Contacts of the helix formed by residues 47 - 77 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLU* 4.9 1.5 + - - +
36D THR* 5.0 6.3 + - - +
37D GLN* 2.3 39.5 + - - +
46D GLY* 1.3 71.8 - - - +
48D LEU* 1.3 60.3 + - + +
49D ALA* 2.8 30.7 - - + +
50D PHE* 3.0 9.6 + - - -
51D GLU* 2.6 33.3 + - - +
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Residues in contact with LEU 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLY 3.1 16.6 - - - +
47D THR* 1.3 77.7 - - + +
49D ALA* 1.3 50.2 + - - +
51D GLU* 4.2 11.2 - - + -
52D ARG* 2.8 41.8 + - - +
104D GLU 5.1 6.4 - - - +
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLU* 2.9 25.6 - - - +
47D THR* 2.8 17.6 - - + +
48D LEU* 1.3 80.7 - - - +
50D PHE* 1.3 58.4 + - - +
51D GLU 3.4 0.2 - - - -
52D ARG* 3.6 4.5 + - - +
53D VAL* 3.2 25.3 + - - +
102D LEU* 4.6 3.6 - - - +
104D GLU 6.1 0.2 - - - -
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D VAL* 4.8 6.1 - - + -
33D GLU* 3.3 48.9 + - + +
34D SER* 3.7 23.1 - - - -
37D GLN* 3.6 25.6 - - - +
42D PHE* 6.0 0.2 - - + -
43D GLN* 2.8 36.1 - - + -
44D ARG* 3.3 27.4 - - - -
45D THR 3.8 11.0 - - - -
47D THR* 3.0 7.4 + - - +
49D ALA* 1.3 77.4 - - - +
51D GLU* 1.3 63.6 + - - +
52D ARG 3.2 1.1 - - - -
53D VAL* 4.3 1.2 - - + +
54D TYR* 3.0 36.8 + + + +
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Residues in contact with GLU 51 (chain D).
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 3.3 24.4 - - - +
45D THR* 4.2 17.9 - - + +
46D GLY 4.0 8.3 - - - +
47D THR 2.6 21.7 + - - +
48D LEU* 4.2 9.9 - - + -
50D PHE* 1.3 76.9 - - + +
52D ARG* 1.3 58.0 + - - +
54D TYR* 4.3 5.2 - - - -
55D THR* 3.1 37.5 + - - -
43E GLN* 4.1 14.7 - - - +
44E ARG* 3.6 25.1 + - - +
45E THR* 5.1 5.2 - - - +
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Residues in contact with ARG 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D LEU* 2.8 26.6 + - - +
49D ALA* 3.8 6.7 - - - +
50D PHE 3.2 0.2 - - - -
51D GLU* 1.3 81.8 - - - +
53D VAL* 1.3 56.3 + - - +
55D THR* 3.9 6.0 - - + +
56D ALA* 3.2 17.7 + - - +
101D TYR* 3.4 32.3 - - + +
102D LEU* 3.1 30.5 + - + +
103D GLY* 4.6 0.4 - - - -
104D GLU 4.1 11.7 + - - +
105D ARG* 4.9 1.7 - - - +
106D THR* 3.6 24.9 + - - +
107D GLN* 3.7 20.4 - - - +
108D SER 3.7 23.9 + - - -
109D THR* 4.6 4.5 + - - -
41E SER* 4.4 13.3 + - - -
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Residues in contact with VAL 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LYS* 3.4 30.1 - - + +
30D VAL* 3.4 30.1 - - + -
33D GLU* 4.3 9.6 - - + -
49D ALA 3.2 15.3 + - - +
50D PHE* 3.6 3.8 + - + +
51D GLU 3.3 0.2 - - - -
52D ARG* 1.3 75.4 - - - +
54D TYR* 1.3 69.4 + - - +
55D THR 2.9 1.6 - - - -
56D ALA* 3.1 1.8 + - - +
57D ASN* 2.8 24.9 + - - +
98D PHE* 4.6 8.5 - - + -
102D LEU* 3.0 33.4 - - + -
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Residues in contact with TYR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 4.5 13.7 - - + -
43D GLN 5.2 3.6 - - - -
44D ARG* 4.5 15.5 - - + -
50D PHE* 3.0 26.1 + + + +
51D GLU* 4.3 7.4 - - - +
53D VAL* 1.3 85.1 - - + +
55D THR* 1.3 57.3 + - - +
57D ASN* 4.5 3.1 - - - -
58D GLN* 2.9 49.1 + - + +
44E ARG* 3.6 37.7 - - - -
58F GLN* 3.9 21.3 + - - +
59F ASN* 4.6 4.3 + - - -
112F TYR* 3.8 28.7 - + - -
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Residues in contact with THR 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLU* 3.1 24.8 + - - +
52D ARG* 3.9 5.4 - - + +
53D VAL 2.9 1.0 - - - -
54D TYR* 1.3 79.1 - - - +
56D ALA* 1.3 69.3 + - - +
57D ASN 3.1 0.9 + - - -
58D GLN* 3.2 9.0 + - - -
59D ASN* 2.8 26.4 + - - +
101D TYR* 3.2 30.5 - - + +
42E PHE* 4.3 13.0 - - + +
43E GLN* 4.2 2.2 - - - -
44E ARG* 3.7 30.2 + - - +
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Residues in contact with ALA 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ARG 3.2 11.5 + - - +
53D VAL* 3.1 6.8 + - + +
55D THR* 1.3 78.8 - - - +
57D ASN* 1.3 62.8 + - - +
59D ASN* 3.3 7.8 - - - +
60D CYS* 3.1 22.5 - - - -
97D TYR* 4.1 0.5 - - - -
98D PHE* 3.6 20.9 - - + +
101D TYR* 2.9 46.4 - - + +
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 3.4 27.1 - - - +
30D VAL* 3.5 19.9 - - + +
53D VAL 2.8 21.2 + - - +
54D TYR* 3.9 3.4 - - - +
56D ALA* 1.3 68.9 - - - +
58D GLN* 1.3 55.5 + - - +
59D ASN 2.5 17.6 + - - -
60D CYS* 2.7 14.7 + - - +
61D VAL* 3.0 29.4 + - - +
98D PHE* 3.5 11.8 - - + -
504D 2CS 3.6 9.5 - - - -
112F TYR* 2.7 32.8 + - - -
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Residues in contact with GLN 58 (chain D).
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* 2.9 48.6 + - + +
55D THR* 3.2 2.2 + - - +
57D ASN* 1.3 73.6 - - - +
59D ASN* 1.3 61.0 + - - +
61D VAL* 4.2 12.5 - - - +
62D ASP* 2.7 32.0 - - - +
44E ARG* 6.1 1.6 - - - -
54E TYR* 4.2 10.9 + - - +
58E GLN* 2.8 33.6 + - - +
58F GLN* 3.1 14.3 + - + +
61F VAL* 5.6 0.2 - - - +
62F ASP* 2.8 34.6 + - - +
112F TYR* 4.2 2.0 + - - -
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Residues in contact with ASN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D THR* 2.8 23.0 - - - +
56D ALA 3.3 10.3 - - - +
57D ASN 2.5 2.4 + - - -
58D GLN* 1.3 81.6 - - - +
60D CYS* 1.3 64.0 + - - +
61D VAL 3.4 0.7 - - - -
62D ASP* 3.8 10.7 + - - +
63D ALA* 3.9 9.9 + - - +
97D TYR* 2.8 28.5 + - + +
101D TYR* 3.4 21.0 + - - -
112D TYR* 3.5 34.9 - - + +
114D PHE* 3.8 13.8 - - - -
42E PHE* 5.0 3.0 - - - +
54E TYR* 4.7 6.6 + - - -
505E 2CS 4.4 4.9 - - - -
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Residues in contact with CYS 60 (chain D).
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* 5.6 0.8 + - - -
26D PHE* 3.9 28.0 - - + -
56D ALA 3.1 22.2 - - - -
57D ASN 2.7 5.1 + - - +
59D ASN* 1.3 77.5 - - - +
61D VAL* 1.3 59.3 + - + +
62D ASP 3.2 2.2 - - - -
63D ALA 3.4 0.8 + - - -
64D TYR* 3.1 24.4 + - - +
94D ARG* 3.2 24.3 + - - +
97D TYR* 3.7 26.0 - - - -
98D PHE* 4.0 9.6 - - - -
114D PHE* 4.0 13.5 - - - -
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASN* 5.5 6.1 - - - +
26D PHE* 6.2 0.4 - - + -
57D ASN* 3.0 37.4 + - - +
58D GLN* 4.2 15.5 - - - +
59D ASN 3.4 0.2 - - - -
60D CYS* 1.3 79.0 - - + +
62D ASP* 1.3 63.6 + - - +
63D ALA 3.4 0.2 - - - -
64D TYR* 4.2 6.8 - - + +
65D PRO* 3.7 13.0 - - - +
504D 2CS 3.8 18.2 - - + -
61E VAL* 4.5 3.5 - - - +
61F VAL* 4.4 4.9 - - + +
62F ASP* 3.5 38.4 - - + +
65F PRO* 5.1 6.5 - - + +
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Residues in contact with ASP 62 (chain D).
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* 2.7 41.7 - - - +
59D ASN* 3.9 4.9 - - - +
60D CYS 3.2 0.2 - - - -
61D VAL* 1.3 79.2 - - - +
63D ALA* 1.3 59.4 + - - +
64D TYR 3.5 0.2 - - - -
65D PRO* 3.3 10.1 - - - +
66D THR* 3.2 17.0 + - - -
112D TYR* 2.8 29.1 + - - +
58E GLN* 2.9 14.5 + - - +
61E VAL* 3.5 21.0 - - + +
505E 2CS 3.2 29.1 - - + -
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Residues in contact with ALA 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN 3.9 1.7 + - - +
60D CYS 3.4 5.8 + - - +
62D ASP* 1.3 78.0 - - - +
64D TYR* 1.3 65.1 + - - +
65D PRO* 3.2 3.5 - - - -
66D THR* 3.5 4.2 + - - -
67D PHE* 3.0 25.5 + - - +
90D TYR* 2.9 24.5 - - - +
94D ARG* 4.6 0.2 - - - +
114D PHE* 3.6 19.1 - - + -
505E 2CS 3.5 28.6 - - + -
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Residues in contact with TYR 64 (chain D).
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* 3.5 12.1 + - - +
19D SER* 2.9 36.7 + - - -
20D VAL* 3.6 11.3 - - + +
23D ASN* 3.4 27.8 - - - +
60D CYS 3.1 11.7 + - - +
61D VAL* 4.5 5.8 - - - +
63D ALA* 1.3 74.8 - - - +
65D PRO* 1.4 58.2 - - + +
67D PHE* 3.1 11.0 + + - +
68D LEU* 2.7 76.5 + - + +
94D ARG* 3.5 21.0 - - - +
65F PRO* 3.9 21.5 - - + -
66F THR* 4.1 18.2 - - + -
69F ALA* 4.7 1.0 - - + +
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Residues in contact with PRO 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D VAL 3.7 9.4 - - - +
62D ASP* 3.3 19.3 - - - +
63D ALA 3.2 3.8 - - - -
64D TYR* 1.4 97.0 - - + +
66D THR* 1.3 62.3 + - - +
67D PHE 2.9 0.3 + - - -
68D LEU* 3.1 10.1 + - + +
69D ALA* 2.9 29.8 + - - +
61E VAL* 5.0 9.2 - - + +
64E TYR* 4.0 27.1 - - + -
65E PRO* 5.3 10.5 - - + -
68E LEU* 5.6 4.9 - - + +
65F PRO* 5.5 9.6 - - + -
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Residues in contact with THR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASP 3.2 20.6 + - - -
63D ALA 3.8 3.5 + - - -
65D PRO* 1.3 77.5 - - - +
67D PHE* 1.3 59.2 + - - +
69D ALA* 3.8 12.4 - - - +
70D VAL* 4.0 7.6 - - - +
119D ILE* 4.3 6.2 - - - +
20E VAL* 3.7 23.0 - - + +
23E ASN* 3.3 36.5 + - + -
64E TYR* 3.7 15.4 - - + -
505E 2CS 3.9 28.7 + - - +
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Residues in contact with PHE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D VAL* 5.4 0.2 - - + -
19D SER* 4.5 2.2 - - - -
63D ALA 3.0 18.0 + - - +
64D TYR* 3.7 15.7 - + - -
66D THR* 1.3 76.7 - - - +
68D LEU* 1.3 95.2 + - + +
69D ALA 3.0 2.1 + - - -
70D VAL* 3.3 4.3 + - - +
71D LEU* 2.9 41.3 + - + +
87D GLY* 3.6 26.5 - - - -
90D TYR* 3.4 61.7 - + + -
91D LEU* 4.0 15.3 - - + -
119D ILE* 4.1 13.9 - - + -
122D LEU* 4.5 6.7 - - + -
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Residues in contact with LEU 68 (chain D).
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* 4.5 7.6 - - + +
19D SER* 4.8 0.7 - - - +
64D TYR* 2.7 73.5 + - + +
65D PRO* 3.5 8.1 - - + +
67D PHE* 1.3 86.4 - - + +
69D ALA* 1.3 66.9 + - - +
71D LEU* 3.9 15.5 - - + -
72D TRP* 3.1 32.3 + - + +
65F PRO* 5.4 7.2 - - + +
69F ALA* 5.6 5.2 - - + -
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PRO 2.9 15.6 + - - +
66D THR* 3.8 3.8 - - - +
67D PHE 3.0 0.4 - - - -
68D LEU* 1.3 81.4 - - - +
70D VAL* 1.3 58.9 + - - +
71D LEU 3.0 0.3 + - - -
72D TRP* 3.0 1.7 + - - +
73D SER* 2.6 29.2 + - - +
16E THR* 4.6 11.9 - - + -
20E VAL* 3.4 29.2 - - + -
64E TYR* 4.4 8.3 - - + +
68E LEU* 5.5 4.3 - - + -
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D THR 4.0 8.1 - - - +
67D PHE 3.4 9.6 - - - +
69D ALA* 1.3 77.0 - - - +
71D LEU* 1.3 60.7 + - - +
72D TRP 3.2 0.4 - - - -
73D SER* 3.5 8.1 - - - -
74D ALA* 2.8 33.5 + - - +
119D ILE* 3.8 20.2 - - + +
122D LEU* 3.5 27.4 - - + +
123D PHE* 3.7 35.7 - - + +
17E LEU* 4.2 6.1 - - + -
20E VAL* 3.9 23.8 - - + -
505E 2CS 5.4 1.3 - - + -
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Residues in contact with LEU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 3.6 20.9 - - + +
15D VAL* 3.7 24.7 - - + -
16D THR* 3.5 13.9 - - - +
67D PHE* 2.9 35.5 + - + +
68D LEU* 3.3 23.8 - - + +
69D ALA 3.0 0.4 + - - -
70D VAL* 1.3 76.8 - - - +
72D TRP* 1.3 80.9 + - + +
75D GLY* 3.5 11.8 + - - -
83D ALA* 3.6 24.4 - - - +
87D GLY* 4.4 2.7 - - - -
122D LEU* 4.1 7.9 - - - -
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Residues in contact with TRP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 3.3 26.5 - - + -
12D LEU* 3.3 38.4 - - + -
13D ALA* 3.8 8.7 - - + -
16D THR* 3.2 36.1 + - + -
68D LEU* 3.1 25.4 - - + +
69D ALA 3.0 2.5 + - - +
71D LEU* 1.3 91.6 - - + +
73D SER* 1.3 55.8 + - - +
74D ALA 3.0 1.8 - - - -
75D GLY* 2.4 22.1 + - - -
76D LEU* 2.7 39.3 + - + +
73F SER* 5.6 3.6 - - - -
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Residues in contact with SER 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ALA* 2.6 31.6 + - - +
70D VAL* 3.5 3.3 - - - -
72D TRP* 1.3 74.5 - - - +
74D ALA* 1.3 56.8 + - - +
76D LEU* 4.2 5.3 - - - +
77D LEU* 2.8 47.2 + - - +
126D SER* 3.5 19.8 - - - -
13E ALA* 5.5 2.5 - - - -
16E THR* 4.9 3.1 - - - +
17E LEU* 3.6 22.3 - - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D VAL 2.8 22.0 + - - +
72D TRP 3.0 0.6 - - - -
73D SER* 1.3 76.6 - - - +
75D GLY* 1.3 51.9 + - - +
78D CYS 2.3 27.1 - - - +
83D ALA* 3.0 2.6 - - + +
122D LEU* 2.9 27.8 - - + +
125D MET* 2.8 38.3 - - + +
126D SER* 3.7 9.6 - - - +
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASN 5.2 0.3 - - - +
12D LEU* 3.8 11.7 - - - -
71D LEU 3.5 7.0 + - - -
72D TRP 2.4 19.9 + - - -
74D ALA* 1.3 73.3 - - - +
76D LEU* 1.3 68.3 + - - +
78D CYS 3.5 7.9 - - - +
79D SER 3.8 0.6 - - - -
80D GLN* 3.6 21.4 + - - +
83D ALA* 3.4 17.3 - - - -
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ASN 4.9 6.5 - - - +
9D VAL* 5.2 4.7 - - + -
12D LEU* 3.8 18.6 - - + -
72D TRP* 2.7 53.3 + - + +
73D SER* 4.2 2.9 - - - +
75D GLY* 1.3 80.0 - - - +
77D LEU* 1.3 63.0 + - + +
78D CYS* 2.7 17.5 + - - -
79D SER 4.9 0.2 + - - -
1E MET* 3.3 50.7 + - + +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D SER* 2.8 29.9 + - - +
76D LEU* 1.3 87.1 - - + +
78D CYS* 1.3 65.1 + - - +
126D SER* 4.0 14.8 - - - +
129D GLY* 2.9 27.2 + - - -
130D ILE* 3.7 28.7 - - + +
1E MET* 5.2 1.3 - - - -
6E VAL* 4.5 24.9 - - + -
9E VAL* 5.7 7.2 - - + -
10E VAL* 5.9 0.9 - - + -
13E ALA* 3.7 30.5 - - + -
17E LEU* 5.7 1.1 - - + -
----------------------------------------------------------
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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
------------------------------------------------------------
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