Contacts of the helix formed by residues 44 - 72 (chain B) in PDB entry 2RBD
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 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 3.1 8.2 - - - +
43B GLY* 1.3 75.0 - - - +
45B GLU* 1.3 59.7 + - - +
46B ASP* 2.9 18.3 + - - +
47B LEU* 2.9 27.3 + - + +
48B LYS 3.0 21.3 + - - -
99B ASP* 3.1 22.6 + - - +
154B LYS* 2.7 33.4 + - - +
156B TRP* 4.2 14.3 - - + -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR 4.1 7.8 - - - +
43B GLY 3.0 22.8 + - - +
44B ASP* 1.3 72.6 + - - +
46B ASP* 1.3 61.7 + - - +
47B LEU 3.3 0.2 - - - -
48B LYS* 3.7 29.2 - - - +
49B ASN* 3.0 41.2 + - - +
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Residues in contact with ASP 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 2.9 6.2 + - - +
45B GLU* 1.3 75.9 - - - +
47B LEU* 1.3 64.9 + - - +
49B ASN* 3.4 9.9 + - - +
50B LEU* 3.3 26.9 + - + +
150B LEU* 3.8 20.0 - - + -
154B LYS* 2.6 25.4 + - - -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 4.1 4.5 - - + -
44B ASP* 2.9 20.9 + - + +
46B ASP* 1.3 76.3 - - - +
48B LYS* 1.3 63.6 + - - +
50B LEU* 3.0 4.4 + - - +
51B ILE* 3.0 43.1 + - + +
99B ASP* 3.5 48.7 - - + +
102B ILE* 4.1 13.2 - - + -
103B SER* 4.3 12.8 - - - -
106B ILE* 4.6 1.3 - - + -
147B MSE 4.3 11.9 - - + -
150B LEU* 3.8 27.7 - - + +
156B TRP* 4.1 6.7 - - + -
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Residues in contact with LYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.9 32.1 - - + +
42B THR* 3.7 15.0 - - + +
44B ASP 3.0 17.3 + - - +
45B GLU* 3.7 28.3 - - - +
46B ASP 3.4 0.2 - - - -
47B LEU* 1.3 76.8 - - - +
49B ASN* 1.3 70.4 + - - +
51B ILE* 3.2 8.5 + - - +
52B ASP* 2.6 52.3 + - - +
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Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU* 3.0 29.4 + - - +
46B ASP* 3.8 10.9 + - - +
47B LEU 3.2 0.2 - - - -
48B LYS* 1.3 83.1 + - - +
50B LEU* 1.3 60.2 + - + +
52B ASP* 3.4 16.0 + - - +
53B GLU* 3.1 25.9 + - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP 3.3 9.5 + - - +
47B LEU* 3.0 8.5 + - + +
49B ASN* 1.3 76.7 - - + +
51B ILE* 1.3 59.3 + - - +
53B GLU* 3.2 23.8 + - - +
54B ALA 2.9 24.1 + - - -
143B PHE* 3.4 21.4 - - + -
146B LYS* 3.7 37.5 - - + +
147B MSE 4.1 20.0 - - - -
150B LEU* 3.7 40.6 - - + -
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 3.6 43.5 - - + +
38B PHE* 4.2 7.4 - - + -
39B ILE* 3.6 16.6 - - + -
42B THR* 3.4 25.1 - - - +
47B LEU* 3.0 22.8 + - + +
48B LYS* 3.6 6.7 - - - +
50B LEU* 1.3 75.7 - - - +
52B ASP* 1.3 62.3 + - - +
54B ALA* 3.2 6.7 + - - +
55B ILE* 3.0 22.7 + - + +
102B ILE* 3.8 20.6 - - + -
106B ILE* 3.5 19.3 - - + -
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Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ILE* 3.0 25.4 - - - +
48B LYS* 2.6 48.5 + - - +
49B ASN* 3.5 14.6 - - - +
50B LEU 3.2 0.2 - - - -
51B ILE* 1.3 77.9 - - - +
53B GLU* 1.3 61.9 + - - +
55B ILE* 3.3 6.5 + - - +
56B GLN* 3.1 23.2 + - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASN 3.1 10.0 + - - +
50B LEU* 3.2 18.3 + - - +
52B ASP* 1.3 79.1 - - - +
54B ALA* 1.3 61.0 - - - +
56B GLN* 3.4 6.3 + - - +
57B ALA* 3.0 25.5 + - + +
143B PHE* 4.0 22.4 - - + +
146B LYS* 2.8 34.7 + - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 4.0 24.7 - - + -
50B LEU 2.9 8.1 + - - +
51B ILE* 3.6 8.7 - - - +
53B GLU* 1.3 77.0 - - - +
55B ILE* 1.3 61.1 + - - +
57B ALA* 3.3 3.4 + - - +
58B MSE 3.0 31.0 + - - +
106B ILE* 5.2 1.1 - - + -
143B PHE* 3.6 26.9 - - + -
171B PG4 4.1 16.4 - - - -
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 4.2 18.1 - - + +
35B TYR* 3.8 17.9 - - + -
36B ARG* 3.8 32.5 - - + +
39B ILE* 3.6 30.7 - - + -
51B ILE 3.0 15.1 + - - +
52B ASP* 3.7 7.4 - - - +
54B ALA* 1.3 76.6 - - - +
56B GLN* 1.3 57.1 + - - +
58B MSE 3.3 12.6 + - + +
59B GLN* 2.9 50.8 + - - +
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Residues in contact with GLN 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP 3.1 16.7 + - - +
53B GLU* 3.9 6.1 - - - +
55B ILE* 1.3 76.4 - - - +
57B ALA* 1.3 58.1 + - - +
59B GLN* 3.2 24.7 + - - +
60B ASP* 2.6 64.7 + - - +
63B HIS* 5.9 2.0 + - - -
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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
----------------------------------------------------------
53B GLU* 3.0 20.8 + - + +
54B ALA* 3.6 5.4 - - - +
55B ILE 3.2 0.2 - - - -
56B GLN* 1.3 76.1 - - - +
58B MSE 1.3 56.3 + - - +
60B ASP* 3.2 12.4 + - - +
61B GLU* 3.0 31.9 + - - +
143B PHE* 6.2 0.4 - - + -
171B PG4 3.7 30.5 - - - -
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Residues in contact with MSE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 3.8 35.0 - - - +
31B LEU* 3.7 26.5 - - - -
32B ILE* 3.9 27.1 - - + +
35B TYR* 3.5 34.5 - - + -
54B ALA* 3.0 25.3 + - + +
55B ILE* 3.7 9.0 - - - +
57B ALA* 1.3 72.5 - - - +
59B GLN* 1.3 61.2 + - - +
61B GLU* 3.4 6.4 + - - +
62B ASN* 2.9 36.6 + - - +
140B LYS* 5.2 0.7 - - - +
171B PG4 4.2 22.0 - - - +
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 3.8 18.2 - - + +
36B ARG* 3.3 28.1 - - - +
55B ILE* 2.9 33.2 + - - +
56B GLN* 3.2 32.8 + - - +
58B MSE 1.3 77.7 - - - +
60B ASP* 1.3 62.0 + - - +
62B ASN* 3.2 7.9 + - - +
63B HIS* 3.1 36.5 + - + +
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 2.6 48.7 + - - +
57B ALA* 3.2 13.3 + - - +
59B GLN* 1.3 74.3 - - - +
61B GLU* 1.3 65.8 + - + +
63B HIS* 3.4 19.8 + - - +
64B GLN* 3.1 23.9 + - - +
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 2.8 29.6 + - - -
28B ASN* 3.3 13.5 + - - +
57B ALA 3.0 17.7 + - - +
58B MSE 3.6 8.8 - - - +
60B ASP* 1.3 76.1 - - + +
62B ASN* 1.3 63.0 + - - +
64B GLN* 3.1 13.7 + - - +
65B LEU* 2.9 27.1 + - + +
136B PHE* 3.5 43.1 - - + +
139B ALA* 5.0 0.7 - - - +
140B LYS* 4.2 2.4 + - - -
171B PG4 2.4 33.2 + - - -
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.2 22.3 - - + +
28B ASN* 2.9 31.8 + - - +
29B ASN* 2.9 25.7 + - - -
32B ILE* 3.5 23.6 - - - +
58B MSE 2.9 16.7 + - - +
59B GLN* 3.5 7.4 - - - +
60B ASP 3.2 0.2 - - - -
61B GLU* 1.3 77.9 - - - +
63B HIS* 1.3 57.2 + - - +
65B LEU* 3.9 4.2 - - - +
66B GLU* 2.8 42.3 + - - +
80B PRO* 5.5 0.4 - - - +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLN* 5.9 1.5 + - - -
59B GLN* 3.1 32.1 + - + +
60B ASP* 3.8 13.9 - - - +
61B GLU 3.2 0.4 - - - -
62B ASN* 1.3 75.4 - - + +
64B GLN* 1.3 63.3 + - + +
66B GLU* 4.1 12.7 + - - +
67B GLU* 3.1 24.4 + - - +
70B ARG* 5.1 1.6 + - - -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ASP* 3.1 27.1 + - - +
61B GLU* 3.1 6.9 + - - +
63B HIS* 1.3 77.9 - - + +
65B LEU* 1.3 56.5 + - - +
67B GLU* 3.4 5.5 + - - +
68B LEU* 3.0 27.2 + - - +
132B MSE 4.2 28.5 - - + +
135B GLN* 4.9 6.9 - - - +
136B PHE* 3.7 26.6 - - + -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 4.3 17.9 - - + +
24B TYR* 3.6 28.9 - - + -
25B LEU* 4.1 21.3 - - + -
28B ASN* 4.3 0.2 - - - +
61B GLU 2.9 22.0 + - - +
62B ASN* 3.3 20.2 + - - +
64B GLN* 1.3 75.0 - - - +
66B GLU* 1.3 60.4 + - - +
68B LEU* 3.3 6.7 + - + +
69B LEU* 2.9 36.3 + - + +
132B MSE 3.9 15.7 - - - -
133B PHE* 3.7 28.9 - - + -
136B PHE* 4.1 5.8 - - + -
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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
----------------------------------------------------------
25B LEU* 3.6 29.4 - - + +
29B ASN* 4.8 8.1 + - - +
62B ASN* 2.8 26.8 + - - +
63B HIS* 4.1 13.7 + - - +
65B LEU* 1.3 75.5 - - - +
67B GLU* 1.3 57.9 + - - +
69B LEU* 3.8 0.3 - - - -
70B ARG* 2.9 45.7 + - - +
76B LEU* 3.8 32.6 - - + +
77B PRO 5.2 3.6 - - - +
79B ALA* 5.1 10.0 - - - +
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Residues in contact with GLU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B HIS 3.1 18.6 + - - +
64B GLN* 3.7 5.6 - - - +
65B LEU 3.2 0.2 - - - -
66B GLU* 1.3 75.9 - - - +
68B LEU* 1.3 52.2 + - - +
70B ARG* 3.0 30.0 + - - +
71B SER* 2.7 55.8 + - - +
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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
----------------------------------------------------------
13B LEU* 4.5 14.1 - - + -
21B THR* 4.2 32.1 - - + +
64B GLN 3.0 14.7 + - - +
65B LEU* 3.6 9.6 - - + +
67B GLU* 1.3 76.0 - - - +
69B LEU* 1.3 63.7 + - + +
71B SER* 2.9 8.8 + - - +
72B ASN* 2.7 36.6 + - - +
126B ARG* 3.6 27.8 - - - +
128B ASP* 4.0 8.3 - - - +
129B VAL* 4.3 14.6 - - + -
132B MSE 4.5 23.8 - - + -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 5.0 6.5 - - + -
18B VAL* 4.4 11.0 - - + +
21B THR* 3.4 25.8 - - - +
22B TRP* 3.8 33.7 - - + +
25B LEU* 3.8 24.5 - - + -
65B LEU 2.9 15.9 + - - +
68B LEU* 1.3 78.9 - - + +
70B ARG* 1.3 65.7 + - - +
72B ASN* 3.1 7.9 + - - -
74B VAL* 3.0 53.6 + - + +
76B LEU* 3.6 15.9 - - + -
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B HIS 5.1 0.8 + - - -
66B GLU* 2.9 30.9 + - - +
67B GLU* 3.0 40.6 + - - +
69B LEU* 1.3 72.8 - - - +
71B SER* 1.3 63.4 + - - +
72B ASN 3.1 1.4 + - - -
73B GLY* 3.2 12.3 + - - -
74B VAL 4.1 7.4 + - - +
76B LEU* 3.7 30.5 - - + +
----------------------------------------------------------
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP* 5.3 1.7 - - - +
67B GLU* 2.7 39.8 + - - +
68B LEU* 2.9 15.6 + - - +
70B ARG* 1.3 76.1 - - - +
72B ASN* 1.3 67.2 + - - +
73B GLY 3.5 0.8 + - - -
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Residues in contact with ASN 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A HIS* 2.7 36.4 + - + -
165A ASP* 3.3 20.7 - - + +
11B GLU 5.0 0.2 - - - +
12B PRO* 5.3 1.7 - - - +
13B LEU* 3.7 26.4 + - + +
68B LEU* 2.7 39.4 + - - +
69B LEU 3.1 3.4 + - - +
70B ARG 3.1 0.8 - - - -
71B SER* 1.3 92.7 + - - +
73B GLY* 1.3 53.8 + - - +
74B VAL* 3.4 3.4 - - + -
126B ARG* 3.3 25.3 + - - +
----------------------------------------------------------
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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