Contacts of the helix formed by residues 67 - 98 (chain E) in PDB entry 5TWV
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 LYS 67 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ASP 3.5 3.2 + - - +
66E LEU* 1.3 74.4 - - - +
68E TRP* 1.3 60.1 + - - +
69E PRO* 3.5 14.8 - - + -
70E HIS* 3.6 20.3 + - + +
71E THR* 2.4 30.1 + - - -
55F SER 5.3 1.4 + - - -
56F SER* 3.8 30.6 - - - +
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Residues in contact with TRP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLN* 5.9 4.5 - - - -
60C PHE* 4.2 33.1 - + - -
162C ILE* 6.2 6.5 - - + -
67E LYS* 1.3 70.9 - - - +
69E PRO* 1.3 74.0 - - + +
71E THR* 3.7 21.6 - - + -
72E LEU* 3.2 30.8 + - + +
167E ILE* 4.7 16.6 - - + -
170E LYS* 4.0 30.3 - - + -
173E GLN* 5.1 10.8 - - - +
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Residues in contact with PRO 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LYS* 3.6 17.9 - - + -
68E TRP* 1.3 97.5 - - + +
70E HIS* 1.3 69.7 + - + +
72E LEU* 3.7 5.6 + - + +
73E LEU* 3.5 18.2 + - - +
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Residues in contact with HIS 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66E LEU* 4.9 18.8 - - + +
67E LYS* 3.6 24.8 + - + +
69E PRO* 1.3 83.3 - - + +
71E THR* 1.3 61.0 + - - +
73E LEU* 3.0 15.0 + - + +
74E ILE* 2.9 34.6 + - + +
51F TRP* 4.0 29.9 - + - -
52F GLY* 4.1 28.1 + - - -
55F SER* 4.9 10.3 - - - -
56F SER* 6.0 3.0 - - - -
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Residues in contact with THR 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU 4.6 7.7 + - - +
66E LEU* 3.0 17.7 + - - +
67E LYS 2.4 25.8 + - - -
68E TRP* 3.7 27.7 - - + -
69E PRO 3.3 0.2 - - - -
70E HIS* 1.3 78.9 - - - +
72E LEU* 1.3 58.9 + - - +
74E ILE* 3.5 12.6 + - + +
75E PHE* 3.1 55.0 + - + -
166E CYS* 6.1 1.8 - - - +
167E ILE* 5.6 2.2 - - + -
170E LYS* 6.1 2.9 - - + -
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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
----------------------------------------------------------
158C MET* 4.3 27.1 - - + -
162C ILE* 6.4 0.7 - - + -
68E TRP* 3.2 20.8 + - + +
69E PRO* 3.9 6.5 - - + +
70E HIS 3.2 0.4 - - - -
71E THR* 1.3 77.8 - - - +
73E LEU* 1.3 53.4 + - - +
75E PHE* 3.5 6.0 + - - +
76E THR* 2.7 52.9 + - + +
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Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E PRO 3.5 10.8 + - - +
70E HIS* 3.0 19.0 + - + +
72E LEU* 1.3 78.6 - - - +
74E ILE* 1.3 63.8 + - + +
76E THR* 3.1 17.2 + - - +
77E MET* 3.1 41.6 + - + +
48F PHE* 5.6 9.6 - - + -
51F TRP* 4.6 22.2 - - + -
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Residues in contact with ILE 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E LEU* 5.0 21.5 - - + -
66E LEU* 4.3 24.7 - - + -
70E HIS* 2.9 21.5 + - + +
71E THR* 3.8 15.7 - - + +
72E LEU 3.3 0.2 - - - -
73E LEU* 1.3 79.6 - - + +
75E PHE* 1.3 73.8 + - + +
77E MET* 4.6 1.0 - - - +
78E SER* 2.8 33.7 + - - +
45F PRO* 5.5 14.4 - - + +
48F PHE* 5.1 17.0 - - + -
49F ILE* 5.1 10.8 - - + +
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Residues in contact with PHE 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 4.6 3.6 - - - +
158C MET* 4.3 14.8 - - + -
63E LEU* 5.5 7.6 - - + -
71E THR* 3.1 41.5 + - + +
72E LEU* 4.1 3.4 - - - +
73E LEU 3.4 0.2 - - - -
74E ILE* 1.3 90.3 - - + +
76E THR* 1.3 63.6 + - - +
77E MET 3.5 0.2 - - - -
78E SER* 3.5 6.9 + - - -
79E PHE* 3.2 29.9 - + - +
162E ILE* 6.3 1.6 - - + -
163E MET* 3.8 36.3 - - + -
166E CYS* 3.8 35.4 - - + -
167E ILE* 3.8 22.0 - - + -
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Residues in contact with THR 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 4.1 27.7 - - + +
158C MET* 5.6 2.9 - - + -
72E LEU* 2.7 41.5 + - + +
73E LEU* 3.1 15.1 + - - +
75E PHE* 1.3 78.3 - - + +
77E MET* 1.3 70.3 + - - +
79E PHE* 3.6 4.0 + - - +
80E LEU* 3.2 31.7 + - - +
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Residues in contact with MET 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E LEU* 3.1 35.5 + - + +
74E ILE* 4.6 1.3 - - - +
76E THR* 1.3 78.1 + - - +
78E SER* 1.3 55.8 + - - +
79E PHE 3.1 1.6 - - - -
80E LEU* 3.5 18.0 - - - +
81E CYS* 2.6 38.9 + - - +
44F PHE* 5.2 25.1 - - + -
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Residues in contact with SER 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E ILE* 2.8 25.9 + - - +
75E PHE* 3.5 13.7 + - - -
77E MET* 1.3 77.8 - - - +
79E PHE* 1.3 66.8 + - - +
81E CYS* 3.9 7.4 - - - +
82E SER* 2.9 27.7 + - - -
159E ILE* 5.0 1.5 - - - +
44F PHE* 6.0 0.2 - - - +
45F PRO* 4.6 22.9 - - - -
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Residues in contact with PHE 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C ILE* 4.3 12.6 - - + -
157C LEU* 4.6 15.9 - - + -
75E PHE* 3.2 23.1 + + + +
76E THR* 3.6 5.8 + - - +
77E MET 3.1 0.6 - - - -
78E SER* 1.3 86.9 + - - +
80E LEU* 1.3 59.7 + - - +
82E SER* 3.1 5.6 + - - -
83E TRP* 2.8 71.6 + + + +
129E VAL* 6.1 2.2 - - + -
156E GLY 5.7 1.1 - - - -
159E ILE* 3.9 31.9 - - + -
160E ASN* 4.0 28.7 - - + -
163E MET* 3.8 25.1 - - + -
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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
----------------------------------------------------------
150C ILE* 4.7 14.8 - - + -
76E THR* 3.2 23.4 + - - +
77E MET* 3.6 19.3 - - - +
79E PHE* 1.3 76.5 - - - +
81E CYS* 1.3 66.8 + - - +
83E TRP* 3.2 29.2 + - + +
84E LEU* 3.1 24.6 + - - +
121E PHE* 4.8 13.8 - - + -
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Residues in contact with CYS 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E MET 2.6 23.2 + - - +
78E SER* 3.9 8.7 - - - +
79E PHE 3.2 0.2 - - - -
80E LEU* 1.3 73.5 - - - +
82E SER* 1.3 60.3 + - - +
84E LEU 3.9 0.3 + - - -
85E LEU* 3.8 4.5 + - - +
41F PHE* 3.3 67.6 - - + +
44F PHE* 4.4 14.1 - - + -
45F PRO* 5.7 0.2 - - + -
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Residues in contact with SER 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E SER 2.9 17.2 + - - -
79E PHE 3.1 8.9 + - - -
80E LEU 3.1 0.6 - - - -
81E CYS* 1.3 75.5 - - - +
83E TRP* 1.3 67.5 + - - +
84E LEU 3.1 2.0 - - - -
85E LEU* 3.0 19.6 + - - +
86E PHE* 2.9 39.6 + - - -
155E VAL* 6.2 0.2 - - - +
159E ILE* 4.1 20.4 - - - +
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Residues in contact with TRP 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ILE* 3.6 36.3 - - + -
153C ASN* 5.5 4.7 - - + -
154C ILE* 4.8 16.2 - - + -
79E PHE* 2.8 61.1 + + + +
80E LEU* 3.2 28.2 + - + +
82E SER* 1.3 82.2 - - - +
84E LEU* 1.3 57.7 + - - +
85E LEU 3.4 0.2 - - - -
86E PHE* 4.0 5.4 - - - -
87E ALA* 3.4 21.3 + - - +
121E PHE* 3.8 11.9 - + + -
124E SER* 3.5 8.9 + - - -
125E ILE* 3.1 39.7 - - + -
128E GLN* 4.3 26.6 - - + +
129E VAL* 4.5 19.0 - - + +
159E ILE* 5.7 2.6 - - - +
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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
----------------------------------------------------------
80E LEU 3.1 13.5 + - - +
81E CYS 4.2 0.7 - - - +
82E SER 3.1 1.2 - - - -
83E TRP* 1.3 76.4 - - - +
85E LEU* 1.3 60.4 + - - +
87E ALA* 3.7 6.4 - - - +
88E MET* 3.2 29.1 + - - +
121E PHE* 4.3 10.1 - - + -
41F PHE* 3.7 29.2 - - + -
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Residues in contact with LEU 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E CYS 3.8 3.5 + - - +
82E SER* 3.0 13.1 + - - +
84E LEU* 1.3 80.0 - - - +
86E PHE* 1.3 73.4 + - + +
87E ALA 3.1 2.3 + - - -
88E MET* 3.6 6.1 + - + +
89E VAL* 3.6 22.2 + - - +
34F VAL* 5.0 6.5 - - + +
37F VAL* 5.3 1.1 - - + -
38F PHE* 4.4 35.7 - - + +
41F PHE* 3.9 31.6 - - + -
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Residues in contact with PHE 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E SER* 2.9 45.0 + - - +
83E TRP* 4.1 1.8 - + - -
85E LEU* 1.3 89.5 - - + +
87E ALA* 1.3 56.5 + - - +
89E VAL* 3.8 13.6 - - + +
90E TRP* 3.5 24.0 - - + +
124E SER* 2.8 24.1 + - - +
128E GLN* 3.1 40.4 - - + +
148E ILE* 6.6 0.2 - - + -
151E VAL* 4.6 4.5 - - + -
152E GLN* 3.8 30.1 - - + -
155E VAL* 4.5 21.3 - - + -
156E GLY* 4.9 4.0 - - - -
159E ILE* 5.8 0.4 - - + -
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Residues in contact with ALA 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E TRP 3.4 16.3 + - - +
84E LEU 3.8 4.9 - - - +
85E LEU 3.1 0.6 - - - -
86E PHE* 1.3 80.7 - - - +
88E MET* 1.3 64.4 + - - +
89E VAL 3.4 0.2 - - - -
90E TRP* 3.4 5.1 + - - +
91E TRP* 3.1 23.4 + - - +
117E PHE* 5.6 5.0 - - + +
120E ALA* 3.9 4.9 - - - +
121E PHE* 3.3 42.2 - - + +
124E SER* 3.9 5.2 - - - -
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Residues in contact with MET 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E LEU 3.2 17.1 + - - +
85E LEU* 3.6 7.6 + - + +
87E ALA* 1.3 73.4 - - - +
89E VAL* 1.3 56.2 - - - +
90E TRP 3.1 4.7 - - - -
91E TRP* 3.2 35.6 + - + +
92E LEU* 3.1 27.3 + - + +
117E PHE* 4.5 18.8 - - + -
30F ALA* 5.3 5.4 - - - +
33F VAL* 3.7 30.5 - - + -
34F VAL* 4.5 24.7 - - + +
37F VAL* 5.3 11.2 - - + -
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Residues in contact with VAL 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E LEU 3.6 17.0 + - - +
86E PHE* 3.8 16.6 - - + +
88E MET* 1.3 78.4 - - - +
90E TRP* 1.3 70.7 + - + +
92E LEU* 3.7 20.4 - - + +
93E ILE* 3.0 29.3 + - + +
148E ILE* 4.4 24.2 - - + -
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Residues in contact with TRP 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E PHE* 3.5 21.3 - - - +
87E ALA* 3.7 7.0 - - - +
88E MET 3.1 0.8 - - - -
89E VAL* 1.3 83.2 - - + +
91E TRP* 1.3 58.4 + - - +
92E LEU 3.0 5.4 - - - -
93E ILE* 3.1 36.2 + - + +
94E ALA* 3.8 8.1 + - - +
111E VAL* 3.8 22.3 - - + +
114E ILE* 5.5 4.7 - - + +
120E ALA* 4.1 16.3 - - + +
123E PHE* 2.8 54.6 - + + -
127E VAL* 6.0 0.2 - - + -
138E VAL* 5.8 2.0 - - + -
145E ALA* 3.4 23.6 - - + -
148E ILE* 3.6 32.1 - - + -
149E LEU* 3.5 26.7 - - + -
152E GLN* 5.1 7.4 - - + -
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Residues in contact with TRP 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ALA 3.1 15.4 + - - +
88E MET* 3.2 24.4 + - + +
90E TRP* 1.3 77.2 - - - +
92E LEU* 1.3 58.8 - - + +
93E ILE 3.6 0.2 - - - -
94E ALA* 4.1 5.6 - - - +
95E PHE* 3.3 52.4 + + - +
100E LEU* 5.1 10.0 - - + +
114E ILE* 5.9 1.6 - - + -
116E SER 4.5 5.6 - - - -
117E PHE* 3.1 65.2 - + + +
120E ALA* 4.0 11.9 - - + +
6F CYS* 6.2 2.5 - - + -
30F ALA* 4.3 24.2 - - + -
105F HIS* 5.0 15.5 - - + -
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E MET* 3.1 15.1 + - + +
89E VAL* 3.7 22.0 - - + +
90E TRP 3.0 0.2 - - - -
91E TRP* 1.3 81.8 - - + +
93E ILE* 1.3 60.8 + - + +
94E ALA 3.1 2.2 - - - -
95E PHE* 4.1 10.1 - - + -
96E ALA* 2.8 35.7 + - + +
27F PHE* 5.8 5.8 - - + +
30F ALA* 4.8 24.9 - - + +
31F LEU* 5.4 14.8 - - + +
34F VAL* 5.7 9.2 - - + -
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Residues in contact with ILE 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E VAL* 3.0 22.2 + - + +
90E TRP* 3.1 52.5 - - + +
92E LEU* 1.3 78.3 - - + +
94E ALA* 1.3 59.5 + - + +
96E ALA* 3.9 7.0 - - - +
97E HIS* 3.4 24.6 + - - +
110E CYS* 5.5 6.6 - - + +
111E VAL* 4.6 9.9 - - + -
142E CYS* 5.3 5.9 - - - -
144E LEU* 5.3 12.3 - - + -
145E ALA* 3.6 37.0 - - + +
148E ILE* 5.6 5.2 - - + -
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Residues in contact with ALA 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E TRP 3.8 12.3 + - - +
91E TRP* 4.2 4.9 - - - +
92E LEU 3.1 0.4 - - - -
93E ILE* 1.3 80.6 - - + +
95E PHE* 1.3 61.1 + - - +
96E ALA 3.3 0.7 - - - -
97E HIS* 4.5 1.1 - - - +
98E GLY* 2.8 28.0 + - - -
99E ASP* 3.8 12.8 + - - +
100E LEU* 3.6 29.0 - - + +
114E ILE* 4.5 15.5 - - + -
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Residues in contact with PHE 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E TRP* 3.3 51.9 + + + +
92E LEU* 3.3 14.5 + - + +
94E ALA* 1.3 80.2 - - - +
96E ALA* 1.3 59.6 + - - +
97E HIS 3.3 0.8 + - - -
98E GLY* 3.7 10.1 + - - +
100E LEU* 4.7 18.2 - - + -
6F CYS* 4.7 11.9 - - + -
12F SER* 5.3 14.4 - - - -
15F TYR* 5.6 9.2 - - + +
16F ARG* 5.7 1.6 - - - -
21F VAL* 6.0 2.1 - - - +
26F CYS* 3.8 35.0 - - + -
27F PHE* 4.6 15.8 - - + +
30F ALA* 5.4 7.2 - - + -
105F HIS* 6.1 0.7 - - + -
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E LEU* 2.8 23.8 + - + +
93E ILE* 4.2 7.9 - - - +
94E ALA 3.3 0.2 - - - -
95E PHE* 1.3 77.6 - - - +
97E HIS* 1.3 61.1 + - - +
144E LEU* 6.4 2.5 - - + -
21F VAL* 5.7 10.3 - - - +
----------------------------------------------------------
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Residues in contact with HIS 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ILE 3.4 18.5 + - - +
94E ALA* 4.3 1.6 - - - +
96E ALA* 1.3 78.9 - - - +
98E GLY* 1.3 63.3 + - - +
99E ASP* 3.0 33.9 + - + +
107E ASN* 6.1 2.9 - - - -
108E VAL 4.7 10.3 + - - -
110E CYS* 5.1 6.3 + - + -
141E GLU* 4.8 14.1 - - + +
142E CYS* 4.2 25.7 - - + +
16F ARG* 4.1 12.0 - - - +
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Residues in contact with GLY 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E ALA 2.8 16.0 + - - -
95E PHE* 3.7 9.8 - - - -
96E ALA 3.4 1.2 - - - -
97E HIS* 1.3 77.6 - - - +
99E ASP* 1.3 57.9 + - - +
100E LEU* 3.2 5.7 + - - +
101E ALA 4.0 1.0 + - - -
102E PRO* 3.1 24.3 - - - +
12F SER* 4.5 4.3 - - - +
16F ARG* 3.3 25.6 - - - +
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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