Contacts of the helix formed by residues 32 - 69 (chain G) in PDB entry 3H1J
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 ASP 32 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 5.6 4.9 + - - -
73F ARG* 2.6 31.5 + - - -
27G PRO 5.3 1.0 - - - +
28G ASN* 2.9 30.3 + - + +
30G PHE 3.0 1.0 - - - -
31G SER* 1.3 83.0 - - - +
33G ALA* 1.3 63.0 + - - +
35G PRO* 3.3 10.8 - - - +
36G ASN* 2.6 36.5 + - - +
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Residues in contact with ALA 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ARG* 6.1 0.9 - - - +
2003D CDL 4.1 30.4 + - - +
73F ARG* 4.3 11.9 - - - +
26G ILE* 6.1 1.1 - - + -
27G PRO 4.9 3.3 + - - +
28G ASN 2.8 10.0 + - - +
29G ILE* 3.1 27.8 - - + +
32G ASP* 1.3 77.5 - - - +
34G LEU* 1.3 64.8 + - - +
35G PRO* 3.8 0.2 - - - +
36G ASN* 2.9 12.3 + - - +
37G VAL* 3.2 13.8 + - - +
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2003D CDL 3.8 22.7 - - - +
29G ILE* 3.1 17.0 + - + +
30G PHE* 4.0 26.7 - - + +
33G ALA* 1.3 76.6 - - - +
35G PRO* 1.3 72.0 - - + +
37G VAL* 2.9 20.0 + - + +
38G TRP* 2.8 24.8 + - - +
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Residues in contact with PRO 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G PHE 2.9 29.6 - - - +
31G SER 4.0 9.6 - - - +
32G ASP* 3.3 15.5 - - - +
33G ALA 3.3 0.2 - - - -
34G LEU* 1.3 93.0 - - + +
36G ASN* 1.3 58.2 + - - +
38G TRP* 3.5 9.4 + - + +
39G ARG* 2.9 22.9 + - - +
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Residues in contact with ASN 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2003D CDL 4.9 2.5 - - - +
72F HIS 4.4 2.7 - - - +
73F ARG* 3.3 31.6 - - - +
74F ILE 5.5 0.2 + - - -
32G ASP* 2.6 41.4 + - - -
33G ALA 2.9 7.1 + - - +
35G PRO* 1.3 76.3 - - - +
37G VAL* 1.3 68.7 + - - +
38G TRP 3.0 1.3 - - - -
39G ARG* 2.4 37.9 + - - +
40G ARG* 2.7 32.6 + - + +
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Residues in contact with VAL 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2003D CDL 4.4 25.3 + - - +
33G ALA 3.2 18.3 + - - +
34G LEU* 2.9 28.3 + - + +
36G ASN* 1.3 75.0 - - - +
38G TRP* 1.3 60.0 + - - +
40G ARG* 3.4 12.1 + - - +
41G PHE* 2.9 32.5 + - + +
2004G CDL 4.0 29.4 - - + +
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Residues in contact with TRP 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU 2.8 11.0 + - - +
35G PRO* 3.5 11.4 - - + +
37G VAL* 1.3 75.7 - - - +
39G ARG* 1.3 65.3 + - - +
41G PHE* 3.0 36.5 + + - +
42G SER* 2.7 56.6 + - - -
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Residues in contact with ARG 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007C PEE 4.6 8.9 + - - -
72F HIS 3.7 18.2 + - - -
73F ARG* 4.3 3.5 - - - +
74F ILE* 4.0 44.7 - - - +
35G PRO 2.9 16.3 + - - +
36G ASN* 2.4 58.5 + - - +
38G TRP* 1.3 79.4 - - - +
40G ARG* 1.3 85.5 + - - +
42G SER* 3.4 7.0 - - - -
43G SER* 3.0 25.6 + - - +
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Residues in contact with ARG 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007C PEE 4.2 7.4 - - - +
2003D CDL 3.5 33.9 + - - -
72F HIS* 3.5 40.2 + - - +
36G ASN* 2.7 27.2 + - - +
37G VAL* 3.7 8.3 - - - +
39G ARG* 1.3 96.4 - - - +
41G PHE* 1.3 69.0 + - - +
43G SER* 2.8 20.7 + - - -
44G GLN* 3.2 12.0 + - - +
2004G CDL 2.5 92.7 + - - +
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Residues in contact with PHE 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G VAL* 2.9 23.1 + - + +
38G TRP* 3.4 33.0 - + + +
40G ARG* 1.3 74.3 - - - +
42G SER* 1.3 68.4 + - - +
44G GLN* 3.0 9.2 + - - +
45G VAL* 3.0 40.4 + - + -
2004G CDL 3.7 35.9 - - + +
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Residues in contact with SER 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G TRP* 2.7 60.3 + - - -
39G ARG* 3.4 7.2 - - - -
41G PHE* 1.3 77.7 - - - +
43G SER* 1.3 62.4 + - - +
44G GLN 3.3 0.5 + - - -
45G VAL* 3.5 18.5 - - - +
46G PHE* 4.3 9.4 - - - -
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Residues in contact with SER 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007C PEE 5.7 2.9 + - - -
39G ARG* 3.0 13.3 + - - +
40G ARG* 2.8 19.2 + - - -
41G PHE 3.1 0.2 + - - -
42G SER* 1.3 78.3 - - - +
44G GLN* 1.3 70.2 + - - +
46G PHE* 5.1 2.7 + - - +
47G LYS* 4.0 14.4 - - - +
2004G CDL 5.4 0.2 + - - -
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Residues in contact with GLN 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C TYR* 4.1 3.6 + - - -
323C GLN* 3.3 17.9 + - - +
327C TRP* 4.6 9.5 - - - +
2007C PEE 3.4 37.8 + - - +
40G ARG 3.2 8.4 + - - +
41G PHE 3.0 3.2 + - - +
43G SER* 1.3 85.2 + - - +
45G VAL* 1.3 61.3 + - - +
46G PHE 3.2 2.9 - - - -
47G LYS* 2.9 49.0 + - - +
48G VAL* 3.0 15.5 + - + +
2004G CDL 3.4 42.6 - - - +
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Residues in contact with VAL 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G PHE* 3.0 39.7 + - + +
42G SER* 3.5 18.4 - - - +
44G GLN* 1.3 76.4 - - - +
46G PHE* 1.3 78.9 + - + +
48G VAL 4.6 0.7 - - - +
49G ALA* 2.9 48.0 + - + +
2004G CDL 4.6 14.1 - - + +
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Residues in contact with PHE 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C THR* 5.3 0.9 + - - -
42G SER 4.3 9.1 + - - +
43G SER 5.7 2.0 - - - +
44G GLN* 3.2 1.4 - - - +
45G VAL* 1.3 96.7 - - + +
47G LYS* 1.3 62.7 + - + +
50G PRO* 3.1 26.6 - - + +
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Residues in contact with LYS 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C THR 5.2 0.8 + - - -
320C PRO* 3.8 23.1 - - + +
323C GLN* 2.9 46.9 + - + +
324C THR* 4.2 21.6 + - - +
327C TRP* 4.0 13.7 - - + +
23F ALA 4.6 8.7 + - - -
24F ALA 5.8 0.6 + - - -
43G SER 4.0 13.0 - - - +
44G GLN* 2.9 29.7 + - - +
46G PHE* 1.3 84.4 - - + +
48G VAL* 1.3 64.6 + - + +
50G PRO* 3.9 1.0 - - - +
51G PRO* 3.6 16.1 - - - +
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Residues in contact with VAL 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C TRP* 3.6 37.4 - - + +
2007C PEE 3.9 25.8 - - + +
44G GLN* 3.0 18.8 + - - +
45G VAL 4.6 0.2 - - - +
47G LYS* 1.3 75.7 - - - +
49G ALA* 1.3 69.6 + - - +
50G PRO 3.3 0.2 - - - -
51G PRO* 3.0 21.5 - - - +
52G PHE* 3.7 31.6 + - + +
2004G CDL 4.4 20.4 - - + +
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G VAL* 2.9 33.7 + - + +
48G VAL* 1.3 80.6 - - - +
50G PRO* 1.3 57.7 - - + +
52G PHE* 3.1 6.8 + - - -
53G LEU* 2.6 40.2 + - + +
2004G CDL 5.6 0.6 - - + +
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Residues in contact with PRO 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C THR* 6.3 0.9 - - + -
45G VAL 3.4 4.0 - - - +
46G PHE* 3.1 34.8 - - + +
47G LYS 4.6 0.4 - - - +
48G VAL 3.4 4.0 - - - -
49G ALA* 1.3 92.3 - - + +
51G PRO* 1.4 66.8 - - + +
53G LEU* 3.1 10.7 + - + +
54G GLY* 2.7 29.5 + - - -
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Residues in contact with PRO 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C THR* 4.7 7.9 - - + +
327C TRP* 3.6 29.8 - - + +
328C LEU* 3.2 44.4 - - + +
331C ALA* 3.6 7.5 - - + +
47G LYS 3.6 9.0 - - - +
48G VAL 3.0 21.5 - - - +
50G PRO* 1.4 89.5 - - + +
52G PHE* 1.3 55.9 + - + +
54G GLY* 3.5 1.6 + - - +
55G ALA* 2.9 26.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C TRP* 4.1 20.2 - + - -
330C VAL* 3.7 22.0 - - + -
331C ALA* 3.4 37.9 - - + -
334C LEU* 4.2 19.1 - - + -
2007C PEE 4.3 20.0 - - + -
48G VAL* 3.9 29.8 - - + +
49G ALA* 3.1 8.9 + - - +
51G PRO* 1.3 73.2 - - - +
53G LEU* 1.3 69.0 + - - +
54G GLY 3.0 1.1 - - - -
55G ALA* 3.0 3.9 + - - +
56G TYR* 2.7 24.1 + - - +
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Residues in contact with LEU 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ALA* 2.6 24.6 + - + +
50G PRO* 3.5 8.3 - - + +
52G PHE* 1.3 71.5 - - - +
54G GLY* 1.3 67.1 + - - +
56G TYR* 3.0 27.1 - - + +
57G LEU* 3.1 30.0 + - + +
----------------------------------------------------------
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Residues in contact with GLY 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G PRO 2.7 15.7 + - - -
51G PRO* 3.7 2.0 - - - -
53G LEU* 1.3 79.1 - - - +
55G ALA* 1.3 63.4 + - - +
57G LEU* 2.8 23.9 + - - +
58G LEU* 3.1 10.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ALA* 4.1 13.5 - - + +
334C LEU* 5.5 7.0 - - + -
335C ILE* 3.8 37.7 - - + +
51G PRO 2.9 18.6 + - - +
52G PHE* 3.6 4.9 - - + +
54G GLY* 1.3 71.5 - - - +
56G TYR* 1.3 64.2 + - - +
58G LEU* 3.1 6.7 + - - +
59G TYR* 2.9 22.3 + - - +
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Residues in contact with TYR 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G PHE 2.7 16.6 + - - +
53G LEU* 3.0 20.6 - - + +
54G GLY 2.9 0.2 + - - -
55G ALA* 1.3 72.3 - - - +
57G LEU* 1.3 88.0 + - + +
59G TYR* 3.0 35.0 - + - +
60G SER* 3.2 26.4 + - - -
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Residues in contact with LEU 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LEU* 3.3 31.6 - - + +
54G GLY* 2.8 15.4 + - - +
56G TYR* 1.3 90.2 - - + +
58G LEU* 1.3 65.2 + - - +
59G TYR 2.7 2.4 + - - -
60G SER* 2.7 19.4 + - - +
61G TRP* 2.9 13.6 + - - -
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Residues in contact with LEU 58 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C ILE* 3.7 29.2 - - + -
338C TRP* 3.7 8.7 - - + -
351C ILE* 3.8 39.7 - - + -
54G GLY 3.1 8.3 + - - +
55G ALA* 3.4 10.3 - - - +
57G LEU* 1.3 78.0 - - - +
59G TYR* 1.3 63.4 - - - +
61G TRP* 4.0 17.7 - - + -
62G GLY 3.1 14.7 + - - -
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Residues in contact with TYR 59 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C TRP* 3.2 48.4 - + + -
342C GLN* 5.3 0.9 - - - -
55G ALA 2.9 11.3 + - - +
56G TYR* 3.0 28.5 - + - +
57G LEU 2.7 4.2 + - - -
58G LEU* 1.3 74.6 - - - +
60G SER* 1.3 64.6 + - - +
62G GLY* 3.6 0.3 - - - -
63G THR* 2.7 65.5 + - + +
----------------------------------------------------------
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Residues in contact with SER 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G TYR* 3.2 39.5 + - - -
57G LEU* 2.7 13.2 + - - -
59G TYR* 1.3 79.4 - - - +
61G TRP* 1.3 57.5 + - - -
63G THR* 3.5 4.2 - - - -
64G GLN* 2.7 57.0 + - - +
----------------------------------------------------------
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Residues in contact with TRP 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C HIS* 5.1 6.1 - + - -
347C PRO* 3.5 34.1 - - + -
350C ILE* 5.9 1.8 - - + -
351C ILE* 3.9 11.9 - - + -
57G LEU 2.9 13.2 + - - +
58G LEU* 4.0 21.5 - - + +
60G SER* 1.3 78.6 - - - +
62G GLY* 1.3 71.1 + - - +
64G GLN* 3.7 5.5 - - + +
65G GLU* 2.7 63.2 + - + +
----------------------------------------------------------
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Residues in contact with GLY 62 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C TRP* 4.1 7.9 - - - -
347C PRO* 3.5 16.1 - - - +
348C PHE* 3.8 8.0 - - - -
351C ILE* 4.2 1.1 - - - -
58G LEU 3.1 10.0 + - - -
59G TYR 3.6 2.2 - - - -
61G TRP* 1.3 98.7 - - - +
63G THR* 1.3 56.8 + - - +
66G PHE* 3.0 28.2 + - - +
----------------------------------------------------------
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Residues in contact with THR 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C TRP* 3.8 5.9 + - - -
348C PHE* 4.7 4.7 - - + -
59G TYR* 2.7 60.3 + - + +
60G SER* 3.5 6.3 - - - -
62G GLY* 1.3 69.8 - - - +
64G GLN* 1.3 72.2 + - + +
66G PHE* 3.0 9.8 + - + +
67G GLU* 3.0 30.6 + - + +
----------------------------------------------------------
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Residues in contact with GLN 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G SER* 2.7 50.2 + - - +
61G TRP* 3.7 4.2 - - + +
63G THR* 1.3 76.7 - - + +
65G GLU* 1.3 58.6 + - - +
67G GLU* 3.0 9.9 + - - +
68G ARG* 2.7 29.8 + - - +
----------------------------------------------------------
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Residues in contact with GLU 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C HIS* 4.5 7.6 + - - +
347C PRO* 4.1 15.7 - - + -
61G TRP* 2.7 55.7 + - + +
62G GLY 4.0 2.9 - - - +
64G GLN* 1.3 73.4 - - - +
66G PHE* 1.3 62.7 + - - +
68G ARG* 2.9 38.3 + - - -
69G LEU* 3.2 40.6 + - + +
----------------------------------------------------------
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Residues in contact with PHE 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C GLN* 5.7 1.3 - - - -
343C PRO* 4.0 18.2 - - + -
345C GLU* 3.5 32.1 - - + -
346C HIS 3.4 17.9 - - - -
347C PRO* 3.8 9.6 - - + -
348C PHE* 3.7 28.3 - + + -
2D GLU* 3.9 7.2 - - - -
62G GLY 3.0 19.8 + - - +
63G THR* 3.0 7.0 + - + +
65G GLU* 1.3 78.6 - - - +
67G GLU* 1.3 71.9 + - + +
69G LEU* 3.5 13.9 + - + +
70G LYS* 3.5 43.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 5.9 1.0 - - - +
63G THR* 3.0 21.7 + - + +
64G GLN* 3.3 12.3 - - - +
66G PHE* 1.3 85.1 - - + +
68G ARG* 1.3 59.6 + - - +
70G LYS* 2.8 60.9 + - - +
71G ARG* 3.6 8.8 + - - +
----------------------------------------------------------
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Residues in contact with ARG 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLN 2.7 15.2 + - - +
65G GLU* 2.9 34.8 + - - +
67G GLU* 1.3 67.6 - - - +
69G LEU* 1.3 84.2 + - - +
70G LYS 2.6 16.3 + - - -
71G ARG* 2.9 31.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C HIS* 3.8 35.9 - - + +
2D GLU* 5.6 1.9 - - - +
65G GLU* 3.2 30.9 + - + +
66G PHE* 3.6 10.3 - - + +
67G GLU 3.2 0.4 - - - -
68G ARG* 1.3 109.4 - - - +
70G LYS* 1.3 60.3 + - - +
71G ARG 4.1 4.5 - - - +
----------------------------------------------------------
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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