1.3 56.5 + - - +
86E THR* 3.6 7.4 - - - +
87E SER* 2.9 37.0 + - - -
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Residues in contact with LEU 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 4.6 3.1 - - + +
32C LEU* 4.0 39.7 - - + +
35C VAL* 3.8 16.2 - - + +
71C MET* 6.1 2.5 - - - -
46E LEU* 5.6 4.0 - - + -
49E LEU* 5.1 17.5 - - + -
50E VAL* 5.7 5.2 - - + -
80E PHE* 2.9 43.9 + - + +
81E ILE* 3.5 12.1 - - + +
82E ALA 3.1 0.2 - - - -
83E GLN* 1.3 76.1 - - - +
85E GLN* 1.3 67.2 + - + +
87E SER* 3.3 3.3 + - - -
88E ILE* 3.0 40.6 + - + +
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Residues in contact with GLN 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E LEU* 3.6 23.2 - - + +
50E VAL* 4.7 12.9 - - + +
81E ILE* 3.0 36.2 + - - +
82E ALA* 3.3 15.6 - - - +
84E LEU* 1.3 79.2 - - + +
86E THR* 1.3 68.1 + - + +
88E ILE* 3.1 12.0 - - - +
89E ARG* 2.9 51.7 + - - +
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Residues in contact with THR 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E ALA* 2.9 21.4 + - + +
83E GLN* 3.6 11.3 + - - +
85E GLN* 1.3 84.1 - - + +
87E SER* 1.3 62.8 + - - +
89E ARG* 4.1 8.7 - - - +
90E GLU* 2.9 31.4 + - - +
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Residues in contact with SER 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C TYR* 3.4 39.8 - - - -
34C GLU* 4.9 1.4 + - - -
35C VAL* 5.5 2.7 - - - -
83E GLN* 2.9 27.5 + - - -
84E LEU* 3.7 4.9 - - - -
86E THR* 1.3 79.3 + - - +
88E ILE* 1.3 56.3 - - - +
90E GLU* 3.4 7.6 + - - +
91E GLU* 3.0 24.4 + - - +
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Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 3.3 66.5 - - + +
31C TYR* 4.4 7.0 - - + -
75C PHE* 5.1 3.1 - - + -
42E VAL* 6.5 0.9 - - + -
45E PHE* 4.1 13.7 - - + -
46E LEU* 3.4 30.7 - - + -
49E LEU* 5.5 2.2 - - + -
84E LEU* 3.0 27.8 + - + +
85E GLN 3.1 13.5 - - - +
87E SER* 1.3 75.4 - - - +
89E ARG* 1.3 64.4 + - + +
91E GLU* 3.0 20.8 + - - +
92E ILE* 3.0 13.0 + - - +
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Residues in contact with ARG 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E VAL* 5.5 6.7 - - + -
43E ASP* 2.9 35.1 + - - +
46E LEU* 3.3 28.3 - - + +
47E GLN* 5.7 4.0 - - - +
85E GLN* 2.9 37.2 + - - +
86E THR* 4.1 8.5 - - - +
88E ILE* 1.3 73.6 - - + +
90E GLU* 1.3 66.2 + - - +
92E ILE* 3.1 18.0 - - + +
93E SER* 3.0 27.0 + - - -
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ARG* 5.2 9.1 + - - +
31C TYR* 6.0 0.2 - - - -
86E THR 2.9 21.9 + - - +
87E SER* 3.4 9.2 - - - +
88E ILE 3.3 0.2 - - - -
89E ARG* 1.3 75.6 - - - +
91E GLU* 1.3 56.2 + - - +
93E SER* 3.6 9.4 + - - -
94E ASP* 2.7 48.5 + - - +
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Residues in contact with GLU 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 5.8 2.6 - - + -
27C ALA* 3.8 26.9 - - + +
28C PHE* 3.9 18.8 - - + -
31C TYR* 3.1 38.1 + - + -
87E SER 3.0 5.8 + - - +
88E ILE* 3.0 12.9 + - - +
90E GLU* 1.3 75.8 - - - +
92E ILE* 1.3 61.3 + - - +
94E ASP* 2.7 29.7 + - - +
95E ILE* 3.0 32.7 + - + +
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Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ILE* 5.2 6.1 - - + -
28C PHE* 3.7 28.7 - - + -
86C PHE* 5.9 2.5 - - + -
38E LEU* 5.4 5.6 - - + -
39E ASP* 3.6 23.8 - - - +
42E VAL* 3.8 31.9 - - + -
88E ILE 3.0 5.9 + - - +
89E ARG* 3.1 27.6 - - + +
91E GLU* 1.3 75.2 - - + +
93E SER* 1.3 76.7 + - - +
95E ILE* 3.1 20.4 - - + +
96E LYS* 3.0 37.4 + - + +
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Residues in contact with SER 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E ARG 3.0 18.9 + - - -
90E GLU* 3.9 11.7 - - - -
92E ILE* 1.3 85.7 - - - +
94E ASP* 1.3 63.3 + - - +
96E LYS* 3.6 12.5 + - - +
97E GLU* 3.4 34.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B ARG* 2.7 51.6 + - - +
154B LYS* 5.7 4.5 - - - +
31C TYR* 4.7 4.5 + - - -
90E GLU* 2.7 36.5 + - - +
91E GLU* 2.7 31.9 + - - +
93E SER* 1.3 79.4 - - - +
95E ILE* 1.3 58.0 + - + +
97E GLU* 3.5 3.5 + - - +
98E GLU* 3.4 21.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ARG* 6.4 2.0 - - + -
24C ILE* 4.6 28.7 - - + -
38E LEU* 5.6 5.2 - - + -
91E GLU* 3.0 31.2 + - + +
92E ILE* 3.1 32.1 - - + +
94E ASP* 1.3 75.1 - - + +
96E LYS* 1.3 68.1 + - + +
97E GLU 3.3 0.2 - - - -
98E GLU* 3.1 29.3 - - + +
101E LEU* 3.9 15.2 - - + +
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Residues in contact with LYS 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E VAL* 3.8 23.9 - - + +
36E LYS* 5.4 0.4 - - - +
38E LEU* 3.7 23.6 - - + -
39E ASP* 3.3 30.9 + - - -
92E ILE* 3.0 30.4 + - + +
93E SER* 4.0 13.2 + - - +
94E ASP 3.3 0.4 - - - -
95E ILE* 1.3 83.9 - - + +
97E GLU* 1.3 59.3 + - + +
98E GLU 3.4 0.2 - - - -
100E ASN 4.0 0.2 + - - -
101E LEU* 3.2 23.5 + - + -
102E GLU* 2.8 39.3 - - - +
105E LEU* 6.0 1.3 - - + -
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Residues in contact with GLU 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLN* 5.6 3.6 - - - +
147B THR* 4.4 7.6 + - - -
150B ARG* 4.1 23.3 + - - +
93E SER* 3.4 23.0 + - - +
94E ASP* 3.5 4.8 + - - +
95E ILE 3.3 0.2 - - - -
96E LYS* 1.3 78.5 - - + +
98E GLU* 1.3 66.4 + - - +
99E GLY 3.5 1.1 - - - -
100E ASN 4.4 4.0 + - - +
102E GLU* 4.6 11.7 - - - +
----------------------------------------------------------
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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