Contacts of the helix formed by residues 99 - 133 (chain B) in PDB entry 3VBB
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 99 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 5.3 0.2 - - - -
78B GLU* 3.2 55.8 + - - +
79B SER 3.2 26.0 + - - -
80B VAL* 4.0 6.1 - - - +
98B LEU* 1.3 75.4 - - - +
100B VAL* 1.3 58.1 + - - +
101B SER 4.2 1.3 - - - +
102B GLN* 2.7 54.8 + - - +
103B ILE* 3.1 10.1 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.9 29.4 - - + +
67B LYS* 3.2 44.2 - - + +
68B MET* 4.4 20.9 - - + -
98B LEU 3.7 0.8 + - - -
99B LYS* 1.3 72.0 - - - +
101B SER* 1.3 60.7 + - - +
103B ILE* 3.5 8.2 + - - -
104B LYS* 3.1 27.7 + - + +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP 4.8 12.3 - - - +
78B GLU 3.1 28.9 + - - -
79B SER* 3.2 23.1 - - - -
80B VAL 4.1 2.6 + - - -
99B LYS* 3.0 2.6 + - - +
100B VAL* 1.3 80.3 - - - +
102B GLN* 1.3 62.2 + - - +
104B LYS* 3.5 10.2 - - - +
105B LYS* 3.2 34.5 + - - +
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.0 37.8 - - - +
81B PRO 4.7 1.1 - - - +
82B GLU* 2.7 42.2 - - + +
98B LEU* 3.0 35.8 - - + +
99B LYS* 2.7 38.7 + - - +
101B SER* 1.3 76.0 + - - +
103B ILE* 1.3 64.1 + - - +
104B LYS 3.1 1.8 - - - -
105B LYS* 3.2 7.9 + - + +
106B VAL* 3.1 27.6 + - + +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 3.7 28.0 - - - +
63B THR* 3.5 28.5 - - + -
64B ILE* 3.2 26.7 - - + -
67B LYS* 3.9 19.7 - - + -
95B LEU* 3.6 26.0 - - + +
98B LEU* 4.0 14.1 - - + +
99B LYS 3.1 10.2 + - - +
100B VAL* 4.0 2.9 - - - +
102B GLN* 1.3 76.3 - - - +
104B LYS* 1.3 56.8 + - - +
106B VAL* 3.4 6.0 + - - +
107B ARG* 2.9 27.9 + - - +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.4 23.5 - - + +
68B MET* 4.4 24.1 - - - +
100B VAL* 3.1 17.5 + - - +
101B SER* 3.5 13.9 - - - +
102B GLN 3.1 0.8 - - - -
103B ILE* 1.3 77.4 - - - +
105B LYS* 1.3 59.2 + - + +
107B ARG* 3.3 21.5 + - - +
108B LEU* 2.9 29.5 + - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER* 5.0 9.2 - - - -
80B VAL 3.8 21.2 + - - +
81B PRO* 4.3 15.2 - - - +
101B SER* 3.2 24.5 - - - +
102B GLN* 3.2 10.3 + - - +
104B LYS* 1.3 77.3 - - + +
106B VAL* 1.3 61.4 + - + +
108B LEU* 3.8 14.2 - - + +
109B LEU* 3.5 26.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B CYS* 3.7 12.1 - - - -
82B GLU 5.7 3.1 - - - +
83B ASN* 5.7 5.8 - - + -
85B LEU* 4.5 29.6 - - + +
87B PHE* 4.8 6.3 - - + -
90B LEU* 3.4 31.4 - - + -
98B LEU* 5.4 2.5 - - + -
102B GLN* 3.1 18.0 + - + +
103B ILE* 3.7 7.0 - - - +
104B LYS 3.1 0.2 - - - -
105B LYS* 1.3 76.9 - - + +
107B ARG* 1.3 61.3 + - - +
108B LEU 3.1 1.1 - - - -
109B LEU* 2.8 26.7 + - + +
110B ILE* 3.0 17.0 + - + +
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 4.2 15.3 - - + +
60B CYS* 4.0 21.3 - - + -
61B SER* 2.5 50.7 + - - +
64B ILE* 4.3 18.0 - - + +
103B ILE 2.9 17.6 + - - +
104B LYS* 3.3 29.0 + - - +
106B VAL* 1.3 75.7 - - - +
108B LEU* 1.3 58.3 + - - +
110B ILE* 3.2 6.2 + - - +
111B ASP* 3.0 41.9 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS 2.9 17.6 + - - +
105B LYS* 3.8 14.6 - - + +
107B ARG* 1.3 78.4 - - - +
109B LEU* 1.3 63.2 + - + +
111B ASP* 4.6 4.3 - - + +
112B GLU* 3.0 41.9 + - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU 5.7 4.3 - - - +
87B PHE* 3.6 23.1 - - + -
105B LYS 3.5 15.3 + - - +
106B VAL* 2.8 20.3 + - + +
108B LEU* 1.3 81.7 - - + +
110B ILE* 1.3 60.3 + - - +
112B GLU* 3.9 23.3 - - - +
113B ALA* 3.2 24.4 + - - +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 3.4 35.4 - - + +
56B LEU* 3.5 42.2 - - + +
57B LYS* 3.7 15.0 - - + +
60B CYS* 4.3 11.9 - - - -
87B PHE* 3.6 23.6 - - + -
90B LEU* 4.6 2.2 - - + -
106B VAL* 3.0 17.6 + - + +
107B ARG* 3.5 7.2 - - - +
109B LEU* 1.3 74.2 - - - +
111B ASP* 1.3 56.1 + - - +
112B GLU 3.1 1.3 - - - -
113B ALA* 2.8 8.7 + - - +
114B ILE* 2.7 34.6 + - + +
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 3.0 49.9 - - - +
107B ARG* 3.0 25.4 + - - +
108B LEU* 4.6 3.8 - - + +
110B ILE* 1.3 71.2 - - - +
112B GLU* 1.3 57.2 + - - +
114B ILE* 4.1 10.0 - - - +
115B LEU* 3.1 39.5 + - + +
----------------------------------------------------------
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.0 36.2 + - + +
109B LEU* 3.9 22.6 - - - +
110B ILE 3.1 0.8 - - - -
111B ASP* 1.3 78.0 - - - +
113B ALA* 1.3 57.1 + - - +
115B LEU* 3.9 7.6 - - - +
116B LYS* 3.3 20.8 + - - +
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ARG* 4.0 15.7 + - - +
53B LEU* 3.8 17.6 - - + +
87B PHE* 4.5 7.2 - - + -
109B LEU 3.2 14.7 + - - +
110B ILE* 2.8 10.1 + - - +
112B GLU* 1.3 76.1 - - - +
114B ILE* 1.3 64.1 + - - +
115B LEU 3.1 1.8 - - - -
116B LYS* 3.1 18.1 + - + +
117B CYS* 3.2 15.6 + - - +
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Residues in contact with ILE 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 4.4 13.5 - - + +
53B LEU* 3.4 30.7 - - + +
54B ASN* 3.5 39.0 - - - +
57B LYS* 4.6 10.8 - - + -
110B ILE* 2.7 22.5 + - + +
111B ASP* 3.8 11.0 - - - +
113B ALA* 1.3 72.9 - - - +
115B LEU* 1.3 69.0 + - + +
117B CYS* 3.4 10.5 - - - +
118B ASP* 3.2 26.7 - - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ASP* 3.1 30.6 + - + +
112B GLU* 4.1 7.2 - - - +
113B ALA 3.1 0.2 - - - -
114B ILE* 1.3 86.6 - - + +
116B LYS* 1.3 64.7 + - - +
117B CYS 3.0 1.8 - - - -
118B ASP* 3.1 16.0 + - + +
119B ALA* 3.0 22.7 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU 3.3 13.0 + - - +
113B ALA* 3.1 14.4 + - + +
115B LEU* 1.3 78.4 - - - +
117B CYS* 1.3 58.9 + - - +
119B ALA* 3.5 8.1 + - + +
120B GLU* 2.9 53.3 + - + +
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Residues in contact with CYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B CYS* 3.9 26.8 - - + -
49B ARG* 3.9 24.2 - - - -
50B ALA* 3.7 29.4 - - + -
53B LEU* 5.0 1.1 - - - -
113B ALA 3.2 12.8 + - - +
114B ILE 3.4 11.4 - - - +
116B LYS* 1.3 76.2 - - - +
118B ASP* 1.3 57.9 + - - +
120B GLU* 3.2 7.4 + - - +
121B ARG* 2.6 41.2 + - - +
----------------------------------------------------------
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 5.1 3.8 - - - +
114B ILE* 3.2 24.9 - - - +
115B LEU* 3.1 19.0 + - + +
117B CYS* 1.3 79.3 - - - +
119B ALA* 1.3 60.5 + - - +
121B ARG* 3.9 15.9 + - - +
122B ILE* 3.2 31.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU 3.0 12.2 + - - +
116B LYS* 3.7 13.2 - - + +
117B CYS 3.1 0.2 - - - -
118B ASP* 1.3 75.7 - - - +
120B GLU* 1.3 67.5 + - + +
122B ILE* 3.4 6.6 + - - +
123B LYS* 3.1 23.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B CYS* 4.1 17.9 - - - -
116B LYS* 2.9 48.5 + - + +
117B CYS* 3.6 5.8 - - - +
119B ALA* 1.3 75.6 - - - +
121B ARG* 1.3 67.2 + - - +
122B ILE 3.0 0.5 + - - -
123B LYS* 3.1 27.9 + - - +
124B LEU* 2.7 34.9 + - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 3.3 53.9 + - + +
46B CYS* 3.8 26.9 - - + -
47B ARG* 3.2 42.1 - - - +
50B ALA* 5.5 1.7 - - - +
117B CYS* 2.6 26.7 + - - +
118B ASP* 4.1 14.7 + - - +
120B GLU* 1.3 72.2 - - - +
122B ILE* 1.3 52.8 + - + +
124B LEU* 3.5 3.9 - - - +
125B GLU* 2.8 49.2 + - - +
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Residues in contact with ILE 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 3.2 20.7 + - + +
119B ALA* 3.8 5.8 - - - +
120B GLU 3.1 0.6 - - - -
121B ARG* 1.3 75.8 - - + +
123B LYS* 1.3 69.3 - - + +
124B LEU 3.0 1.6 + - - -
125B GLU* 3.4 24.3 + - - +
126B ALA* 3.5 12.8 + - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU* 5.1 4.8 + - - -
119B ALA 3.1 11.5 + - - +
120B GLU* 3.1 25.7 + - - +
122B ILE* 1.3 82.7 - - + +
124B LEU* 1.3 71.5 + - - +
126B ALA* 4.0 4.8 + - - +
127B GLU* 3.2 42.9 + - + +
----------------------------------------------------------
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.6 24.0 - - + +
42B GLU* 3.6 26.9 - - + +
43B TRP* 3.3 41.3 - - + +
46B CYS* 5.1 1.3 - - - -
120B GLU* 2.7 33.2 + - + +
121B ARG 3.5 4.9 - - - +
123B LYS* 1.3 88.0 - - - +
125B GLU* 1.3 67.1 + - - +
126B ALA 2.9 2.1 + - - -
127B GLU* 2.9 21.3 + - - +
128B ARG* 2.8 28.2 + - - +
----------------------------------------------------------
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 3.1 34.8 + - + +
121B ARG* 2.8 39.0 + - - +
122B ILE* 3.4 17.3 + - - +
124B LEU* 1.3 73.1 - - - +
126B ALA* 1.3 55.8 + - - +
128B ARG* 3.6 21.9 + - - +
129B PHE* 3.3 23.4 + - - +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ILE 3.5 13.0 + - - +
123B LYS* 4.1 4.7 - - - +
124B LEU 2.9 0.4 - - - -
125B GLU* 1.3 76.4 - - - +
127B GLU* 1.3 57.2 + - - +
128B ARG 2.9 5.2 - - - -
129B PHE* 2.8 22.1 + - - +
130B GLU* 2.8 18.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLN* 4.5 11.2 - - + +
36B LEU* 5.2 0.7 - - - +
39B ALA* 4.0 23.1 - - + +
123B LYS* 3.2 37.9 + - - +
124B LEU* 2.9 12.1 + - - +
126B ALA* 1.3 77.9 - - - +
128B ARG* 1.3 59.1 + - - +
130B GLU* 4.2 9.0 - - - +
131B ASN* 3.6 27.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.8 25.7 - - + +
9B ARG* 3.9 1.0 - - - +
36B LEU* 3.1 30.1 - - + +
39B ALA* 5.1 6.2 - - + +
40B ASP* 2.9 41.7 + - + +
43B TRP* 3.4 46.1 - - - -
124B LEU 2.8 15.2 + - - +
125B GLU* 3.6 18.1 + - - +
127B GLU* 1.3 78.6 - - - +
129B PHE* 1.3 58.5 + - - +
131B ASN* 3.3 3.8 + - - +
132B LEU* 3.0 31.1 + - + +
----------------------------------------------------------
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 5.2 9.6 - - + -
125B GLU 3.3 13.3 + - - +
126B ALA* 2.8 7.6 + - - +
128B ARG* 1.3 78.0 - - - +
130B GLU* 1.3 64.2 + - - +
132B LEU* 4.4 18.6 - - + -
133B ARG* 3.2 51.6 + - + +
405B ARG* 4.1 27.6 - - - -
----------------------------------------------------------
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA* 2.8 16.7 + - + +
127B GLU* 4.4 7.8 - - - +
129B PHE* 1.3 78.1 - - - +
131B ASN* 1.3 65.0 + - - +
133B ARG* 4.0 7.8 + - - +
134B GLU* 3.7 23.4 + - + +
----------------------------------------------------------
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Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.0 45.0 + - - +
35B GLN* 3.4 30.9 + - - +
36B LEU* 3.5 18.1 - - + +
127B GLU* 3.6 19.9 + - - +
128B ARG 3.3 4.3 + - - +
129B PHE 3.2 0.2 - - - -
130B GLU* 1.3 82.5 - - - +
132B LEU* 1.3 64.9 + - - +
133B ARG 3.2 1.6 - - - -
134B GLU* 3.2 10.1 + - - +
135B ILE* 3.1 22.7 + - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 3.4 41.0 - - + +
3B LEU* 3.8 19.6 + - + +
5B LEU* 4.9 15.9 - - + +
8B PHE* 3.7 22.4 - - + -
36B LEU* 3.5 26.6 - - + +
128B ARG* 3.0 17.3 + - + +
129B PHE* 3.6 17.5 + - + +
131B ASN* 1.3 76.4 - - - +
133B ARG* 1.3 62.8 + - - +
134B GLU 3.2 0.5 + - - -
135B ILE* 3.3 20.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B VAL* 4.1 7.5 - - + +
129B PHE* 3.2 48.7 + - + +
130B GLU* 4.0 9.6 - - - +
131B ASN 3.2 0.2 - - - -
132B LEU* 1.3 76.1 - - - +
134B GLU* 1.3 64.6 + - + +
135B ILE 3.4 1.0 + - - -
235B GLN* 4.0 22.8 + - - +
238B ALA 4.3 5.5 + - - -
239B GLN* 4.5 2.8 - - - +
240B LEU* 4.2 27.1 - - - +
243B PHE* 4.8 6.1 - - - -
371B HIS* 3.4 18.9 - - - -
401B TYR* 3.8 7.4 + - - -
405B ARG* 2.8 39.9 - - - +
----------------------------------------------------------
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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