Contacts of the helix formed by residues 82 - 111 (chain B) in PDB entry 3BVI
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 GLY 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP* 3.5 22.3 - - - -
80B PHE 3.6 1.6 - - - -
81B GLU* 1.3 80.0 - - - +
83B LEU* 1.3 64.3 + - - -
84B THR 3.3 2.5 - - - -
85B GLN* 3.4 4.4 + - - +
86B ILE* 3.1 24.9 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP* 4.3 3.8 - - - -
31B CYS* 4.5 5.6 - - - -
36B LEU* 3.6 23.0 - - + +
39B ALA* 3.8 16.8 - - + -
82B GLY* 1.3 72.9 - - - -
84B THR* 1.3 62.3 + - - +
86B ILE* 3.4 5.5 + - + +
87B PHE* 3.2 63.4 + - + +
141B ILE* 4.1 17.0 - - + +
146B ASN* 5.9 0.2 - - - +
151B LEU* 3.9 31.4 - - + +
154B ALA* 4.0 23.6 - - + -
155B ASP* 4.8 9.0 - - - +
158B VAL* 5.7 1.8 - - + -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY 3.3 0.4 - - - -
83B LEU* 1.3 76.9 - - - +
85B GLN* 1.3 58.7 + - - +
87B PHE* 3.2 4.0 + - - +
88B GLN* 2.9 53.5 + - + +
138B LEU* 4.3 4.3 - - + +
141B ILE* 3.3 24.9 + - + +
142B GLU* 3.8 25.1 + - - +
146B ASN* 4.3 12.9 + - - -
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS 5.4 1.6 + - - -
80B PHE* 3.4 21.3 - - - +
81B GLU* 2.9 62.8 + - + +
82B GLY 3.4 8.3 + - - +
83B LEU 3.3 0.2 - - - -
84B THR* 1.3 76.4 - - - +
86B ILE* 1.3 66.0 + - - +
88B GLN* 3.8 8.6 - - + +
89B LYS* 3.0 53.3 + - + +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 3.8 22.1 - - + +
30B TRP* 3.5 42.8 - - + -
31B CYS* 3.8 14.1 - - - -
43B LEU* 4.0 26.2 - - + -
80B PHE* 3.7 27.8 - - + -
82B GLY 3.1 13.6 + - - +
83B LEU* 3.7 8.5 - - - +
85B GLN* 1.3 77.9 - - - +
87B PHE* 1.3 65.4 + - + +
89B LYS* 3.3 5.0 + - - +
90B ALA* 2.9 26.6 + - + +
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Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.2 7.4 - - + -
42B PHE* 4.0 16.4 - + - -
43B LEU* 4.0 26.2 - - + -
83B LEU* 3.2 46.6 + - + +
84B THR 3.2 2.4 + - - +
86B ILE* 1.3 79.6 - - + +
88B GLN* 1.3 61.1 + - - +
90B ALA* 3.9 2.6 - - + +
91B TYR* 2.9 30.7 + - - +
134B PHE* 3.8 37.7 - + - +
137B ILE* 3.6 27.8 - - + -
138B LEU* 3.9 15.5 - - + +
141B ILE* 3.6 17.3 - - + -
158B VAL* 4.5 9.2 - - + -
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B THR* 2.9 35.2 + - - +
85B GLN* 3.8 8.1 + - + +
87B PHE* 1.3 75.1 - - - +
89B LYS* 1.3 60.4 + - + +
91B TYR* 3.5 2.3 + - - +
92B GLU* 3.0 45.8 + - - +
138B LEU* 3.8 28.1 - - + +
142B GLU* 3.8 12.1 + - - +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET* 4.1 12.6 - - + -
77B GLU* 5.1 14.3 + - + +
79B LYS 5.6 2.0 + - - -
80B PHE* 4.8 13.0 - - + -
85B GLN* 3.0 52.5 + - + +
86B ILE* 3.6 3.8 - - - +
88B GLN* 1.3 79.6 - - + +
90B ALA* 1.3 57.3 + - - +
92B GLU* 3.4 13.8 + - - +
93B HIS* 2.9 29.3 + - - +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 3.4 18.3 + - + +
27B MET* 4.2 9.2 - - - +
43B LEU* 5.3 1.6 - - + -
86B ILE 2.9 17.5 + - - +
87B PHE* 3.9 5.4 - - + +
88B GLN 3.3 0.2 - - - -
89B LYS* 1.3 76.0 - - - +
91B TYR* 1.3 58.6 + - - +
93B HIS* 3.1 7.5 + - - +
94B GLU* 2.9 33.9 + - - +
134B PHE* 3.6 30.5 - - + -
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Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE 2.9 18.8 + - - +
88B GLN 3.8 3.4 - - - +
90B ALA* 1.3 73.6 - - - +
92B GLU* 1.3 64.8 + - + +
94B GLU* 3.2 2.9 + - + +
95B GLN* 3.1 61.8 + - + +
131B GLU* 3.6 32.6 + - + -
134B PHE* 4.2 14.5 - - + +
135B LYS* 3.7 41.1 - - + +
138B LEU* 4.1 22.0 - - + -
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN* 3.0 35.1 + - - +
89B LYS* 3.7 11.8 - - - +
91B TYR* 1.3 76.6 - - + +
93B HIS* 1.3 63.0 + - - +
95B GLN* 3.4 18.3 + - - +
96B HIS* 3.2 20.8 + - - +
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Residues in contact with HIS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS 5.4 0.4 - - - -
20B SER* 2.8 43.7 + - - -
23B LEU* 4.1 23.7 - - + +
24B TYR* 3.6 24.4 - + - -
89B LYS 2.9 17.6 + - - +
90B ALA* 3.1 7.8 + - - +
92B GLU* 1.3 77.8 - - - +
94B GLU* 1.3 61.2 + - - +
96B HIS* 3.1 15.7 + + - +
97B ILE* 3.0 45.4 + - + +
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 2.6 33.9 + - - +
46B HIS* 2.9 22.6 + - - -
50B GLU* 3.5 2.4 - - - +
90B ALA 2.9 14.0 + - - +
91B TYR* 3.2 6.2 + - + +
93B HIS* 1.3 76.3 - - - +
95B GLN* 1.3 61.4 + - - +
97B ILE* 3.3 3.9 + - - +
98B SER* 2.9 15.9 + - - -
127B GLN* 2.8 35.1 + - - +
130B GLU* 4.0 3.9 - - - +
131B GLU* 4.3 16.6 - - + -
134B PHE* 3.9 19.7 - - + -
1007B FE 2.4 26.8 - - - -
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Residues in contact with GLN 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 3.1 55.2 + - + +
92B GLU* 3.5 21.8 - - - +
94B GLU* 1.3 76.6 - - - +
96B HIS* 1.3 62.1 + - - +
98B SER* 3.4 2.6 + - - -
99B GLU* 3.0 24.9 + - - +
131B GLU* 3.6 24.8 - - - +
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 3.4 39.1 - - + -
92B GLU 3.2 11.7 + - - +
93B HIS* 3.1 18.8 + + - +
95B GLN* 1.3 75.0 - - - +
97B ILE* 1.3 73.2 + - + +
99B GLU* 3.2 10.9 + - + +
100B SER* 3.0 22.3 + - - -
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 4.2 5.6 - - - +
16B LYS* 4.4 26.0 - - + +
17B GLU* 4.0 9.9 - - - +
20B SER* 4.9 7.6 - - - +
50B GLU* 5.1 2.5 - - - +
93B HIS* 3.0 40.1 + - + +
94B GLU* 3.3 10.7 + - - +
96B HIS* 1.3 90.3 - - + +
98B SER* 1.3 60.9 + - - +
100B SER* 2.8 20.9 + - - +
101B ILE* 3.0 17.0 + - + +
127B GLN* 3.6 24.2 - - - +
1006B FE 3.9 12.1 - - - -
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLU 2.9 11.5 + - - -
95B GLN 3.6 5.4 - - - -
96B HIS 3.3 0.2 - - - -
97B ILE* 1.3 76.7 - - - +
99B GLU* 1.3 61.5 + - - +
101B ILE* 3.4 4.2 + - - +
102B ASN* 3.1 33.0 + - - +
127B GLN* 3.0 32.3 + - - +
128B HIS* 5.0 0.7 + - - -
131B GLU* 2.6 30.3 + - - +
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLN 3.0 14.0 + - - +
96B HIS* 3.2 15.0 + - + +
98B SER* 1.3 76.4 - - - +
100B SER* 1.3 63.5 + - - +
102B ASN* 3.4 12.2 + - + +
103B ASN* 3.0 22.9 + - + +
----------------------------------------------------------
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 3.1 27.8 + - - -
16B LYS* 4.0 22.7 - - - +
96B HIS* 3.0 15.9 + - - -
97B ILE* 2.8 21.5 + - - -
99B GLU* 1.3 76.5 - - - +
101B ILE* 1.3 61.8 + - - +
103B ASN* 3.4 8.3 + - - +
104B ILE* 3.3 25.5 + - - +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 3.9 7.4 - - - +
97B ILE* 3.0 14.7 + - + +
98B SER* 3.7 6.1 - - - +
99B GLU 3.3 0.2 - - - -
100B SER* 1.3 81.5 + - - +
102B ASN* 1.3 64.8 + - - +
104B ILE* 3.1 11.5 + - + +
105B VAL* 3.0 24.4 + - + +
120B LEU* 5.3 2.5 - - + +
123B TYR* 3.5 49.8 - - + +
124B VAL* 3.8 30.1 - - + -
127B GLN* 3.6 38.8 - - + -
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Residues in contact with ASN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER* 3.1 25.6 + - - +
99B GLU* 3.5 11.9 - - + +
101B ILE* 1.3 80.1 - - - +
103B ASN* 1.3 52.1 + - - +
105B VAL* 3.4 7.7 + - - +
106B ASP* 2.8 36.2 + - - +
124B VAL* 5.1 10.7 - - - +
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.8 25.7 - - - +
99B GLU* 3.0 14.1 + - + +
100B SER* 3.4 13.8 - - - +
102B ASN* 1.3 73.4 - - - +
104B ILE* 1.3 61.0 + - - +
106B ASP* 3.3 11.7 + - - +
107B HIS* 2.9 28.7 + - - +
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.3 9.5 - - + +
9B LEU* 3.8 47.1 - - + +
10B LEU* 4.2 20.2 - - + -
13B GLN* 3.7 35.9 - - + +
100B SER 3.4 11.9 - - - +
101B ILE* 3.1 9.5 + - + +
103B ASN* 1.3 77.5 - - - +
105B VAL* 1.3 57.7 + - - +
107B HIS* 3.0 3.5 + - - +
108B ALA* 2.9 27.0 + - - +
116B THR* 5.0 1.3 - - + -
120B LEU* 3.7 25.4 - - + -
123B TYR* 5.4 1.3 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ILE* 3.0 21.3 + - + +
102B ASN* 3.7 7.4 - - - +
104B ILE* 1.3 74.9 - - - +
106B ASP* 1.3 64.0 - - - +
108B ALA* 3.2 6.5 + - - +
109B ILE* 3.1 24.8 + - + +
117B PHE* 3.3 32.5 - - + -
120B LEU* 3.8 26.7 - - + -
121B GLN* 4.4 4.3 - - - +
124B VAL* 3.8 27.8 - - + -
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN 2.8 23.2 + - - +
103B ASN* 3.5 13.5 + - - +
105B VAL* 1.3 73.8 - - - +
107B HIS* 1.3 58.4 + - - +
109B ILE* 3.3 14.3 + - - +
110B LYS* 3.1 57.0 + - - +
----------------------------------------------------------
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Residues in contact with HIS 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 5.7 0.2 + - - -
5B ASP* 3.3 41.6 + - + +
6B ILE* 3.8 16.6 - - + -
9B LEU* 3.8 19.4 - - + +
103B ASN* 2.9 18.3 + - - +
104B ILE 3.0 4.7 + - - +
106B ASP* 1.3 74.5 - - - +
108B ALA* 1.3 60.5 + - - +
110B LYS* 3.8 14.8 - - + +
111B SER* 2.9 44.3 + - - -
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.9 13.1 - - + +
104B ILE 2.9 12.4 + - - +
105B VAL* 3.2 11.2 + - - +
107B HIS* 1.3 76.5 - - - +
109B ILE* 1.3 60.3 + - - +
111B SER* 3.5 4.9 + - - -
112B LYS 3.1 2.9 + - - -
113B ASP* 2.8 48.9 + - - +
114B HIS* 5.1 0.5 + - - -
116B THR* 4.4 7.6 - - + -
117B PHE* 4.1 18.8 - - + +
----------------------------------------------------------
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 3.1 16.8 + - + +
106B ASP* 3.5 14.6 - - - +
108B ALA* 1.3 75.1 - - - +
110B LYS* 1.3 67.1 + - + +
112B LYS* 3.1 18.0 + - - +
114B HIS* 4.6 21.0 + - + -
117B PHE* 3.6 33.4 - - + -
----------------------------------------------------------
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP* 3.1 46.4 + - - +
107B HIS* 3.8 16.8 - - + +
108B ALA 3.4 0.2 - - - -
109B ILE* 1.3 81.0 - - + +
111B SER* 1.3 59.1 + - - +
112B LYS* 3.3 6.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 4.7 8.1 + - - -
6B ILE* 4.1 5.4 - - - +
107B HIS* 2.9 37.8 + - - -
108B ALA* 3.6 8.7 + - - -
109B ILE 3.2 0.2 - - - -
110B LYS* 1.3 75.1 - - - +
112B LYS* 1.3 67.2 + - - +
113B ASP* 3.2 11.8 + - - +
----------------------------------------------------------
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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