Contacts of the helix formed by residues 47 - 77 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 3.9 5.6 - - - +
46B GLY* 1.3 95.6 + - - +
48B LEU* 1.3 56.8 + - - +
49B ALA* 2.3 23.8 + - - +
50B PHE* 2.9 13.7 + - - +
51B GLU* 3.2 27.6 + - - +
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B THR* 1.3 70.3 - - - +
49B ALA* 1.3 61.4 + - + +
50B PHE 3.5 0.2 - - - -
51B GLU* 3.8 12.2 + - - -
52B ARG* 2.8 53.2 + - - +
103B GLY* 5.3 0.2 - - - -
104B GLU* 5.2 7.4 - - - +
105B ARG 5.7 3.1 - - - +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU* 3.5 22.1 - - - +
47B THR 2.3 19.4 + - - +
48B LEU* 1.3 73.4 - - + +
50B PHE* 1.3 58.7 + - - +
51B GLU 3.4 0.2 - - - -
52B ARG* 3.7 3.6 - - - +
53B VAL* 3.2 29.3 + - - +
102B LEU* 5.0 7.9 - - + +
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 4.0 14.1 - - + -
33B GLU* 3.4 40.6 - - + +
34B SER* 3.8 8.3 - - - -
39B GLY* 5.7 1.3 - - - -
42B PHE* 3.1 35.0 - + - -
43B GLN 2.7 26.2 - - - -
44B ARG* 4.3 5.8 - - - -
45B THR 3.6 3.1 - - - -
46B GLY* 2.8 30.3 - - - -
47B THR 2.9 11.8 + - - +
49B ALA* 1.3 75.5 - - - +
51B GLU* 1.3 61.3 + - + +
52B ARG 3.2 1.6 - - - -
53B VAL* 5.3 0.7 - - + -
54B TYR* 3.1 39.5 + + + +
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Residues in contact with GLU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG 5.4 0.7 - - - +
45B THR* 2.8 39.3 + - - +
46B GLY 4.2 0.2 - - - +
47B THR* 3.2 35.7 + - - +
48B LEU* 3.8 13.9 + - - +
50B PHE* 1.3 78.4 - - + +
52B ARG* 1.3 59.3 + - - +
54B TYR* 4.9 3.3 - - - +
55B THR* 3.0 29.7 + - - -
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 2.8 46.6 + - - +
49B ALA 3.8 3.6 - - - +
50B PHE 3.2 0.4 - - - -
51B GLU* 1.3 80.4 - - - +
53B VAL* 1.3 57.3 + - - +
55B THR* 3.8 6.5 - - - +
56B ALA* 3.2 18.0 + - - +
101B TYR* 3.4 21.3 - - + +
102B LEU 3.3 21.5 - - - +
103B GLY* 3.2 19.8 - - - -
105B ARG* 2.9 34.2 + - - +
106B THR 3.9 0.2 + - - -
108B SER* 2.3 36.4 + - - -
41C SER* 3.1 25.0 + - - -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LYS* 3.2 31.4 - - + +
30B VAL* 3.0 29.4 - - + -
33B GLU* 4.1 10.5 - - + +
49B ALA 3.2 19.8 + - - +
50B PHE* 4.2 1.6 - - + +
51B GLU 3.4 0.2 - - - -
52B ARG* 1.3 75.9 - - - +
54B TYR* 1.3 57.5 + - - +
55B THR 2.8 5.7 + - - -
56B ALA* 3.1 3.7 + - + +
57B ASN* 2.8 29.6 + - - +
98B PHE* 4.1 13.1 - - + -
101B TYR 5.3 2.2 - - - +
102B LEU* 4.5 19.7 - - + -
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 5.5 0.8 - - + +
58A GLN* 3.4 18.6 + - + +
59A ASN* 3.3 19.7 + - - -
112A TYR* 3.8 18.6 - + - -
30B VAL* 3.6 20.2 - - + -
42B PHE* 4.6 10.8 - + - -
44B ARG* 4.2 36.6 + - + -
50B PHE* 3.1 32.8 + + + +
51B GLU* 4.9 2.7 - - - +
53B VAL* 1.3 77.9 - - - +
55B THR* 1.3 56.8 + - - +
57B ASN* 4.0 5.6 - - - -
58B GLN* 3.0 62.2 + - + +
44C ARG* 6.0 1.6 - - - -
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU 3.0 22.8 + - - +
52B ARG* 3.8 7.4 - - - +
53B VAL 2.8 1.0 - - - -
54B TYR* 1.3 78.6 - - - +
56B ALA* 1.3 67.9 + - - +
57B ASN 3.2 1.0 + - - -
58B GLN* 3.2 10.1 + - - +
59B ASN* 2.9 26.0 - - - +
101B TYR* 3.6 34.1 - - + +
42C PHE* 3.7 17.8 + - + +
43C GLN* 4.7 1.9 - - - -
44C ARG* 4.7 13.3 + - - +
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG 3.2 12.2 + - - +
53B VAL* 3.1 6.1 + - + +
55B THR* 1.3 80.3 - - - +
57B ASN* 1.3 63.5 + - - +
59B ASN* 3.3 14.2 - - - +
60B CYS* 3.4 9.9 + - - -
97B TYR* 4.0 1.6 - - - -
98B PHE* 3.6 26.4 - - + +
101B TYR* 3.4 46.2 - - + +
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Residues in contact with ASN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A TYR* 2.4 26.8 + - - -
503A 2CS 3.8 19.4 - - - -
26B PHE* 3.9 18.8 + - + +
30B VAL* 3.8 11.4 - - + -
53B VAL 2.8 19.9 + - - +
54B TYR* 3.6 5.0 - - - +
56B ALA* 1.3 69.1 - - - +
58B GLN* 1.3 86.8 + - - +
59B ASN 2.6 16.7 + - - -
60B CYS* 2.7 17.8 + - - +
61B VAL* 2.9 13.4 + - - +
98B PHE* 3.4 18.5 - - + -
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Residues in contact with GLN 58 (chain B).
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* 3.1 28.3 - - + +
62A ASP* 3.0 33.8 + - - +
54B TYR* 3.0 42.5 + - + +
55B THR* 3.2 3.6 + - - +
57B ASN* 1.3 109.4 + - - +
59B ASN* 1.3 58.6 + - - +
61B VAL* 3.6 12.7 - - - +
62B ASP* 2.3 28.4 - - - +
54C TYR* 3.7 15.0 + - - +
58C GLN* 4.4 6.3 - - - +
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Residues in contact with ASN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 2.9 18.7 + - - +
56B ALA 3.3 7.9 - - - +
57B ASN 2.6 2.6 + - - -
58B GLN* 1.3 81.2 - - - +
60B CYS* 1.3 63.6 + - - +
61B VAL 3.4 0.9 - - - -
62B ASP* 3.0 12.4 - - - +
63B ALA* 3.9 8.0 + - - +
97B TYR* 2.8 28.8 + - - +
101B TYR* 3.1 25.1 + - - -
111B GLY 4.2 1.4 + - - -
112B TYR* 3.3 28.0 - - + +
114B PHE* 3.9 14.9 - - - -
42C PHE* 3.9 21.0 - - - -
54C TYR* 4.2 4.0 + - - -
501C 2CS 4.8 1.4 - - - -
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Residues in contact with CYS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 3.7 27.1 - - + -
56B ALA 3.8 6.5 - - - +
57B ASN 2.7 7.5 + - - +
59B ASN* 1.3 80.3 - - - +
61B VAL* 1.3 58.4 + - + +
62B ASP 3.2 2.0 - - - -
63B ALA* 3.3 6.8 + - - +
64B TYR* 3.0 24.8 + - - +
94B ARG* 3.2 42.1 + - - +
97B TYR* 3.5 30.5 - - - -
98B PHE* 4.2 5.4 - - - -
114B PHE* 4.4 0.7 - - - -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 4.9 2.7 - - - +
61A VAL 4.6 3.6 - - - +
62A ASP* 3.7 38.8 - - + +
65A PRO* 5.4 6.8 - - + +
66A THR* 5.8 0.4 - - - +
503A 2CS 3.8 21.3 - - + -
23B ASN* 6.3 1.8 - - - +
57B ASN* 2.9 17.9 + - - +
58B GLN* 3.6 24.0 - - - +
59B ASN 3.4 0.4 - - - +
60B CYS* 1.3 79.5 - - + +
62B ASP* 1.3 66.8 + - - +
64B TYR* 4.2 6.1 - - + +
65B PRO* 3.6 13.7 - - - +
58C GLN* 5.1 0.2 - - - +
61C VAL* 5.1 4.6 - - + +
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Residues in contact with ASP 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 2.3 30.1 - - - +
59B ASN* 3.0 6.0 - - - +
60B CYS 3.2 0.2 - - - -
61B VAL* 1.3 83.2 - - - +
63B ALA* 1.3 59.7 + - - +
64B TYR 3.6 0.2 - - - -
65B PRO* 3.3 9.1 - - - +
66B THR* 3.3 13.9 + - - -
112B TYR* 2.8 38.0 + - + +
58C GLN* 3.1 22.0 - - - +
61C VAL* 3.7 19.9 - - + +
501C 2CS 3.1 26.6 - - + -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ASN 3.9 3.9 + - - +
60B CYS* 3.3 7.5 + - - +
62B ASP* 1.3 80.6 - - - +
64B TYR* 1.3 64.8 + - - +
65B PRO* 3.3 1.5 - - - -
66B THR* 3.5 3.4 + - - -
67B PHE* 3.1 23.7 + - - +
90B TYR* 2.9 22.2 + - - +
114B PHE* 3.5 18.4 - - + -
501C 2CS 3.5 28.5 - - + -
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Residues in contact with TYR 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO* 3.8 26.2 - - + -
66A THR* 4.2 15.3 - - + -
69A ALA* 4.6 1.4 - - + +
16B THR* 3.6 11.3 + - - +
19B SER* 3.2 33.7 + - - -
20B VAL* 3.7 12.5 + - - +
23B ASN* 3.2 28.5 - - - +
60B CYS 3.0 15.3 + - - +
61B VAL* 4.3 7.2 - - + +
63B ALA* 1.3 74.5 - - - +
65B PRO* 1.3 59.1 - - + +
67B PHE* 3.1 16.9 + + - +
68B LEU* 2.8 66.6 + - + +
94B ARG* 3.5 18.6 - - - +
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Residues in contact with PRO 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO* 5.4 10.1 - - + -
61B VAL 3.6 13.0 - - - +
62B ASP* 3.3 17.3 - - - +
63B ALA 3.3 0.4 - - - -
64B TYR* 1.3 95.1 - - + +
66B THR* 1.3 65.5 + - - +
67B PHE 2.9 10.3 + - - -
68B LEU* 3.1 7.8 + - + +
69B ALA* 2.9 24.5 + - - +
61C VAL* 5.3 7.6 - - + +
64C TYR* 4.0 24.0 - - + -
65C PRO* 5.6 9.6 - - + -
68C LEU* 5.9 2.5 - - + +
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Residues in contact with THR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP 3.3 19.4 + - - -
63B ALA 3.5 3.5 + - - -
65B PRO* 1.3 76.7 - - - +
67B PHE* 1.3 58.2 + - - +
69B ALA* 3.9 2.6 - - - +
70B VAL* 4.0 8.0 - - - +
119B ILE* 4.4 6.2 - - - +
20C VAL* 3.5 37.0 - - + +
23C ASN* 2.8 48.9 + - + +
64C TYR* 3.6 10.5 - - + -
501C 2CS 4.1 18.1 - - + +
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Residues in contact with PHE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B VAL* 4.9 1.6 - - + -
19B SER* 4.6 3.4 - - - -
63B ALA 3.1 17.7 + - - +
64B TYR* 3.2 18.2 - + - +
65B PRO 2.9 0.2 - - - -
66B THR* 1.3 77.1 - - - +
68B LEU* 1.3 93.6 + - + +
69B ALA 2.9 1.8 + - - -
70B VAL* 3.2 5.0 + - - +
71B LEU* 2.8 41.7 + - + +
87B GLY* 3.5 29.6 - - - -
90B TYR* 3.3 58.3 - + + -
91B LEU* 4.1 10.5 - - + -
118B ILE* 5.0 0.7 - - + -
119B ILE* 4.1 14.1 - - + -
122B LEU* 4.7 6.5 - - + -
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO* 5.7 1.8 - - + +
69A ALA* 5.5 4.7 - - + -
16B THR* 3.9 15.7 - - + +
19B SER* 5.0 0.4 - - - +
64B TYR* 2.8 59.2 + - + +
65B PRO* 3.6 7.0 - - + +
67B PHE* 1.3 98.8 - - + +
69B ALA* 1.3 67.7 + - - +
71B LEU* 3.1 25.8 + - + -
72B TRP* 3.1 29.0 - - + +
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO 2.9 15.5 + - - +
66B THR* 3.9 2.5 - - - +
67B PHE 2.9 0.4 - - - -
68B LEU* 1.3 81.0 - - - +
70B VAL* 1.3 62.1 + - + +
71B LEU 3.0 0.2 + - - -
72B TRP* 3.8 1.7 - - - +
73B SER* 3.0 26.7 + - - -
16C THR* 4.8 12.3 - - + -
20C VAL* 3.5 27.4 - - + -
64C TYR* 4.6 8.5 - - + +
68C LEU* 5.8 3.1 - - + -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B THR 4.0 4.9 - - - +
67B PHE 3.4 11.4 - - - +
69B ALA* 1.3 78.9 - - + +
71B LEU* 1.3 58.0 + - - +
72B TRP 3.2 0.2 - - - -
73B SER* 4.3 0.9 - - - -
74B ALA* 3.0 31.1 + - - +
119B ILE* 3.9 24.9 - - + +
122B LEU* 3.4 28.2 - - + +
123B PHE* 3.8 28.9 - - + +
126B SER* 4.2 8.7 - - - +
17C LEU* 4.9 5.6 - - + -
20C VAL* 3.9 27.4 - - + -
501C 2CS 5.6 0.7 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.9 8.2 - - + +
15B VAL* 4.0 21.3 - - + -
16B THR* 3.6 24.0 - - - +
67B PHE* 2.8 33.2 + - + +
68B LEU* 3.3 23.3 - - + +
69B ALA 3.0 0.6 + - - -
70B VAL* 1.3 77.7 - - - +
72B TRP* 1.3 69.6 + - + +
75B GLY* 3.5 14.4 + - - -
83B ALA* 3.1 31.5 - - - +
84B ALA* 4.3 6.3 - - - -
87B GLY* 4.0 10.3 - - - -
122B LEU* 4.1 6.1 - - + -
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Residues in contact with TRP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 3.9 20.4 - - + -
12B LEU* 3.2 67.1 - - + -
13B ALA* 3.7 7.6 - - + -
16B THR* 3.5 21.4 + - + +
68B LEU* 3.1 33.5 + - + +
69B ALA 3.0 5.1 + - - +
71B LEU* 1.3 81.9 - - + +
73B SER* 1.3 56.7 + - - +
74B ALA 2.9 1.8 - - - -
75B GLY* 2.3 23.9 + - - +
76B LEU* 2.7 39.5 + - + +
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA 3.0 16.4 + - - -
70B VAL* 4.3 1.6 - - - -
72B TRP* 1.3 76.2 - - - +
74B ALA* 1.3 56.1 + - - +
76B LEU* 4.7 2.2 - - - -
77B LEU* 2.9 47.1 + - - +
126B SER* 2.8 19.5 + - - -
13C ALA* 5.2 3.8 - - - +
16C THR* 4.2 9.4 - - - +
17C LEU* 3.6 24.1 - - - +
72C TRP* 5.4 4.7 - - - -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B VAL 3.0 16.1 + - - +
72B TRP 2.9 0.8 - - - -
73B SER* 1.3 75.5 - - - +
75B GLY* 1.3 52.0 + - - +
76B LEU 3.6 0.2 - - - -
78B CYS* 2.3 28.3 - - - +
83B ALA* 2.9 13.6 - - - +
122B LEU* 2.8 31.0 - - + +
125B MET* 2.9 30.1 - - + +
126B SER* 2.7 11.3 + - - +
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.0 11.4 - - - -
71B LEU 3.5 7.0 + - - -
72B TRP* 2.3 25.3 + - - -
74B ALA* 1.3 68.9 - - - +
76B LEU* 1.3 67.5 + - - +
78B CYS 3.3 9.6 - - - +
79B SER 3.8 0.6 - - - -
80B GLN* 3.5 20.3 + - - +
83B ALA* 3.4 15.5 - - - -
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASN 4.5 10.3 - - - +
9B VAL* 5.5 2.5 - - + -
12B LEU* 4.2 13.5 - - + -
72B TRP* 2.7 62.6 + - + +
73B SER* 4.3 1.1 - - - +
75B GLY* 1.3 78.2 - - - +
77B LEU* 1.3 57.4 + - + +
78B CYS* 2.6 17.4 + - - -
1C MET* 3.0 57.5 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER* 2.9 29.8 + - - +
76B LEU* 1.3 74.9 - - + +
78B CYS* 1.3 63.6 + - - +
126B SER* 4.1 11.0 - - - +
129B GLY* 2.9 23.7 + - - -
130B ILE* 3.1 38.6 - - + +
1C MET* 3.2 27.1 - - + -
6C VAL* 4.0 20.2 - - + -
9C VAL* 5.6 4.5 - - + -
10C VAL* 5.9 1.1 - - + -
13C ALA* 3.6 20.9 - - + -
17C LEU* 4.7 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