Contacts of the helix formed by residues 62 - 88 (chain E) in PDB entry 5AJI
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 ASP 62 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60E LYS 3.9 2.2 + - - -
61E ILE* 1.3 76.1 - - - +
63E ALA* 1.3 61.4 + - - +
64E THR* 2.8 39.5 + - - -
65E VAL* 3.3 22.6 + - + +
66E ALA* 2.9 27.9 + - - +
122E VAL* 4.2 14.6 - - - +
125E VAL* 4.4 17.2 - - - +
126E MET* 4.2 17.3 - - + +
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ILE* 4.6 17.7 - - + +
61E ILE 3.5 3.0 + - - -
62E ASP* 1.3 76.7 + - - +
64E THR* 1.3 59.8 + - - +
66E ALA* 3.9 4.9 - - - +
67E R1A 3.0 27.0 + - - +
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Residues in contact with THR 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62E ASP* 2.8 17.5 + - - -
63E ALA* 1.3 72.5 - - - +
65E VAL* 1.3 59.3 + - - +
67E R1A 3.4 6.8 - - + +
68E PHE* 2.8 29.5 + - - +
118E LEU* 3.4 39.9 - - + +
122E VAL* 4.0 14.8 - - + +
150E ILE* 5.1 5.8 - - + +
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Residues in contact with VAL 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ILE* 4.1 12.6 - - + -
62E ASP* 3.3 24.9 + - + +
64E THR* 1.3 76.6 - - - +
66E ALA* 1.3 57.8 + - - +
68E PHE* 3.3 6.5 + - + +
69E LEU* 3.0 56.0 + - + +
122E VAL* 3.8 26.2 - - + -
126E MET* 5.0 3.4 - - + -
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Residues in contact with ALA 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ASN* 3.7 14.5 - - - +
56E MET* 3.4 38.5 - - + +
57E ILE* 4.0 11.2 - - + -
61E ILE* 4.0 3.1 - - + +
62E ASP 2.9 18.0 + - - +
63E ALA 3.9 3.1 - - - +
65E VAL* 1.3 76.8 - - - +
67E R1A 1.3 56.9 + - - +
70E SER* 2.4 35.2 + - - -
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Residues in contact with R1A 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E SER* 5.0 6.1 - - - +
50E ASN* 4.1 19.3 - - - +
53E ASN* 3.8 28.0 + - - +
63E ALA 3.0 19.9 + - - +
64E THR* 3.4 10.1 - - + +
65E VAL 3.2 0.2 - - - -
66E ALA* 1.3 74.9 + - - +
68E PHE* 1.3 67.9 + - - +
70E SER* 3.3 13.5 + - - -
71E ALA* 3.0 52.6 + - + +
74E ARG* 2.4 47.3 + - - +
75E TYR* 3.6 24.2 - - - +
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Residues in contact with PHE 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E THR* 2.8 21.2 + - + +
65E VAL* 3.7 5.8 - - + +
67E R1A 1.3 72.6 + - - +
69E LEU* 1.3 78.0 + - + +
71E ALA* 3.2 18.7 + - + +
72E LEU* 3.3 40.9 + - + +
115E LEU* 3.7 31.9 - - + -
118E LEU* 4.4 22.4 - - + -
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Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E MET* 4.0 24.7 - - + -
61E ILE* 5.7 0.7 - - + -
65E VAL* 3.0 38.6 + - + +
68E PHE* 1.3 91.2 - - + +
70E SER* 1.3 61.8 + - - +
72E LEU* 3.3 18.9 + - + +
73E VAL* 3.1 25.8 + - + +
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Residues in contact with SER 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E SER* 3.6 22.1 - - - -
52E VAL* 3.5 10.4 - - - +
53E ASN* 3.2 23.2 - - - +
56E MET* 3.2 13.9 - - - +
66E ALA 2.4 25.8 + - - -
67E R1A 3.6 9.6 - - - -
69E LEU* 1.3 72.9 - - - +
71E ALA* 1.3 59.6 + - - +
73E VAL* 3.2 4.3 + - - +
74E ARG* 2.9 28.5 + - - +
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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
----------------------------------------------------------
67E R1A 3.0 44.3 + - + +
68E PHE* 3.2 14.6 + - + +
70E SER* 1.3 75.3 - - - +
72E LEU* 1.3 62.6 + - + +
74E ARG* 3.3 3.8 - - - +
75E TYR* 2.8 41.5 + - + -
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Residues in contact with LEU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E PHE* 3.3 45.6 + - + +
69E LEU* 3.5 20.9 - - + +
70E SER 3.2 0.4 - - - -
71E ALA* 1.3 75.8 - - + +
73E VAL* 1.3 60.5 + - + +
74E ARG 3.2 0.2 + - - -
75E TYR* 3.2 8.1 + - + +
76E GLY* 2.8 30.0 + - - -
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Residues in contact with VAL 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ILE* 4.0 26.5 - - + +
49E SER* 4.2 11.7 - - - -
52E VAL* 4.2 24.7 - - + -
56E MET* 5.9 0.7 - - + -
69E LEU* 3.1 16.5 + - + +
70E SER* 3.2 9.2 + - - +
72E LEU* 1.3 75.9 - - + +
74E ARG* 1.3 63.6 + - - +
76E GLY* 4.2 1.6 - - - -
77E ILE* 3.3 22.7 + - + +
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Residues in contact with ARG 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E LEU* 5.5 7.1 + - - +
45E ALA* 4.1 9.1 - - + +
46E ARG* 3.9 39.3 - - - +
49E SER* 3.4 24.9 - - - +
67E R1A 2.4 55.1 + - - +
70E SER 2.9 13.7 + - - +
71E ALA* 3.3 11.7 - - - +
72E LEU 3.1 0.2 - - - -
73E VAL* 1.3 76.5 - - - +
75E TYR* 1.3 71.6 + - + +
77E ILE* 2.9 22.2 + - - +
78E ILE* 3.1 28.7 + - + +
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Residues in contact with TYR 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E R1A 3.6 25.3 - - + +
71E ALA* 2.8 37.0 + - + +
72E LEU* 4.2 7.6 - - + +
74E ARG* 1.3 87.7 + - - +
76E GLY* 1.3 56.9 + - - +
78E ILE* 3.6 20.2 - - + +
79E ALA* 2.7 35.5 + - - +
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Residues in contact with GLY 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E LEU 2.8 16.4 + - - -
73E VAL* 4.2 2.7 - - - -
75E TYR* 1.3 77.2 - - - +
77E ILE* 1.3 56.8 + - - +
79E ALA* 3.4 7.6 - - - +
80E PHE* 3.0 42.8 + - - -
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Residues in contact with ILE 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLY 4.0 7.9 - - - +
44E ILE* 4.3 9.6 - - + -
45E ALA* 3.7 27.8 - - + +
48E ILE* 3.6 44.2 - - + -
73E VAL* 3.3 19.2 + - + +
74E ARG 2.9 7.6 + - - +
76E GLY* 1.3 74.1 - - - +
78E ILE* 1.3 55.2 + - - +
79E ALA 3.1 1.3 - - - -
80E PHE* 3.2 16.1 + - + +
81E THR* 2.7 40.1 + - - +
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Residues in contact with ILE 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E GLY 5.6 0.2 - - - -
42E LEU* 3.7 30.5 - - + -
45E ALA* 3.9 17.0 - - + -
74E ARG* 3.1 52.7 + - + +
75E TYR* 3.3 21.5 + - + +
77E ILE* 1.3 75.0 - - - +
79E ALA* 1.3 56.7 + - - +
81E THR* 3.2 7.8 + - - -
82E LEU* 2.8 48.9 + - + +
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Residues in contact with ALA 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E TYR 2.7 21.2 + - - +
76E GLY* 3.4 9.4 - - - +
77E ILE 3.1 0.2 - - - -
78E ILE* 1.3 71.8 - - - +
80E PHE* 1.3 67.0 + - + +
82E LEU* 3.4 2.7 + - - +
83E ILE* 3.0 34.5 + - + +
100E LEU* 4.3 20.9 - - + +
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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
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76E GLY* 3.0 31.4 + - - -
77E ILE* 3.6 14.8 - - + +
79E ALA* 1.3 77.4 - - + +
81E THR* 1.3 62.1 + - - +
83E ILE* 3.5 16.3 + - + +
84E ALA* 3.1 24.1 + - - +
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Residues in contact with THR 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 3.2 35.7 - - + +
38E ILE* 3.6 17.3 - - + +
41E GLY* 3.5 25.6 + - - -
42E LEU* 5.8 1.3 - - + -
44E ILE* 5.5 0.2 - - - +
77E ILE* 2.7 29.2 + - - +
78E ILE* 3.4 9.2 - - - -
79E ALA 3.2 0.2 - - - -
80E PHE* 1.3 74.2 - - - +
82E LEU* 1.3 55.8 + - + +
84E ALA* 3.3 3.8 + - - +
85E ALA* 2.8 36.4 + - - +
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Residues in contact with LEU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E ILE* 5.0 18.4 - - + -
78E ILE* 2.8 43.9 + - + +
79E ALA* 3.8 4.0 - - - +
81E THR* 1.3 72.6 - - + +
83E ILE* 1.3 55.6 + - - +
85E ALA* 4.3 3.8 - - - -
86E LEU* 2.7 64.3 + - + +
96E VAL* 4.4 0.4 - - - -
100E LEU* 4.5 27.8 - - + -
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Residues in contact with ILE 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ALA* 3.0 30.7 + - + +
80E PHE* 3.7 17.5 - - + +
82E LEU* 1.3 75.5 - - - +
84E ALA* 1.3 60.4 + - + +
86E LEU* 4.3 0.3 - - - +
87E GLY* 2.9 26.2 + - - -
88E ARG* 5.0 0.7 + - - -
93E THR* 3.8 27.2 - - - +
96E VAL* 3.4 30.6 - - + +
97E ILE* 4.3 22.4 - - + -
100E LEU* 5.1 3.1 - - + -
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Residues in contact with ALA 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ILE* 4.4 14.4 - - + +
80E PHE 3.1 15.7 + - - +
81E THR* 3.8 3.4 - - - +
83E ILE* 1.3 78.4 - - - +
85E ALA* 1.3 64.9 + - - +
87E GLY* 3.4 0.3 + - - -
88E ARG* 3.1 54.4 + - - +
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Residues in contact with ALA 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ALA* 3.4 42.9 - - - +
37E ILE* 3.9 18.3 - - + +
38E ILE* 3.6 21.1 - - + -
81E THR 2.8 22.4 + - - +
82E LEU* 3.9 2.5 - - - +
84E ALA* 1.3 70.7 - - - +
86E LEU* 1.3 64.9 + - + +
88E ARG* 3.3 10.6 + - - +
89E VAL* 3.5 3.5 + - - +
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Residues in contact with LEU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D PHE* 3.8 38.8 - - + -
38E ILE* 6.2 2.0 - - + -
82E LEU* 2.7 50.8 + - + +
85E ALA* 1.3 75.0 - - + +
87E GLY* 1.3 59.5 + - - +
89E VAL* 3.2 15.6 + - + +
91E VAL* 3.0 47.7 + - + +
96E VAL* 4.0 13.2 - - + -
100E LEU* 6.3 0.9 - - + -
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Residues in contact with GLY 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E ILE 2.9 21.5 + - - -
84E ALA 3.6 3.1 - - - -
85E ALA 3.1 0.6 - - - -
86E LEU* 1.3 77.3 - - - +
88E ARG* 1.3 67.0 - - - +
89E VAL 3.2 0.2 - - - -
90E GLY* 2.9 20.8 + - - -
91E VAL 3.5 12.9 + - - -
93E THR* 6.0 0.9 - - - -
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Residues in contact with ARG 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASN* 3.1 42.3 + - + +
33E ALA* 5.3 4.7 - - + -
34E ALA 5.1 0.9 - - - +
37E ILE* 4.4 19.5 - - + +
83E ILE 5.0 0.4 + - - -
84E ALA* 3.1 40.4 + - - +
85E ALA 3.3 6.6 + - - +
87E GLY* 1.3 85.2 - - - +
89E VAL* 1.3 58.7 + - - +
90E GLY 3.3 1.7 + - - -
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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