Contacts of the helix formed by residues 47 - 77 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.9 7.3 + - - +
37C GLN* 2.7 39.3 + - - +
46C GLY* 1.3 82.8 + - - +
48C LEU* 1.3 81.5 + - - +
49C ALA* 3.0 17.9 - - + +
50C PHE 3.9 3.4 - - - -
51C GLU* 2.9 25.9 - - - +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 5.2 6.7 - - - -
44A ARG* 4.5 12.6 - - - +
47C THR* 1.3 89.0 - - - +
49C ALA* 1.3 59.9 + - - +
50C PHE 3.5 0.4 - - - -
51C GLU* 4.3 10.8 - - + +
52C ARG* 2.8 74.8 - - + +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLU* 3.3 29.8 - - - +
37C GLN* 3.8 0.9 - - - +
47C THR* 3.0 11.8 - - + +
48C LEU* 1.3 81.7 - - - +
50C PHE* 1.3 59.1 + - - +
51C GLU 3.4 0.2 - - - -
52C ARG* 3.7 2.0 + - - -
53C VAL* 3.2 19.6 + - - +
102C LEU* 3.8 14.0 - - + +
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Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C VAL* 3.9 9.9 - - + -
33C GLU* 3.3 37.9 - - + +
34C SER* 3.8 18.4 - - - -
37C GLN* 3.5 20.3 - - + +
42C PHE* 3.7 21.8 - + - -
43C GLN 3.2 27.6 - - - -
44C ARG 4.2 9.9 - - - -
45C THR 4.4 4.0 - - - -
46C GLY 4.0 19.5 - - - -
47C THR* 3.7 3.1 - - - +
49C ALA* 1.3 79.2 - - - +
51C GLU* 1.3 61.8 + - - +
52C ARG 3.2 1.3 - - - -
53C VAL* 3.8 0.9 - - + +
54C TYR* 3.0 38.8 + + + +
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A SER* 3.1 27.4 + - - +
43A GLN* 3.1 21.1 + - + +
44A ARG* 2.3 44.7 + - - +
44C ARG 3.6 18.2 - - - +
45C THR* 2.6 25.0 + - - +
46C GLY 3.8 2.9 - - - +
47C THR 2.9 20.9 + - - +
48C LEU* 4.3 8.5 - - + -
50C PHE* 1.3 80.2 - - + +
52C ARG* 1.3 60.0 + - - +
55C THR* 3.2 26.3 + - - -
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 3.0 56.2 - - - +
41A SER* 4.7 8.0 - - - +
48C LEU* 2.8 53.7 + - + +
49C ALA* 3.7 2.7 + - - +
50C PHE 3.2 0.2 - - - -
51C GLU* 1.3 80.6 - - - +
53C VAL* 1.3 56.8 + - - +
55C THR* 3.0 21.9 - - + +
56C ALA 3.3 4.9 + - - -
101C TYR* 3.5 13.2 - - + +
102C LEU* 3.4 38.0 - - + +
105C ARG* 3.4 36.6 - - - +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE 5.2 1.6 - - - +
29C LYS* 3.2 37.2 - - + +
30C VAL* 3.0 29.8 - - + -
33C GLU* 4.0 12.3 - - + -
49C ALA 3.2 14.4 + - - +
50C PHE 4.2 0.4 - - - +
52C ARG* 1.3 75.8 - - - +
54C TYR* 1.3 66.4 + - - +
55C THR 2.9 1.9 + - - -
56C ALA* 3.1 3.4 + - - +
57C ASN* 2.8 25.6 + - + +
98C PHE* 4.4 5.9 - - + -
102C LEU* 3.4 34.5 - - + -
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Residues in contact with TYR 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLN* 2.8 41.3 - - - +
58B GLN* 3.7 20.3 + - - +
59B ASN* 4.2 2.5 + - - -
112B TYR* 4.0 20.2 - + - -
30C VAL* 3.4 20.4 - - + -
42C PHE* 3.9 33.4 - + - -
44C ARG* 4.5 18.6 - - + +
50C PHE* 3.0 26.8 + + + +
53C VAL* 1.3 79.8 - - - +
55C THR* 1.3 56.3 + - - +
57C ASN* 3.9 1.1 - - - +
58C GLN* 3.0 56.2 + - + +
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Residues in contact with THR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG 3.7 9.4 - - - +
41A SER* 4.3 2.2 - - - -
42A PHE* 3.5 18.7 + - - -
43A GLN* 2.5 23.0 + - - +
51C GLU 3.2 12.5 + - - +
52C ARG* 3.0 17.3 - - - +
53C VAL 2.9 1.8 - - - -
54C TYR* 1.3 73.9 - - - +
56C ALA* 1.3 69.7 - - - +
57C ASN 3.0 1.2 + - - -
58C GLN* 3.0 8.6 + - - -
59C ASN* 2.3 32.2 + - - +
101C TYR* 2.9 25.3 - - + -
112C TYR* 3.4 19.5 + - - -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ARG 3.6 8.7 - - - +
53C VAL* 3.1 4.8 + - - +
55C THR* 1.3 81.5 - - - +
57C ASN* 1.3 62.4 + - - +
59C ASN* 3.4 11.2 + - - +
60C CYS* 3.4 21.0 - - - -
97C TYR* 4.0 1.9 - - - -
98C PHE* 3.5 24.2 - - + -
101C TYR* 3.3 41.7 - - + +
102C LEU* 5.0 0.4 - - + -
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Residues in contact with ASN 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B TYR* 3.1 37.6 + - - -
26C PHE* 3.1 39.9 - - - +
27C ALA* 3.9 2.2 - - - +
30C VAL* 4.2 10.8 - - + +
53C VAL 2.8 16.0 + - - +
54C TYR* 3.9 3.9 - - - +
56C ALA* 1.3 72.6 - - - +
58C GLN* 1.3 54.5 + - - +
59C ASN 2.6 17.7 + - - -
60C CYS* 2.7 17.2 + - - +
61C VAL* 3.0 13.8 + - - +
98C PHE* 3.8 13.2 - - + -
501C 2CS 4.6 10.6 - - - -
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Residues in contact with GLN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLN* 5.3 0.9 - - - +
54A TYR* 3.5 19.4 + - - +
58A GLN* 2.9 25.7 - - + +
58B GLN* 4.3 5.7 - - + +
61B VAL* 5.1 0.2 - - - +
62B ASP* 3.1 21.2 + - - +
112B TYR* 3.1 26.3 + - - -
54C TYR* 3.0 50.0 + - + +
55C THR* 3.0 1.5 + - - +
57C ASN* 1.3 74.0 - - - +
59C ASN* 1.3 63.7 + - - +
61C VAL* 3.3 17.3 - - - +
62C ASP* 3.3 17.2 - - - +
112C TYR* 5.8 0.2 - - - +
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Residues in contact with ASN 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A 2CS 4.9 3.1 - - - -
55C THR* 2.3 29.4 + - - +
56C ALA* 3.5 5.3 - - - +
57C ASN 2.6 2.6 + - - -
58C GLN* 1.3 79.7 - - - +
60C CYS* 1.3 64.3 + - - +
61C VAL 3.4 1.1 - - - -
62C ASP* 3.9 11.8 + - - +
63C ALA* 3.8 9.0 + - - +
97C TYR* 2.7 30.1 + - - +
101C TYR* 3.4 24.7 - - - -
112C TYR* 3.1 44.6 + - + +
113C ILE 5.8 0.3 + - - -
114C PHE* 3.6 13.9 - - - -
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Residues in contact with CYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASN* 5.7 1.3 - - - +
26C PHE* 3.4 37.2 - - + -
56C ALA 3.4 14.6 - - - -
57C ASN* 3.4 7.2 - - - +
59C ASN* 1.3 79.2 - - - +
61C VAL* 1.3 58.7 + - - +
62C ASP 3.1 1.6 - - - -
63C ALA* 3.1 0.9 + - - -
64C TYR* 3.0 25.6 + - - +
94C ARG* 3.4 27.3 + - - +
97C TYR* 3.6 27.4 - - - -
98C PHE* 4.2 1.8 - - - -
114C PHE* 4.1 8.3 - - - -
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Residues in contact with VAL 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A GLN* 5.0 0.9 - - - +
61A VAL* 4.6 3.4 - - + +
61B VAL* 5.1 4.5 - - + +
62B ASP* 3.7 37.0 - - + +
65B PRO* 5.3 6.9 - - + +
112B TYR* 4.9 2.0 - - - +
23C ASN* 5.2 7.0 - - - +
57C ASN* 3.0 16.5 + - - +
58C GLN* 3.3 31.4 - - - +
59C ASN 3.8 0.2 - - - +
60C CYS* 1.3 80.5 - - - +
62C ASP* 1.3 65.8 + - - +
64C TYR* 4.1 6.0 - - + +
65C PRO* 3.5 14.9 - - - +
501C 2CS 3.8 20.4 - - + -
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Residues in contact with ASP 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 5.8 0.2 + - - -
54A TYR* 3.9 5.7 + - - -
57A ASN* 4.3 4.7 - - - +
58A GLN* 2.9 37.8 + - - +
61A VAL* 3.6 18.9 - - + +
502A 2CS 3.6 29.9 - - + -
58C GLN 3.3 18.1 - - - +
59C ASN* 3.9 6.0 + - - +
60C CYS 3.1 0.4 - - - -
61C VAL* 1.3 84.6 - - - +
63C ALA* 1.3 58.2 + - - +
65C PRO* 3.3 10.2 - - - +
66C THR* 3.2 16.5 + - - -
112C TYR* 4.1 14.8 - - + -
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Residues in contact with ALA 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A 2CS 3.5 21.0 - - + -
59C ASN 3.9 1.6 - - - +
60C CYS 3.1 4.1 + - - +
62C ASP* 1.3 78.3 - - - +
64C TYR* 1.3 65.1 + - - +
65C PRO* 3.2 3.4 - - - -
66C THR* 3.5 2.7 + - - -
67C PHE* 3.1 25.5 + - - +
90C TYR* 3.0 24.2 + - - +
114C PHE* 3.2 29.6 - - + -
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Residues in contact with TYR 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PRO* 4.0 22.9 - - + -
66B THR* 3.6 17.5 - - + -
69B ALA* 4.6 4.2 - - + +
16C THR* 3.6 5.9 + - - +
19C SER* 2.8 33.5 + - - -
20C VAL* 3.5 16.3 + - + +
23C ASN* 3.0 31.4 - - - +
60C CYS 3.0 12.1 + - - +
61C VAL* 4.2 6.5 - - - +
63C ALA* 1.3 73.1 - - - +
65C PRO* 1.3 65.8 - - + +
67C PHE* 3.5 11.7 - + - -
68C LEU* 2.8 59.0 + - + +
94C ARG* 3.4 27.5 - - - +
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Residues in contact with PRO 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.8 9.2 - - + +
64A TYR* 3.6 27.7 - - + -
65A PRO* 5.5 8.5 - - + -
68A LEU* 6.1 0.8 - - + +
65B PRO* 5.6 9.4 - - + -
61C VAL 3.5 10.3 - - - +
62C ASP* 3.3 17.9 - - - +
63C ALA 3.2 3.1 - - - -
64C TYR* 1.3 99.0 - - + +
66C THR* 1.3 64.0 + - - +
67C PHE 2.9 0.3 + - - -
68C LEU* 3.1 8.4 + - + +
69C ALA* 2.9 29.6 + - - +
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 3.4 31.7 - - + +
23A ASN* 3.1 46.7 + - + +
64A TYR* 3.6 9.0 - - + -
502A 2CS 3.8 24.0 - - + +
62C ASP 3.2 20.8 + - - -
63C ALA 3.7 3.8 + - - -
65C PRO* 1.3 76.5 - - - +
67C PHE* 1.3 58.1 + - - +
69C ALA* 3.7 6.3 - - - +
70C VAL* 4.1 2.8 + - - +
119C ILE* 4.0 10.4 - - - +
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Residues in contact with PHE 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C VAL* 5.4 2.2 - - + -
16C THR* 6.3 0.2 - - - -
19C SER* 4.7 3.8 - - - -
63C ALA 3.1 16.1 + - - +
64C TYR* 3.5 26.9 - + - -
65C PRO 3.0 0.8 - - - -
66C THR* 1.3 77.2 - - - +
68C LEU* 1.3 93.8 + - + +
69C ALA 2.9 1.9 + - - -
70C VAL* 3.2 5.0 + - - +
71C LEU* 2.9 41.3 + - + +
87C GLY* 3.8 23.8 - - - -
90C TYR* 3.4 58.6 - + + +
91C LEU* 4.0 9.2 - - + -
119C ILE* 3.8 15.7 - - + -
122C LEU* 4.5 6.7 - - + -
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Residues in contact with LEU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PRO* 5.9 2.7 - - + +
69B ALA* 5.8 4.3 - - + -
16C THR* 3.7 25.1 - - + +
19C SER* 5.2 0.4 - - - +
64C TYR* 2.8 60.6 + - + +
65C PRO* 3.5 7.4 - - + +
67C PHE* 1.3 92.3 - - + +
69C ALA* 1.3 67.9 + - - +
71C LEU* 3.2 9.0 + - + -
72C TRP* 3.3 31.3 + - + +
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Residues in contact with ALA 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 4.6 13.7 - - + -
17A LEU* 5.8 0.4 - - + -
20A VAL* 3.4 29.2 - - + -
64A TYR* 4.3 8.5 - - + +
68A LEU* 5.9 2.0 - - + -
65C PRO 2.9 15.2 + - - +
66C THR* 3.7 2.5 - - - +
67C PHE 2.9 0.4 - - - -
68C LEU* 1.3 82.0 - - - +
70C VAL* 1.3 60.7 + - - +
71C LEU 3.0 2.9 + - - -
72C TRP* 3.1 1.4 + - - +
73C SER* 3.1 23.9 + - - -
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Residues in contact with VAL 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.4 6.5 - - + -
20A VAL* 3.7 29.6 - - + -
502A 2CS 5.7 0.7 - - + -
66C THR 4.1 2.7 - - - +
67C PHE 3.2 10.0 + - - +
69C ALA* 1.3 73.3 - - + +
71C LEU* 1.3 59.2 + - - +
72C TRP 3.2 0.4 - - - -
73C SER* 3.5 8.3 - - - +
74C ALA* 2.9 32.3 + - - +
119C ILE* 3.7 22.4 - - + +
122C LEU* 3.0 34.7 - - + +
123C PHE* 3.7 28.0 - - + +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.7 9.6 - - + +
15C VAL* 3.3 26.7 - - + -
16C THR* 3.9 3.4 - - - +
67C PHE* 2.9 36.1 + - + +
68C LEU* 3.4 13.5 - - + +
69C ALA 3.0 0.2 + - - -
70C VAL* 1.3 77.4 - - - +
72C TRP* 1.3 89.2 + - + +
75C GLY* 3.4 16.6 + - - -
83C ALA* 3.0 32.6 - - - +
84C ALA* 4.4 4.7 - - - -
87C GLY* 3.8 13.2 - - - -
122C LEU* 4.1 7.0 - - + -
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Residues in contact with TRP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER* 5.4 4.3 - - - -
9C VAL* 3.7 23.6 - - + -
12C LEU* 3.2 48.5 - - + -
13C ALA* 3.8 8.7 - - + -
16C THR* 3.2 20.5 + - + -
68C LEU* 3.3 22.7 - - + +
69C ALA 3.1 2.7 + - - +
71C LEU* 1.3 104.2 - - + +
73C SER* 1.3 55.8 + - - +
74C ALA 3.0 1.3 - - - -
75C GLY* 2.4 23.2 + - - +
76C LEU* 2.7 36.9 + - + +
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Residues in contact with SER 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA* 5.5 2.9 - - - -
16A THR* 5.6 3.1 - - - -
17A LEU* 3.2 25.4 - - - +
69C ALA 3.1 11.5 + - - -
70C VAL* 3.5 10.6 - - - -
72C TRP* 1.3 76.3 - - - +
74C ALA* 1.3 57.1 + - - +
76C LEU* 4.1 3.6 - - - +
77C LEU* 2.8 46.9 + - - +
126C SER* 2.8 29.6 + - - -
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Residues in contact with ALA 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C VAL 2.9 16.1 + - - +
72C TRP 3.0 0.8 - - - -
73C SER* 1.3 79.7 + - - +
75C GLY* 1.3 51.3 + - - +
78C CYS 2.3 28.1 - - - +
83C ALA* 3.0 11.0 - - + +
122C LEU 2.8 30.5 - - - +
125C MET* 3.1 27.9 - - + +
126C SER* 3.6 8.5 - - - +
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Residues in contact with GLY 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASN 5.1 0.2 - - - +
12C LEU* 3.9 10.3 - - - -
71C LEU 3.4 7.0 + - - -
72C TRP 2.4 24.7 + - - -
74C ALA* 1.3 69.9 - - - +
76C LEU* 1.3 68.4 + - - +
78C CYS 3.7 2.4 - - - +
79C SER 3.8 0.4 - - - -
80C GLN* 3.5 25.8 + - - +
83C ALA* 3.4 16.6 - - - -
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.5 57.8 + - + +
8C ASN 4.7 9.4 - - - +
9C VAL* 5.2 3.6 - - + -
12C LEU* 3.6 18.2 - - + -
72C TRP* 2.7 58.1 + - + +
73C SER* 4.1 2.2 - - - +
75C GLY* 1.3 80.7 - - - +
77C LEU* 1.3 58.9 + - + +
78C CYS* 2.7 16.7 + - - -
79C SER 5.0 0.2 + - - -
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.0 5.8 - - + -
6A VAL* 3.9 28.7 - - + -
9A VAL* 5.7 5.6 - - + -
10A VAL* 5.9 1.8 - - + -
13A ALA* 3.7 31.2 - - + -
17A LEU* 5.5 0.9 - - + -
73C SER* 2.8 33.1 + - - +
76C LEU* 1.3 87.3 - - + +
78C CYS* 1.3 65.1 + - - +
125C MET 4.3 0.4 - - - -
126C SER* 4.1 14.8 - - - +
129C GLY* 2.9 26.8 + - - -
130C ILE* 4.3 20.6 - - + +
----------------------------------------------------------
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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