Contacts of the helix formed by residues 42 - 80 (chain F) in PDB entry 1J1D
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 SER 42 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU* 4.1 4.7 + - - -
41F ILE* 1.3 76.4 - - - +
43F ALA* 1.3 54.0 + - - +
44F SER* 2.9 20.9 + - - -
45F ARG* 2.7 45.6 + - - +
46F LYS 3.2 5.0 + - - -
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Residues in contact with ALA 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 5.0 18.6 - - - +
3D ASP 4.9 1.7 - - - +
6D LYS* 4.7 22.2 - - + +
7D ALA* 3.1 16.9 - - + +
10D GLU* 3.5 22.8 + - - +
41F ILE 2.9 8.3 + - - +
42F SER* 1.3 70.4 - - - +
44F SER* 1.3 58.6 + - - +
45F ARG 3.2 0.4 - - - -
46F LYS* 4.0 20.4 + - + +
47F LEU* 4.1 5.7 + - - +
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Residues in contact with SER 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ALA* 3.7 14.8 + - - -
10D GLU* 2.6 36.3 + - - +
11D GLN* 3.5 19.6 + - - -
42F SER* 2.9 10.2 - - - -
43F ALA* 1.3 77.5 - - - +
45F ARG* 1.3 60.6 + - - +
46F LYS 3.6 0.2 - - - -
47F LEU* 4.1 8.5 + - - +
48F GLN* 3.6 14.8 + - - +
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Residues in contact with ARG 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D GLU* 4.3 5.3 + - - +
127D THR 3.0 29.3 + - - -
128D ILE* 4.2 0.8 - - - +
129D THR* 4.7 4.8 + - - +
132D ASP* 2.7 39.9 + - - -
41F ILE* 4.6 9.4 - - + -
42F SER* 2.7 25.9 + - - +
44F SER* 1.3 77.4 - - - +
46F LYS* 1.3 56.5 + - - +
47F LEU 3.1 1.6 - - - -
48F GLN* 2.5 61.9 + - - +
49F LEU* 2.7 36.4 + - + +
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Residues in contact with LYS 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 3.3 48.0 + - + +
135D GLU* 4.1 24.7 + - + -
136D LEU* 4.4 15.9 - - + +
139D ASP* 3.1 40.6 + - - +
41F ILE* 4.1 19.7 - - + +
42F SER 3.2 8.8 + - - +
43F ALA* 4.1 14.1 - - - +
44F SER 3.6 0.2 - - - -
45F ARG* 1.3 79.7 - - - +
47F LEU* 1.3 54.6 + - - +
49F LEU* 2.8 4.0 + - - +
50F LYS* 2.7 46.2 + - - +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ASP 6.0 0.9 - - - -
4D ILE* 3.9 46.7 - - + +
7D ALA* 4.4 8.5 - - + -
160D VAL* 6.0 7.0 - - + -
43F ALA 4.1 8.6 + - - +
44F SER 4.2 9.9 - - - +
45F ARG 3.1 0.2 - - - -
46F LYS* 1.3 79.0 - - - +
48F GLN* 1.3 58.8 + - - +
50F LYS* 4.5 8.3 - - - -
51F THR* 2.7 44.5 + - - +
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Residues in contact with GLN 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D GLU* 2.9 33.3 + - - +
44F SER 3.6 6.4 + - - +
45F ARG* 2.5 60.2 + - + +
47F LEU* 1.3 76.6 - - - +
49F LEU* 1.3 56.2 + - + -
51F THR* 4.2 1.3 - - - -
52F LEU* 2.9 40.0 + - + +
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Residues in contact with LEU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D LEU* 4.1 14.1 - - + -
124D THR* 4.9 3.5 - - - +
126D GLU* 4.3 20.0 - - + -
128D ILE* 4.9 5.2 - - + -
132D ASP* 3.3 41.7 - - + +
136D LEU* 3.6 26.9 - - + -
41F ILE* 6.4 0.7 - - + -
45F ARG* 2.7 47.7 + - + +
46F LYS* 3.8 4.5 - - - +
48F GLN* 1.3 74.8 - - - +
50F LYS* 1.3 53.1 + - - +
52F LEU* 3.2 5.4 + - + +
53F LEU* 2.6 41.2 + - - +
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Residues in contact with LYS 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP 4.8 4.6 + - - -
3D ASP* 5.6 4.6 - - - +
136D LEU* 3.8 18.4 - - + -
139D ASP* 2.6 31.4 + - - -
156D PHE* 2.9 50.3 + - + +
157D MET* 3.9 22.2 - - + -
160D VAL* 3.6 16.8 - - + -
46F LYS* 2.7 33.3 + - + +
47F LEU* 4.5 4.0 - - - +
49F LEU* 1.3 71.5 - - - +
51F THR* 1.3 63.3 + - - +
53F LEU* 3.3 4.3 + - + +
54F LEU* 3.2 28.4 + - - +
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Residues in contact with THR 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D VAL* 3.5 17.7 - - - +
161D GLU 3.4 19.4 + - - +
47F LEU* 2.7 36.4 + - + +
48F GLN* 4.2 3.1 - - - -
49F LEU 3.3 0.6 - - - -
50F LYS* 1.3 79.4 - - - +
52F LEU* 1.3 64.2 + - + +
54F LEU* 3.4 3.3 + - - +
55F GLN* 3.0 28.1 + - + +
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D THR* 4.2 23.4 - - - +
126D GLU* 3.1 41.5 - - + +
48F GLN* 2.9 32.3 + - + +
49F LEU* 3.2 7.5 + - + +
50F LYS 3.2 0.4 - - - -
51F THR* 1.3 78.5 - - + +
53F LEU* 1.3 64.1 + - - +
54F LEU 3.1 1.8 - - - -
55F GLN* 3.1 32.3 + - - +
56F ILE* 3.0 26.3 + - - +
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D PHE* 3.7 21.6 - - + -
117D LEU* 4.5 9.4 - - + -
120D MET* 3.9 16.6 - - + -
121D LEU* 3.6 54.3 - - + +
124D THR* 3.9 4.0 - - + -
136D LEU* 4.4 9.4 - - + -
156D PHE* 4.8 4.0 - - + -
157D MET* 4.1 17.9 - - + -
49F LEU 2.6 28.3 + - - +
50F LYS* 3.3 10.1 + - - +
52F LEU* 1.3 73.9 - - - +
54F LEU* 1.3 58.3 + - - +
56F ILE* 2.7 21.8 - - + +
57F ALA* 3.3 10.7 + - - +
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Residues in contact with LEU 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LYS* 4.2 22.4 - - + -
97D LEU* 3.9 22.4 - - + -
100D LEU* 4.2 16.4 - - + +
104D PHE* 3.8 26.0 - - + -
153D PHE* 4.2 6.3 - - + -
157D MET* 3.6 32.3 - - + -
160D VAL* 3.8 18.4 - - + -
161D GLU 5.1 1.8 - - - +
50F LYS 3.2 14.6 + - - +
51F THR 3.9 3.6 - - - +
52F LEU 3.1 0.6 - - - -
53F LEU* 1.3 73.8 - - - +
55F GLN* 1.3 61.9 + - - +
56F ILE 3.0 2.0 - - - -
57F ALA* 3.8 3.1 - - - +
58F LYS* 2.9 30.8 + - - +
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Residues in contact with GLN 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LYS* 5.9 1.1 - - - +
51F THR* 3.0 19.4 + - + +
52F LEU* 3.1 37.0 + - - +
54F LEU* 1.3 76.4 - - - +
56F ILE* 1.3 60.6 + - - +
58F LYS* 3.4 8.5 - - + +
59F GLN* 3.3 33.4 + - + +
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Residues in contact with ILE 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D MET* 3.3 23.1 - - + +
123D ALA* 4.5 26.0 - - + +
124D THR* 4.6 10.5 - - + -
52F LEU 3.0 13.8 + - - +
53F LEU* 2.7 33.7 - - - +
55F GLN* 1.3 75.7 - - - +
57F ALA* 1.3 58.6 + - - +
58F LYS 2.9 1.8 - - - -
59F GLN* 2.6 41.9 + - - +
60F GLU* 2.9 45.2 + - + +
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 4.0 14.8 - - + +
103D MET* 3.6 17.6 - - + +
104D PHE* 3.7 16.8 - - + -
120D MET* 3.4 23.6 - - + -
53F LEU 3.3 3.8 + - - +
54F LEU* 3.4 3.6 + - - +
56F ILE* 1.3 89.2 - - - +
58F LYS* 1.3 56.8 + - - +
60F GLU* 3.5 2.5 - - - +
61F LEU* 2.8 30.7 + - - +
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Residues in contact with LYS 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D LYS* 2.9 35.3 - - - +
96D GLU* 3.2 21.4 + - - +
100D LEU* 4.0 19.2 - - + +
54F LEU 2.9 16.6 + - - +
55F GLN* 3.4 11.2 - - + +
56F ILE 2.9 0.2 - - - -
57F ALA* 1.3 74.1 - - - +
59F GLN* 1.3 68.7 + - - +
61F LEU* 3.2 16.7 + - + +
62F GLU* 3.2 14.3 + - + +
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F GLN* 3.3 27.8 + - + +
56F ILE* 2.6 26.4 + - - +
58F LYS* 1.3 77.2 - - - +
60F GLU* 1.3 64.9 + - + +
62F GLU* 3.1 6.8 + - - +
63F ARG* 2.9 21.0 + - - +
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Residues in contact with GLU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D MET* 3.1 29.7 - - + +
106D LYS* 2.7 31.9 + - - -
120D MET* 4.2 0.7 - - - +
123D ALA* 5.4 4.2 - - - +
56F ILE* 2.9 37.4 + - + +
57F ALA* 3.5 7.0 - - - +
59F GLN* 1.3 82.4 - - + +
61F LEU* 1.3 50.8 + - - +
63F ARG* 2.8 16.0 + - - +
64F GLU 2.7 32.1 + - - -
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D GLU* 6.4 0.4 - - + -
99D ASP* 3.5 30.5 - - + +
100D LEU* 4.0 14.8 - - + -
102D ARG* 3.8 22.9 - - - +
103D MET* 3.0 28.7 - - + +
57F ALA 2.8 20.5 + - - +
58F LYS* 3.2 10.5 + - + +
60F GLU* 1.3 70.8 - - - +
62F GLU* 1.3 57.2 + - - +
64F GLU* 3.4 12.9 + - - +
65F ALA* 3.1 25.1 + - - +
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F LYS* 3.2 8.8 + - + +
59F GLN* 3.1 9.9 + - - +
61F LEU* 1.3 76.4 - - - +
63F ARG* 1.3 60.3 + - - +
65F ALA* 3.7 15.2 - - - +
66F GLU* 3.1 33.8 + - - +
69F ARG* 4.3 10.8 + - - -
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Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C SER* 5.2 7.9 + - - -
78C THR* 2.4 36.5 + - - +
81C GLN* 4.8 18.2 - - - +
59F GLN 2.9 12.3 + - - +
60F GLU* 2.8 17.7 + - - +
62F GLU* 1.3 76.8 - - - +
64F GLU* 1.3 65.6 + - - +
66F GLU* 3.1 14.9 + - - +
67F GLU* 2.3 52.4 + - - +
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Residues in contact with GLU 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ARG* 3.3 29.1 + - - -
103D MET* 4.0 15.3 - - + +
256E GLN* 5.6 0.6 + - - -
60F GLU 2.7 11.0 + - - +
61F LEU* 3.5 19.2 - - - +
63F ARG* 1.3 77.2 - - - +
65F ALA* 1.3 55.6 + - - +
67F GLU* 3.2 13.7 + - - +
68F ARG* 2.8 52.4 + - - +
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Residues in contact with ALA 65 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F LEU 3.1 16.6 + - - +
62F GLU* 3.7 20.4 - - - +
63F ARG 3.1 0.2 - - - -
64F GLU* 1.3 73.5 - - - +
66F GLU* 1.3 64.2 + - - +
67F GLU 3.1 1.8 - - - -
68F ARG* 3.1 23.3 + - - +
69F ARG* 2.8 32.8 + - - +
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLU* 3.1 25.4 + - - +
63F ARG* 3.1 7.4 + - + +
65F ALA* 1.3 75.5 - - - +
67F GLU* 1.3 64.1 + - + +
69F ARG* 2.6 42.4 + - - +
70F GLY* 3.3 13.7 + - - -
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Residues in contact with GLU 67 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ARG 5.6 0.5 - - - +
78C THR* 3.9 1.6 + - - -
63F ARG* 2.3 58.9 + - - +
64F GLU* 3.5 12.9 - - - +
65F ALA 3.1 0.2 - - - -
66F GLU* 1.3 78.4 - - + +
68F ARG* 1.3 54.4 + - - +
69F ARG 3.1 0.2 - - - -
70F GLY* 2.7 20.2 + - - +
71F GLU* 2.7 34.5 + - + +
74F ARG* 4.7 2.5 + - - +
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Residues in contact with ARG 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ARG* 5.1 1.4 - - - +
248E PHE* 4.2 6.3 - - + -
252E GLU* 2.8 55.5 + - + +
256E GLN* 5.3 6.4 - - - +
64F GLU* 2.8 52.3 + - - +
65F ALA* 3.3 18.0 - - - +
67F GLU* 1.3 77.0 - - - +
69F ARG* 1.3 65.8 + - - +
71F GLU* 3.3 14.9 + - - +
72F LYS* 2.9 28.8 + - + +
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Residues in contact with ARG 69 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62F GLU* 4.3 13.7 + - - -
65F ALA* 2.8 29.9 + - - +
66F GLU* 2.6 49.8 + - - +
68F ARG* 1.3 79.2 - - - +
70F GLY* 1.3 57.6 + - - +
72F LYS* 3.9 7.2 - - - +
73F GLY* 3.0 24.9 + - - -
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Residues in contact with GLY 70 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F GLU 3.3 6.0 + - - -
67F GLU* 2.7 10.6 + - - -
69F ARG* 1.3 77.5 - - - +
71F GLU* 1.3 64.7 + - - -
73F GLY* 2.9 11.8 + - - -
74F ARG* 2.9 36.9 + - - +
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Residues in contact with GLU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E PHE* 4.0 13.1 - - + -
252E GLU* 4.4 8.7 - - - +
67F GLU* 2.7 33.6 + - + +
68F ARG* 3.7 21.7 + - - +
70F GLY* 1.3 70.7 - - - -
72F LYS* 1.3 57.9 + - - +
74F ARG* 3.2 18.7 + - - +
75F ALA* 2.8 29.6 + - - +
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Residues in contact with LYS 72 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245E ALA* 4.0 30.4 + - - +
248E PHE* 3.2 39.2 - - + -
249E ASP* 2.9 38.8 + - - +
68F ARG* 2.9 14.6 + - + +
69F ARG* 4.0 5.8 - - - +
71F GLU* 1.3 77.2 - - - +
73F GLY* 1.3 58.3 + - - +
75F ALA* 3.6 0.9 - - - +
76F LEU* 3.0 45.9 + - + +
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Residues in contact with GLY 73 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F ARG 3.0 13.2 + - - -
70F GLY 2.9 8.4 + - - -
72F LYS* 1.3 76.6 - - - +
74F ARG* 1.3 63.6 + - - +
76F LEU* 3.6 8.0 + - - +
77F SER* 3.4 18.9 + - - -
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Residues in contact with ARG 74 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLU* 3.7 22.7 - - - +
74C ARG* 3.3 57.5 - - - +
67F GLU* 4.7 2.0 + - - +
70F GLY* 2.9 38.6 + - - -
71F GLU* 3.7 16.1 - - - +
73F GLY* 1.3 74.7 - - - +
75F ALA* 1.3 67.8 + - - +
77F SER* 2.9 20.9 + - - -
78F THR* 3.3 14.0 + - + +
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Residues in contact with ALA 75 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E PHE* 3.9 22.9 - - + -
71F GLU 2.8 17.7 + - - +
72F LYS 3.6 5.8 - - - +
74F ARG* 1.3 77.6 - - - +
76F LEU* 1.3 58.4 + - + +
78F THR* 3.1 10.5 + - - -
79F ARG* 3.0 53.3 + - - +
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Residues in contact with LEU 76 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E TYR* 3.1 46.6 - - + +
244E GLU* 3.7 16.8 - - + +
245E ALA* 3.5 42.6 - - + +
248E PHE* 5.3 2.2 - - + -
72F LYS* 3.0 37.1 + - + +
73F GLY* 4.1 7.0 - - - +
74F ARG 3.3 0.2 - - - -
75F ALA* 1.3 77.3 - - + +
77F SER* 1.3 60.9 + - - +
78F THR 3.3 0.2 - - - -
79F ARG* 5.0 2.0 - - - -
80F ALA* 3.3 29.9 + - + +
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Residues in contact with SER 77 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F GLY 3.4 11.5 + - - -
74F ARG* 2.9 14.1 + - - -
76F LEU* 1.3 78.9 - - - +
78F THR* 1.3 61.8 + - - +
80F ALA 4.8 1.3 - - - -
81F GLN* 3.4 27.7 - - - +
82F PRO* 4.7 5.8 - - - +
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Residues in contact with THR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ARG* 5.8 9.2 - - - -
67C GLU* 5.7 4.7 - - - +
74F ARG* 3.6 13.2 - - + +
75F ALA* 3.1 11.2 + - - -
77F SER* 1.3 81.3 - - - +
79F ARG* 1.3 72.9 + - - +
80F ALA 3.1 2.3 + - - -
81F GLN* 4.0 17.8 + - - +
103F ARG* 5.5 0.9 + - - -
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Residues in contact with ARG 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240E ILE* 5.0 0.3 - - - +
244E GLU* 3.3 47.4 + - + +
247E LYS* 4.6 9.3 - - - +
248E PHE* 4.4 23.4 - - - +
251E GLN* 3.3 31.4 + - - +
75F ALA* 3.0 33.6 + - - +
76F LEU* 5.0 0.7 - - - -
78F THR* 1.3 86.1 + - - +
80F ALA* 1.3 59.7 + - - +
81F GLN 3.9 0.2 - - - -
103F ARG* 3.1 23.6 + - - -
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Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237E TRP* 3.2 21.6 - - + +
240E ILE* 4.7 9.4 - - + -
241E TYR* 4.4 29.7 - - + -
244E GLU* 4.8 7.9 - - + -
76F LEU 3.3 21.8 + - - +
78F THR 3.1 0.2 - - - -
79F ARG* 1.3 82.2 - - - +
81F GLN* 1.3 65.2 + - - +
82F PRO* 3.3 2.9 - - - +
103F ARG* 4.6 6.5 - - - +
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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