Contacts of the helix formed by residues 47 - 77 (chain F) in PDB entry 2Q7M
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 47 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F GLU* 5.6 0.2 - - - +
37F GLN* 2.9 44.1 - - + +
46F GLY* 1.3 86.2 - - - +
48F LEU* 1.3 70.0 + - + +
49F ALA* 3.2 20.9 - - + +
50F PHE* 3.4 19.6 - - - +
51F GLU* 2.8 21.3 - - - +
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Residues in contact with LEU 48 (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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46F GLY 4.4 2.0 - - - +
47F THR* 1.3 84.9 - - + +
49F ALA* 1.3 58.3 + - - +
51F GLU* 4.3 13.7 - - + +
52F ARG* 2.8 50.5 + - - +
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Residues in contact with ALA 49 (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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33F GLU* 3.3 26.4 - - + +
47F THR* 3.2 12.2 - - + +
48F LEU* 1.3 81.9 - - - +
50F PHE* 1.3 58.6 + - - +
51F GLU 3.4 0.2 - - - -
52F ARG* 3.8 2.0 - - - -
53F VAL* 3.2 20.8 + - - +
102F LEU* 3.9 10.0 - - + +
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Residues in contact with PHE 50 (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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30F VAL 5.2 1.6 - - - -
33F GLU* 3.3 48.2 - - + +
34F SER* 3.8 17.0 - - - -
37F GLN* 5.1 4.0 - - + -
39F GLY 4.3 10.8 - - - -
40F ARG* 4.2 12.1 - - - -
41F SER 3.2 34.3 - - - -
42F PHE* 4.4 7.0 - - + -
45F THR 3.6 9.4 - - - -
46F GLY* 3.8 17.3 - - - -
47F THR* 3.4 15.6 - - - +
49F ALA* 1.3 77.7 - - - +
51F GLU* 1.3 68.9 + - + +
52F ARG 3.3 0.2 - - - -
53F VAL* 4.3 0.7 - - - +
54F TYR* 3.0 40.1 + + + +
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Residues in contact with GLU 51 (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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44D ARG* 2.3 65.3 + - - +
43F GLN* 5.0 0.6 + - - -
44F ARG* 3.1 33.2 + - - +
45F THR* 3.3 18.2 + - - +
46F GLY 3.1 18.0 - - - +
47F THR 2.8 16.2 + - - +
48F LEU* 4.3 12.5 - - + +
49F ALA 3.4 0.2 - - - -
50F PHE* 1.3 86.5 - - + +
52F ARG* 1.3 58.5 + - - +
54F TYR* 5.0 2.2 - - - -
55F THR* 3.0 13.5 + - - -
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Residues in contact with ARG 52 (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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40D ARG 4.5 1.2 + - - -
41D SER* 3.2 21.6 + - - -
42D PHE 5.6 0.4 + - - -
44D ARG* 4.1 17.3 - - - +
48F LEU* 2.8 39.9 + - - +
49F ALA 3.9 0.4 - - - +
50F PHE 3.3 0.4 - - - -
51F GLU* 1.3 81.8 - - - +
53F VAL* 1.3 55.8 + - - +
55F THR* 4.7 0.7 - - - -
56F ALA* 3.3 18.0 + - - +
101F TYR* 3.4 36.6 + - + +
102F LEU* 3.4 24.9 - - + +
103F GLY 3.1 30.7 + - - +
104F GLU* 5.3 1.3 + - - -
105F ARG* 3.0 38.4 - - - +
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Residues in contact with VAL 53 (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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29F LYS* 3.2 32.8 - - + +
30F VAL* 3.4 21.3 - - + -
33F GLU* 4.6 7.4 - - + +
49F ALA 3.2 15.2 + - - +
50F PHE 4.3 2.5 - - - +
51F GLU 3.4 0.2 - - - -
52F ARG* 1.3 74.8 - - - +
54F TYR* 1.3 66.7 + - - +
55F THR 2.9 4.9 - - - -
56F ALA* 3.1 2.5 + - + +
57F ASN* 2.8 25.6 + - + +
98F PHE* 4.2 14.2 - - + -
102F LEU* 3.0 40.4 - - + -
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Residues in contact with TYR 54 (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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44D ARG* 6.4 1.8 - - + -
58E GLN* 3.5 26.4 + - + +
59E ASN* 3.9 4.8 + - - -
62E ASP* 3.6 4.7 + - - -
112E TYR* 3.4 33.4 - + - -
30F VAL* 3.8 23.6 - - + -
42F PHE* 4.8 28.9 - + + -
43F GLN 6.0 0.4 - - - -
50F PHE* 3.0 30.6 + + + +
51F GLU* 4.9 3.1 - - - +
53F VAL* 1.3 79.4 - - - +
55F THR* 1.3 58.5 + - - +
57F ASN* 4.8 0.4 - - - -
58F GLN* 3.0 46.5 + - + +
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Residues in contact with THR 55 (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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42D PHE* 4.4 5.8 - - + -
43D GLN 5.6 1.3 - - - +
44D ARG* 2.8 43.2 + - + +
51F GLU 3.0 13.8 + - - -
52F ARG 4.0 1.1 - - - -
53F VAL 2.9 2.0 - - - -
54F TYR* 1.3 78.1 - - - +
56F ALA* 1.3 65.7 + - - -
58F GLN* 3.3 3.6 + - - -
59F ASN* 2.8 39.2 + - - +
101F TYR* 2.8 34.1 - - + +
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Residues in contact with ALA 56 (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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52F ARG 3.3 9.9 + - - +
53F VAL* 3.1 4.0 + - + +
55F THR* 1.3 74.2 - - - +
57F ASN* 1.3 64.1 + - - +
59F ASN* 3.2 15.4 - - - +
60F CYS* 3.3 9.2 + - - -
97F TYR* 4.6 2.1 - - + -
98F PHE* 3.5 32.0 - - + +
101F TYR* 2.9 48.6 - - + +
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Residues in contact with ASN 57 (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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112E TYR* 2.8 38.8 + - - -
506E 2CS 4.2 8.7 - - - -
26F PHE* 2.9 45.9 - - - +
27F ALA* 3.7 2.6 - - - +
30F VAL* 3.5 12.5 - - + +
53F VAL 2.8 16.1 + - - +
54F TYR 3.9 2.2 - - - +
56F ALA* 1.3 72.4 - - - +
58F GLN* 1.3 53.8 + - - +
59F ASN 2.5 17.3 + - - -
60F CYS* 2.6 18.4 + - - +
61F VAL* 3.0 11.7 + - - +
98F PHE* 3.4 8.6 - - + -
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Residues in contact with GLN 58 (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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54D TYR* 3.9 16.2 + - - +
58D GLN* 3.1 15.2 - - + +
58E GLN* 2.9 28.8 - - + +
62E ASP* 3.4 18.4 + - - +
112E TYR* 3.3 24.0 + - - -
54F TYR* 3.0 37.8 + - + +
55F THR* 3.3 6.0 + - - +
57F ASN* 1.3 75.9 - - - +
59F ASN* 1.3 54.4 + - - +
61F VAL* 3.7 18.5 - - - +
62F ASP* 2.8 32.0 - - - +
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Residues in contact with ASN 59 (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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42D PHE* 3.2 21.5 - - - -
54D TYR* 4.6 5.7 + - - -
504D 2CS 4.6 4.3 - - - -
55F THR* 2.8 28.8 + - - +
56F ALA 3.2 8.7 - - - +
57F ASN 2.5 2.6 + - - -
58F GLN* 1.3 79.4 - - - +
60F CYS* 1.3 62.8 + - - +
61F VAL 3.5 0.4 - - - -
62F ASP* 3.9 9.4 + - - +
63F ALA* 4.0 14.7 + - - +
97F TYR* 3.1 28.9 + - + +
101F TYR* 3.4 13.3 - - - -
112F TYR* 3.4 27.7 - - + +
114F PHE* 4.2 5.9 - - - -
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Residues in contact with CYS 60 (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* 5.8 0.4 - - - +
26F PHE* 4.0 30.5 - - + -
56F ALA 3.3 11.2 + - - +
57F ASN* 2.6 10.9 + - - +
59F ASN* 1.3 80.1 - - - +
61F VAL* 1.3 57.7 + - + +
62F ASP 3.2 4.7 - - - -
63F ALA* 3.2 2.8 + - - +
64F TYR 3.1 22.3 + - - -
94F ARG* 3.1 22.7 + - - +
97F TYR* 4.3 4.7 - - - -
98F PHE* 4.1 12.3 - - - -
114F PHE* 3.4 34.3 - - - -
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Residues in contact with VAL 61 (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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58D GLN* 5.6 0.7 - - - +
61D VAL* 4.4 4.6 - - + +
58E GLN* 5.5 0.2 - - - +
61E VAL* 4.8 3.1 - - + +
62E ASP* 4.0 33.9 - - + +
65E PRO* 4.8 8.2 - - + +
66E THR* 5.0 0.4 - - - +
506E 2CS 4.2 14.1 - - + -
23F ASN* 3.9 23.8 - - - +
57F ASN* 3.0 14.3 + - - +
58F GLN* 3.7 30.7 - - - +
59F ASN 3.5 0.2 - - - -
60F CYS* 1.3 78.0 - - + +
62F ASP* 1.3 59.7 + - - +
64F TYR* 4.1 7.6 - - + +
65F PRO* 3.5 15.2 - - - +
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Residues in contact with ASP 62 (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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23D ASN* 5.4 0.5 + - - -
54D TYR* 4.5 0.2 + - - -
58D GLN* 2.8 24.3 + - - +
61D VAL* 3.5 21.1 - - + +
504D 2CS 3.5 32.3 - - + -
58F GLN* 2.8 38.0 - - - +
59F ASN* 4.0 6.1 - - - +
61F VAL* 1.3 81.5 - - - +
63F ALA* 1.3 58.6 + - - +
64F TYR 3.6 0.2 - - - -
65F PRO* 3.4 15.7 - - - +
66F THR* 3.8 5.7 + - - -
112F TYR* 3.0 18.8 + - + +
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Residues in contact with ALA 63 (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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504D 2CS 3.1 30.5 - - + +
59F ASN 4.0 2.6 + - - +
60F CYS 3.2 7.7 + - - +
62F ASP* 1.3 79.1 - - - +
64F TYR* 1.3 66.4 + - - +
65F PRO* 3.4 1.3 - - - -
66F THR* 3.6 3.3 + - - -
67F PHE* 3.1 23.4 + - - +
90F TYR* 3.0 23.8 - - - +
114F PHE* 3.6 17.0 - - + -
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Residues in contact with TYR 64 (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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65E PRO* 3.9 24.2 - - + -
66E THR* 3.9 28.9 - - + -
69E ALA* 4.7 1.9 - - + +
16F THR* 3.6 8.5 + - - +
19F SER* 2.8 35.0 + - - -
20F VAL* 3.6 14.4 + - + +
23F ASN* 3.9 23.1 - - - +
60F CYS 3.1 15.5 + - - +
61F VAL* 4.3 7.9 - - + +
63F ALA* 1.3 76.8 - - - +
65F PRO* 1.3 59.9 - - + +
67F PHE* 3.3 17.2 - + - +
68F LEU* 2.7 65.0 + - + +
90F TYR* 5.7 0.9 - + - -
91F LEU* 6.3 0.2 - - + -
94F ARG* 4.3 10.0 - - - +
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Residues in contact with PRO 65 (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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23D ASN* 5.5 0.7 - - - +
61D VAL* 5.1 8.3 - - + +
64D TYR* 3.9 26.2 - - + -
65D PRO* 5.5 9.0 - - + -
68D LEU* 5.4 5.7 - - + +
65E PRO* 5.4 9.9 - - + -
61F VAL 3.5 14.8 - - - +
62F ASP* 3.4 14.6 - - - +
63F ALA 3.4 1.8 - - - -
64F TYR* 1.3 95.7 - - + +
66F THR* 1.3 63.7 + - - +
67F PHE 2.8 6.6 + - - -
68F LEU* 3.0 7.8 + - + +
69F ALA* 2.9 24.3 + - - +
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Residues in contact with THR 66 (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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20D VAL* 3.3 51.4 - - + +
23D ASN* 3.0 34.8 + - + +
24D GLY 5.0 0.7 - - - +
64D TYR* 4.1 4.2 - - + -
504D 2CS 4.4 17.3 - - + +
62F ASP 3.8 13.2 + - - -
63F ALA 3.6 4.6 + - - -
64F TYR 3.5 0.2 - - - -
65F PRO* 1.3 75.9 - - - +
67F PHE* 1.3 57.3 + - - +
69F ALA* 4.1 1.8 - - - -
70F VAL* 3.6 20.1 - - - +
119F ILE* 4.3 5.8 - - - +
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Residues in contact with PHE 67 (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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504D 2CS 6.2 0.2 - - - -
15F VAL* 5.2 0.9 - - + -
16F THR* 5.7 0.2 - - - -
19F SER* 4.6 4.9 - - - -
63F ALA 3.1 16.8 + - - +
64F TYR* 3.1 27.6 + + - -
65F PRO 2.9 0.6 - - - -
66F THR* 1.3 76.2 - - - +
68F LEU* 1.3 103.5 + - + +
69F ALA 2.9 2.0 + - - -
70F VAL* 3.2 8.1 - - + +
71F LEU* 2.9 37.4 + - + +
87F GLY* 3.9 19.3 - - - -
90F TYR* 3.0 62.8 - + + +
91F LEU* 4.6 10.8 - - + -
118F ILE* 5.4 1.1 - - + -
119F ILE* 4.0 13.7 - - + -
122F LEU* 5.4 2.2 - - + -
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Residues in contact with LEU 68 (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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65E PRO* 6.1 0.4 - - + +
69E ALA* 5.8 2.5 - - + -
16F THR* 3.7 14.1 - - + +
64F TYR* 2.7 59.7 + - + +
65F PRO* 3.5 6.5 - - + +
67F PHE* 1.3 84.0 - - + +
69F ALA* 1.3 67.2 + - - +
71F LEU* 3.2 19.9 + - + -
72F TRP* 2.9 54.6 - - + +
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Residues in contact with ALA 69 (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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16D THR* 4.4 14.4 - - + -
17D LEU* 5.7 0.2 - - + -
20D VAL* 3.2 31.6 - - + -
64D TYR* 4.7 4.9 - - + +
68D LEU* 5.6 3.4 - - + -
65F PRO 2.9 15.2 + - - +
66F THR* 4.0 1.6 - - - +
67F PHE 2.9 0.6 - - - -
68F LEU* 1.3 82.6 - - - +
70F VAL* 1.3 62.9 + - - +
71F LEU 2.9 0.2 + - - -
72F TRP* 3.0 9.6 + - - +
73F SER* 3.0 18.8 + - - -
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Residues in contact with VAL 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 5.6 3.1 - - + +
20D VAL* 3.7 25.8 - - + -
66F THR 3.6 15.0 - - - +
67F PHE* 3.2 10.5 - - + +
69F ALA* 1.3 73.3 - - - +
71F LEU* 1.3 65.9 + - - +
73F SER* 4.3 1.8 - - - -
74F ALA* 2.9 29.8 + - - +
119F ILE* 4.0 25.1 - - + +
122F LEU* 3.3 30.1 - - + +
123F PHE* 3.9 20.4 - - + +
126F SER* 4.3 8.3 - - - -
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Residues in contact with LEU 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 3.7 12.3 - - + +
15F VAL* 3.3 28.0 - - + -
16F THR* 3.4 16.8 - - - +
67F PHE* 2.9 30.2 + - + +
68F LEU* 3.3 18.8 - - + +
69F ALA 2.9 0.6 + - - -
70F VAL* 1.3 80.2 - - - +
72F TRP* 1.3 75.3 + - + +
75F GLY* 3.4 15.4 + - - -
83F ALA* 3.1 33.0 - - - +
84F ALA* 4.3 2.7 - - - -
87F GLY* 4.2 9.0 - - - -
122F LEU* 4.4 4.7 - - + -
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Residues in contact with TRP 72 (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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9F VAL* 3.6 21.1 - - + -
12F LEU* 3.0 54.5 - - + -
13F ALA* 3.7 7.9 - - + -
16F THR* 3.3 26.0 + - + +
68F LEU* 2.9 50.6 - - + +
69F ALA 3.0 5.3 + - - +
71F LEU* 1.3 78.5 - - + +
73F SER* 1.3 57.1 + - - +
74F ALA 2.9 1.8 - - - -
75F GLY 2.4 22.2 + - - -
76F LEU* 2.7 35.7 + - + +
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Residues in contact with SER 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ALA* 5.2 5.0 - - - +
16D THR* 4.4 7.1 - - - +
17D LEU* 3.6 22.1 - - - +
72D TRP* 5.6 3.6 - - - -
69F ALA* 3.0 17.1 + - - -
70F VAL* 4.3 1.6 - - - -
72F TRP* 1.3 76.6 - - - +
74F ALA* 1.3 55.6 + - - +
76F LEU* 4.8 0.9 - - - -
77F LEU* 2.9 48.6 + - - +
126F SER* 2.8 23.7 + - - -
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F VAL 2.9 14.7 + - - +
72F TRP 2.9 0.6 - - - -
73F SER* 1.3 75.5 - - - +
75F GLY* 1.3 50.8 + - - +
76F LEU 3.7 0.2 - - - -
78F CYS* 2.3 28.5 - - - +
83F ALA* 2.8 15.0 - - + +
122F LEU* 2.8 37.5 - - + +
125F MET* 2.9 25.0 - - + +
126F SER* 2.7 10.0 + - - +
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F LEU* 3.8 9.6 - - - -
71F LEU 3.4 6.6 + - - -
72F TRP 2.4 24.2 + - - -
74F ALA* 1.3 68.9 - - - +
76F LEU* 1.3 70.7 + - - +
78F CYS 3.6 5.4 - - - +
79F SER 3.8 0.4 - - - -
80F GLN* 3.5 24.0 + - - +
83F ALA* 3.4 15.7 - - - -
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.2 55.3 + - + +
8F ASN 4.4 15.7 - - - +
9F VAL* 5.6 4.3 - - + -
12F LEU* 4.5 7.0 - - + -
72F TRP* 2.7 63.0 + - + +
73F SER* 4.8 1.1 - - - -
75F GLY* 1.3 82.0 - - - +
77F LEU* 1.3 58.2 + - + +
78F CYS* 2.7 16.3 + - - -
79F SER 4.9 0.2 + - - -
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 3.7 23.8 - - + -
6D VAL* 4.4 17.7 - - + -
9D VAL* 5.7 5.2 - - + -
10D VAL* 5.7 1.8 - - + -
13D ALA* 3.6 31.0 - - + -
17D LEU* 5.5 0.7 - - + -
73F SER* 2.9 28.7 + - - +
76F LEU* 1.3 76.8 - - + +
78F CYS* 1.3 64.3 + - - +
126F SER* 4.0 14.8 - - - +
129F GLY* 2.9 23.5 - - - -
130F ILE* 3.7 27.1 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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