Contacts of the helix formed by residues 59 - 86 (chain H) in PDB entry 1DPS
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 PHE 59 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H HIS 4.4 1.1 - - - -
54H MET* 3.2 42.8 - - + +
55H ARG 4.2 0.2 - - - -
56H GLY 3.2 10.8 + - - +
57H ALA 3.3 0.2 - - - -
58H ASN* 1.3 76.8 - - - +
60H ILE* 1.3 79.7 + - + +
62H VAL* 3.7 1.5 - - - +
63H HIS* 2.8 68.0 + + + +
114H VAL* 4.1 7.9 - - + -
160K TRP* 4.2 9.4 - + - -
161K PHE* 3.7 31.4 - + - -
164K CYS* 3.3 42.4 - - + +
165K ASN* 3.6 18.0 + - - +
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Residues in contact with ILE 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H PHE* 1.3 84.5 - - + +
61H ALA* 1.3 60.4 + - - +
63H HIS* 3.3 3.5 + - + +
64H GLU* 3.0 60.3 + - + +
58K ASN* 4.7 3.4 - - - +
61K ALA* 3.9 32.1 - - + +
62K VAL* 4.7 1.8 - - + +
65K MET* 4.1 17.5 - - + -
161K PHE* 3.5 44.9 - - + -
165K ASN* 3.4 26.6 + - - +
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Residues in contact with ALA 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.7 24.3 - - + +
61A ALA* 4.1 19.3 - - + -
58H ASN* 3.7 15.2 + - - +
59H PHE 3.5 0.4 - - - -
60H ILE* 1.3 82.5 - - - +
62H VAL* 1.3 57.5 + - - +
64H GLU* 3.6 7.5 + - - +
65H MET* 2.9 30.0 + - - +
61K ALA* 4.2 10.1 - - + -
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Residues in contact with VAL 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 4.8 1.1 - - + -
54H MET* 3.7 27.8 - - + -
58H ASN* 3.3 41.1 + - + +
59H PHE 3.9 1.6 - - - +
60H ILE 3.3 0.6 - - - -
61H ALA* 1.3 75.4 - - - +
63H HIS* 1.3 66.8 + - - +
65H MET* 3.2 10.1 + - + +
66H LEU* 3.0 32.7 + - + +
114H VAL* 4.4 11.2 - - + -
118H LEU* 4.1 16.8 - - + -
165H ASN* 4.2 22.0 - - + +
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Residues in contact with HIS 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F GLU* 4.6 7.2 + - - -
51H HIS* 2.7 81.4 + + - -
52H TRP* 4.5 2.2 - + - -
54H MET* 4.1 8.2 - - - -
59H PHE* 2.8 45.4 + + + +
60H ILE* 3.5 5.4 - - + +
62H VAL* 1.3 75.9 - - - +
64H GLU* 1.3 69.4 + - + +
66H LEU* 3.5 1.0 + - - +
67H ASP 3.4 7.3 + - - -
160K TRP* 3.9 23.2 - + - -
161K PHE* 4.1 23.1 - + - -
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Residues in contact with GLU 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ILE* 3.0 48.7 + - + +
61H ALA* 4.1 5.5 - - - +
63H HIS* 1.3 79.1 - - + +
65H MET* 1.3 66.8 + - - +
67H ASP* 3.2 17.1 + - - +
68H GLY* 3.3 9.5 + - - -
161K PHE* 5.0 3.7 - - + -
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Residues in contact with MET 65 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.9 25.4 - - + -
61H ALA 2.9 18.9 + - - +
62H VAL* 3.5 14.4 - - + +
64H GLU* 1.3 76.7 - - - +
66H LEU* 1.3 76.7 + - + +
68H GLY* 3.1 12.5 + - - -
69H PHE* 3.2 51.0 + - + -
118H LEU* 4.9 2.2 - - + -
161H PHE* 4.0 14.6 - - + +
162H ILE* 4.3 12.6 - - + -
165H ASN* 3.7 28.5 - - - +
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Residues in contact with LEU 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H THR* 3.2 22.8 - - + +
48H LYS* 5.6 0.2 - - - -
51H HIS* 3.9 22.0 - - + +
54H MET* 3.5 31.4 - - + -
62H VAL* 3.0 23.3 + - + +
63H HIS 3.9 4.5 - - - +
64H GLU 3.3 0.2 - - - -
65H MET* 1.3 82.4 - - + +
67H ASP* 1.3 65.4 + - - +
69H PHE* 3.2 28.8 + - + +
70H ARG* 3.1 18.5 + - - +
118H LEU* 5.6 0.7 - - + -
121H LEU* 3.6 27.4 - - + -
125H TYR* 4.9 1.6 - - + +
162H ILE* 4.6 6.7 - - + -
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Residues in contact with ASP 67 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ASP* 4.4 0.7 - - - +
48H LYS* 2.9 34.6 + - - +
51H HIS* 3.9 18.5 + - + -
63H HIS 3.4 4.3 + - - +
64H GLU* 3.2 13.2 + - - +
66H LEU* 1.3 77.2 - - - +
68H GLY* 1.3 63.6 + - - +
70H ARG* 3.2 19.1 + - - +
71H THR* 3.3 18.5 + - - -
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Residues in contact with GLY 68 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H GLU 3.3 5.7 + - - -
65H MET* 3.1 8.9 + - - -
67H ASP* 1.3 82.4 + - - +
69H PHE* 1.3 62.6 + - - +
71H THR* 3.3 10.3 + - - -
72H ALA* 3.3 19.9 + - - +
158H PHE* 5.5 0.4 - - - -
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Residues in contact with PHE 69 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65H MET* 3.2 39.2 + - + -
66H LEU* 3.2 20.8 + - + +
68H GLY* 1.3 77.5 - - - +
70H ARG* 1.3 63.3 + - - +
72H ALA* 3.1 4.3 + - - +
73H LEU* 2.9 27.0 + - - +
125H TYR* 3.5 28.0 - + - +
158H PHE* 3.4 62.1 - + + -
161H PHE* 3.8 21.8 - + + -
162H ILE* 3.8 24.9 - - + -
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Residues in contact with ARG 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F ILE* 4.0 34.4 - - - +
75F ASP* 5.1 3.2 + - - -
77F LEU* 5.9 2.2 - - - +
78F ASP* 3.0 28.9 + - - -
44H SER* 3.8 26.4 + - - +
47H THR* 4.3 7.4 - - + +
48H LYS* 3.5 36.3 - - + +
66H LEU 3.1 9.9 + - - +
67H ASP* 3.2 13.0 + - - +
69H PHE* 1.3 79.1 - - - +
71H THR* 1.3 69.0 + - - +
73H LEU* 3.2 11.4 + - - +
74H ILE* 3.1 45.9 + - - +
----------------------------------------------------------
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Residues in contact with THR 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H ASP* 3.3 14.8 + - - -
68H GLY* 3.3 12.6 + - - -
69H PHE 3.3 0.2 - - - -
70H ARG* 1.3 84.9 + - - +
72H ALA* 1.3 62.5 + - - +
74H ILE* 3.4 14.3 + - + +
75H ASP* 3.2 32.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H GLY 3.3 6.5 + - - +
69H PHE 3.1 4.3 + - - +
71H THR* 1.3 78.6 - - - +
73H LEU* 1.3 63.1 + - - +
75H ASP* 3.2 8.4 + - - +
76H HIS* 3.0 31.3 + - + -
154H ASP* 4.0 12.1 - - - +
158H PHE* 3.4 32.8 - - + -
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Residues in contact with LEU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H PHE* 3.9 19.7 - - + +
43H LEU* 4.1 17.7 - - + -
44H SER* 3.8 37.0 - - - +
47H THR* 3.9 4.3 - - - +
69H PHE 2.9 19.7 + - - +
70H ARG* 3.2 7.2 + - - +
72H ALA* 1.3 77.5 - - - +
74H ILE* 1.3 57.3 + - - +
76H HIS* 3.3 5.3 + - + +
77H LEU* 3.0 31.5 + - - +
125H TYR* 3.6 21.5 - - + +
155H LEU* 3.7 30.7 - - + -
158H PHE* 4.5 11.2 - - + -
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Residues in contact with ILE 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ARG* 4.0 31.6 - - - +
74F ILE* 3.8 28.9 - - + -
44H SER* 4.0 19.3 - - - +
70H ARG* 3.1 34.3 + - - +
71H THR* 3.4 17.3 - - + +
73H LEU* 1.3 75.5 - - - +
75H ASP* 1.3 65.7 + - - +
77H LEU* 3.6 13.7 - - + +
78H ASP* 3.1 29.8 + - - +
----------------------------------------------------------
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Residues in contact with ASP 75 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F ARG* 5.2 1.7 + - - -
71H THR* 3.2 24.6 + - - +
72H ALA* 3.2 12.2 + - - +
74H ILE* 1.3 81.4 - - - +
76H HIS* 1.3 66.6 + - + +
78H ASP* 3.4 8.8 + - - +
79H THR* 3.0 27.4 + - - -
----------------------------------------------------------
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Residues in contact with HIS 76 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H PHE* 3.9 18.4 - + + -
72H ALA* 3.0 29.0 + - + +
73H LEU* 3.8 5.8 - - - +
75H ASP* 1.3 77.5 - - + +
77H LEU* 1.3 62.3 + - - +
79H THR* 3.3 9.8 + - - -
80H MET* 3.1 27.0 + - + +
147H ILE* 4.9 4.5 + - - +
150H ALA* 3.6 31.7 - - + +
151H ALA* 3.6 23.4 + - + +
154H ASP* 2.8 36.6 + - + +
155H LEU* 5.4 2.0 - - + -
158H PHE* 5.6 0.4 - + - -
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Residues in contact with LEU 77 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F TRP* 3.9 17.3 - - + -
70F ARG* 5.7 2.5 - - - +
37H VAL* 4.0 13.3 - - + +
40H PHE* 3.7 22.2 - - + +
41H ILE* 3.7 47.1 - - + +
44H SER* 4.8 0.2 - - - +
73H LEU 3.0 21.5 + - - +
74H ILE* 3.6 24.7 - - + +
76H HIS* 1.3 72.7 - - - +
78H ASP* 1.3 73.6 + - - +
80H MET* 3.3 10.9 + - - +
81H ALA* 2.9 29.5 + - - +
----------------------------------------------------------
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Residues in contact with ASP 78 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 2.9 31.8 + - - +
52F TRP* 3.2 29.1 + - - +
67F ASP* 4.6 0.3 - - - +
70F ARG* 2.9 19.5 + - - -
74H ILE 3.1 21.4 + - - +
75H ASP* 3.7 9.0 - - - +
77H LEU* 1.3 81.2 - - - +
79H THR* 1.3 56.4 + - - +
81H ALA* 3.3 1.4 + - - +
82H GLU* 2.9 44.7 + - - +
----------------------------------------------------------
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Residues in contact with THR 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75H ASP* 3.0 13.9 + - - +
76H HIS* 3.4 12.0 - - - -
78H ASP* 1.3 79.5 - - - +
80H MET* 1.3 56.2 + - - +
82H GLU* 3.5 11.3 + - - +
83H ARG* 3.1 26.3 + - - +
147H ILE* 3.8 22.1 - - + +
153J ARG* 3.5 28.8 + - - +
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Residues in contact with MET 80 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LEU* 3.7 25.8 - - + +
36H GLN* 3.6 31.9 - - + -
37H VAL* 4.0 11.0 - - + -
40H PHE* 3.8 22.0 - - + -
76H HIS* 3.1 19.4 + - + +
77H LEU* 3.6 13.0 - - - +
78H ASP 3.2 0.2 - - - -
79H THR* 1.3 74.2 - - - +
81H ALA* 1.3 64.5 + - - +
83H ARG* 3.3 4.9 + - - +
84H ALA* 3.1 19.6 + - - +
132H VAL* 4.8 0.4 - - + -
147H ILE* 3.8 18.2 - - + -
148H LEU* 3.9 16.2 - - + -
151H ALA* 3.5 31.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F TRP* 3.4 45.5 - - + +
37H VAL* 4.0 10.7 - - + +
77H LEU 2.9 14.7 + - - +
78H ASP 3.7 0.2 - - - +
80H MET* 1.3 75.4 - - - +
82H GLU* 1.3 63.5 + - - +
84H ALA* 3.1 7.6 + - - +
85H VAL* 3.1 25.6 + - - +
91H ALA* 3.7 14.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 82 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 5.7 0.3 + - - -
51F HIS* 4.7 7.4 + - - -
52F TRP* 4.4 11.6 - - + -
63F HIS* 4.7 8.7 + - + -
78H ASP* 2.9 29.8 + - - +
79H THR* 3.8 9.0 - - - +
81H ALA* 1.3 76.4 - - - +
83H ARG* 1.3 61.3 + - - +
85H VAL* 3.2 10.5 - - - +
86H GLN* 3.0 41.0 + - - +
157J LYS* 4.0 24.3 + - - +
160J TRP* 3.8 22.8 - - + -
161J PHE* 5.9 0.6 - - - -
----------------------------------------------------------
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Residues in contact with ARG 83 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H ASN* 4.8 1.2 - - - +
33H LEU* 3.7 10.3 - - + -
79H THR 3.1 14.6 + - - +
80H MET* 3.6 8.1 - - - +
81H ALA 3.2 0.2 - - - -
82H GLU* 1.3 77.3 - - - +
84H ALA* 1.3 62.8 + - - +
86H GLN* 3.2 18.7 + - - +
87H LEU* 3.1 42.8 + - + +
141H ASP* 3.0 36.6 + - - -
143H ASP* 3.2 28.0 + - - +
144H THR* 3.5 17.0 + - - +
147H ILE* 3.7 23.8 - - + -
133J ARG* 4.1 5.3 - - - +
152J SER 4.9 0.2 + - - -
153J ARG* 5.0 3.8 - - - +
156J ASP* 2.8 40.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 84 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H VAL* 3.5 25.7 - - + +
33H LEU* 3.6 22.6 - - + +
34H ASN* 4.8 4.3 - - - +
80H MET 3.1 12.7 + - - +
81H ALA* 3.1 13.0 + - - +
83H ARG* 1.3 76.2 - - - +
85H VAL* 1.3 58.5 - - - +
87H LEU* 3.4 7.0 + - - -
89H GLY* 2.9 23.3 + - - -
91H ALA* 4.7 14.4 - - + +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F TRP* 3.6 14.8 - - + +
53F ASN* 3.3 27.1 - - - +
55F ARG* 4.2 15.2 + - - +
81H ALA 3.1 13.3 + - - +
82H GLU* 3.2 17.5 - - - +
84H ALA* 1.3 72.2 - - - +
86H GLN* 1.3 65.8 + - - +
87H LEU 3.2 0.7 - - - -
88H GLY* 3.0 14.2 + - - -
89H GLY 3.6 14.5 - - - +
91H ALA* 3.8 13.9 - - + +
160J TRP* 3.3 37.3 - - + +
----------------------------------------------------------
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Residues in contact with GLN 86 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H THR* 3.9 17.7 + - - +
19H ASN* 4.2 11.4 + - - +
82H GLU* 3.0 32.7 + - - +
83H ARG* 3.5 38.0 + - - +
85H VAL* 1.3 77.1 - - - +
87H LEU* 1.3 59.8 + - + +
88H GLY 3.2 3.3 + - - -
153J ARG 4.7 2.3 - - - +
156J ASP* 3.9 7.1 - - + +
157J LYS* 3.7 26.9 + - - +
160J TRP* 3.4 53.8 - - + +
----------------------------------------------------------
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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