Contacts of the helix formed by residues 114 - 143 (chain F) in PDB entry 1NU9
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 THR 114 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F SER 2.8 28.6 + - - +
17F LYS 3.9 7.6 - - - +
19F GLY* 3.5 24.5 - - - +
20F THR 3.4 22.7 - - - +
21F LEU* 4.1 3.8 - - + -
22F ILE* 4.0 3.8 - - - -
113F LEU* 1.3 79.9 - - - +
115F MET* 1.3 66.2 + - - +
116F ARG* 3.4 5.7 + - - +
117F GLU* 2.9 40.1 + - - +
118F TYR* 3.0 13.5 + - - +
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Residues in contact with MET 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LYS* 3.3 31.2 - - - +
94C GLU* 6.0 0.2 - - - +
20F THR 4.3 2.6 + - - -
22F ILE* 3.9 26.0 - - + +
26F TYR* 4.0 18.6 - - + +
30F ARG* 4.7 3.1 - - - +
114F THR* 1.3 74.2 - - - +
116F ARG* 1.3 64.4 + - - +
118F TYR* 3.6 28.0 - - + +
119F ASN* 2.8 46.4 + - - +
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Residues in contact with ARG 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F ASN* 5.8 2.2 - - - +
15F ASN* 5.6 1.8 + - - +
16F SER* 3.2 27.6 + - - +
19F GLY* 6.0 2.0 - - - -
114F THR* 3.0 11.2 + - - +
115F MET* 1.3 80.0 - - - +
117F GLU* 1.3 61.5 + - - +
119F ASN* 3.9 5.4 - - - +
120F GLU* 2.9 52.0 + - - +
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Residues in contact with GLU 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 4.5 5.6 - - + +
16F SER* 3.9 17.5 - - - -
17F LYS* 3.3 19.1 - - - +
21F LEU* 5.6 0.3 - - - +
72F TYR* 2.4 33.2 + - + +
76F ARG* 3.3 13.7 + - - -
112F ASP 4.2 1.7 - - - +
113F LEU* 3.2 26.4 - - + +
114F THR* 2.9 45.5 + - - +
116F ARG* 1.3 75.4 - - - +
118F TYR* 1.3 64.1 + - - +
120F GLU* 3.2 1.4 + - - +
121F LEU* 2.9 36.1 + - + +
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Residues in contact with TYR 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE* 5.1 0.4 - - + -
30F ARG* 3.0 59.5 + - + -
33F SER* 2.7 24.3 + - - -
34F LEU* 3.8 20.9 - - + -
37F GLN* 3.5 6.9 + - - -
113F LEU* 4.2 10.9 - - + +
114F THR 3.0 11.5 + - - +
115F MET* 3.6 24.7 - - + +
117F GLU* 1.3 77.9 - - - +
119F ASN* 1.3 75.6 + - - +
121F LEU* 3.3 7.8 + - - +
122F THR* 2.8 54.0 + - + +
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Residues in contact with ASN 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F MET* 2.8 40.8 + - - +
116F ARG* 4.0 5.4 - - - +
118F TYR* 1.3 94.7 - - - +
120F GLU* 1.3 60.1 + - + +
122F THR* 3.4 4.7 + - - +
123F GLU* 2.8 37.7 + - + +
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Residues in contact with GLU 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ARG* 4.9 4.3 - - - +
12F VAL* 3.2 18.3 - - + +
13F ASN* 2.7 43.1 + - - +
16F SER* 2.6 23.6 + - - -
116F ARG* 2.9 44.7 + - - +
117F GLU 3.8 2.9 - - - +
119F ASN* 1.3 76.5 - - + +
121F LEU* 1.3 59.8 + - - +
123F GLU* 3.8 4.5 - - - +
124F SER* 2.8 31.7 + - - -
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 3.8 12.8 - - + -
34F LEU* 3.8 22.2 - - + -
37F GLN* 4.8 0.4 - - - -
38F PHE* 5.0 0.7 - - + -
69F GLU* 3.4 46.6 - - + +
72F TYR* 4.0 13.2 - - + -
73F LEU* 3.5 36.3 - - + -
113F LEU* 4.7 1.1 - - + -
117F GLU* 2.9 27.4 + - + +
118F TYR 3.7 3.4 - - - +
120F GLU* 1.3 75.4 - - - +
122F THR* 1.3 64.2 + - - +
124F SER* 3.2 5.7 + - - -
125F LEU* 3.0 31.6 + - + +
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Residues in contact with THR 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 4.1 0.9 - - - +
37F GLN* 3.0 41.9 + - - +
118F TYR* 2.8 41.7 + - + +
119F ASN* 3.6 7.6 - - - +
121F LEU* 1.3 77.6 - - - +
123F GLU* 1.3 66.4 + - - +
125F LEU 3.5 0.3 + - - -
126F LYS* 3.0 46.8 + - - +
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Residues in contact with GLU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ASN* 2.8 26.8 + - + +
120F GLU* 4.1 4.5 - - - +
122F THR* 1.3 73.9 - - - +
124F SER* 1.3 61.9 + - - +
126F LYS* 3.5 36.4 + - - +
127F SER* 2.9 32.2 + - - -
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Residues in contact with SER 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ARG* 3.0 13.7 - - - +
65F ARG* 2.9 32.2 + - - +
69F GLU* 2.6 35.9 + - - +
120F GLU 2.8 20.3 + - - -
121F LEU 3.5 4.0 - - - -
123F GLU* 1.3 80.3 - - - +
125F LEU* 1.3 58.5 + - - +
127F SER* 3.2 0.8 + - - -
128F ALA* 2.8 25.5 + - - +
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Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F LEU* 5.5 2.5 - - + -
37F GLN* 3.8 36.3 - - + +
38F PHE* 3.9 46.7 - - + +
41F ALA* 4.9 9.0 - - + -
65F ARG 4.6 1.1 - - - +
66F ILE* 4.1 26.5 - - + +
69F GLU* 4.1 15.9 - - + -
121F LEU 3.0 19.1 + - - +
122F THR 4.0 2.7 - - - +
124F SER* 1.3 73.7 - - - +
126F LYS* 1.3 58.6 + - - +
128F ALA* 3.0 7.3 + - + +
129F VAL* 2.9 35.6 + - + +
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Residues in contact with LYS 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F GLN* 5.6 0.4 - - - -
122F THR* 3.0 34.1 + - - +
123F GLU* 3.5 35.3 + - - +
125F LEU* 1.3 77.2 - - - +
127F SER* 1.3 58.9 + - - +
129F VAL* 3.3 7.2 + - - +
130F LYS* 2.9 42.4 + - - +
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Residues in contact with SER 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ARG* 4.0 13.9 + - - -
123F GLU 2.9 19.0 + - - -
124F SER* 3.5 4.5 - - - -
126F LYS* 1.3 76.8 - - - +
128F ALA* 1.3 63.4 + - - +
130F LYS* 3.3 8.1 + - - +
131F ASP* 3.0 33.0 + - - +
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F LEU* 3.8 16.9 - - + +
65F ARG* 3.6 44.1 - - + +
66F ILE* 5.3 0.4 - - + +
124F SER 2.8 13.6 + - - +
125F LEU* 3.0 13.9 + - + +
127F SER* 1.3 77.0 - - - +
129F VAL* 1.3 62.8 + - - +
131F ASP* 3.3 5.6 + - - +
132F PHE* 3.0 21.0 + - - +
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Residues in contact with VAL 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F ASN* 5.2 4.5 - - - +
41F ALA* 4.2 28.3 - - + -
44F ILE* 3.9 25.6 - - + -
62F LEU* 4.3 9.4 - - + -
125F LEU* 2.9 21.4 + - + +
126F LYS* 3.7 6.3 - - - +
128F ALA* 1.3 75.0 - - - +
130F LYS* 1.3 64.6 + - - +
132F PHE* 3.0 10.0 + - + +
133F GLU* 2.8 44.9 + - + +
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Residues in contact with LYS 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F LYS* 2.9 29.9 + - - +
127F SER* 3.5 9.6 - - - +
128F ALA 3.3 0.2 - - - -
129F VAL* 1.3 77.0 - - - +
131F ASP* 1.3 65.2 + - - +
133F GLU* 3.2 23.4 + - + +
134F LYS* 3.0 22.1 + - - +
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Residues in contact with ASP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F LYS* 4.8 17.9 - - + +
65F ARG* 3.7 17.8 + - - -
127F SER* 3.0 26.1 + - - +
128F ALA* 3.7 5.8 - - - +
130F LYS* 1.3 78.1 - - - +
132F PHE* 1.3 53.5 + - - +
134F LYS* 3.1 8.8 + - - +
135F ASP* 2.8 43.3 + - - +
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Residues in contact with PHE 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ILE* 4.0 20.2 - - + -
45F LEU* 4.8 2.2 - - - -
50F TYR* 3.9 32.1 - + + -
55F TYR* 5.4 0.9 - + + -
58F ALA* 3.4 42.4 - - + -
59F LYS* 3.7 24.5 - - + -
61F LYS* 5.7 1.7 - - - +
62F LEU* 3.5 31.4 - - + -
128F ALA 3.0 12.4 + - - +
129F VAL* 3.0 11.7 + - + +
131F ASP* 1.3 76.9 - - - +
133F GLU* 1.3 61.7 + - + +
135F ASP* 3.2 6.8 + - - +
136F VAL* 2.8 50.5 + - + +
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Residues in contact with GLU 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ILE* 4.9 7.9 - - + +
50F TYR* 6.1 0.7 - - - +
129F VAL* 2.8 35.8 + - + +
130F LYS* 3.6 29.4 + - + +
132F PHE* 1.3 79.9 - - + +
134F LYS* 1.3 64.7 + - - +
136F VAL* 3.8 7.3 - - - +
137F GLU* 3.0 24.1 + - - +
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Residues in contact with LYS 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F LYS 3.0 13.3 + - - +
131F ASP* 3.1 11.6 + - - +
133F GLU* 1.3 75.7 - - - +
135F ASP* 1.3 67.4 + - - +
137F GLU* 3.2 18.7 + - - +
138F ILE* 3.1 45.5 + - + +
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Residues in contact with ASP 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F ALA* 3.8 23.9 - - + -
61F LYS* 3.0 43.4 + - - +
131F ASP* 2.8 21.4 + - - +
132F PHE* 3.5 6.8 - - - +
134F LYS* 1.3 82.4 - - - +
136F VAL* 1.3 61.4 + - - +
138F ILE* 3.2 14.6 + - - +
139F ILE* 3.0 29.1 + - + +
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Residues in contact with VAL 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F TYR* 3.6 32.3 - - + +
55F TYR* 3.9 12.6 - - + -
58F ALA* 5.1 0.2 - - + -
132F PHE* 2.8 44.1 + - + +
133F GLU* 3.8 7.2 - - - +
135F ASP* 1.3 76.6 - - - +
137F GLU* 1.3 59.3 + - - +
139F ILE* 3.1 10.8 + - + +
140F GLU* 2.9 56.2 + - - +
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Residues in contact with GLU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLU 3.0 17.2 + - - +
134F LYS* 3.2 20.3 + - - +
136F VAL* 1.3 80.5 - - - +
138F ILE* 1.3 57.0 + - + +
140F GLU* 3.5 7.9 + - - +
141F ASN* 2.7 44.5 + - - +
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Residues in contact with ILE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F LYS* 3.1 42.8 + - + +
135F ASP* 3.6 13.9 - - - +
137F GLU* 1.3 76.1 - - + +
139F ILE* 1.3 69.9 + - + +
141F ASN* 3.2 17.8 + - - +
142F GLN* 3.4 17.1 + - + +
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Residues in contact with ILE 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLU* 3.1 48.2 - - + +
55F TYR* 3.6 31.0 - - + -
58F ALA* 4.0 17.0 - - + -
135F ASP* 3.0 21.4 + - + +
136F VAL 3.4 6.1 - - - +
138F ILE* 1.3 77.9 - - + +
140F GLU* 1.3 57.3 + - - +
142F GLN* 3.2 5.8 + - - -
143F HIS* 3.1 33.6 + - + +
146F LEU* 4.0 14.1 - - + -
----------------------------------------------------------
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Residues in contact with GLU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F HIS* 3.2 14.2 + - - -
50F TYR* 4.2 0.9 - - - -
55F TYR* 2.6 30.3 + - - +
136F VAL* 2.9 37.2 + - - +
137F GLU* 4.0 7.2 - - - +
138F ILE 3.2 0.2 - - - -
139F ILE* 1.3 75.5 - - - +
141F ASN* 1.3 61.8 + - - +
143F HIS 3.5 20.1 - - - +
144F HIS* 4.0 5.7 + - - -
146F LEU* 3.6 17.3 - - + +
147F LYS* 4.0 27.2 - - + +
148F PRO* 3.1 20.4 - - - +
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Residues in contact with ASN 141 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F GLU* 2.7 36.5 + - - +
138F ILE* 3.2 9.4 + - - +
139F ILE 3.2 1.0 - - - -
140F GLU* 1.3 77.5 - - - +
142F GLN* 1.3 58.4 + - - +
143F HIS 3.5 0.4 - - - -
144F HIS* 3.0 27.7 - - + -
147F LYS* 5.2 11.0 + - - +
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Residues in contact with GLN 142 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138F ILE* 3.4 13.9 + - + +
139F ILE* 3.2 9.2 + - - +
141F ASN* 1.3 81.8 - - - +
143F HIS* 1.3 81.4 + - + +
144F HIS* 3.9 3.0 + - - -
----------------------------------------------------------
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Residues in contact with HIS 143 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLU* 3.5 39.6 + - + +
139F ILE* 3.1 26.7 + - + +
140F GLU 3.5 9.3 - - - +
141F ASN 3.5 0.2 - - - -
142F GLN* 1.3 103.5 + - + +
144F HIS* 1.3 59.1 + - - +
145F ASP* 3.1 16.7 + - - +
146F LEU* 2.8 34.4 + - + +
209F ARG* 5.0 1.2 + - - -
----------------------------------------------------------
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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