Contacts of the helix formed by residues 66 - 88 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E VAL* 3.5 33.4 - - + -
58E HIS* 3.8 30.5 - - + +
64E ILE 3.1 3.8 - - - +
65E PHE* 1.3 96.8 - - + +
67E GLY* 1.3 61.2 + - - +
68E VAL* 4.2 5.8 - - + -
69E LEU* 2.9 38.7 + - + +
70E ILE* 3.2 10.4 + - - +
1005E CL 4.2 0.2 - - + -
27F MET* 4.0 16.8 - - + -
72F GLU* 5.1 1.1 - - - +
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Residues in contact with GLY 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E PHE 3.4 2.0 + - - -
66E PRO* 1.3 71.8 - - - +
68E VAL* 1.3 60.8 + - - +
70E ILE* 3.0 18.5 + - - +
71E VAL* 3.2 6.8 + - - +
109E PHE* 3.1 43.5 - - - -
1005E CL 3.3 22.4 - - - +
72F GLU* 5.6 0.2 + - - -
101F PHE* 5.0 1.1 - - - -
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Residues in contact with VAL 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E PRO* 4.2 11.9 - - + -
67E GLY* 1.3 75.7 - - - +
69E LEU* 1.3 64.6 + - + +
71E VAL* 3.4 10.2 + - - +
72E GLU* 3.0 20.4 + - - +
109E PHE* 4.2 0.6 - - - -
27F MET* 4.7 0.4 - - + -
68F VAL* 3.5 42.2 - - + +
69F LEU* 4.5 9.0 - - + -
71F VAL* 4.7 3.4 - - + -
72F GLU* 3.5 36.1 + - + +
101F PHE* 3.7 21.9 - - + -
104F ILE* 4.4 10.1 - - + -
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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
----------------------------------------------------------
51C ASN* 6.0 1.3 - - - +
26E PRO 6.1 0.7 - - - +
27E MET* 4.5 14.8 - - - -
29E LEU* 3.5 29.2 - - + +
54E VAL* 3.9 29.8 - - + -
65E PHE* 3.7 25.8 - - + -
66E PRO* 2.9 26.4 + - + +
68E VAL* 1.3 82.4 - - + +
70E ILE* 1.3 59.6 + - - +
72E GLU* 3.7 3.4 - - + -
73E GLY* 3.0 21.5 + - - -
121E TYR* 4.5 0.5 + - - -
27F MET* 5.1 4.0 - - - -
68F VAL* 4.4 15.5 - - + -
69F LEU* 4.7 9.9 - - + -
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Residues in contact with ILE 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E PHE* 3.8 20.4 - - + +
66E PRO 3.2 10.2 + - - +
67E GLY* 3.0 19.8 + - - +
69E LEU* 1.3 76.0 - - - +
71E VAL* 1.3 63.7 + - + +
73E GLY 3.2 1.2 + - - -
74E MET* 3.0 26.2 + - - +
109E PHE* 4.6 12.1 - - + -
111E ILE 5.4 1.6 - - - +
113E VAL* 3.5 32.1 - - + +
119E LEU* 3.8 13.5 - - + -
121E TYR* 3.6 3.6 - - - -
139E ALA* 3.6 29.4 - - + -
146E VAL* 4.9 0.7 - - + +
147E ALA* 4.1 15.7 - - + -
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Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLY 3.2 10.0 + - - +
68E VAL* 3.6 10.1 - - - +
70E ILE* 1.3 76.5 - - + +
72E GLU* 1.3 59.7 + - - +
74E MET* 3.1 11.1 + - - +
75E ALA* 2.9 26.9 + - - +
101E PHE* 3.9 21.8 - - + -
104E ILE* 4.3 21.5 - - + -
107E VAL* 4.6 9.9 - - + -
109E PHE* 4.3 17.7 - - + -
147E ALA* 6.5 0.2 - - + -
149E ALA* 4.3 19.7 - - + -
151E LEU* 4.0 7.5 - - + +
68F VAL* 4.4 3.6 - - + -
104F ILE* 5.1 4.3 - - + -
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Residues in contact with GLU 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E HIS* 3.5 18.4 + - - -
27E MET* 3.8 19.5 - - + +
29E LEU* 3.8 10.3 - - + -
68E VAL 3.0 14.3 + - - +
69E LEU* 3.6 12.8 - - - +
70E ILE 3.3 0.2 - - - -
71E VAL* 1.3 76.4 - - - +
73E GLY* 1.3 57.9 + - - +
75E ALA* 3.2 7.5 + - - +
76E GLN* 2.9 57.0 + - - +
101E PHE* 3.6 14.9 - - - -
58F HIS* 4.5 7.5 + - - -
66F PRO* 5.1 1.0 - - - +
67F GLY 5.5 0.9 + - - -
68F VAL* 3.5 28.0 + - + +
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Residues in contact with GLY 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 4.2 13.0 - - - -
30E VAL* 3.7 6.2 - - - +
69E LEU 3.0 12.5 + - - -
70E ILE 3.6 1.6 - - - -
71E VAL 3.1 0.4 - - - -
72E GLU* 1.3 78.3 - - - +
74E MET* 1.3 58.4 - - - +
76E GLN* 3.5 3.4 + - - -
77E SER* 3.1 24.3 + - - -
121E TYR* 3.4 31.2 - - - -
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Residues in contact with MET 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E ILE* 3.0 20.7 + - - +
71E VAL* 3.1 10.3 + - - +
73E GLY* 1.3 74.1 - - - +
75E ALA* 1.3 65.5 + - - +
77E SER* 3.2 4.2 + - - -
78E GLY* 3.0 18.2 + - - -
121E TYR* 3.4 20.0 - - + -
123E LEU* 3.5 32.6 - - + +
135E VAL* 5.0 0.2 - - - +
137E GLY 3.5 35.0 - - - +
138E THR* 3.5 13.9 - - - +
139E ALA* 4.2 13.7 - - + -
147E ALA* 5.2 1.8 - - - +
148E GLU 4.7 1.8 - - - -
149E ALA* 3.8 27.6 - - + +
151E LEU* 4.2 7.1 - - + +
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Residues in contact with ALA 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E VAL 2.9 6.3 + - - +
72E GLU* 3.4 10.3 - - - +
74E MET* 1.3 77.6 - - - +
76E GLN* 1.3 52.3 + - + +
78E GLY* 3.0 3.0 + - - -
79E GLY* 2.7 32.1 + - - -
99E VAL* 5.9 2.4 - - - +
101E PHE* 3.5 38.8 - - + -
135E VAL* 5.5 0.2 - - - -
151E LEU* 3.6 21.9 - - + +
153E ALA* 5.6 3.6 - - + -
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Residues in contact with GLN 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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21E LEU* 3.7 18.2 - - + +
23E HIS* 3.5 30.8 - - + +
27E MET 2.8 24.6 + - - +
28E LEU* 3.6 12.8 - - - +
29E LEU* 2.7 32.5 + - - +
30E VAL* 3.7 15.9 + - + +
72E GLU* 2.9 43.6 + - - +
73E GLY 3.8 0.4 - - - +
74E MET 3.3 0.2 - - - -
75E ALA* 1.3 76.6 - - + +
77E SER* 1.3 58.1 + - - +
79E GLY* 3.2 3.3 + - - +
80E PHE* 2.9 24.4 + - - +
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Residues in contact with SER 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E VAL* 4.0 7.7 - - - +
42E ILE* 3.4 24.3 - - - +
44E ALA* 3.6 16.8 - - - +
73E GLY 3.1 14.3 + - - -
74E MET 3.4 9.2 - - - -
75E ALA 3.1 0.4 - - - -
76E GLN* 1.3 72.3 - - - +
78E GLY* 1.3 66.0 + - - +
80E PHE* 3.3 4.4 + - - +
81E LEU* 3.1 17.8 + - - +
121E TYR* 3.4 20.1 - - - +
123E LEU* 3.9 17.0 - - - -
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Residues in contact with GLY 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E ILE* 4.7 1.6 - - - -
74E MET 3.0 13.2 + - - -
75E ALA 3.5 3.1 - - - -
77E SER* 1.3 76.4 - - - +
79E GLY* 1.3 52.0 + - - +
81E LEU* 3.1 9.2 + - - +
82E ALA* 2.6 37.6 + - - +
123E LEU* 4.3 4.9 - - - +
133E TRP* 5.5 1.2 - - - -
135E VAL* 4.4 27.2 - - - +
151E LEU* 6.3 0.2 - - - -
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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
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21E LEU* 4.1 10.3 - - - +
75E ALA 2.7 14.7 + - - -
76E GLN* 3.2 4.9 + - - -
77E SER 3.2 0.2 - - - -
78E GLY* 1.3 76.3 - - - +
80E PHE* 1.3 56.6 + - - +
82E ALA* 3.2 7.7 + - - +
83E PHE* 2.9 30.7 + - - +
99E VAL* 5.2 17.3 - - - -
153E ALA* 6.2 2.0 - - - -
155E ILE* 4.3 4.2 - - - +
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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
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12E PHE* 3.7 25.4 - + - -
16E HIS 4.1 1.1 - - - -
17E ILE* 4.0 20.4 - - + -
20E ILE* 3.7 36.6 - - + -
21E LEU* 3.8 16.0 - - + +
30E VAL* 6.4 1.1 - - + -
33E ILE* 3.4 35.7 - - + -
36E LEU* 3.8 17.5 - - + -
42E ILE* 4.0 10.8 - - + -
76E GLN 2.9 12.4 + - - +
77E SER* 3.6 10.1 - - - +
78E GLY 3.3 0.2 - - - -
79E GLY* 1.3 75.2 - - - +
81E LEU* 1.3 62.1 + - - +
83E PHE* 3.5 0.5 + - - -
84E THR* 2.9 51.5 + - + +
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Residues in contact with LEU 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E LEU* 3.2 27.4 - - + -
37E GLN 3.5 14.6 - - - +
38E ALA* 4.4 0.2 - - - -
39E ASN 4.1 1.8 - - - +
40E GLN 4.3 0.2 - - - +
41E LYS* 3.5 20.2 - - - +
42E ILE* 3.7 23.6 - - + -
77E SER 3.1 9.4 + - - +
78E GLY* 3.1 12.3 + - - +
80E PHE* 1.3 80.9 - - - +
82E ALA* 1.3 59.2 + - - +
84E THR* 3.5 4.6 + - - +
85E SER* 2.8 42.8 + - - +
123E LEU 4.5 3.1 - - - +
125E VAL* 3.5 31.2 - - + +
133E TRP* 4.9 1.3 - - + -
135E VAL* 5.0 4.5 - - + -
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Residues in contact with ALA 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E GLY 2.6 20.8 + - - +
79E GLY* 3.5 8.1 - - - +
81E LEU* 1.3 74.6 - - - +
83E PHE* 1.3 62.8 + - - +
85E SER* 3.7 2.4 - - - -
86E LEU* 3.2 25.9 + - - +
133E TRP* 3.6 45.9 - - + -
155E ILE* 3.8 16.4 - - + -
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Residues in contact with PHE 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 3.9 29.4 - - + -
21E LEU* 6.2 0.4 - - + -
79E GLY 2.9 15.8 + - - +
82E ALA* 1.3 77.8 - - - +
84E THR* 1.3 62.0 + - + +
86E LEU* 3.2 5.3 + - - +
87E TRP* 3.0 59.1 + + + -
88E GLY 3.5 19.1 - - - -
90E ASP 3.5 16.4 - - - -
93E ILE* 3.9 7.4 - - + -
94E ALA* 3.3 44.4 - - + -
97E LYS* 4.0 13.2 - - + -
155E ILE* 3.7 13.8 - - + +
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Residues in contact with THR 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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9E GLN* 5.9 5.1 + - - -
12E PHE* 5.4 2.5 - - + -
20E ILE* 4.4 6.5 - - + -
36E LEU* 3.6 21.5 - - + +
38E ALA* 5.9 0.4 - - - -
80E PHE* 2.9 42.1 + - + +
81E LEU* 3.5 4.0 + - - -
83E PHE* 1.3 81.5 - - + +
85E SER* 1.3 63.3 + - - +
86E LEU 3.2 0.2 - - - -
88E GLY* 2.8 47.3 + - - +
89E PHE* 4.5 9.9 - - + -
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Residues in contact with SER 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ALA* 3.6 15.3 - - - +
39E ASN* 2.8 52.0 + - - +
81E LEU* 2.8 25.9 + - - +
82E ALA 3.7 0.7 - - - -
83E PHE 3.2 0.2 - - - -
84E THR* 1.3 78.6 + - - +
86E LEU* 1.3 64.7 + - - +
88E GLY 4.8 0.2 + - - -
133E TRP* 3.5 12.7 - - - -
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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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39E ASN* 5.5 0.9 - - - +
82E ALA 3.2 13.0 + - - +
83E PHE 3.4 7.0 - - - +
84E THR 3.2 0.2 - - - -
85E SER* 1.3 82.8 - - - +
87E TRP* 1.3 89.0 + - + +
88E GLY 3.6 0.4 - - - -
128E HIS* 5.6 2.0 - - + +
130E GLY* 4.0 7.2 - - - +
131E MET* 3.8 32.1 - - + -
133E TRP* 3.4 41.1 - - + +
155E ILE* 4.2 9.0 - - + -
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Residues in contact with TRP 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E PHE* 3.0 55.3 + + + +
86E LEU* 1.3 106.9 - - + +
88E GLY* 1.3 62.8 + - - +
89E PHE 3.9 0.3 + - - -
90E ASP* 4.0 11.4 - - + +
93E ILE* 3.8 36.5 - - + +
97E LYS* 3.6 29.4 - - - -
131E MET* 3.8 33.2 - - + -
155E ILE* 4.2 8.3 - - + -
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Residues in contact with GLY 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E GLN* 5.9 3.8 - - - -
83E PHE* 3.5 9.7 - - - -
84E THR* 2.8 41.0 + - - +
86E LEU 3.6 1.0 - - - -
87E TRP* 1.3 81.5 - - - +
89E PHE* 1.3 58.5 + - - -
90E ASP 3.1 6.4 + - - -
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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