Contacts of the helix formed by residues 45 - 73 (chain G) in PDB entry 5AVB
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 ALA 45 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ARG* 5.0 5.4 + - - +
31G HIS* 4.7 10.3 - - + -
43G VAL 3.7 1.2 + - - -
44G GLY* 1.3 72.3 - - - -
46G GLY* 1.3 61.5 + - - +
48G PRO* 3.4 14.9 - - - +
49G VAL* 3.8 11.8 - - - +
121H TYR* 4.5 21.3 + - + +
38I A 2.9 27.0 + - - +
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Residues in contact with GLY 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44G GLY* 3.2 1.4 - - - -
45G ALA* 1.3 78.5 - - - +
47G ALA* 1.3 63.7 + - - +
48G PRO 3.5 0.2 - - - -
49G VAL* 3.1 10.3 + - - +
50G TYR* 3.0 23.6 + - - +
91H SER* 3.9 15.9 - - - +
118H VAL* 3.8 13.1 - - - +
121H TYR* 5.6 3.8 - - - -
38I A 4.7 0.8 + - - -
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 4.5 4.9 - - + -
43G VAL* 4.1 6.3 - - + -
44G GLY 3.3 5.0 + - - +
46G GLY* 1.3 76.1 - - - +
48G PRO* 1.3 65.2 - - + +
50G TYR* 3.4 2.0 + - - +
51G LEU* 2.9 31.3 + - - +
89H ILE* 3.6 28.0 - - + +
90H THR 3.7 13.9 - - - +
91H SER* 3.9 14.5 - - - +
94H ILE* 3.9 10.4 - - + +
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Residues in contact with PRO 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ARG* 4.3 5.4 - - - +
27G VAL* 3.8 11.9 - - + +
30G VAL* 3.8 13.3 - - + +
31G HIS* 3.4 54.3 - - + +
34G LEU* 4.2 3.6 - - + -
43G VAL* 4.1 6.5 - - + -
44G GLY 3.1 15.9 - - - +
45G ALA 3.4 11.2 - - - +
47G ALA* 1.3 92.5 - - + +
49G VAL* 1.3 56.4 + - - +
52G ALA* 3.0 30.1 + - - +
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Residues in contact with VAL 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G ARG* 6.1 0.2 - - - +
21G ALA* 3.9 9.4 - - + -
23G LEU* 3.7 3.9 - - + +
27G VAL* 3.9 24.5 - - + -
45G ALA 3.8 15.0 - - - +
46G GLY* 3.1 8.4 + - - +
48G PRO* 1.3 75.1 - - - +
50G TYR* 1.3 66.8 + - - +
52G ALA 3.3 1.0 + - - -
53G ALA* 3.0 23.4 + - - +
117H ALA* 3.5 39.0 - - + +
118H VAL* 3.8 9.9 - - + -
121H TYR* 3.9 31.4 - - + -
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Residues in contact with TYR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLY 3.0 16.1 + - - +
47G ALA 3.8 3.6 - - - +
49G VAL* 1.3 75.7 - - - +
51G LEU* 1.3 58.1 + - - +
53G ALA* 3.3 3.3 + - - +
54G VAL* 3.0 41.8 + - + +
91H SER* 4.2 18.6 - - - -
94H ILE* 3.5 21.1 - - + -
95H GLN* 2.7 51.9 + - + +
98H VAL* 4.5 3.6 - - + -
110H ALA 4.5 1.1 - - - -
111H VAL* 3.3 27.4 + - - +
114H GLY* 3.5 31.2 - - - -
115H THR* 3.6 6.7 - - - -
118H VAL* 3.9 13.7 - - + +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G VAL* 3.9 12.1 - - + -
34G LEU* 4.0 19.5 - - + -
47G ALA 2.9 17.5 + - - +
48G PRO 4.2 1.8 - - - +
50G TYR* 1.3 74.6 - - - +
52G ALA* 1.3 66.1 + - - +
54G VAL* 3.4 3.3 + - + +
55G LEU* 3.0 43.9 + - + +
70H PHE* 3.5 35.7 - - + +
73H ILE* 3.7 42.0 - - + -
74H ALA* 5.1 1.3 - - + -
94H ILE* 4.1 18.4 - - + +
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Residues in contact with ALA 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 4.1 13.0 - - + -
25G PHE* 3.8 15.9 - - + +
27G VAL* 4.2 12.6 - - + -
30G VAL* 4.1 22.2 - - + +
48G PRO 3.0 21.4 + - - +
49G VAL 3.7 4.0 - - - +
51G LEU* 1.3 77.0 - - - +
53G ALA* 1.3 58.4 + - - +
55G LEU* 3.4 5.4 + - - +
56G GLU* 3.0 29.6 + - - +
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Residues in contact with ALA 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 3.8 17.2 - - + +
49G VAL 3.0 13.3 + - - +
50G TYR 3.4 9.2 - - - +
51G LEU 3.2 0.2 - - - -
52G ALA* 1.3 75.1 - - - +
54G VAL* 1.3 60.1 + - - +
56G GLU* 3.3 2.1 + - - +
57G TYR* 2.9 31.3 + - - +
113H GLU* 3.7 18.9 - - + +
114H GLY* 3.9 4.5 - - - -
117H ALA* 3.7 24.5 - - + -
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Residues in contact with VAL 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.0 39.0 + - + +
51G LEU* 3.8 7.2 - - + +
53G ALA* 1.3 75.4 - - - +
55G LEU* 1.3 58.8 + - - +
57G TYR* 3.4 6.7 + - - +
58G LEU* 3.0 41.0 + - + +
73H ILE* 3.9 25.8 - - + -
98H VAL* 4.0 16.2 - - + -
102H LEU* 4.6 1.8 - - + -
110H ALA* 3.6 35.7 - - + +
114H GLY* 4.7 0.7 - - - -
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Residues in contact with LEU 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 4.1 14.6 - - + -
30G VAL* 4.8 7.6 - - + -
51G LEU* 3.0 31.9 + - + +
52G ALA* 3.8 8.1 - - - +
53G ALA 3.2 0.2 - - - -
54G VAL* 1.3 75.3 - - - +
56G GLU* 1.3 62.7 + - - +
58G LEU* 3.5 4.4 + - + +
59G THR* 2.8 30.4 + - - -
37H TYR* 4.9 2.5 - - + +
65H PHE* 5.3 1.8 - - + -
66H VAL* 3.9 20.1 - - + +
69H ILE* 3.8 31.4 - - + -
70H PHE* 3.8 44.4 - - + +
73H ILE* 4.8 1.1 - - + -
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Residues in contact with GLU 56 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLY 4.7 2.4 - - - +
23G LEU* 3.5 19.2 - - - +
24G GLN* 2.5 45.1 + - - +
25G PHE* 3.0 31.9 + - + -
52G ALA 3.0 17.6 + - - +
53G ALA* 3.7 5.2 - - - +
55G LEU* 1.3 75.2 - - - +
57G TYR* 1.3 59.0 + - - +
59G THR* 3.3 3.6 + - - -
60G ALA* 2.9 27.9 + - + +
44H VAL* 3.9 11.7 - - + +
47H GLN* 4.9 5.5 + - - +
----------------------------------------------------------
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Residues in contact with TYR 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G ALA 2.9 16.3 + - - +
54G VAL* 3.7 4.0 - - - +
56G GLU* 1.3 78.4 - - - +
58G LEU* 1.3 81.5 + - + +
60G ALA* 3.2 9.2 + - + +
61G GLU* 3.1 38.5 + - + +
105H GLU 5.3 0.2 - - - -
106H LEU* 3.8 37.6 - - + +
109H HIS* 3.1 38.6 - + + +
110H ALA* 4.0 13.9 - - + -
113H GLU* 3.8 33.4 - - + +
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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
----------------------------------------------------------
54G VAL* 3.0 34.7 + - + +
55G LEU* 3.8 5.6 - - - +
57G TYR* 1.3 92.9 - - + +
59G THR* 1.3 63.3 + - - +
61G GLU* 3.4 5.1 + - - +
62G ILE* 3.3 27.0 + - - +
93G LEU* 5.4 3.0 - - + +
96G LEU* 4.8 8.1 - - + -
65H PHE* 3.9 19.7 - - + -
69H ILE* 3.6 33.9 - - + -
102H LEU* 4.1 26.7 - - + -
106H LEU* 4.3 20.0 - - + -
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Residues in contact with THR 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 3.3 25.6 - - + -
55G LEU 2.8 22.0 + - - -
56G GLU 3.5 5.2 - - - -
58G LEU* 1.3 78.1 - - - +
60G ALA* 1.3 62.1 + - - +
62G ILE* 3.4 2.1 + - - +
63G LEU* 3.0 40.2 + - + +
41H VAL* 4.3 11.7 - - + -
44H VAL* 4.3 8.3 - - + -
62H MET* 3.8 24.2 - - + -
65H PHE* 4.3 4.6 - - - -
66H VAL* 3.7 13.0 - - - +
----------------------------------------------------------
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Residues in contact with ALA 60 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G GLU* 2.9 14.3 + - + +
57G TYR* 3.2 15.5 + - + +
59G THR* 1.3 77.2 - - - +
61G GLU* 1.3 56.1 + - - +
63G LEU* 3.3 2.6 + - - +
64G GLU* 2.8 34.2 + - - +
44H VAL* 3.7 19.7 - - + +
48H VAL* 4.4 15.9 - - + +
----------------------------------------------------------
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Residues in contact with GLU 61 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TYR* 3.1 36.5 + - + +
58G LEU* 3.7 10.5 - - - +
59G THR 3.4 0.2 - - - -
60G ALA* 1.3 76.3 - - - +
62G ILE* 1.3 61.3 + - - +
64G GLU* 3.6 8.1 + - - +
65G LEU* 3.2 39.3 + - + +
90G ASP* 4.7 6.1 - - - +
93G LEU* 4.4 15.7 - - + -
106H LEU* 4.2 20.1 - - + +
----------------------------------------------------------
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G LEU 3.3 12.7 + - - +
59G THR 3.9 3.1 - - - +
60G ALA 3.3 0.4 - - - -
61G GLU* 1.3 75.6 - - - +
63G LEU* 1.3 55.8 + - - +
65G LEU* 3.2 2.8 + - - +
66G ALA* 2.7 34.7 + - + +
83G LEU* 3.8 25.8 - - + +
86G ALA* 4.5 2.1 - - + +
87G ILE* 4.5 23.8 - - + -
93G LEU* 3.9 30.1 - - + -
97G LEU* 4.6 0.4 - - + -
62H MET* 4.1 11.9 - - + -
65H PHE* 3.5 47.3 - - + -
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Residues in contact with LEU 63 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G THR* 3.0 35.9 + - + +
60G ALA 3.8 3.1 - - - +
62G ILE* 1.3 77.0 - - - +
64G GLU* 1.3 57.5 + - - +
66G ALA* 4.4 2.5 - - - -
67G GLY* 2.8 27.4 + - - -
78G ILE* 4.0 19.5 - - + +
83G LEU* 4.9 4.0 - - + -
41H VAL* 3.5 27.4 - - + +
44H VAL* 4.1 3.8 - - + -
45H LEU* 3.7 25.8 - - + +
48H VAL* 4.2 10.8 - - + -
49H HIS* 3.6 6.5 - - - -
54H ILE* 4.5 11.0 - - + -
62H MET* 4.3 26.5 - - + -
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Residues in contact with GLU 64 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G ALA 2.8 18.6 + - - +
61G GLU* 3.7 10.5 - - - +
63G LEU* 1.3 76.6 - - - +
65G LEU* 1.3 69.3 + - + +
68G ASN* 3.1 39.1 + - - +
48H VAL* 4.0 20.4 - - + +
49H HIS* 3.1 32.2 + - - -
----------------------------------------------------------
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLU* 3.2 26.5 + - - +
62G ILE* 3.8 1.6 - - - +
64G GLU* 1.3 87.0 - - + +
66G ALA* 1.3 58.9 + - - +
68G ASN* 3.4 18.2 + - - +
69G ALA* 3.1 24.1 + - - +
86G ALA* 3.6 20.7 - - + +
90G ASP* 3.7 26.7 - - + +
93G LEU* 3.6 28.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 66 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ILE 2.7 21.7 + - - +
63G LEU* 4.1 2.9 - - - +
65G LEU* 1.3 70.1 - - - +
67G GLY* 1.3 61.0 + - - +
69G ALA* 3.2 3.9 + - - +
70G ALA* 3.0 26.9 + - - +
78G ILE* 4.0 13.5 - - + +
82G HIS* 3.7 19.9 - - - +
83G LEU* 3.6 27.6 - - + -
86G ALA* 3.5 11.1 - - + +
----------------------------------------------------------
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Residues in contact with GLY 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU 2.8 19.0 + - - -
64G GLU 3.9 0.2 - - - -
66G ALA* 1.3 77.6 - - - +
68G ASN* 1.3 54.9 + - - +
70G ALA* 3.2 5.7 + - - +
71G ARG* 3.0 26.6 + - - +
78G ILE* 3.8 14.1 - - - +
49H HIS* 3.5 21.1 - - - -
52H THR* 4.7 6.5 + - - +
----------------------------------------------------------
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Residues in contact with ASN 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLU* 3.1 31.1 + - - +
65G LEU* 3.6 19.0 - - + +
67G GLY* 1.3 73.0 - - - +
69G ALA* 1.3 58.8 + - - +
71G ARG* 3.1 8.8 + - - +
72G ASP* 2.8 40.7 + - - +
49H HIS* 3.4 20.8 + - - -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G LEU 3.1 13.4 + - - +
66G ALA 3.2 9.8 + - - +
68G ASN* 1.3 75.5 - - - +
70G ALA* 1.3 62.0 + - - +
72G ASP* 3.4 9.5 + - - +
73G ASN* 2.9 31.5 + - - +
82G HIS* 3.7 28.0 - - + +
85G LEU* 4.4 15.9 - - + -
86G ALA* 4.7 2.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ALA 3.0 12.3 + - - +
67G GLY* 3.4 9.9 - - - +
69G ALA* 1.3 73.4 - - - +
71G ARG* 1.3 60.1 + - - +
73G ASN 3.2 2.4 + - - -
74G LYS 3.1 4.5 + - - -
75G LYS* 2.7 43.3 + - - +
76G THR 5.0 2.0 - - - -
77G ARG 4.4 4.5 - - - +
78G ILE* 4.3 12.1 - - + -
82G HIS* 3.8 30.2 - - + +
52H THR* 5.1 2.0 - - + -
----------------------------------------------------------
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Residues in contact with ARG 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G GLY 3.0 12.0 + - - +
68G ASN* 3.1 14.3 + - - +
70G ALA* 1.3 75.7 - - - +
72G ASP* 1.3 63.3 + - - +
74G LYS* 2.9 23.4 + - - +
75G LYS 3.8 7.5 + - - +
76G THR* 6.2 2.8 - - - +
49H HIS* 5.2 10.9 + - - -
51H ASP* 5.8 7.1 + - - +
52H THR* 4.9 10.1 + - - -
----------------------------------------------------------
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Residues in contact with ASP 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASN* 2.8 31.2 + - - +
69G ALA* 3.6 9.5 - - - +
70G ALA 3.3 0.2 - - - -
71G ARG* 1.3 77.2 - - - +
73G ASN* 1.3 62.9 + - - +
74G LYS* 3.1 10.4 + - - +
----------------------------------------------------------
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Residues in contact with ASN 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ALA* 2.9 19.9 + - - +
70G ALA 3.2 4.4 + - - +
72G ASP* 1.3 79.8 - - - +
74G LYS* 1.3 72.2 + - - +
75G LYS* 3.1 24.2 + - + +
81G ARG* 5.1 6.1 - - - +
82G HIS* 4.0 24.0 + - - +
85G LEU* 4.2 19.5 - - - +
----------------------------------------------------------
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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