Contacts of the helix formed by residues 72 - 96 (chain E) in PDB entry 5JRE
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 PHE 72 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LEU* 3.4 37.0 - - + -
18E LYS* 4.9 0.9 - - + -
19E LYS* 3.7 36.6 - - + -
22E ILE* 3.9 15.3 - - + +
66E LEU* 3.5 6.8 - - - +
69E TYR* 2.9 24.1 + + + +
71E MET* 1.3 108.7 - - + +
73E TYR* 1.3 66.7 + - - +
74E SER 3.2 2.9 - - - -
75E ASN* 3.0 33.1 + - + +
76E GLY 3.4 7.6 + - - -
109F TRP* 3.9 35.0 - + - -
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Residues in contact with TYR 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E LEU* 3.9 34.5 - - + +
69E TYR 3.9 0.8 + - - -
70E PRO* 3.1 21.3 + - + +
71E MET 3.5 0.4 - - - -
72E PHE* 1.3 75.6 - - - +
74E SER* 1.3 67.9 + - - +
76E GLY* 3.1 4.2 + - - -
77E PHE* 3.1 45.6 + + - -
80E LEU* 5.9 0.9 - - + -
107E ASP* 2.7 37.1 + - - -
109E TRP* 4.3 0.8 - + - +
110E VAL* 3.6 13.3 + - + +
70F PRO* 3.8 22.2 - - + +
71F MET* 3.5 43.7 - - + +
73F TYR* 5.6 0.2 - - + -
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Residues in contact with SER 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E MET 5.1 2.7 + - - -
72E PHE 3.2 0.8 - - - -
73E TYR* 1.3 86.5 - - - +
75E ASN* 1.3 65.4 + - - +
76E GLY 3.4 0.3 + - - -
77E PHE* 3.5 16.8 + - - +
78E ILE* 4.8 4.9 + - - +
74F SER* 5.9 7.4 - - - -
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Residues in contact with ASN 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LYS* 3.7 25.4 - - + +
22E ILE* 4.0 10.9 - - + +
23E VAL* 3.8 26.6 - - + +
26E SER* 3.7 17.3 + - - -
71E MET 4.3 1.6 - - - +
72E PHE* 3.0 38.7 + - + +
74E SER* 1.3 79.1 - - - +
76E GLY* 1.3 57.8 + - - +
78E ILE 5.2 0.6 + - - -
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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
----------------------------------------------------------
22E ILE* 3.8 6.2 - - - +
26E SER* 3.9 3.7 + - - -
62E GLN* 3.8 22.9 + - - -
66E LEU* 4.3 11.7 - - - -
72E PHE 3.4 3.6 + - - -
73E TYR 3.1 7.5 + - - -
75E ASN* 1.3 77.5 - - - +
77E PHE* 1.3 66.3 + - - +
78E ILE 3.4 2.8 + - - -
79E GLY* 3.4 2.8 + - - -
80E LEU* 3.3 22.3 + - - +
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Residues in contact with PHE 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E LEU* 5.4 0.4 - - - -
73E TYR* 3.1 37.8 + + - +
74E SER* 3.5 18.4 + - - +
76E GLY* 1.3 77.3 - - - +
78E ILE* 1.3 64.1 + - + +
80E LEU* 3.1 7.7 + - - +
81E GLN* 2.9 47.9 + - + +
109E TRP* 3.7 16.8 - + - -
110E VAL* 3.4 28.9 - - + +
113E PHE* 3.7 43.7 - + + -
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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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163B ARG* 6.0 7.6 - - - +
26E SER* 4.4 5.3 + - - +
30E SER* 5.6 3.6 - - - -
74E SER 4.8 4.2 + - - +
75E ASN 5.2 0.6 + - - -
76E GLY 3.4 0.6 - - - -
77E PHE* 1.3 82.2 - - + +
79E GLY* 1.3 57.9 + - - +
81E GLN* 3.3 17.9 + - - +
82E GLU* 2.9 47.9 + - + +
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Residues in contact with GLY 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E SER* 3.0 39.2 + - - -
29E MET* 3.4 23.5 - - - +
30E SER* 4.7 2.0 - - - -
76E GLY 3.4 1.3 + - - -
77E PHE 3.3 0.2 - - - -
78E ILE* 1.3 77.8 - - - +
80E LEU* 1.3 56.2 + - - +
82E GLU* 3.4 7.4 + - - +
83E TYR* 3.0 21.3 + - - +
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Residues in contact with LEU 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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29E MET* 3.8 20.2 - - + -
59E ALA* 4.2 4.9 - - + +
62E GLN* 4.3 10.1 - - + -
63E ILE* 3.8 35.7 - - + -
66E LEU* 3.6 30.5 - - + -
73E TYR* 5.9 1.8 - - + -
76E GLY 3.3 9.1 + - - +
77E PHE* 3.1 7.4 + - - +
79E GLY* 1.3 73.2 - - - +
81E GLN* 1.3 66.4 + - - +
83E TYR* 3.2 15.3 + - + +
84E VAL* 3.0 26.7 + - - +
106E VAL* 4.4 4.5 - - + -
110E VAL* 4.1 26.2 - - + -
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Residues in contact with GLN 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E PHE* 2.9 38.4 + - + +
78E ILE* 3.4 19.8 - - - +
80E LEU* 1.3 78.4 - - - +
82E GLU* 1.3 60.3 + - + +
84E VAL* 3.3 1.8 + - - +
85E GLU* 3.0 24.2 + - - +
110E VAL* 4.5 9.3 - - + +
113E PHE* 3.5 18.8 + - - +
114E GLY* 3.6 26.2 - - - +
117E ASP* 2.6 27.4 + - - +
165E LYS* 3.8 12.9 - - - +
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Residues in contact with GLU 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ARG* 5.8 0.2 + - - -
30E SER* 3.3 23.8 + - - +
33E SER* 3.0 24.0 + - - +
34E LYS* 2.8 33.3 + - - +
37E ILE* 5.2 0.2 - - - +
78E ILE* 2.9 37.2 + - + +
79E GLY 3.8 4.0 - - - +
81E GLN* 1.3 77.6 - - + +
83E TYR* 1.3 59.7 + - - +
85E GLU* 3.6 19.0 - - - +
86E ALA* 3.0 24.9 + - - +
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Residues in contact with TYR 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E MET* 3.7 11.0 - - + -
33E SER* 3.5 8.2 + - - -
55E LEU* 3.8 14.4 - - + -
56E THR* 4.1 18.9 - - - +
59E ALA* 3.7 31.7 - - + +
63E ILE* 4.9 0.8 - - + +
79E GLY 3.0 13.9 + - - +
80E LEU* 3.3 19.7 - - + +
82E GLU* 1.3 74.4 - - - +
84E VAL* 1.3 67.1 + - + +
86E ALA* 3.4 0.5 + - - +
87E LEU* 3.0 56.7 + - + +
103E GLU 5.0 0.2 + - - -
104E LEU* 2.7 45.6 + - + +
106E VAL* 3.8 16.2 - - + -
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Residues in contact with VAL 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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80E LEU 3.0 17.3 + - - +
81E GLN 3.3 6.5 + - - +
83E TYR* 1.3 76.2 - - + +
85E GLU* 1.3 59.8 + - - +
87E LEU* 4.1 0.5 - - - +
88E ALA* 2.9 29.3 + - + +
104E LEU* 3.9 23.2 - - + +
106E VAL* 3.9 22.9 - - + -
110E VAL* 3.9 21.1 - - + -
111E TYR* 3.9 28.3 - - + +
114E GLY* 4.0 9.0 - - - -
115E ILE* 4.0 12.6 - - + +
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Residues in contact with GLU 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 3.9 9.6 - - + +
81E GLN* 3.0 16.8 + - - +
82E GLU* 3.6 20.5 - - - +
84E VAL* 1.3 78.4 - - - +
86E ALA* 1.3 60.6 + - - +
88E ALA* 3.7 2.4 - - - +
89E LEU* 3.1 22.7 + - - +
114E GLY 3.8 13.4 + - - +
117E ASP* 3.7 39.4 - - + +
118E ILE* 3.9 8.8 - - + +
121E GLU* 2.9 40.5 - - + +
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Residues in contact with ALA 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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33E SER* 3.8 32.1 - - - +
36E LEU* 4.0 18.4 - - + +
37E ILE* 3.9 16.5 - - + +
40E MET* 5.9 0.3 - - - +
55E LEU* 4.1 2.2 - - + -
82E GLU 3.0 18.3 + - - +
83E TYR 3.9 2.9 - - - +
85E GLU* 1.3 78.1 - - - +
87E LEU* 1.3 57.8 + - - +
89E LEU* 3.3 4.0 + - - +
90E TYR* 2.9 27.0 + - - +
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Residues in contact with LEU 87 (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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36E LEU* 4.0 11.2 - - + -
52E LYS* 4.5 22.4 - - + -
55E LEU* 3.8 18.4 - - + -
56E THR* 4.0 15.3 - - + +
83E TYR* 3.0 50.6 + - + +
84E VAL 4.1 0.9 - - - +
86E ALA* 1.3 74.2 - - - +
88E ALA* 1.3 60.0 + - - +
90E TYR* 3.3 5.0 - - + +
91E TYR* 2.9 42.5 + - + -
99E PRO* 4.4 0.9 - - - -
104E LEU* 3.5 33.2 - - + -
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Residues in contact with ALA 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E VAL* 2.9 20.1 + - + +
85E GLU 3.7 0.2 - - - +
87E LEU* 1.3 77.9 - - - +
89E LEU* 1.3 56.4 + - - +
91E TYR 3.8 0.5 - - - -
92E TYR* 2.8 29.9 + - - +
97E ARG 4.0 3.8 - - - +
98E ILE* 4.1 7.8 - - + +
99E PRO* 3.6 22.3 - - + +
115E ILE* 4.1 14.6 - - + -
118E ILE* 3.6 25.4 - - + -
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Residues in contact with LEU 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ILE* 3.7 44.0 - - + +
40E MET* 4.7 2.5 - - + -
41E ILE* 4.5 7.0 - - + -
85E GLU 3.1 13.8 + - - +
86E ALA* 3.6 8.5 - - - +
88E ALA* 1.3 73.0 - - - +
90E TYR* 1.3 66.5 + - - +
92E TYR* 3.2 6.0 + - + +
93E ILE* 3.0 50.6 + - + +
118E ILE* 4.9 4.6 - - + +
121E GLU* 3.9 37.0 - - + +
122E ILE* 4.2 15.9 - - + +
125E LYS* 5.0 2.2 - - + -
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Residues in contact with TYR 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LEU* 4.1 12.1 - - + -
40E MET* 3.6 43.7 - - + +
45E TYR* 5.8 1.3 - + - -
48E ALA* 4.7 3.6 - - + -
49E ASP* 2.7 28.4 + - - -
52E LYS* 3.4 43.8 + - + +
86E ALA 2.9 14.9 + - - +
87E LEU* 3.2 12.3 + - - +
89E LEU* 1.3 77.0 - - - +
91E TYR* 1.3 77.7 + + - +
94E LYS* 2.9 72.4 + - + +
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Residues in contact with TYR 91 (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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52E LYS* 3.4 30.1 + - - -
87E LEU* 2.9 38.0 + - + +
90E TYR* 1.3 93.4 - + - +
92E TYR* 1.3 61.5 + - - +
94E LYS* 4.6 1.1 - - + -
95E GLU* 2.9 50.7 + - + +
96E ASN 3.1 6.4 + - - -
97E ARG* 3.1 46.2 + - + +
99E PRO* 4.0 25.4 - - + -
103E GLU* 4.3 12.3 + - + +
104E LEU* 5.1 1.8 - - + -
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Residues in contact with TYR 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E ALA 2.8 18.5 + - - +
89E LEU* 3.2 10.0 + - + +
91E TYR* 1.3 77.5 - - - +
93E ILE* 1.3 64.6 + - + +
96E ASN* 3.1 31.5 + - - +
97E ARG* 3.1 15.4 + - - +
98E ILE* 4.2 9.0 - - + -
122E ILE* 4.0 34.3 - - + +
125E LYS* 5.9 0.7 - - + -
137E TYR* 3.6 26.4 + + - -
140E LYS* 4.2 5.7 + - - +
141E ALA* 3.6 16.6 + - - +
144E ASP* 2.6 37.3 + - + +
1F MET* 3.9 28.5 - - + -
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Residues in contact with ILE 93 (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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40E MET* 3.8 34.8 - - + +
41E ILE* 4.7 0.7 - - - +
45E TYR* 3.8 23.3 - - + +
89E LEU* 3.0 46.5 + - + +
92E TYR* 1.3 81.8 - - + +
94E LYS* 1.3 63.5 + - - +
96E ASN* 4.5 1.4 + - - +
125E LYS* 4.0 30.3 - - + -
137E TYR* 4.0 19.5 - - + +
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Residues in contact with LYS 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E MET* 4.5 8.1 - - + -
45E TYR* 5.5 9.9 - - + -
49E ASP* 5.1 2.5 + - - -
90E TYR* 2.9 56.0 + - + +
91E TYR* 4.6 1.5 - - - +
93E ILE* 1.3 80.4 - - - +
95E GLU* 1.3 82.0 + - + +
96E ASN 3.7 0.4 - - - -
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Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TYR* 2.9 31.0 + - + +
94E LYS* 1.3 102.7 + - + +
96E ASN* 1.3 72.5 + - - +
97E ARG* 2.8 45.6 + - - +
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Residues in contact with ASN 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TYR 3.1 2.6 + - - -
92E TYR* 3.1 25.0 + - - +
93E ILE 4.5 1.0 + - - +
94E LYS 3.7 1.4 - - - -
95E GLU* 1.3 79.9 - - - +
97E ARG* 1.3 58.0 + - - +
140E LYS* 2.6 38.6 + - - +
144E ASP* 4.2 2.4 - - - +
1F MET* 6.1 1.2 - - - +
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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