Contacts of the helix formed by residues 47 - 77 (chain A) in PDB entry 5AM8
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 4.2 1.9 + - - -
45A ASN* 3.1 28.0 + - - +
46A ILE* 1.3 82.3 - - - +
48A ALA* 1.3 65.0 + - - +
49A GLU* 3.5 8.1 + - - +
50A ASN* 3.0 28.3 + - - +
51A ALA* 3.0 23.6 + - - +
120A ARG* 6.5 0.4 - - - -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 1.3 74.3 - - - +
49A GLU* 1.3 56.8 + - - +
51A ALA* 3.4 7.5 + - - +
52A ARG* 2.9 28.5 + - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.2 8.1 + - - +
48A ALA* 1.3 79.6 - - - +
50A ASN* 1.3 58.3 + - - +
52A ARG* 2.7 40.0 + - - +
53A ARG* 2.9 71.3 + - - +
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 4.6 1.6 - - - +
41A ALA* 3.4 21.2 + - + +
42A HIS* 3.8 23.1 - - - +
45A ASN* 2.9 40.9 + - - +
47A THR* 3.0 21.1 + - - +
49A GLU* 1.3 73.0 - - - +
51A ALA* 1.3 60.6 + - - +
53A ARG* 3.4 30.7 + - - +
54A GLN* 2.9 29.8 + - - +
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A HIS* 3.6 20.7 - - + +
47A THR 3.0 17.7 + - - +
48A ALA* 3.5 7.6 - - - +
49A GLU 3.2 0.2 - - - -
50A ASN* 1.3 74.0 - - - +
52A ARG* 1.3 65.7 + - - +
54A GLN* 3.1 4.0 + - - +
55A GLU* 2.9 35.3 + - - +
116A SER* 3.9 19.5 + - - +
117A GLN* 5.1 6.7 - - - +
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Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA 2.9 14.6 + - - +
49A GLU* 2.7 53.6 + - - +
51A ALA* 1.3 76.1 - - - +
53A ARG* 1.3 71.2 + - - +
55A GLU* 3.3 13.4 + - + +
56A GLU* 3.0 49.4 + - - +
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 4.1 8.0 - - + +
41A ALA* 6.4 1.3 - - - -
49A GLU* 2.9 51.3 + - - +
50A ASN* 3.5 25.2 + - - +
52A ARG* 1.3 84.1 - - - +
54A GLN* 1.3 63.1 + - - +
56A GLU* 3.3 16.3 + - - +
57A ALA* 3.0 22.5 + - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 5.0 4.9 + - - -
38A ALA* 3.8 15.5 - - + +
39A SER* 3.5 38.6 + - - +
42A HIS* 4.5 7.9 - - + -
50A ASN 2.9 17.8 + - - +
51A ALA* 3.1 6.5 + - - +
53A ARG* 1.3 78.0 - - - +
55A GLU* 1.3 63.3 + - - +
57A ALA* 3.2 3.0 + - + +
58A ALA* 2.8 38.5 + - - +
112A ASN* 4.8 2.8 - - - +
115A LEU* 5.9 1.7 - - - +
116A SER* 3.6 17.7 + - - -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 2.9 24.9 + - - +
52A ARG* 3.6 12.3 - - + +
54A GLN* 1.3 79.5 - - - +
56A GLU* 1.3 58.7 + - - +
58A ALA* 3.3 7.6 + - - +
59A LEU* 2.9 30.1 + - - +
109A GLN 5.1 1.0 - - - +
112A ASN* 3.8 22.1 + - + +
113A ALA* 3.7 24.7 + - - +
116A SER* 2.5 36.1 + - - +
117A GLN* 5.0 2.3 + - - -
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.0 39.3 + - - +
53A ARG* 3.6 12.2 - - - +
54A GLN 3.3 0.2 - - - -
55A GLU* 1.3 72.9 - - - +
57A ALA* 1.3 66.9 + - - +
59A LEU* 3.2 12.2 + - - +
60A LEU* 3.2 20.6 + - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 3.1 37.6 + - - +
35A SER* 3.9 9.2 - - - -
38A ALA* 3.6 26.9 - - + -
53A ARG 3.0 8.6 + - - +
54A GLN 3.5 8.3 - - - +
56A GLU* 1.3 77.9 - - - +
58A ALA* 1.3 62.6 + - - +
60A LEU* 3.2 3.1 + - - +
61A SER* 3.1 19.2 + - - -
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 4.7 6.2 + - - +
54A GLN* 2.8 30.8 + - - +
55A GLU* 3.6 7.2 - - - +
56A GLU 3.3 0.2 - - - -
57A ALA* 1.3 78.2 - - - +
59A LEU* 1.3 56.1 + - - +
61A SER* 3.3 9.1 + - - -
62A GLN* 3.0 34.2 + - - +
112A ASN* 3.9 21.3 - - + +
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU 2.9 15.9 + - - +
56A GLU* 3.2 13.2 + - - +
58A ALA* 1.3 75.7 - - - +
60A LEU* 1.3 57.9 + - - +
62A GLN* 3.4 19.5 + - - +
63A GLU* 3.0 28.3 + - - +
105A LEU* 4.0 22.9 - - + -
108A ARG* 3.8 25.8 + - + +
109A GLN* 4.0 25.1 - - + +
112A ASN* 3.8 6.5 - - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.0 25.4 - - + -
2A ASP 5.7 0.7 - - - +
5A LEU* 4.9 8.5 - - + -
31A VAL* 4.5 10.5 - - + -
34A GLN* 3.7 31.2 - - + +
56A GLU 3.2 8.3 + - - +
57A ALA 3.2 8.6 + - - +
59A LEU* 1.3 76.8 - - - +
61A SER* 1.3 66.6 + - - +
63A GLU* 3.2 17.0 + - - +
64A PHE* 3.0 23.4 + - - +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.7 17.2 + - - +
32A LEU* 5.0 7.3 + - - +
34A GLN* 3.3 19.1 + - - -
35A SER* 3.4 15.5 - - - -
57A ALA 3.1 7.1 + - - -
58A ALA* 3.3 11.0 + - - -
60A LEU* 1.3 78.3 - - - +
62A GLN* 1.3 57.4 + - - +
64A PHE* 3.3 4.4 + - - +
65A ALA* 2.9 30.4 + - - +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 3.0 17.6 + - - +
59A LEU* 3.4 17.1 - - - +
60A LEU 3.3 0.2 - - - -
61A SER* 1.3 76.5 - - - +
63A GLU* 1.3 58.8 + - - +
65A ALA* 4.5 2.0 - - - +
66A GLU* 2.9 28.2 + - - +
100A SER* 2.8 38.3 + - - +
101A ALA* 3.3 21.7 - - + +
108A ARG* 3.7 27.3 + - - +
111A TYR* 4.3 2.6 - - - -
112A ASN* 2.8 41.8 + - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 2.6 49.3 + - + +
59A LEU 3.0 13.4 + - - +
60A LEU* 3.2 21.4 + - - +
62A GLN* 1.3 76.5 - - - +
64A PHE* 1.3 63.2 + - - +
66A GLU* 3.4 12.1 + - - +
67A ALA* 3.1 23.4 + - - +
108A ARG* 4.1 13.2 - - - +
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Residues in contact with PHE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 4.0 12.5 - - + +
5A LEU* 3.6 17.9 - - + -
24A TYR* 3.5 33.7 - + - -
27A SER* 3.9 15.7 - - - -
28A ALA* 3.7 32.3 - - + -
31A VAL* 4.0 32.5 - - + -
32A LEU* 6.1 3.6 - - + -
60A LEU 3.0 17.1 + - - +
61A SER 3.6 4.5 - - - +
63A GLU* 1.3 73.6 - - - +
65A ALA* 1.3 66.9 + - + +
67A ALA 3.2 1.6 + - - -
68A TRP* 3.1 62.0 + + - -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 6.0 2.0 - - - -
61A SER 2.9 16.9 + - - +
62A GLN* 3.9 3.8 - - - +
64A PHE* 1.3 81.3 - - + +
66A GLU* 1.3 58.7 + - - +
68A TRP* 4.7 2.7 - - - +
69A GLY* 2.8 30.6 + - - +
95A VAL 4.7 1.9 - - - +
97A THR 5.6 1.8 - - - +
98A LEU* 4.0 16.4 - - - +
101A ALA* 4.3 10.3 - - + -
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN 2.9 17.9 + - - +
63A GLU* 3.5 12.3 - - - +
64A PHE 3.2 0.2 - - - -
65A ALA* 1.3 78.3 - - - +
67A ALA* 1.3 63.6 + - - +
70A GLN* 2.9 57.7 + - - +
98A LEU* 3.8 17.5 - - + -
101A ALA* 4.0 6.7 - - + +
108A ARG* 2.8 32.3 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LEU* 3.7 21.3 - - + -
6A GLN* 3.8 14.6 - - - +
7A PRO* 3.7 13.8 - - + +
63A GLU 3.1 13.6 + - - +
64A PHE 3.2 7.5 + - - +
66A GLU* 1.3 78.4 + - - +
68A TRP* 1.3 64.2 + - + +
70A GLN* 4.1 8.1 - - - +
71A LYS* 3.3 23.0 + - - +
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Residues in contact with TRP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU 2.7 25.7 + - - -
6A GLN 3.9 3.1 - - - -
7A PRO* 3.4 40.6 - - + +
10A PHE* 4.6 2.2 - + - -
20A PHE* 3.6 38.5 - + - -
23A SER* 3.5 20.6 - - - -
24A TYR* 3.4 61.5 - + + -
27A SER* 4.8 4.7 - - - -
64A PHE* 3.1 42.7 + + - +
65A ALA* 4.5 1.8 - - - +
67A ALA* 1.3 76.3 - - + +
69A GLY* 1.3 59.7 + - - +
71A LYS* 3.3 4.5 + - - +
72A ALA* 2.8 30.7 + - - +
95A VAL* 3.9 5.4 - - + -
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 2.8 18.6 + - - -
68A TRP* 1.3 74.8 - - - +
70A GLN* 1.3 63.5 + - - +
72A ALA* 3.3 2.9 + - - +
73A LYS* 3.1 27.4 + - - +
95A VAL* 3.2 26.6 + - - +
96A ARG* 4.3 0.5 - - - -
98A LEU* 3.9 13.5 - - - -
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 2.9 47.8 + - + +
67A ALA* 4.1 6.4 - - - +
69A GLY* 1.3 74.9 - - - +
71A LYS* 1.3 57.8 + - - +
73A LYS* 3.3 10.4 + - - +
74A GLU* 2.8 33.7 + - - +
98A LEU* 4.4 10.3 - - + +
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.9 28.1 + - + -
8A GLY 4.0 15.7 + - - +
9A GLN* 4.2 15.2 + - - +
20A PHE* 3.6 20.9 - - + -
67A ALA 3.3 16.7 + - - +
68A TRP 3.5 4.5 - - - +
69A GLY 3.2 0.4 - - - -
70A GLN* 1.3 80.0 - - - +
72A ALA* 1.3 57.3 + - - +
74A GLU* 3.4 31.6 + - - +
75A LEU* 2.8 51.8 + - + +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.8 14.8 - - + -
68A TRP 2.8 20.3 + - - +
69A GLY 3.5 5.8 - - - +
71A LYS* 1.3 72.9 - - - +
73A LYS* 1.3 52.6 + - - +
76A TYR* 2.7 45.0 + - - +
77A GLU 3.6 0.7 + - - -
80A TRP* 5.8 0.2 - - - -
92A ILE* 4.8 11.1 - - + +
95A VAL* 3.9 20.2 - - + -
96A ARG* 4.4 13.7 - - + +
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Residues in contact with LYS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.1 21.8 + - - +
70A GLN* 3.7 9.6 - - - +
72A ALA* 1.3 72.7 - - - +
74A GLU* 1.3 70.4 + - - +
77A GLU* 3.0 57.0 + - + +
78A PRO* 4.0 2.1 - - - +
96A ARG* 3.6 35.2 + - + +
98A LEU* 3.9 17.2 - - + +
102A ASN* 4.8 4.0 + - - -
188A GLN 4.5 14.3 + - - -
189A ASP* 4.8 1.6 + - - -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLN* 2.8 17.4 + - - +
71A LYS* 3.4 39.6 + - - +
73A LYS* 1.3 78.8 - - - +
75A LEU* 1.3 68.2 + - + +
78A PRO* 4.8 4.9 - - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.4 35.2 - - + +
12A ALA* 3.6 26.2 - - + +
20A PHE* 4.1 3.8 - - + -
71A LYS* 2.8 46.1 + - + +
74A GLU* 1.3 88.3 - - + +
76A TYR* 1.3 102.6 + - + +
77A GLU 3.9 0.2 - - - -
78A PRO* 4.5 5.4 - - - +
79A ILE* 3.8 6.1 - - - +
----------------------------------------------------------
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.5 12.0 - - - +
11A SER 2.9 28.8 + - - -
12A ALA* 3.8 6.5 - - - -
13A ASP 3.6 14.1 - - - -
16A GLY 3.1 7.4 + - - -
17A ALA* 3.1 25.8 + - + -
20A PHE* 3.7 20.5 - + + +
72A ALA* 2.7 26.8 + - - +
75A LEU* 1.3 98.4 - - + +
77A GLU* 1.3 64.3 + - - +
78A PRO* 3.2 3.6 - - - -
79A ILE* 3.0 12.3 + - + -
80A TRP* 2.8 43.6 + - + -
83A PHE* 4.0 14.8 - + - -
92A ILE* 4.3 13.0 - - + -
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 3.6 2.9 + - - +
73A LYS* 3.0 40.4 + - + +
76A TYR* 1.3 74.1 - - - +
78A PRO* 1.3 64.1 - - + +
79A ILE 3.2 4.3 + - - -
80A TRP* 3.3 28.7 + - - -
81A GLN* 5.4 3.6 + - - +
96A ARG* 3.3 33.6 + - - +
----------------------------------------------------------
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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