Contacts of the helix formed by residues 69 - 97 (chain B) in PDB entry 5LSJ
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 GLN 69 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LYS* 4.5 24.2 - - - +
49A GLY 5.9 0.6 + - - -
65B PHE* 4.5 10.2 - - - -
67B GLN 4.0 0.8 + - - -
68B LEU* 1.3 95.6 - - - +
70B PRO* 1.3 66.3 - - - +
71B ALA* 3.0 8.5 - - + +
72B MET* 3.0 32.0 + - + +
73B THR* 3.3 10.4 + - - +
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Residues in contact with PRO 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.9 3.2 + - - +
66B TYR* 3.6 33.9 - - + +
67B GLN* 4.5 7.2 - - - +
68B LEU 3.6 0.6 - - - -
69B GLN* 1.3 87.3 - - - +
71B ALA* 1.3 57.8 + - - +
72B MET 3.5 0.2 - - - -
73B THR* 3.0 24.4 + - + +
74B GLN* 3.5 12.3 + - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 3.0 3.6 - - + -
70B PRO* 1.3 78.5 - - - +
72B MET* 1.3 61.3 + - - +
74B GLN* 3.5 4.1 + - - +
75B GLN* 3.0 31.8 + - - +
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Residues in contact with MET 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 5.2 12.8 - - + -
46A LYS* 3.6 42.4 - - + -
65B PHE* 4.3 15.5 - - + -
69B GLN* 3.0 24.7 + - + +
71B ALA* 1.3 77.8 - - - +
73B THR* 1.3 58.5 + - - +
75B GLN* 3.7 24.1 - - - +
76B ILE* 2.9 37.9 + - + +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.5 8.6 + - - -
58B PHE* 4.0 6.3 - - - -
59B THR* 5.1 5.2 - - - -
65B PHE* 3.5 39.3 - - + +
66B TYR* 3.5 27.7 - - + -
69B GLN 3.3 14.4 - - - +
70B PRO* 3.0 15.9 + - + +
72B MET* 1.3 75.9 - - - +
74B GLN* 1.3 65.1 + - - +
76B ILE* 3.1 11.6 - - - +
77B TYR* 2.9 29.7 + - - +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TYR* 3.1 43.5 - - + +
70B PRO 3.5 10.1 + - - +
71B ALA* 4.1 4.0 - - - +
72B MET 3.3 0.2 - - - -
73B THR* 1.3 77.3 + - - +
75B GLN* 1.3 64.7 + - - +
77B TYR* 4.2 3.2 - - - -
78B ASP* 2.7 60.2 + - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 3.0 20.7 + - - +
72B MET* 3.7 26.2 - - + +
74B GLN* 1.3 81.3 + - - +
76B ILE* 1.3 59.1 + - + +
78B ASP* 3.3 5.5 + - - +
79B LYS* 2.9 28.9 + - + +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.3 48.6 - - + +
42A VAL* 3.5 25.6 - - + -
43A ILE* 3.5 22.4 - - + -
58B PHE* 4.4 9.6 - - + -
65B PHE* 5.0 1.3 - - + -
72B MET* 2.9 20.7 + - + +
73B THR* 3.1 21.1 - - - +
75B GLN* 1.3 74.9 - - - +
77B TYR* 1.3 61.5 + - - +
79B LYS* 3.8 10.3 - - + +
80B PHE* 2.9 27.2 + - - +
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 5.1 0.7 - + - -
50B VAL* 4.5 6.8 + - - +
53B GLY 2.6 30.3 + - - -
54B SER* 3.8 3.1 - - - -
55B TYR* 3.1 38.1 + + + +
58B PHE* 3.4 38.6 - + + -
73B THR 2.9 19.1 + - - +
74B GLN* 3.7 6.7 - - - +
75B GLN 3.3 0.2 - - - -
76B ILE* 1.3 78.1 - - - +
78B ASP* 1.3 70.9 + - - +
80B PHE* 3.2 26.9 + + - +
81B ILE* 2.9 47.3 + - + +
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Residues in contact with ASP 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLN* 2.7 53.8 + - - +
75B GLN* 3.3 6.0 + - - +
77B TYR* 1.3 86.5 - - - +
79B LYS* 1.3 60.5 + - - +
81B ILE* 3.3 11.5 - - + +
82B ALA* 2.9 31.6 + - - +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 5.3 11.4 - - + -
39A VAL* 6.0 2.2 - - + -
42A VAL* 6.2 4.3 - - + -
75B GLN* 2.9 18.2 + - + +
76B ILE* 3.8 12.1 - - + +
78B ASP* 1.3 75.4 - - - +
80B PHE* 1.3 60.4 + - - +
82B ALA* 4.6 3.8 - - - -
83B GLN* 2.9 70.6 + - + +
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.6 7.4 - - + -
35A VAL* 3.5 36.7 - - + +
36A MET* 3.4 32.1 - - + -
39A VAL* 3.5 19.1 - - + -
67A PHE* 4.2 19.1 - + - -
71A MET* 4.8 7.6 - - + -
53B GLY* 5.6 0.7 - - - -
58B PHE* 5.5 2.0 - + + -
76B ILE 2.9 18.9 + - - +
77B TYR* 3.2 27.3 + + - +
79B LYS* 1.3 79.9 - - - +
81B ILE* 1.3 85.6 + - + +
84B LEU* 2.9 48.9 + - + +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU 5.7 0.2 - - - -
50B VAL* 3.6 48.9 - - + +
52B ALA 5.4 1.1 - - - +
53B GLY 5.1 1.6 - - - +
77B TYR* 2.9 36.0 + - + +
78B ASP* 3.3 17.5 - - - +
80B PHE* 1.3 98.7 - - + +
82B ALA* 1.3 68.7 + - + +
84B LEU* 3.7 8.6 - - + +
85B GLN* 3.0 38.0 + - - +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ASP 2.9 18.7 + - - +
79B LYS* 4.0 4.5 - - - +
81B ILE* 1.3 81.2 - - + +
83B GLN* 1.3 57.5 + - - +
85B GLN* 3.3 11.3 - - - +
86B THR* 2.9 39.8 + - + +
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Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.0 20.1 - - + +
38A ALA* 4.8 8.0 - - - +
79B LYS* 2.9 48.2 + - + +
82B ALA* 1.3 76.7 - - - +
84B LEU* 1.3 58.5 + - - +
86B THR* 3.5 7.9 - - - +
87B SER* 2.9 35.8 + - - -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE 5.4 0.2 - - - +
31A TYR* 4.4 5.8 - - + -
32A LEU* 4.0 47.8 - - + +
35A VAL* 3.7 16.0 - - + +
71A MET* 6.1 1.3 - - - -
46B LEU* 5.6 4.9 - - + -
49B LEU* 4.9 18.2 - - + -
50B VAL* 5.6 4.3 - - + -
80B PHE* 2.9 34.2 + - + +
81B ILE* 3.7 12.3 - - + +
82B ALA 3.2 0.2 - - - -
83B GLN* 1.3 76.8 - - - +
85B GLN* 1.3 61.7 + - + +
87B SER* 3.2 3.7 + - - -
88B ILE* 2.9 44.2 + - + +
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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
----------------------------------------------------------
46B LEU* 3.6 22.2 - - + +
50B VAL* 5.1 11.3 - - + +
81B ILE* 3.0 37.3 + - - +
82B ALA* 3.3 15.4 - - - +
84B LEU* 1.3 80.0 - - + +
86B THR* 1.3 67.1 + - + +
88B ILE* 3.1 11.4 - - - +
89B ARG* 2.9 52.7 + - - +
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Residues in contact with THR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 2.9 27.6 + - + +
83B GLN* 3.5 11.4 - - - +
85B GLN* 1.3 82.2 - - + +
87B SER* 1.3 62.4 + - - +
89B ARG* 4.1 9.5 - - - +
90B GLU* 2.9 42.3 + - - +
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A TYR* 3.4 39.5 - - - -
34A GLU* 4.9 1.6 + - - -
35A VAL* 5.7 2.0 - - - -
83B GLN* 2.9 27.3 + - - -
84B LEU* 3.6 4.9 - - - -
86B THR* 1.3 78.9 + - - +
88B ILE* 1.3 56.1 - - - +
90B GLU* 3.5 9.7 + - - +
91B GLU* 3.0 27.0 + - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PHE* 3.4 62.4 - - + +
31A TYR* 4.7 5.8 - - + -
75A PHE* 5.1 2.7 - - + -
42B VAL* 6.4 2.0 - - + -
45B PHE* 4.2 13.9 - - + -
46B LEU* 3.5 31.2 - - + -
49B LEU* 5.5 2.2 - - + -
84B LEU* 2.9 26.7 + - + +
85B GLN 3.1 13.5 - - - +
87B SER* 1.3 73.0 - - - +
89B ARG* 1.3 65.6 + - + +
91B GLU* 3.1 7.4 + - - +
92B ILE* 3.0 29.4 + - + +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL* 5.7 5.2 - - + -
43B ASP* 3.0 31.8 + - - +
46B LEU* 3.4 27.0 - - + +
47B GLN* 6.3 0.8 - - - +
85B GLN* 2.9 40.1 + - - +
86B THR* 4.1 8.7 - - - +
88B ILE* 1.3 76.8 - - + +
90B GLU* 1.3 59.6 + - + +
92B ILE* 3.1 15.9 - - + +
93B SER* 2.9 32.7 + - - +
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR* 2.9 28.7 + - - +
87B SER* 3.8 8.1 - - - +
89B ARG* 1.3 76.9 - - - +
91B GLU* 1.3 56.5 + - - +
93B SER* 3.8 5.3 - - - -
94B ASP* 2.9 39.0 + - - +
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 3.8 22.4 - - + +
28A PHE* 4.1 12.6 - - + -
31A TYR* 2.8 40.3 + - + -
87B SER 3.0 15.4 + - - +
88B ILE* 3.3 11.4 - - - +
89B ARG 3.1 0.6 - - - -
90B GLU* 1.3 74.6 - - - +
92B ILE* 1.3 61.4 + - - +
94B ASP* 2.9 25.5 + - - +
95B ILE* 2.9 42.4 + - + +
154E LYS* 5.1 1.4 + - - -
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ILE* 5.1 8.5 - - + -
28A PHE* 3.5 31.4 - - + -
86A PHE* 6.0 2.5 - - + -
38B LEU* 6.0 5.8 - - + -
39B ASP* 3.4 26.2 - - - +
42B VAL* 4.3 29.2 - - + -
88B ILE 3.0 11.1 + - - +
89B ARG* 3.1 23.6 - - + +
91B GLU* 1.3 75.3 - - + +
93B SER* 1.3 77.1 + - - +
95B ILE* 3.2 10.7 + - + +
96B LYS* 2.9 34.3 + - + +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ARG* 2.9 20.4 + - - +
90B GLU* 4.0 6.7 - - - -
92B ILE* 1.3 85.7 - - - +
94B ASP* 1.3 63.2 + - - +
96B LYS* 3.5 27.8 + - - +
97B GLU* 3.6 20.7 + - - +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLU* 2.9 28.5 + - - +
91B GLU* 2.9 16.3 + - - +
93B SER* 1.3 81.1 - - - +
95B ILE* 1.3 62.4 + - + +
97B GLU* 3.3 11.0 + - - +
98B GLU* 3.3 17.5 + - - +
150E ARG* 4.0 36.4 + - - +
151E HIS* 5.9 1.9 + - - -
154E LYS* 5.8 4.3 - - - +
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS* 5.2 8.3 - - - -
23A ARG* 5.1 11.4 - - + +
24A ILE* 4.0 31.4 - - + +
27A ALA* 5.7 0.2 - - + -
91B GLU* 2.9 42.1 + - + +
92B ILE* 3.2 9.1 + - + +
94B ASP* 1.3 74.8 - - + +
96B LYS* 1.3 62.7 + - - +
97B GLU 3.3 1.1 - - - -
98B GLU* 3.5 34.8 + - + +
101B LEU* 3.8 22.7 - - + +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B VAL* 5.4 3.3 - - + +
36B LYS* 5.7 0.2 - - - +
38B LEU* 4.7 23.3 - - + -
39B ASP* 3.1 36.0 + - - +
92B ILE* 2.9 22.2 + - + +
93B SER* 3.7 23.9 + - - +
94B ASP 3.2 0.4 - - - -
95B ILE* 1.3 79.4 - - - +
97B GLU* 1.3 57.0 + - + +
98B GLU 3.3 0.9 - - - -
100B ASN* 3.9 2.8 - - - -
101B LEU* 3.1 31.2 + - + -
102B GLU* 3.2 52.2 + - + +
105B LEU* 6.4 1.1 - - + -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 3.6 14.2 + - - +
94B ASP* 3.3 11.4 + - - +
95B ILE 3.3 0.4 - - - -
96B LYS* 1.3 77.6 - - + +
98B GLU* 1.3 64.7 + - - +
99B GLY 3.6 1.3 - - - -
100B ASN* 4.2 9.5 + - - +
102B GLU* 5.2 6.7 - - - +
143E GLN* 5.7 5.0 - - - +
147E THR* 4.5 5.4 + - - -
150E ARG* 3.4 44.6 + - - +
----------------------------------------------------------
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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