Contacts of the helix formed by residues 118 - 150 (chain F) in PDB entry 1NF4
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 ASP 118 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F LYS* 6.0 0.2 - - - -
12F VAL* 3.6 27.4 - - + +
66F ARG* 3.2 18.0 + - - -
70F LEU* 4.0 8.3 - - - +
113F CYS* 2.6 21.3 + - - +
114F LYS* 4.5 0.6 + - - +
116F GLN 4.5 2.2 - - - +
117F GLY* 1.3 71.5 - - - +
119F ILE* 1.3 56.5 + - - +
120F VAL* 3.4 3.1 + - - +
121F THR* 2.7 40.7 + - - -
122F ALA* 3.0 28.0 + - - +
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Residues in contact with ILE 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LYS* 5.6 8.3 - - + +
117F GLY* 3.7 8.1 + - - +
118F ASP* 1.3 73.2 + - - +
120F VAL* 1.3 64.2 + - - +
122F ALA* 3.3 8.4 + - + +
123F ARG* 2.9 22.5 + - - +
107P SER* 3.6 36.3 + - - +
110P LEU* 4.2 20.2 - - + -
114P LYS* 5.1 8.5 - - - +
126P GLU* 4.0 28.8 - - + +
129P ILE* 4.2 29.6 - - + -
130P GLU* 6.0 1.1 - - + -
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Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ARG* 3.7 34.8 - - - +
69F GLU* 5.1 0.9 - - - +
118F ASP* 3.3 2.0 + - - +
119F ILE* 1.3 76.3 - - - +
121F THR* 1.3 63.2 + - - +
123F ARG* 3.2 4.7 + - - +
124F LEU* 3.0 22.1 + - + +
127F ARG* 4.9 2.0 + - - +
103P ILE* 5.6 3.1 - - + -
129P ILE* 3.9 25.1 - - + +
130P GLU* 4.3 23.6 - - + +
133P GLN* 4.1 33.7 - - + +
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Residues in contact with THR 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F VAL* 3.6 13.5 - - + +
16F LEU* 3.7 29.2 - - + -
66F ARG* 2.8 26.1 + - + +
70F LEU* 4.1 0.3 - - - +
113F CYS* 3.5 21.1 - - - -
118F ASP* 2.7 33.8 + - - -
120F VAL* 1.3 73.5 - - - +
122F ALA* 1.3 66.8 + - - +
124F LEU* 3.2 7.5 + - + +
125F PHE* 3.1 22.5 + - + -
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Residues in contact with ALA 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU* 3.4 22.6 - - + +
113F CYS* 3.7 18.0 - - + +
114F LYS* 4.0 22.4 - - + -
118F ASP 3.0 18.2 + - - +
119F ILE* 3.3 8.0 + - + +
121F THR* 1.3 77.5 - - - +
123F ARG* 1.3 60.3 + - - +
125F PHE 3.4 1.4 + - - +
126F GLU* 3.1 19.8 + - - +
126P GLU* 5.5 0.7 - - - +
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Residues in contact with ARG 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119F ILE* 2.9 17.0 + - + +
120F VAL 3.7 4.3 - - - +
121F THR 3.2 0.4 - - - -
122F ALA* 1.3 72.7 - - - +
124F LEU* 1.3 65.4 + - - +
126F GLU* 3.2 35.2 + - - +
127F ARG* 2.9 66.9 + - - +
130F GLU* 4.8 2.2 + - - -
123K ARG* 3.7 19.7 - - - +
123P ARG* 3.5 33.2 - - - +
126P GLU* 3.1 28.9 + - + +
130P GLU* 3.3 32.1 + - - +
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F LEU* 4.4 4.0 - - + -
62F ASN* 3.8 36.6 - - + +
63F PHE* 4.0 19.1 - - + -
66F ARG* 4.0 22.2 - - + -
120F VAL* 3.0 14.6 + - + +
121F THR* 3.2 9.8 + - + +
123F ARG* 1.3 78.3 - - - +
125F PHE* 1.3 62.5 + - - +
127F ARG* 3.4 29.1 + - - +
128F ILE* 3.0 40.9 + - + +
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Residues in contact with PHE 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F VAL* 4.1 8.5 - - + -
16F LEU* 3.7 24.7 - - + -
19F ALA* 3.7 23.3 - - + -
63F PHE* 3.7 24.5 - + - -
106F TYR* 4.0 28.9 - + + +
109F PHE* 3.6 26.5 - + + -
110F LEU* 3.8 20.4 - - + -
113F CYS* 3.8 23.3 - - - -
121F THR* 3.1 23.7 + - + -
122F ALA 3.7 7.2 - - - +
124F LEU* 1.3 76.7 - - + +
126F GLU* 1.3 53.1 + - - +
128F ILE* 3.3 3.5 + - - +
129F ILE* 2.7 40.6 + - + +
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Residues in contact with GLU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F LEU* 3.5 14.1 - - + +
122F ALA 3.1 15.9 + - - +
123F ARG* 3.2 41.7 + - - +
125F PHE* 1.3 77.5 - - - +
127F ARG* 1.3 62.4 + - - +
129F ILE* 3.3 3.0 + - - +
130F GLU* 3.2 27.6 + - + +
119K ILE* 4.4 18.4 - - + +
122K ALA* 6.1 0.2 - - - +
123K ARG* 3.7 33.2 + - + +
126K GLU* 4.3 7.3 - - - +
126P GLU* 3.5 11.3 - - - +
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Residues in contact with ARG 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ASN* 6.0 1.6 - - - +
120F VAL* 4.9 2.0 + - - +
123F ARG* 2.9 55.8 + - - +
124F LEU* 3.6 39.9 - - - +
126F GLU* 1.3 75.5 - - - +
128F ILE* 1.3 64.0 + - + +
130F GLU* 3.4 11.2 + - - +
131F GLU* 3.3 25.9 + - - +
130P GLU* 4.0 21.0 + - - -
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Residues in contact with ILE 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F HIS* 3.6 38.4 - - + +
62F ASN* 4.5 5.4 - - - +
63F PHE* 3.5 31.2 - - + -
106F TYR* 3.8 21.3 - - + -
124F LEU* 3.0 36.0 + - + +
125F PHE* 3.8 3.4 - - - +
127F ARG* 1.3 80.6 - - + +
129F ILE* 1.3 62.1 + - - +
131F GLU* 3.0 11.0 + - - +
132F GLU* 2.9 39.9 + - - +
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Residues in contact with ILE 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ILE* 4.2 21.1 - - + +
106F TYR* 3.5 38.8 - - + +
107F SER* 3.8 21.5 - - - +
110F LEU* 4.1 16.8 - - + -
125F PHE 2.7 27.8 + - - +
126F GLU* 3.3 4.2 + - - +
128F ILE* 1.3 72.9 - - - +
130F GLU* 1.3 63.1 + - + +
132F GLU* 3.3 8.7 + - - +
133F GLN* 3.1 21.1 + - - +
119K ILE* 4.1 18.2 - - + -
120K VAL* 3.9 19.1 - - + -
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Residues in contact with GLU 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F ARG* 4.8 5.4 + - - -
126F GLU* 3.2 16.2 + - + +
127F ARG* 3.6 10.6 - - - +
128F ILE 3.2 0.4 - - - -
129F ILE* 1.3 77.8 - - + +
131F GLU* 1.3 61.1 + - + +
133F GLN* 3.4 4.6 + - - +
134F ALA* 3.2 18.2 + - - +
119K ILE* 6.1 0.9 - - + -
120K VAL* 4.4 24.1 - - + +
123K ARG* 3.1 27.7 + - + +
127K ARG* 2.6 36.9 + - - -
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Residues in contact with GLU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E VAL* 3.4 38.1 - - + +
55F ASP* 5.2 0.2 - - - -
58F ARG* 3.2 16.7 + - - -
59F HIS* 2.6 38.4 + - + +
127F ARG* 3.3 15.9 - - - +
128F ILE* 3.0 9.7 + - - +
130F GLU* 1.3 77.6 - - + +
132F GLU* 1.3 66.9 + - - +
134F ALA* 3.0 13.9 + - - +
135F HIS* 3.1 18.4 + - + -
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Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLU* 3.1 6.2 - - - +
59F HIS* 3.1 9.8 + - - -
99F GLU* 3.4 13.3 - - - +
102F THR* 4.1 11.4 - - + +
103F ILE* 3.7 21.5 - - + +
106F TYR* 3.6 14.4 - - + -
128F ILE* 2.9 24.4 + - + +
129F ILE* 3.3 4.9 + - - +
131F GLU* 1.3 75.2 - - - +
133F GLN* 1.3 57.7 + - - +
135F HIS* 3.1 8.7 + - - +
136F LEU* 2.8 27.2 + - - +
200F FE2 2.0 29.2 - - - -
201F FE2 2.0 32.9 - - - -
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Residues in contact with GLN 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ILE* 3.7 14.5 - - + +
129F ILE 3.1 12.7 + - - +
130F GLU* 3.6 9.4 - - - +
131F GLU 3.2 0.2 - - - -
132F GLU* 1.3 73.5 - - - +
134F ALA* 1.3 67.5 + - - +
136F LEU* 3.7 23.7 - - - +
137F THR* 2.9 49.7 + - - +
140F GLU* 5.4 1.0 - - - +
66K ARG* 3.1 35.9 + - - +
69K GLU* 4.2 15.6 - - - +
120K VAL* 4.1 18.8 - - + +
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Residues in contact with ALA 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E PHE* 4.2 10.5 - - + -
172E VAL* 3.6 22.4 - - + -
130F GLU 3.2 9.1 + - - +
131F GLU* 3.0 9.9 + - - +
133F GLN* 1.3 80.4 - - - +
135F HIS* 1.3 60.6 + - - +
137F THR* 3.4 6.2 + - - -
138F TYR* 3.0 22.0 + - - +
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Residues in contact with HIS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E PHE* 3.9 9.4 - + - -
172E VAL* 4.0 3.7 - - + +
52F ILE* 3.8 25.0 - - + +
55F ASP* 2.8 44.1 + - + +
56F GLU* 3.4 11.6 + - - -
59F HIS* 4.2 6.3 - + - -
99F GLU* 3.4 15.5 + - - +
131F GLU* 3.1 14.3 + - + -
132F GLU* 3.1 14.8 + - - +
134F ALA* 1.3 74.1 - - - +
136F LEU* 1.3 57.8 + - - +
138F TYR* 3.1 8.3 + - - +
139F TYR* 2.9 39.8 + - + -
201F FE2 2.3 27.5 - - - -
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ALA* 3.3 30.1 - - + +
99F GLU* 3.8 15.0 - - + +
100F ASP* 4.1 22.0 - - + +
103F ILE* 4.1 15.7 - - + -
132F GLU 2.8 14.9 + - - +
133F GLN* 3.5 24.9 - - - +
135F HIS* 1.3 74.4 - - - +
137F THR* 1.3 66.5 + - - +
139F TYR* 3.3 2.8 + - - +
140F GLU* 2.9 59.4 + - + +
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Residues in contact with THR 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLN* 2.9 30.7 + - - +
134F ALA* 3.8 5.3 - - - -
136F LEU* 1.3 75.8 - - - +
138F TYR* 1.3 65.6 + - - +
140F GLU* 3.2 12.3 + - + +
141F ASN* 2.9 45.1 + - - +
69K GLU* 4.2 17.7 + - + +
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Residues in contact with TYR 138 (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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171E PHE* 3.8 28.3 - + + -
45F LEU* 3.7 18.4 + - - +
48F ASN* 3.3 42.5 + - + +
49F MET* 5.3 1.1 - - + -
52F ILE* 3.5 21.1 - - + -
92F TYR* 4.3 4.9 + + - -
134F ALA 3.0 14.4 + - - +
135F HIS* 3.1 8.5 + - - +
137F THR* 1.3 76.6 - - - +
139F TYR* 1.3 85.7 + + - +
141F ASN* 3.1 21.8 + - + +
142F ILE* 3.1 46.0 + - + +
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Residues in contact with TYR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.4 10.2 - + - -
49F MET* 3.3 30.8 - - + -
52F ILE* 3.2 31.7 - - + +
92F TYR* 3.8 28.9 - + - +
95F ASP* 3.6 34.3 - - + -
96F ALA* 3.8 20.8 - - + +
99F GLU* 3.7 32.8 - - + -
135F HIS* 2.9 21.6 + - + +
136F LEU 4.0 1.1 - - - +
138F TYR* 1.3 97.0 - + - +
140F GLU* 1.3 62.6 + - - +
142F ILE* 3.5 1.7 + - - +
143F GLY* 3.0 21.3 + - - -
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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
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96F ALA* 4.0 11.8 - - + +
100F ASP* 5.6 0.7 - - - +
133F GLN* 5.4 0.9 - - - +
136F LEU* 2.9 50.5 + - + +
137F THR* 3.7 11.8 + - + +
139F TYR* 1.3 78.3 - - - +
141F ASN* 1.3 63.0 + - - +
143F GLY* 3.5 1.4 + - - +
144F SER* 3.0 24.7 + - - -
69K GLU 5.4 4.2 - - - +
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Residues in contact with ASN 141 (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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137F THR* 2.9 36.1 + - - +
138F TYR* 3.1 13.8 + - + +
140F GLU* 1.3 77.3 - - - +
142F ILE* 1.3 65.6 + - + +
144F SER* 3.2 8.3 + - - -
145F HIS* 3.0 28.4 + - + -
38L ASP 5.1 2.0 + - - +
39L ASP 4.0 13.0 - - - +
41L ASP* 3.7 42.1 + - - +
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Residues in contact with ILE 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 3.9 10.3 - - + -
92F TYR* 3.6 28.5 - - + -
138F TYR* 3.1 54.6 + - + +
139F TYR 4.0 0.2 - - - +
141F ASN* 1.3 76.7 - - + +
143F GLY* 1.3 66.9 + - - +
145F HIS* 3.0 11.9 + - + +
146F ILE* 2.9 42.2 + - + +
153F TYR* 3.3 26.7 - - + +
41L ASP* 5.5 1.1 - - - +
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Residues in contact with GLY 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F PRO 6.0 0.4 - - - -
92F TYR* 3.9 18.1 - - - +
93F GLU* 5.4 3.1 - - - -
139F TYR 3.0 16.0 + - - -
140F GLU* 4.0 1.8 - - - -
142F ILE* 1.3 76.1 - - - +
144F SER* 1.3 56.8 + - - +
146F ILE* 3.8 6.0 - - - +
147F LYS* 2.8 32.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 144 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F GLU 3.0 18.8 + - - -
141F ASN* 3.3 8.3 - - - -
143F GLY* 1.3 76.6 - - - +
145F HIS* 1.3 60.9 + - - +
147F LYS* 4.6 3.6 - - - -
148F ASN* 2.9 47.7 + - - +
39L ASP 6.1 0.9 - - - -
40L MET* 4.9 11.3 + - - -
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Residues in contact with HIS 145 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F ASN 3.0 16.6 + - - -
142F ILE* 3.0 10.4 + - + +
144F SER* 1.3 77.3 - - - +
146F ILE* 1.3 59.6 + - - +
148F ASN* 4.6 1.1 - - + -
149F LEU* 2.6 49.9 + - + +
150F GLY 3.4 0.2 + - - -
153F TYR* 3.6 37.2 + + + +
40L MET 3.6 8.8 + - - -
41L ASP* 2.7 53.8 + - + +
42L TYR* 4.6 7.4 - + - -
158L ALA* 3.5 18.6 - - + +
159L GLY* 3.7 12.3 - - - -
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Residues in contact with ILE 146 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 5.5 0.4 - - + -
88F VAL* 3.5 21.3 - - + +
89F PRO* 4.1 31.2 - - + -
92F TYR* 3.5 35.9 - - + -
142F ILE* 2.9 26.0 + - + +
143F GLY* 3.8 4.5 - - - +
145F HIS* 1.3 76.2 - - - +
147F LYS* 1.3 60.7 + - - +
150F GLY* 2.8 36.6 + - - +
153F TYR* 4.2 17.5 - - + -
154F LEU* 5.0 8.5 - - + -
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Residues in contact with LYS 147 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F GLY 2.8 18.5 + - - +
144F SER* 4.0 4.9 - - - +
146F ILE* 1.3 82.0 - - - +
148F ASN* 1.3 64.4 + - - +
150F GLY* 4.7 0.7 + - - -
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Residues in contact with ASN 148 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F SER* 2.9 35.0 + - - +
145F HIS* 4.2 1.8 - - + +
147F LYS* 1.3 80.9 - - - +
149F LEU* 1.3 72.7 + - + +
42L TYR* 5.0 7.2 - - - +
151L ASP* 3.6 14.9 - - - +
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Residues in contact with LEU 149 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F HIS* 2.6 30.3 + - + +
148F ASN* 1.3 87.4 - - + +
150F GLY* 1.3 63.1 + - - +
151F ASP 3.4 0.3 + - - -
152F THR* 3.3 21.6 + - - -
153F TYR* 3.7 14.4 - - + +
42L TYR* 4.1 20.0 - - - +
151L ASP* 4.0 38.5 - - - +
154L LEU* 4.4 6.7 - - + -
155L ALA* 3.7 28.7 - - + +
158L ALA* 3.9 20.0 - - + -
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Residues in contact with GLY 150 (chain F).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F HIS 3.4 1.2 + - - -
146F ILE* 2.8 27.2 + - - -
147F LYS 4.6 0.8 + - - -
148F ASN 3.8 0.4 - - - -
149F LEU* 1.3 76.4 - - - +
151F ASP* 1.3 59.4 + - - -
153F TYR* 3.0 20.3 + - - +
154F LEU* 3.3 15.9 + - - +
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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