Contacts of the helix formed by residues 47 - 77 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 4.3 1.6 - - - -
45B ASN* 3.1 26.1 + - - +
46B ILE* 1.3 82.7 - - - +
48B ALA* 1.3 64.7 + - - +
49B GLU* 3.4 8.9 + - - +
50B ASN* 2.9 29.8 + - - +
51B ALA* 3.0 23.6 + - - +
120B ARG* 6.4 1.3 - - - -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 1.3 72.7 - - - +
49B GLU* 1.3 58.0 + - - +
51B ALA* 3.4 7.3 + - - +
52B ARG* 3.0 28.4 + - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 3.2 7.4 + - - +
48B ALA* 1.3 80.1 - - - +
50B ASN* 1.3 59.1 + - - +
52B ARG* 2.7 46.2 + - - +
53B ARG* 2.9 56.7 + - - +
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Residues in contact with ASN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA 4.6 1.7 - - - +
41B ALA* 3.4 18.7 + - + +
42B HIS* 3.8 17.6 - - - +
45B ASN* 2.8 47.3 + - - +
47B THR* 2.9 20.5 + - - +
49B GLU* 1.3 77.7 - - - +
51B ALA* 1.3 60.8 + - - +
53B ARG* 3.4 25.5 + - - +
54B GLN* 3.0 27.9 + - - +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B HIS* 3.7 20.3 - - + +
47B THR 3.0 16.1 + - - +
48B ALA* 3.7 7.2 - - - +
50B ASN* 1.3 74.3 - - - +
52B ARG* 1.3 60.0 + - - +
54B GLN* 3.2 4.7 + - - +
55B GLU* 2.9 41.0 + - - +
116B SER* 4.1 20.6 + - - +
117B GLN* 5.2 7.0 - - - +
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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 ALA 3.0 15.0 + - - +
49B GLU* 2.7 46.2 + - - +
51B ALA* 1.3 76.3 - - - +
53B ARG* 1.3 72.6 + - - +
55B GLU* 3.3 10.8 + - + +
56B GLU* 3.0 61.5 + - + +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 4.1 8.4 - - + +
41B ALA* 6.5 1.3 - - + -
49B GLU* 2.9 42.4 + - - +
50B ASN* 3.8 21.3 + - - +
51B ALA 3.2 0.4 - - - -
52B ARG* 1.3 89.9 - - - +
54B GLN* 1.3 65.2 + - - +
56B GLU* 3.3 15.7 + - - +
57B ALA* 3.0 23.2 + - - +
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 5.1 5.2 + - - +
38B ALA* 3.8 17.4 - - + +
39B SER* 3.7 38.7 + - - +
42B HIS* 4.5 8.5 - - + +
50B ASN 3.0 16.6 + - - +
51B ALA* 3.2 5.6 + - - +
53B ARG* 1.3 75.3 - - - +
55B GLU* 1.3 63.0 + - - +
57B ALA* 3.3 2.9 + - + +
58B ALA* 2.9 38.0 + - - +
112B ASN* 4.9 1.9 - - - +
115B LEU* 6.0 1.4 - - - +
116B SER* 3.7 17.2 + - - -
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ALA* 2.9 24.3 + - - +
52B ARG* 3.7 9.0 - - - +
53B ARG 3.3 0.2 - - - -
54B GLN* 1.3 79.4 - - - +
56B GLU* 1.3 62.9 + - - +
58B ALA* 3.4 6.9 + - - +
59B LEU* 3.0 24.3 + - - +
109B GLN 4.9 1.6 - - - +
112B ASN* 3.8 20.8 + - + +
113B ALA* 3.7 25.6 + - - +
116B SER* 2.6 35.7 + - - +
117B GLN* 5.0 3.5 + - - -
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 3.0 42.4 + - + +
53B ARG* 3.3 16.2 - - - +
55B GLU* 1.3 77.2 - - - +
57B ALA* 1.3 61.7 + - - +
59B LEU* 3.3 10.1 + - - +
60B LEU* 3.1 22.2 + - - +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLN* 3.1 40.0 + - - +
35B SER* 4.0 9.6 - - - +
38B ALA* 3.9 19.7 - - + -
53B ARG 3.0 9.0 + - - +
54B GLN* 3.3 8.7 + - - +
56B GLU* 1.3 76.6 - - - +
58B ALA* 1.3 61.4 + - - +
60B LEU* 3.2 2.6 + - - -
61B SER* 2.9 26.9 + - - -
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 5.0 4.2 + - - -
54B GLN* 2.9 29.5 + - - +
55B GLU* 3.6 6.5 - - - +
57B ALA* 1.3 76.8 - - - +
59B LEU* 1.3 58.1 + - - +
61B SER* 3.1 9.3 + - - -
62B GLN* 2.9 34.5 + - - +
112B ASN* 3.8 23.6 - - + +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU 3.0 17.7 + - - +
56B GLU* 3.6 8.5 - - - +
58B ALA* 1.3 75.8 - - - +
60B LEU* 1.3 57.5 + - - +
62B GLN* 3.3 19.3 + - - +
63B GLU* 3.0 40.2 + - + +
105B LEU* 3.9 28.3 - - + -
108B ARG* 3.7 24.2 + - + +
109B GLN* 4.3 20.4 - - + +
112B ASN* 3.8 7.5 - - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 4.0 22.5 - - + +
2B ASP 5.3 1.8 - - - +
5B LEU* 5.0 11.2 - - + -
31B VAL* 4.7 6.3 - - + -
34B GLN* 3.8 29.2 - - + +
56B GLU 3.1 13.4 + - - +
57B ALA* 3.2 8.5 + - - +
59B LEU* 1.3 76.2 - - - +
61B SER* 1.3 57.9 + - - +
63B GLU* 3.2 23.2 + - - +
64B PHE* 3.0 27.8 + - - +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 3.5 25.0 - - - +
32B LEU* 5.4 3.1 - - - +
34B GLN* 3.5 5.9 + - - +
35B SER* 3.6 14.5 - - - -
57B ALA 2.9 15.1 + - - -
58B ALA* 3.1 11.2 + - - -
60B LEU* 1.3 73.7 - - - +
62B GLN* 1.3 61.8 + - - +
64B PHE* 3.5 2.5 - - - +
65B ALA* 2.8 30.7 + - - +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 2.9 15.2 + - - +
59B LEU* 3.4 21.3 - - - +
61B SER* 1.3 79.3 - - - +
63B GLU* 1.3 57.1 + - - +
65B ALA* 4.4 1.3 - - - -
66B GLU* 2.9 27.0 + - - +
100B SER* 2.9 35.4 + - - +
101B ALA* 3.3 24.8 - - + +
108B ARG* 3.6 27.2 + - - +
111B TYR* 4.2 4.0 - - - -
112B ASN* 3.0 40.7 + - - +
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 2.9 42.4 + - + +
59B LEU* 3.0 23.6 + - + +
60B LEU* 3.2 20.5 + - - +
62B GLN* 1.3 75.0 - - - +
64B PHE* 1.3 58.4 + - - +
66B GLU* 3.4 5.0 + - - +
67B ALA* 3.0 29.5 + - - +
105B LEU* 6.0 2.7 - - + +
108B ARG* 3.9 17.0 - - - +
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 3.7 14.5 - - + +
5B LEU* 3.6 12.8 - - + -
24B TYR* 3.5 33.2 - + - -
27B SER* 3.6 15.5 - - - -
28B ALA* 3.5 33.9 - - + -
31B VAL* 3.7 31.2 - - + -
32B LEU* 6.3 0.7 - - + -
60B LEU 3.0 13.5 + - - +
61B SER 3.5 8.5 - - - +
63B GLU* 1.3 73.3 - - - +
65B ALA* 1.3 70.6 + - + +
67B ALA* 3.1 2.1 + - - +
68B TRP* 3.0 60.3 + + - -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 6.2 1.1 - - - -
61B SER 2.8 21.3 + - - +
62B GLN* 3.8 4.0 - - - +
64B PHE* 1.3 78.1 - - + +
66B GLU* 1.3 58.0 + - - +
68B TRP* 5.3 1.1 - - - -
69B GLY* 2.8 28.9 + - - -
95B VAL 4.6 2.5 - - - +
97B THR 5.4 3.3 - - - +
98B LEU* 4.2 14.8 - - - +
101B ALA* 4.0 13.7 - - + -
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Residues in contact with GLU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B GLN 2.9 17.3 + - - +
63B GLU* 3.8 4.8 - - - +
65B ALA* 1.3 77.8 - - - +
67B ALA* 1.3 57.0 + - - +
70B GLN* 3.0 45.6 + - + +
98B LEU* 4.2 14.8 - - + +
101B ALA* 4.0 9.4 - - - +
108B ARG* 2.9 31.5 + - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 4.0 17.7 - - + -
6B GLN* 5.0 4.0 - - + -
7B PRO* 4.1 18.7 - - + +
63B GLU 3.0 16.5 + - - +
64B PHE 3.1 3.8 + - - +
66B GLU* 1.3 80.0 - - - +
68B TRP* 1.3 63.3 + - + +
70B GLN* 4.1 2.7 - - - +
71B LYS* 3.1 25.1 + - - +
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Residues in contact with TRP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU 2.7 24.0 + - - -
6B GLN 3.7 6.3 - - - -
7B PRO* 3.5 42.8 - - + +
10B PHE* 4.4 2.2 - + - -
20B PHE* 3.6 36.3 - + - -
23B SER* 3.6 16.6 - - - -
24B TYR* 3.5 65.7 - + + -
27B SER* 4.3 11.2 - - - -
64B PHE* 3.0 43.2 + + - +
65B ALA* 4.6 1.1 - - - +
67B ALA* 1.3 76.5 - - + +
69B GLY* 1.3 60.5 + - - +
71B LYS* 3.5 2.6 + - - -
72B ALA* 2.9 31.4 + - - +
95B VAL* 3.6 4.3 - - + +
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA 2.8 21.0 + - - -
68B TRP* 1.3 77.5 - - - +
70B GLN* 1.3 60.3 + - - +
72B ALA* 3.2 6.9 + - - +
73B LYS* 3.1 25.0 + - - +
95B VAL 3.4 21.7 + - - -
96B ARG* 4.4 1.4 - - - -
98B LEU* 3.7 14.4 - - - -
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.0 36.6 + - + +
67B ALA* 4.1 2.9 - - - +
69B GLY* 1.3 69.2 - - - +
71B LYS* 1.3 60.3 + - - +
73B LYS* 3.3 24.4 + - - +
74B GLU* 3.0 33.6 + - - +
98B LEU* 3.2 25.1 - - - +
102B ASN* 5.1 0.2 - - - +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO* 3.9 22.9 - - + -
8B GLY 3.9 20.1 + - - +
9B GLN* 5.6 6.2 - - - +
10B PHE* 5.1 0.4 - - + +
20B PHE* 3.7 19.7 - - + -
67B ALA 3.1 19.5 + - - +
68B TRP 3.8 3.8 - - - +
70B GLN* 1.3 77.3 - - - +
72B ALA* 1.3 61.9 + - - +
74B GLU* 3.8 28.3 + - - +
75B LEU* 3.1 47.4 + - + +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.6 21.7 - - + -
68B TRP 2.9 19.2 + - - +
69B GLY* 3.5 5.4 - - - +
71B LYS* 1.3 77.4 - - - +
73B LYS* 1.3 56.5 + - - +
76B TYR* 3.0 37.5 + - + +
77B GLU 3.7 1.0 + - - -
92B ILE* 4.6 14.7 - - + +
95B VAL* 3.9 15.9 - - + -
96B ARG* 4.8 6.3 - - + +
----------------------------------------------------------
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 3.1 10.8 + - - +
70B GLN* 3.7 28.5 + - - +
71B LYS 3.3 0.2 - - - -
72B ALA* 1.3 74.5 - - - +
74B GLU* 1.3 68.9 + - - +
75B LEU 3.1 0.2 - - - -
77B GLU* 2.9 50.6 + - + +
78B PRO* 4.4 0.7 - - - +
96B ARG* 3.2 48.1 + - + +
98B LEU* 4.2 13.8 - - - +
102B ASN* 5.2 2.2 + - - -
188B GLN 4.9 7.9 + - - -
189B ASP* 4.6 8.5 + - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B GLN* 3.0 18.5 + - - +
71B LYS* 3.8 33.3 + - - +
72B ALA 3.5 0.2 - - - -
73B LYS* 1.3 78.8 - - - +
75B LEU* 1.3 65.7 + - + +
78B PRO* 5.3 2.6 - - - +
----------------------------------------------------------
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 5.9 3.1 - - - +
10B PHE* 3.2 40.2 - - + +
12B ALA* 3.5 32.1 - - + +
20B PHE* 4.4 2.2 - - + -
71B LYS* 3.1 44.3 + - + +
74B GLU* 1.3 84.7 - - + +
76B TYR* 1.3 97.4 + - + +
77B GLU 3.8 0.4 - - - -
78B PRO* 4.7 3.9 - - - +
79B ILE* 4.1 5.4 - - - +
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE* 3.6 12.1 - - - +
11B SER 2.9 29.2 + - - -
12B ALA* 3.9 0.9 - - - -
13B ASP 3.7 16.4 - - - -
16B GLY 3.2 5.9 + - - -
17B ALA* 3.0 20.9 + - + -
20B PHE* 3.8 25.3 - + + +
72B ALA* 3.0 22.5 + - - +
75B LEU* 1.3 109.0 - - + +
77B GLU* 1.3 67.7 + - - +
78B PRO* 3.3 3.6 - - - -
79B ILE* 3.0 8.8 + - + -
80B TRP* 2.9 41.9 + - + -
83B PHE* 3.9 19.3 - + + -
92B ILE* 4.3 13.7 - - + -
----------------------------------------------------------
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA 3.7 1.8 + - - -
73B LYS* 2.9 36.1 + - + +
76B TYR* 1.3 78.2 - - - +
78B PRO* 1.3 71.1 - - + +
80B TRP* 3.3 24.2 + - - -
81B GLN* 4.4 7.1 - - - +
96B ARG* 2.8 39.8 + - - +
----------------------------------------------------------
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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