Contacts of the helix formed by residues 114 - 144 (chain Q) in PDB entry 1BFR
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 TYR 114 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ARG* 3.7 20.6 - - - +
105P ILE* 3.6 41.1 - - + -
106P GLY* 3.7 14.1 - - - -
109P ASP* 5.9 1.7 - - + +
117P ARG* 5.4 2.2 - - - -
121P ILE* 4.0 21.1 - - + -
124P LEU* 4.0 14.4 - - + -
109Q ASP* 4.0 31.1 + - - -
112Q HIS* 3.0 50.7 + + + -
113Q ASP* 1.3 71.0 - - - +
115Q VAL* 1.3 56.0 + - - +
117Q ARG* 3.4 20.3 - - - +
118Q ASP* 2.9 32.9 + - - +
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Residues in contact with VAL 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P ARG* 5.1 0.6 - - - +
121P ILE* 4.6 4.9 - - + +
124P LEU* 4.0 11.3 - - + +
125P ARG* 3.7 49.9 + - + +
128P GLU* 3.5 36.1 - - + +
61Q ARG* 3.7 15.9 - - - +
113Q ASP 3.4 0.8 - - - -
114Q TYR* 1.3 76.0 - - - +
116Q SER* 1.3 61.0 + - - +
118Q ASP* 3.4 4.6 + - - +
119Q MET* 3.1 23.2 + - + +
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Residues in contact with SER 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q VAL* 4.0 11.9 - - - +
11Q LEU* 4.8 7.0 - - - -
61Q ARG* 3.0 24.6 + - - +
65Q LEU* 3.8 8.0 - - - +
108Q ALA* 4.6 0.4 - - - -
113Q ASP* 2.8 38.7 + - - -
115Q VAL* 1.3 73.2 - - - +
117Q ARG* 1.3 63.1 + - - +
119Q MET* 3.4 8.6 - - - +
120Q MET* 3.1 35.4 + - - +
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Residues in contact with ARG 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I ASP* 5.0 2.4 + - - -
114I TYR* 5.3 2.8 - - - -
117I ARG* 3.2 28.3 - - - +
117P ARG* 3.1 32.2 - - - +
118P ASP* 5.1 0.2 + - - -
121P ILE* 3.2 15.3 - - - +
105Q ILE* 3.6 28.3 - - + +
108Q ALA* 4.0 8.2 - - + +
109Q ASP* 3.2 38.9 + - - +
113Q ASP 3.0 13.2 + - - +
114Q TYR* 3.4 17.4 + - - +
116Q SER* 1.3 75.9 - - - +
118Q ASP* 1.3 85.7 + - - +
120Q MET* 3.1 15.0 + - - +
121Q ILE* 3.0 25.9 + - + +
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Residues in contact with ASP 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I ARG* 5.2 0.2 + - - -
118I ASP* 5.7 3.1 - - - +
118P ASP* 5.6 3.6 - - - +
121P ILE* 3.3 24.8 - - + +
125P ARG* 3.5 24.4 + - - +
114Q TYR 2.9 19.5 + - - +
115Q VAL 4.0 2.7 - - - +
117Q ARG* 1.3 100.6 + - - +
119Q MET* 1.3 63.3 + - - +
121Q ILE* 3.1 11.2 + - - +
122Q GLU* 3.1 30.2 + - - +
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Residues in contact with MET 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q LEU* 4.3 10.1 - - + -
57Q ARG* 3.7 46.8 + - - +
58Q TYR* 3.5 38.8 - - + -
61Q ARG* 4.0 33.7 - - + -
115Q VAL* 3.1 14.6 + - + +
116Q SER* 3.4 8.5 - - - +
118Q ASP* 1.3 73.5 - - - +
120Q MET* 1.3 73.9 + - + +
122Q GLU* 3.4 4.6 + - - +
123Q ILE* 3.1 26.8 + - + +
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Residues in contact with MET 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7Q VAL* 5.3 2.0 - - + -
10Q TYR* 5.8 1.3 - - + -
11Q LEU* 3.9 15.9 - - + -
14Q LEU* 3.6 26.9 - - - -
58Q TYR* 4.4 6.5 - - + -
101Q LEU* 3.9 12.3 - - + +
104Q ALA* 3.7 25.6 - - + +
105Q ILE* 3.6 15.7 - - + +
108Q ALA* 3.6 30.1 - - + -
116Q SER* 3.1 21.8 + - - +
117Q ARG* 3.1 8.7 + - - +
119Q MET* 1.3 90.2 - - + +
121Q ILE* 1.3 55.8 + - - +
123Q ILE* 3.2 7.3 + - - +
124Q LEU* 2.8 28.8 + - - +
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Residues in contact with ILE 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I TYR* 3.9 27.8 - - + +
115I VAL* 4.8 4.5 - - + +
117I ARG* 3.5 28.3 - - - +
118I ASP* 3.5 24.9 - - - +
105Q ILE* 3.7 31.4 - - + -
117Q ARG* 3.0 27.7 + - - +
118Q ASP* 3.1 11.4 + - - +
120Q MET* 1.3 70.0 - - - +
122Q GLU* 1.3 57.2 + - + +
124Q LEU* 3.2 2.8 + - + +
125Q ARG* 2.9 36.5 + - - +
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Residues in contact with GLU 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125P ARG* 4.7 12.6 + - - -
57Q ARG* 3.0 36.0 + - - +
118Q ASP* 3.1 17.8 + - + +
119Q MET* 3.4 7.1 - - - +
121Q ILE* 1.3 72.9 - - - +
123Q ILE* 1.3 66.4 + - - +
125Q ARG* 3.3 27.7 + - - +
126Q ASP* 3.2 25.8 + - - +
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Residues in contact with ILE 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q GLU* 4.0 6.7 - - - +
54Q HIS* 3.6 46.4 - - + +
57Q ARG* 4.1 18.8 - - + +
58Q TYR* 3.6 45.3 - - + +
101Q LEU* 4.7 4.7 - - + -
119Q MET* 3.1 28.1 + - + +
120Q MET* 3.2 5.6 + - - +
122Q GLU* 1.3 73.3 - - - +
124Q LEU* 1.3 63.2 + - - +
126Q ASP* 3.1 5.5 + - - +
127Q GLU* 3.0 24.6 + - + +
202Q MN 4.1 2.2 - - - +
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Residues in contact with LEU 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I TYR* 4.2 21.1 - - + -
115I VAL* 4.2 11.2 - - + -
98Q ALA* 4.1 24.7 - - + +
101Q LEU* 3.9 27.3 - - + +
102Q ARG* 3.8 31.9 - - + +
105Q ILE* 3.8 22.4 - - + -
120Q MET 2.8 21.4 + - - +
121Q ILE* 3.2 6.0 + - - +
123Q ILE* 1.3 70.6 - - - +
125Q ARG* 1.3 57.3 + - - +
127Q GLU* 3.2 2.8 + - + +
128Q GLU* 2.9 32.7 + - + +
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Residues in contact with ARG 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115I VAL* 3.9 28.7 - - + +
118I ASP* 3.5 36.2 + - - +
122I GLU* 5.0 7.9 + - - -
121Q ILE* 2.9 21.9 + - - +
122Q GLU* 3.5 32.2 + - - +
124Q LEU* 1.3 76.8 - - - +
126Q ASP* 1.3 65.3 + - - +
128Q GLU* 3.4 3.4 + - - +
129Q GLY* 3.2 17.3 + - - -
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Residues in contact with ASP 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q ASP* 5.1 7.0 - - - +
54Q HIS* 2.8 33.3 + - + -
57Q ARG* 5.8 1.7 + - - -
122Q GLU 3.2 14.4 + - - +
123Q ILE* 3.1 7.9 + - - +
125Q ARG* 1.3 77.5 - - - +
127Q GLU* 1.3 62.7 + - - +
129Q GLY* 3.2 4.0 + - - -
130Q HIS* 3.1 32.3 + - - +
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Residues in contact with GLU 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q GLU* 5.3 0.2 - - - +
51Q GLU* 2.9 7.3 - - - +
54Q HIS* 3.1 13.3 - - - -
94Q GLU* 2.8 22.9 - - - +
97Q GLY* 5.8 1.9 - - - -
98Q ALA* 5.2 6.1 - - + +
101Q LEU* 4.1 20.6 - - + -
123Q ILE* 3.0 14.6 + - + +
124Q LEU* 3.6 9.6 - - + +
126Q ASP* 1.3 70.3 - - - +
128Q GLU* 1.3 66.4 + - - +
130Q HIS* 3.0 3.3 + - - -
131Q ILE* 2.9 32.6 + - + +
201Q MN 2.2 28.7 + - - -
202Q MN 2.5 30.7 + - - +
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Residues in contact with GLU 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 3.8 20.9 - - + +
61I ARG* 3.1 35.2 + - - +
64I PHE* 3.8 12.8 - - + -
115I VAL* 3.6 18.0 - - + +
102Q ARG* 2.7 35.4 + - - +
124Q LEU* 2.9 26.7 + - + +
125Q ARG* 3.8 5.6 - - - +
127Q GLU* 1.3 70.8 - - - +
129Q GLY* 1.3 57.7 + - - +
131Q ILE* 3.3 15.9 + - + +
132Q ASP* 2.9 28.2 + - - +
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Residues in contact with GLY 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125Q ARG 3.2 12.7 + - - -
126Q ASP* 3.2 5.6 + - - -
127Q GLU 3.2 0.8 - - - -
128Q GLU* 1.3 73.4 - - - +
130Q HIS* 1.3 65.6 + - - +
132Q ASP* 3.3 8.3 + - - +
133Q TRP* 3.2 20.1 + - - +
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Residues in contact with HIS 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q TYR* 3.5 14.4 + - - +
47Q GLU* 3.5 35.2 - - + +
50Q ASP* 2.8 34.3 + - + -
51Q GLU* 3.4 13.4 + - - -
54Q HIS* 4.9 1.6 - + - -
94Q GLU* 3.2 12.8 - - - +
126Q ASP* 3.1 15.8 + - - +
127Q GLU* 3.0 6.6 + - - +
129Q GLY* 1.3 75.3 - - - +
131Q ILE* 1.3 63.4 + - - +
133Q TRP* 3.2 3.4 + - - +
134Q LEU* 3.0 28.9 + - - +
201Q MN 2.1 33.8 + - - -
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Residues in contact with ILE 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 4.3 22.2 - - + -
64I PHE* 4.8 0.7 - - + -
91Q LEU* 3.8 21.1 - - + -
94Q GLU* 3.6 24.2 - - + +
95Q LEU* 3.7 25.1 - - + -
98Q ALA* 4.3 19.5 - - + -
127Q GLU* 2.9 21.2 + - + +
128Q GLU* 3.5 16.2 - - + +
130Q HIS* 1.3 75.5 - - - +
132Q ASP* 1.3 62.2 + - - +
134Q LEU* 3.3 3.1 + - - +
135Q GLU* 3.0 44.6 + - - +
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Residues in contact with ASP 132 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64I PHE* 3.6 34.5 - - + +
34J ASN* 4.4 11.0 - - - +
128Q GLU 2.9 10.3 + - - +
129Q GLY* 3.6 11.4 - - - +
130Q HIS 3.3 0.2 - - - -
131Q ILE* 1.3 75.5 - - - +
133Q TRP* 1.3 62.8 + - - +
135Q GLU* 3.8 6.0 - - - +
136Q THR* 3.1 37.7 + - - -
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Residues in contact with TRP 133 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q ARG* 4.0 10.9 - - - +
40Q LEU* 4.1 21.1 - - + -
43Q VAL* 3.5 44.4 - - + +
44Q GLU* 3.6 28.7 - - + -
47Q GLU* 3.8 19.3 - - - +
87Q LEU* 4.8 5.8 - - + -
129Q GLY 3.2 9.6 + - - +
130Q HIS 3.2 5.8 + - - +
132Q ASP* 1.3 78.2 - - - +
134Q LEU* 1.3 93.5 + - + +
136Q THR* 3.2 5.1 + - - -
137Q GLU* 3.0 60.9 + - + +
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Residues in contact with LEU 134 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q TYR* 3.8 21.1 - - - +
44Q GLU* 4.1 5.8 - - - +
47Q GLU* 4.6 1.6 - - - +
87Q LEU* 3.8 30.5 - - + +
90Q ASP* 3.9 14.4 - - + -
91Q LEU* 3.8 33.4 - - + +
94Q GLU* 4.1 6.5 - - + -
130Q HIS 3.0 22.5 + - - +
131Q ILE* 3.9 2.9 - - - +
133Q TRP* 1.3 100.2 - - + +
135Q GLU* 1.3 62.0 + - - +
137Q GLU* 3.3 3.1 + - - +
138Q LEU* 3.0 30.7 + - + +
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Residues in contact with GLU 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 2.9 41.5 + - - +
64I PHE* 4.0 11.8 - - - -
66I GLU* 4.4 3.8 - - - +
91Q LEU* 4.1 24.6 - - + +
95Q LEU* 5.5 2.3 - - - +
131Q ILE* 3.0 30.4 + - - +
132Q ASP* 3.8 5.2 - - - +
134Q LEU* 1.3 76.1 - - - +
136Q THR* 1.3 65.1 + - - +
138Q LEU* 3.3 3.6 + - - +
139Q ASP* 3.0 30.4 + - - +
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Residues in contact with THR 136 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J ASN 3.7 12.5 + - - +
35J TRP 3.8 9.9 - - - +
36J GLY* 3.7 32.1 - - - +
132Q ASP* 3.1 25.5 + - - -
133Q TRP* 3.7 4.9 - - - -
135Q GLU* 1.3 77.2 - - - +
137Q GLU* 1.3 67.6 + - - +
139Q ASP* 3.2 7.8 + - - +
140Q LEU* 2.9 30.0 + - + +
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Residues in contact with GLU 137 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39Q ARG* 3.1 37.7 + - - -
87Q LEU* 4.2 10.5 - - + -
133Q TRP* 3.0 46.0 + - + +
134Q LEU* 3.7 6.5 - - - +
136Q THR* 1.3 76.5 - - - +
138Q LEU* 1.3 64.8 + - - +
140Q LEU* 3.1 18.0 + - - +
141Q ILE* 2.9 28.5 + - - +
149Q TYR* 2.6 37.8 + - - +
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Residues in contact with LEU 138 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Q GLU* 3.9 20.4 - - + +
87Q LEU* 3.8 27.4 - - + +
88Q ARG* 3.9 49.4 - - + +
91Q LEU* 3.7 30.3 - - + -
134Q LEU 3.0 18.8 + - - +
135Q GLU* 3.8 4.3 - - - +
137Q GLU* 1.3 75.7 - - - +
139Q ASP* 1.3 62.5 + - - +
141Q ILE* 3.6 9.5 + - + +
142Q GLN* 2.8 30.3 + - - -
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Residues in contact with ASP 139 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J TRP* 5.9 2.0 - - - +
135Q GLU* 3.0 20.6 + - - +
136Q THR* 3.6 10.1 - - + +
138Q LEU* 1.3 73.8 - - - +
140Q LEU* 1.3 62.6 + - + +
142Q GLN* 3.1 11.7 + - - +
143Q LYS* 2.9 53.0 + - - +
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Residues in contact with LEU 140 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J TRP 3.4 20.6 - - - +
36J GLY* 4.5 6.1 - - - +
37J LEU* 4.2 15.5 - - + -
150J LEU* 6.0 0.9 - - + -
154J ILE* 4.5 12.8 - - + -
136Q THR* 2.9 38.4 + - + +
137Q GLU* 3.5 18.6 - - - +
139Q ASP* 1.3 73.0 - - + +
141Q ILE* 1.3 63.3 + - - +
143Q LYS* 3.2 14.8 + - + +
144Q MET* 2.9 56.9 + - + +
149Q TYR* 4.5 9.2 - - + -
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Residues in contact with ILE 141 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Q VAL* 4.6 3.4 - - + -
84Q GLU* 4.2 30.1 - - + +
87Q LEU* 4.1 19.5 - - + -
137Q GLU 2.9 19.3 + - - +
138Q LEU* 3.6 19.5 - - + +
140Q LEU* 1.3 73.7 - - - +
142Q GLN* 1.3 63.8 + - - +
145Q GLY* 3.0 24.1 + - - -
146Q LEU* 3.8 28.9 + - + +
149Q TYR* 3.7 39.2 - - + -
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Residues in contact with GLN 142 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J GLN* 4.8 2.8 + - - -
84Q GLU* 3.2 29.9 + - - +
88Q ARG* 3.4 15.4 + - - +
138Q LEU* 2.8 25.6 + - - +
139Q ASP* 3.1 11.8 + - - +
141Q ILE* 1.3 81.8 - - - +
143Q LYS* 1.3 65.3 + - + +
145Q GLY* 3.7 5.2 + - - -
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Residues in contact with LYS 143 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J TRP* 3.7 44.8 + - - +
37J LEU* 5.8 3.9 - - + +
147J GLN* 3.6 17.0 + - - +
150J LEU* 3.9 29.0 - - + +
139Q ASP* 2.9 44.5 + - - +
140Q LEU* 3.9 13.2 - - + +
142Q GLN* 1.3 76.0 - - + +
144Q MET* 1.3 60.8 + - - +
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Residues in contact with MET 144 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J GLN* 3.5 40.4 + - - +
150J LEU* 4.3 7.2 - - + -
151J GLN* 3.9 38.4 - - - +
154J ILE* 4.0 20.2 - - + -
140Q LEU* 2.9 50.6 + - + +
143Q LYS* 1.3 72.4 - - - +
145Q GLY* 1.3 70.1 + - - +
148Q ASN* 3.3 16.7 + - + +
149Q TYR* 3.8 27.1 - - - +
152Q ALA* 5.1 0.9 - - - -
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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