Contacts of the helix formed by residues 11 - 43 (chain F) in PDB entry 1O9R
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 PRO 11 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASP 3.2 7.6 - - - +
10F LEU* 1.3 97.9 - - + +
12F SER* 1.3 66.6 + - - +
13F ASN* 3.3 3.1 - - + +
14F ALA* 3.0 15.8 + - + +
15F LYS* 2.9 19.8 + - - +
132F GLY 5.6 0.4 - - - +
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Residues in contact with SER 12 (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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10F LEU 3.4 2.9 + - - -
11F PRO* 1.3 72.3 - - - +
13F ASN* 1.3 66.7 + - - +
15F LYS* 3.3 16.1 + - - +
16F SER* 3.0 26.9 + - - -
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Residues in contact with ASN 13 (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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11F PRO* 3.3 3.1 - - + +
12F SER* 1.3 79.6 - - - +
14F ALA* 1.3 58.4 + - - +
16F SER* 3.4 7.5 + - - -
17F THR* 3.0 33.5 + - - +
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Residues in contact with ALA 14 (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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10F LEU* 3.8 23.3 - - + -
11F PRO* 3.0 20.9 + - + +
13F ASN* 1.3 76.5 - - - +
15F LYS* 1.3 66.8 + - - +
17F THR* 3.4 5.0 + - - -
18F VAL* 2.8 29.6 + - + +
131F ALA* 3.3 29.4 - - + +
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Residues in contact with LYS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F THR* 4.1 17.7 + - + +
8F ASN* 2.8 41.5 + - - +
9F ASP 4.3 0.8 - - - -
10F LEU* 2.9 34.5 + - + +
11F PRO 2.9 15.7 + - - +
12F SER* 3.6 16.9 + - - +
14F ALA* 1.3 77.5 - - - +
16F SER* 1.4 57.1 + - - +
18F VAL* 3.8 0.3 - - - +
19F ILE* 2.9 37.8 + - + +
76F LEU* 3.4 37.9 - - + +
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Residues in contact with SER 16 (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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12F SER* 3.0 16.9 + - - -
13F ASN* 3.7 8.2 + - - -
15F LYS* 1.4 76.5 - - - +
17F THR* 1.3 65.5 + - - +
19F ILE* 3.5 9.3 + - - +
20F GLY* 3.3 16.8 + - - -
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Residues in contact with THR 17 (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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13F ASN* 3.0 18.1 + - - +
14F ALA* 3.7 6.1 - - - -
16F SER* 1.3 77.4 - - - +
18F VAL* 1.3 63.1 + - - +
20F GLY* 3.2 11.4 + - - -
21F ILE* 3.2 29.7 + - + +
127F ASP 5.3 0.7 - - - +
131F ALA* 4.2 15.9 - - + -
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Residues in contact with VAL 18 (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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14F ALA 2.8 24.4 + - - +
17F THR* 1.3 70.2 - - - +
19F ILE* 1.3 65.7 + - - +
21F ILE* 3.2 9.3 + - + +
22F LEU* 2.8 31.0 + - + +
76F LEU* 4.0 6.3 - - + -
128F SER* 4.1 12.8 - - - +
131F ALA* 3.8 24.9 - - + -
133F ASP* 3.6 27.6 - - + +
136F THR* 3.4 34.3 - - + +
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Residues in contact with ILE 19 (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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15F LYS* 2.9 25.9 + - + +
16F SER* 3.8 9.2 - - - +
18F VAL* 1.3 73.7 - - - +
20F GLY* 1.3 59.2 + - - +
22F LEU* 3.7 7.4 - - - +
23F ASN* 2.9 46.6 + - - +
73F VAL* 4.0 17.3 - - + +
76F LEU* 3.6 29.2 - - + +
77F GLY 4.3 0.9 - - - -
78F GLY* 3.6 30.3 - - - +
79F THR 5.2 0.9 - - - +
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Residues in contact with GLY 20 (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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16F SER 3.3 6.9 + - - -
17F THR 3.2 8.3 + - - -
19F ILE* 1.3 79.7 - - - +
21F ILE* 1.3 56.2 + - - +
23F ASN* 4.1 3.2 - - - +
24F GLU* 3.0 30.8 + - - +
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Residues in contact with ILE 21 (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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17F THR* 3.2 30.0 + - + +
18F VAL* 3.2 12.9 + - - +
20F GLY* 1.3 75.7 - - - +
22F LEU* 1.3 58.6 + - - +
24F GLU* 3.4 10.5 + - - +
25F SER* 3.0 28.6 + - - +
124F ALA* 3.7 33.4 - - + -
127F ASP* 3.7 39.3 - - + +
128F SER* 4.2 5.6 - - - +
140F PHE* 3.8 11.2 - - + -
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Residues in contact with LEU 22 (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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18F VAL* 2.8 36.3 + - + +
19F ILE* 3.7 1.1 - - - +
21F ILE* 1.3 77.6 - - - +
23F ASN* 1.4 57.7 + - - +
25F SER* 3.2 1.4 + - - -
26F LEU 2.8 24.9 + - - -
69F ILE* 3.3 37.3 - - + +
72F ARG* 3.7 27.6 - - + -
73F VAL* 3.5 29.8 - - + +
76F LEU* 4.1 4.3 - - + -
136F THR* 3.8 7.4 - - + -
139F ILE* 5.1 2.5 - - + -
140F PHE* 3.5 29.8 - - + -
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Residues in contact with ASN 23 (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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19F ILE* 2.9 27.5 + - - +
20F GLY* 4.3 3.4 - - - +
22F LEU* 1.4 72.3 - - - +
24F GLU* 1.4 63.3 + - - +
26F LEU* 3.4 10.6 + - - +
27F ALA* 3.2 21.7 + - - +
73F VAL* 3.7 16.5 - - - +
79F THR 2.9 23.0 + - - -
80F ALA* 3.6 5.7 - - - -
81F LEU* 2.9 48.0 + - + +
90F THR* 4.1 5.2 - - + +
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Residues in contact with GLU 24 (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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20F GLY 3.0 19.5 + - - +
21F ILE* 3.6 11.0 - - - +
23F ASN* 1.4 79.2 - - - +
25F SER* 1.3 64.0 + - - +
27F ALA* 3.4 10.0 + - - +
28F SER* 3.5 9.4 + - - -
90F THR* 3.9 20.2 - - + +
92F LYS* 3.9 28.2 + - + -
120F MET* 4.3 22.4 - - - +
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Residues in contact with SER 25 (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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21F ILE* 3.0 18.6 + - - +
22F LEU 3.7 4.0 - - - -
24F GLU* 1.3 77.5 + - - +
26F LEU* 1.3 63.1 + - - +
28F SER* 3.2 4.0 + - - -
29F VAL* 2.9 27.8 + - - +
69F ILE* 4.6 4.3 - - - -
120F MET* 3.8 21.5 - - - +
121F ILE* 3.3 29.9 - - - +
124F ALA* 4.3 5.2 - - - +
140F PHE* 3.7 15.5 - - - -
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Residues in contact with LEU 26 (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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41E TRP* 4.4 5.8 - - + -
22F LEU 2.8 21.4 + - - +
23F ASN* 3.6 18.6 - - - +
24F GLU 3.3 0.2 - - - -
25F SER* 1.3 72.7 - - - +
27F ALA* 1.4 63.9 + - - +
29F VAL* 3.3 4.4 + - + +
30F ILE* 2.9 47.0 + - + +
66F GLY* 3.4 36.6 - - - +
69F ILE* 3.9 8.7 - - + +
70F ALA* 3.9 24.9 - - + +
73F VAL* 5.5 0.4 - - + -
80F ALA* 4.5 0.2 - - + -
81F LEU 3.6 28.5 - - - +
82F GLY* 4.2 4.0 - - - +
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Residues in contact with ALA 27 (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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23F ASN 3.2 8.8 + - - +
24F GLU 3.8 1.8 - - - +
25F SER 3.3 0.2 - - - -
26F LEU* 1.4 76.1 - - - +
28F SER* 1.3 58.9 + - - +
31F ASP* 3.0 24.4 + - - +
81F LEU 5.0 4.5 + - - +
86F ALA 4.3 0.9 - - - +
87F VAL* 3.5 31.1 - - + +
90F THR* 3.6 38.8 - - + -
91F THR* 3.8 12.1 - - - +
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Residues in contact with SER 28 (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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24F GLU 3.5 4.4 + - - -
25F SER 3.2 3.0 + - - -
27F ALA* 1.3 76.5 - - - +
29F VAL* 1.4 61.6 + - - +
31F ASP* 3.8 1.0 - - - +
32F LEU* 2.9 28.9 + - - +
91F THR* 3.7 9.3 - - - -
92F LYS* 2.9 38.2 + - - +
93F LEU* 3.8 7.1 + - - +
117F VAL* 3.9 13.0 - - - +
120F MET* 3.8 29.4 - - - +
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Residues in contact with VAL 29 (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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25F SER 2.9 22.8 + - - +
26F LEU* 3.8 5.8 - - - +
28F SER* 1.4 77.1 - - - +
30F ILE* 1.3 60.7 + - + +
32F LEU* 3.3 7.0 + - - +
33F ALA* 2.9 27.0 + - + +
62F LEU* 3.6 38.9 - - + +
65F HIS* 4.9 3.1 - - + -
66F GLY* 3.9 18.2 - - - +
69F ILE* 4.5 14.8 - - + -
117F VAL* 4.1 20.4 - - + -
121F ILE* 4.6 8.3 - - + -
147F LEU* 5.5 2.2 - - + -
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Residues in contact with ILE 30 (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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34E LEU* 3.8 27.6 - - + -
41E TRP* 4.4 9.9 - - + -
26F LEU* 2.9 40.9 + - + +
27F ALA 3.9 3.1 - - - +
29F VAL* 1.3 74.8 - - + +
31F ASP* 1.4 68.4 + - - +
33F ALA* 3.0 10.4 + - + +
34F LEU* 3.0 28.1 + - + +
66F GLY* 5.8 1.6 - - - -
82F GLY* 3.7 33.4 - - - +
87F VAL* 3.9 19.7 - - + -
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Residues in contact with ASP 31 (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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84E LEU* 3.7 23.1 + - - +
85E GLN* 5.1 3.3 + - - +
27F ALA 3.0 13.8 + - - +
28F SER 3.8 3.6 - - - +
30F ILE* 1.4 77.5 - - - +
32F LEU* 1.3 57.1 + - - +
34F LEU* 3.1 9.9 + - - +
35F VAL* 2.9 38.5 + - - +
87F VAL* 4.0 10.7 - - + +
91F THR* 2.6 39.0 + - - +
93F LEU* 3.4 20.6 - - + +
94F LYS 5.3 1.2 - - - +
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Residues in contact with LEU 32 (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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28F SER 2.9 18.9 + - - +
29F VAL* 3.6 5.8 - - - +
31F ASP* 1.3 75.0 - - - +
33F ALA* 1.3 58.5 + - - +
35F VAL* 3.3 8.8 + - + +
36F THR* 2.8 33.4 + - - -
62F LEU* 3.9 26.5 - - + -
93F LEU* 3.8 8.0 - - + +
113F ARG* 3.6 36.1 - - + +
114F TYR* 3.6 41.3 - - + -
117F VAL* 3.9 23.1 - - + -
147F LEU* 4.1 2.9 - - + -
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Residues in contact with ALA 33 (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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59E ARG* 6.2 0.2 - - - +
29F VAL 2.9 14.0 + - - +
30F ILE* 3.0 13.0 + - + +
32F LEU* 1.3 75.9 - - - +
34F LEU* 1.4 64.0 + - + +
36F THR* 3.3 8.9 + - - -
37F LYS 3.3 6.2 + - - -
59F ARG* 2.9 45.2 + - - +
62F LEU* 3.8 21.2 - - + +
63F ASP* 4.4 4.5 - - - +
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Residues in contact with LEU 34 (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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30E ILE* 3.8 28.7 - - + -
34E LEU* 4.6 24.2 - - + -
82E GLY 3.9 17.5 - - - +
83E SER* 4.6 1.1 - - - -
84E LEU* 4.0 42.6 - - + +
87E VAL* 5.4 1.1 - - + -
30F ILE* 3.0 25.1 + - + +
31F ASP* 3.5 8.5 - - - +
33F ALA* 1.4 77.8 - - + +
35F VAL* 1.3 57.5 + - - +
36F THR 3.3 0.2 + - - -
37F LYS* 3.3 4.8 + - - +
38F GLN* 2.9 28.6 + - - +
41F TRP* 5.3 0.2 - - - -
59F ARG* 4.1 18.2 - - - +
84F LEU* 5.5 0.9 - - + -
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Residues in contact with VAL 35 (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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83E SER* 5.7 3.6 - - - +
84E LEU 6.1 0.7 - - - +
31F ASP* 2.9 29.9 + - - +
32F LEU* 3.5 20.0 - - + +
34F LEU* 1.3 77.0 - - + +
36F THR* 1.3 64.0 + - - +
38F GLN* 3.2 8.4 + - - +
39F ALA* 3.0 23.9 + - - +
93F LEU* 5.0 0.9 - - + -
94F LYS 5.7 0.4 - - - +
96F TYR* 3.7 41.4 - - + +
110F LEU* 3.6 21.8 - - + -
113F ARG* 4.1 17.5 - - - +
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Residues in contact with THR 36 (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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32F LEU 2.8 20.8 + - - -
33F ALA* 3.5 8.5 - - - -
34F LEU 3.1 0.4 - - - -
35F VAL* 1.3 77.6 - - - +
37F LYS* 1.3 57.3 + - - +
39F ALA* 3.5 3.3 + - - +
40F HIS* 3.0 27.1 + - - +
55F LEU* 3.2 39.5 - - + +
58F PHE* 4.2 1.3 - - + -
59F ARG* 4.0 13.0 - - + +
62F LEU* 3.6 3.0 - - - +
110F LEU* 4.3 7.9 - - - -
114F TYR* 2.7 35.9 + - + +
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Residues in contact with LYS 37 (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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67E ASP* 3.0 41.8 + - - +
1163E FE 4.2 1.2 - - - -
33F ALA 3.3 3.0 + - - -
34F LEU* 3.9 3.8 - - - +
36F THR* 1.3 77.8 - - + +
38F GLN* 1.3 66.5 + - - +
40F HIS* 3.1 23.3 + - + +
41F TRP* 2.9 49.9 + - + -
56F ASP* 2.7 32.4 + - - +
59F ARG* 3.4 48.0 - - + +
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Residues in contact with GLN 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E THR* 4.7 0.7 - - - +
80E ALA 3.0 21.7 + - - +
81E LEU* 4.4 0.8 - - - +
82E GLY* 2.8 34.5 - - - +
83E SER* 3.3 19.2 - - - +
34F LEU 2.9 17.4 + - - +
35F VAL* 3.2 9.8 + - - +
37F LYS* 1.3 76.0 - - - +
39F ALA* 1.3 61.9 + - - +
41F TRP* 3.8 6.1 - - - -
42F ASN* 3.0 39.1 + - - +
96F TYR* 3.7 26.5 - - + -
97F PRO 4.9 0.4 - - - +
98F THR* 4.1 22.3 - - + +
106F HIS* 4.4 1.8 - - + -
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Residues in contact with ALA 39 (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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35F VAL 3.0 15.4 + - - +
36F THR 3.7 4.0 - - - +
38F GLN* 1.3 74.1 - - - +
40F HIS* 1.3 67.1 + - - +
42F ASN 3.1 0.3 + - - -
43F LEU* 3.0 29.1 + - - +
55F LEU* 4.0 5.8 - - + -
96F TYR* 3.6 11.0 - - - +
106F HIS* 3.5 28.7 - - + +
110F LEU* 3.8 23.1 - - + -
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Residues in contact with HIS 40 (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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1163E FE 2.8 21.9 - - - -
36F THR 3.0 17.9 + - - +
37F LYS* 3.4 14.7 + - + +
39F ALA* 1.3 77.0 - - - +
41F TRP* 1.4 84.7 + + - +
43F LEU* 3.1 10.4 - - - +
48F PHE* 4.6 0.2 - - - -
52F HIS* 2.7 76.8 + + - -
55F LEU* 3.7 18.1 - - + +
56F ASP* 3.1 38.0 + - - +
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Residues in contact with TRP 41 (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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152A TRP* 3.6 16.1 + - - -
26E LEU* 4.3 12.1 - - + -
30E ILE* 4.5 10.1 - - + -
66E GLY 4.3 1.6 - - - -
67E ASP* 3.4 37.0 + - - +
70E ALA* 3.3 33.2 - - + +
71E GLU* 4.1 18.3 - - + +
74E VAL* 3.5 19.7 - - + +
80E ALA* 3.9 23.3 - - + -
82E GLY* 4.0 24.9 - - - -
34F LEU 5.3 0.4 - - - -
37F LYS* 2.9 48.9 + - + -
38F GLN* 3.8 9.9 - - - -
40F HIS* 1.4 96.5 + + - +
42F ASN* 1.3 63.4 + - - +
43F LEU* 3.9 1.9 + - - +
52F HIS* 4.8 2.5 - + - -
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Residues in contact with ASN 42 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E VAL* 3.6 8.7 - - - +
78E GLY 4.4 0.7 - - - +
79E THR* 3.5 16.1 - - + +
80E ALA* 3.0 49.8 + - - +
38F GLN* 3.0 33.4 + - - +
39F ALA 3.1 2.6 + - - -
41F TRP* 1.3 78.0 - - - +
43F LEU* 1.3 68.2 + - - +
44F LYS* 3.6 12.8 + - - +
100F ILE 4.4 5.4 - - - +
101F TYR* 3.6 26.6 - - + -
106F HIS* 4.0 13.7 - - + +
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Residues in contact with LEU 43 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TRP* 5.3 0.3 + - - -
156A ALA* 4.3 0.2 - - - +
39F ALA 3.0 19.3 + - - +
40F HIS* 3.1 30.7 - - - +
41F TRP 4.6 0.9 - - - +
42F ASN* 1.3 79.3 - - - +
44F LYS* 1.4 66.3 + - - +
48F PHE* 3.2 39.1 - - + +
51F VAL* 3.5 38.6 - - + -
52F HIS* 4.1 11.7 - - + +
55F LEU* 4.6 3.8 - - + -
101F TYR 3.4 6.1 - - - +
103F ILE* 3.8 23.1 - - + -
106F HIS* 3.7 21.7 + - + -
----------------------------------------------------------
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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