Contacts of the helix formed by residues 45 - 71 (chain E) in PDB entry 1MFR
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 HIS 45 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE 4.6 1.6 - - - -
38E ASP* 3.4 44.4 + - - -
43E ALA* 3.3 14.7 + - - -
44E LEU* 1.3 68.2 - - - +
46E ASN* 1.3 64.7 + - - +
48E ALA* 3.5 7.5 - - - +
49E GLU* 3.1 29.7 + - + +
167E ASP* 3.6 3.8 + - - +
67I LYS* 5.1 4.3 + - - -
142W LYS* 4.0 2.9 - - - -
146W ASP* 3.0 34.7 + - + -
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Residues in contact with ASN 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E HIS* 1.3 76.9 - - - +
47E VAL* 1.3 65.0 + - - +
49E GLU* 3.3 9.4 + - - +
50E PHE 3.0 17.8 + - - -
167E ASP* 3.0 46.0 + - - +
168E LYS* 4.4 11.1 - - - +
171E VAL* 3.2 28.0 - - + +
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Residues in contact with VAL 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 3.9 20.9 - - + -
44E LEU* 3.5 18.2 - - + +
46E ASN* 1.3 77.3 - - - +
48E ALA* 1.3 62.3 + - - +
50E PHE* 3.2 9.1 + - - +
51E PHE* 3.2 45.9 + - + -
92E THR* 4.1 26.2 - - + +
96E MET* 4.6 4.7 - - + -
163E GLU 5.8 0.4 - - - +
166E PHE* 4.3 13.5 - - + -
167E ASP* 3.1 22.9 + - + +
171E VAL* 4.6 4.3 - - + -
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.2 41.1 - - + +
37E PHE* 3.7 24.2 - - + +
38E ASP* 4.1 3.8 - - + +
44E LEU 3.0 14.3 + - - +
45E HIS* 3.5 14.8 - - - +
46E ASN 3.2 0.2 - - - -
47E VAL* 1.3 78.4 - - - +
49E GLU* 1.3 57.1 + - - +
51E PHE* 3.4 2.2 + - - -
52E LYS 3.0 21.3 + - - -
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Residues in contact with GLU 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.6 23.6 + - - -
45E HIS* 3.1 18.4 + - + +
46E ASN* 3.3 11.0 + - - +
48E ALA* 1.3 74.0 - - - +
50E PHE* 1.3 60.3 + - - +
52E LYS* 3.6 24.6 + - - +
53E GLU* 2.9 38.8 + - - +
67I LYS* 5.8 1.2 - - - -
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Residues in contact with PHE 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 5.9 0.2 - + - -
46E ASN 3.0 13.2 + - - +
47E VAL* 3.2 10.5 + - - +
49E GLU* 1.3 77.1 - - - +
51E PHE* 1.3 92.5 + + - +
53E GLU* 3.5 8.8 + - + +
54E HIS* 3.2 55.9 + + - -
96E MET* 4.0 21.1 - - + -
143E ARG* 3.9 18.6 - - - -
144E ILE* 4.5 11.4 - - + -
147E PHE* 3.7 28.3 - + - -
171E VAL* 3.7 20.2 - - + -
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Residues in contact with PHE 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 3.6 49.2 - + + +
33E MET* 3.8 28.3 - - + -
34E TYR 4.0 4.7 - - - +
37E PHE* 3.7 22.7 - + - -
47E VAL* 3.2 36.8 + - + -
48E ALA* 3.9 5.6 - - - +
50E PHE* 1.3 99.1 - + - +
52E LYS* 1.3 58.7 + - - +
54E HIS* 3.2 4.6 + - + +
55E SER* 2.9 24.1 + - - -
95E ALA* 4.1 11.7 - - + -
96E MET* 3.7 23.3 - - + -
99E ALA* 4.2 8.1 - - + -
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Residues in contact with LYS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.7 37.7 + - + +
48E ALA 3.0 17.8 + - - +
49E GLU* 3.6 33.8 + - - +
50E PHE 3.3 0.2 - - - -
51E PHE* 1.3 75.3 - - - +
53E GLU* 1.3 63.4 + - + +
55E SER* 3.2 21.1 + - - +
56E HIS* 3.3 31.2 + - + +
63I GLU* 3.6 24.4 + - - +
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Residues in contact with GLU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLU* 2.9 26.4 + - + +
50E PHE* 3.6 9.3 - - + +
51E PHE 3.2 0.2 - - - -
52E LYS* 1.3 79.3 - - + +
54E HIS* 1.3 63.5 + - + +
56E HIS* 3.3 11.4 + - - +
57E GLU* 3.1 34.9 + - - +
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Residues in contact with HIS 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR* 3.9 22.8 - + + -
50E PHE* 3.2 42.4 + + - +
51E PHE* 3.2 11.0 + - - +
53E GLU* 1.3 82.3 - - + +
55E SER* 1.3 63.5 + - - +
57E GLU* 3.4 17.2 + - - +
58E GLU* 3.2 31.5 + - - +
103E GLU* 3.6 18.1 + - - -
140E ASP* 3.7 26.7 - - + -
143E ARG* 3.1 26.9 + - - -
144E ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E SER* 2.9 47.5 + - - +
30E TYR* 3.7 14.6 - - - +
31E SER* 3.8 14.7 + - - -
34E TYR* 5.8 0.2 - - - +
51E PHE 2.9 9.4 + - - -
52E LYS* 3.2 16.1 + - - +
53E GLU 3.3 0.4 - - - -
54E HIS* 1.3 75.1 - - - +
56E HIS* 1.3 76.0 + - - +
58E GLU 3.4 1.2 + - - -
59E ARG* 3.1 12.0 + - - +
63I GLU* 4.4 5.2 + - - -
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Residues in contact with HIS 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E LYS* 3.3 34.7 + - + +
53E GLU* 3.3 11.5 + - - +
54E HIS 3.2 0.4 - - - -
55E SER* 1.3 92.0 + - - +
57E GLU* 1.3 56.4 + - - +
59E ARG* 3.5 7.5 + - + +
60E GLU* 3.1 26.3 + - - +
59I ARG* 6.0 3.1 - - + +
63I GLU* 3.1 29.2 + - - -
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Residues in contact with GLU 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E GLU* 3.1 21.7 + - - +
54E HIS* 3.6 25.0 + - - +
55E SER 3.2 0.4 - - - -
56E HIS* 1.3 75.9 - - + +
58E GLU* 1.3 64.1 + - + +
60E GLU* 3.2 7.2 + - + +
61E HIS* 2.9 45.9 + - + +
140E ASP* 4.1 17.8 - - - +
143E ARG* 5.8 1.6 + - - -
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Residues in contact with GLU 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU* 2.7 30.2 - - - +
26E ALA* 4.2 9.4 - - + -
27E SER* 3.8 13.5 - - - -
30E TYR* 4.0 16.8 - - + -
54E HIS* 3.2 21.0 + - - +
57E GLU* 1.3 79.9 - - - +
59E ARG* 1.3 57.7 + - - +
61E HIS* 3.1 11.1 + - - +
62E ALA* 3.0 26.2 + - - +
103E GLU* 3.4 15.4 - - - +
106E VAL* 4.9 1.1 - - - +
176E MG 2.0 32.9 - - - -
177E MG 2.6 23.9 - - - -
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Residues in contact with ARG 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LEU* 4.9 12.1 - - + +
27E SER* 3.6 13.4 + - - +
55E SER 3.1 17.6 + - - +
56E HIS* 3.6 10.1 - - + +
57E GLU 3.1 0.2 - - - -
58E GLU* 1.3 74.9 - - - +
60E GLU* 1.3 64.0 + - - +
62E ALA* 3.2 8.6 + - - +
63E GLU* 3.1 36.0 + - + +
56I HIS* 6.0 3.1 - - + +
59I ARG* 5.7 9.2 - - + -
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Residues in contact with GLU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E HIS 3.1 15.7 + - - +
57E GLU* 3.2 11.2 + - - +
59E ARG* 1.3 75.1 - - - +
61E HIS* 1.3 59.9 + - + +
63E GLU* 3.5 11.8 + - - +
64E LYS* 3.1 32.8 + - - +
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Residues in contact with HIS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU* 3.4 16.1 + - - +
57E GLU* 2.9 30.7 + - + +
58E GLU* 3.1 17.5 + - - +
59E ARG 3.2 0.2 - - - -
60E GLU* 1.3 78.4 - - + +
62E ALA* 1.3 64.8 + - - +
64E LYS* 3.4 18.2 + - - -
65E PHE* 3.3 12.9 + - - -
132E GLU 4.6 6.8 + - - -
133E TYR* 3.0 40.0 + + + -
136E GLU* 5.1 15.0 - - + +
137E GLN* 5.1 0.9 - - - -
140E ASP* 5.6 0.4 - - - -
176E MG 2.7 24.7 - - - -
177E MG 4.3 10.5 - - - -
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Residues in contact with ALA 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.7 17.5 - - + +
23E GLU* 3.8 10.5 - - + +
24E LEU* 3.7 34.5 - - + -
58E GLU 3.0 12.7 + - - +
59E ARG 3.2 8.9 + - - +
61E HIS* 1.3 76.3 - - - +
63E GLU* 1.3 64.2 + - - +
65E PHE* 3.3 9.0 + - - +
66E MET* 3.1 26.0 + - + +
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Residues in contact with GLU 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LEU* 6.4 0.4 - - + -
59E ARG* 3.1 25.2 + - + +
60E GLU* 3.8 11.7 - - - +
62E ALA* 1.3 76.8 - - + +
64E LYS* 1.3 62.9 + - - +
66E MET* 3.2 26.1 + - + +
67E LYS* 3.1 24.8 + - - +
31I SER* 4.8 5.6 + - - +
34I TYR* 5.1 10.6 + - + -
52I LYS* 3.6 21.6 - - - +
55I SER* 4.4 5.2 + - - -
56I HIS* 3.1 34.4 + - - -
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Residues in contact with LYS 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E GLU* 3.1 21.2 + - - +
61E HIS* 3.6 17.2 + - - +
62E ALA 3.3 0.4 - - - -
63E GLU* 1.3 75.7 - - - +
65E PHE* 1.3 57.7 + - - +
67E LYS* 3.5 7.4 + - - +
68E TYR* 2.9 27.4 + - - +
128E PHE* 3.7 9.9 - - + -
132E GLU* 2.9 53.6 + - + +
133E TYR* 3.2 21.5 - - + +
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Residues in contact with PHE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16E VAL* 3.9 29.7 - - + +
19E MET* 3.4 33.0 - - + -
20E LEU* 4.2 18.4 - - + -
23E GLU* 4.1 15.0 - - + -
61E HIS 3.3 17.1 + - - -
62E ALA 3.3 8.4 + - - +
63E GLU 3.2 0.4 - - - -
64E LYS* 1.3 77.3 - - - +
66E MET* 1.3 64.4 + - - +
68E TYR* 3.5 2.8 - - + +
69E GLN* 3.0 25.3 + - - +
110E LEU* 4.0 10.5 - - + -
113E LEU* 4.5 7.6 - - + -
125E LEU* 5.3 0.2 - - + -
128E PHE* 3.5 26.0 - + - -
129E LEU* 4.0 12.3 - - + -
133E TYR* 3.4 30.1 - + - -
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Residues in contact with MET 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.8 30.5 - - + +
24E LEU* 5.1 7.2 - - + -
62E ALA* 3.1 21.9 + - + +
63E GLU* 3.2 22.9 + - + +
65E PHE* 1.3 75.5 - - - +
67E LYS* 1.3 61.8 + - - +
69E GLN* 3.4 4.2 - - - +
70E ASN* 3.3 27.4 + - - +
76E VAL* 3.9 20.7 - - + +
78E LEU* 4.7 7.6 - - + -
28I TYR* 5.5 0.4 - - + -
31I SER* 3.3 40.8 - - - +
34I TYR* 4.5 15.7 - - + -
35I ALA* 4.2 13.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 6.0 0.6 - - - +
63E GLU 3.1 9.8 + - - +
64E LYS* 3.6 11.2 - - - +
66E MET* 1.3 79.0 - - - +
68E TYR* 1.3 58.5 + - - +
70E ASN* 3.5 3.3 + - - +
71E LYS* 3.0 43.9 + - + +
34I TYR* 3.4 29.4 - - - +
38I ASP* 3.1 33.6 + - - +
45I HIS* 5.0 5.3 + - - -
49I GLU* 5.8 1.6 - - - -
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Residues in contact with TYR 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 5.6 0.2 - - - -
8E TYR* 3.9 18.4 - + - -
16E VAL* 4.6 8.7 - - + -
64E LYS 2.9 18.5 + - - +
65E PHE* 3.5 7.0 - - - +
66E MET 3.2 0.2 - - - -
67E LYS* 1.3 74.1 - - - +
69E GLN* 1.3 67.9 - - - +
71E LYS* 3.1 17.6 + - + +
72E ARG* 2.8 52.5 + - + +
124E HIS* 2.8 41.2 + + - -
125E LEU* 3.2 35.8 - - + -
128E PHE* 3.6 43.1 - + + -
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Residues in contact with GLN 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR* 3.0 36.5 + - - -
13E GLU* 3.2 27.9 + - - +
16E VAL* 3.5 14.6 - - + +
17E ASN* 3.4 18.6 + - - +
20E LEU* 5.8 1.3 - - + +
65E PHE 3.0 13.6 + - - +
66E MET 3.4 7.0 - - - +
68E TYR* 1.3 83.4 - - - +
70E ASN* 1.3 59.4 + - - +
72E ARG* 3.2 4.9 + - - +
73E GLY 3.1 3.5 + - - -
74E GLY* 2.9 42.3 + - - -
75E ARG 4.0 7.2 - - - -
76E VAL* 3.7 24.2 - - + +
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Residues in contact with ASN 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 3.2 17.9 - - - +
4E VAL* 4.5 0.7 - - - +
66E MET 3.3 12.7 + - - -
67E LYS 3.9 2.7 - - - +
69E GLN* 1.3 76.3 - - - +
71E LYS* 1.3 65.2 + - - +
73E GLY* 3.2 10.3 + - - +
74E GLY 3.9 11.8 - - - +
75E ARG* 4.0 1.5 + - - +
76E VAL* 4.6 8.6 + - - +
35I ALA* 3.0 30.5 + - - +
38I ASP* 3.2 39.2 + - - +
39I ARG* 3.2 28.0 - - - +
40I ASP* 4.8 3.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 2.8 35.6 + - - +
138B VAL* 4.3 24.6 - - + +
139B LYS* 4.6 11.8 - - - +
142B LYS* 4.0 27.8 - - + +
4E VAL* 3.4 18.2 - - - +
67E LYS* 3.0 29.6 + - + +
68E TYR* 3.1 23.2 + - + +
70E ASN* 1.3 76.3 - - - +
72E ARG* 1.3 62.0 + - + +
128E PHE* 6.2 2.8 - - - -
----------------------------------------------------------
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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