Contacts of the helix formed by residues 45 - 71 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 5.0 5.3 + - - -
37F PHE 4.6 1.8 - - - -
38F ASP* 3.4 43.2 + - - -
43F ALA* 3.3 15.2 + - + -
44F LEU* 1.3 69.0 - - - +
46F ASN* 1.3 64.9 + - - +
48F ALA* 3.5 6.7 - - - +
49F GLU* 3.1 29.8 + - - +
167F ASP* 3.6 3.4 + - - +
142V LYS* 4.0 3.1 - - - -
146V ASP* 3.0 35.4 + - + -
150V ASN* 5.9 0.4 - - - -
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Residues in contact with ASN 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F HIS* 1.3 78.9 - - - +
47F VAL* 1.3 67.1 + - - +
49F GLU* 3.3 8.5 + - - +
50F PHE 3.0 17.8 + - - -
167F ASP* 2.9 44.8 + - - +
168F LYS* 4.4 11.1 - - - +
171F VAL* 3.2 27.7 - - + +
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Residues in contact with VAL 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F PHE* 3.9 20.9 - - + -
44F LEU* 3.5 18.8 - - + +
45F HIS 3.3 0.2 - - - -
46F ASN* 1.3 76.3 - - - +
48F ALA* 1.3 62.3 + - - +
50F PHE* 3.2 8.5 + - - +
51F PHE* 3.2 44.4 + - + -
92F THR* 4.1 26.0 - - + +
96F MET* 4.6 4.9 - - + -
163F GLU 5.8 0.2 - - - +
166F PHE* 4.3 13.7 - - + -
167F ASP* 3.1 22.7 + - + +
171F VAL* 4.6 4.7 - - + -
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Residues in contact with ALA 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F TYR* 3.2 40.4 - - + +
37F PHE* 3.7 23.8 - - + +
38F ASP* 4.1 4.3 - - + +
44F LEU 3.0 15.1 + - - +
45F HIS* 3.5 15.0 - - - +
47F VAL* 1.3 77.4 - - - +
49F GLU* 1.3 57.4 + - - +
51F PHE* 3.4 1.9 + - - -
52F LYS 3.0 21.0 + - - -
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 5.7 1.9 - - - -
34F TYR* 3.6 23.4 + - - -
45F HIS* 3.1 18.1 + - + +
46F ASN* 3.3 11.2 + - - +
48F ALA* 1.3 74.9 - - - +
50F PHE* 1.3 60.9 + - - +
52F LYS* 3.6 24.9 + - - +
53F GLU* 2.9 39.9 + - - +
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Residues in contact with PHE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 5.9 0.2 - + - -
46F ASN 3.0 13.6 + - - +
47F VAL* 3.3 10.5 - - - +
49F GLU* 1.3 77.6 - - - +
51F PHE* 1.3 93.8 + + - +
53F GLU* 3.5 8.5 + - - +
54F HIS* 3.2 55.6 + + - -
96F MET* 4.0 20.6 - - + -
143F ARG* 3.9 16.8 - - - -
144F ILE* 4.5 11.7 - - + -
147F PHE* 3.7 30.3 - + - -
171F VAL* 3.7 20.4 - - + +
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Residues in contact with PHE 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.6 49.6 - + + +
33F MET* 3.8 28.9 - - + -
34F TYR 4.0 5.2 - - - +
37F PHE* 3.7 22.0 - + - -
47F VAL* 3.2 36.6 + - + -
48F ALA 3.9 4.9 - - - +
49F GLU 3.2 0.2 - - - -
50F PHE* 1.3 98.1 - + - +
52F LYS* 1.3 59.8 + - - +
54F HIS* 3.2 4.9 + - + +
55F SER* 2.9 23.7 + - - -
95F ALA* 4.1 11.9 - - + -
96F MET* 3.7 24.0 - - + -
99F ALA* 4.2 8.5 - - + -
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Residues in contact with LYS 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 3.6 24.7 + - - +
34F TYR* 3.7 37.9 + - + +
48F ALA 3.0 17.2 + - - +
49F GLU* 3.6 34.0 + - - +
50F PHE 3.3 0.4 - - - -
51F PHE* 1.3 77.4 - - - +
53F GLU* 1.3 62.6 + - + +
55F SER* 3.2 21.5 + - - +
56F HIS* 3.3 29.7 + - + +
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Residues in contact with GLU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F GLU* 2.9 25.2 + - + +
50F PHE* 3.6 8.7 - - + +
51F PHE 3.2 0.2 - - - -
52F LYS* 1.3 78.7 - - + +
54F HIS* 1.3 63.5 + - + +
56F HIS* 3.3 10.5 + - - +
57F GLU* 3.1 35.4 + - - +
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Residues in contact with HIS 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.9 23.5 - + + -
50F PHE* 3.2 40.3 + + - +
51F PHE* 3.2 10.3 + - - +
53F GLU* 1.3 81.6 - - + +
55F SER* 1.3 65.2 + - - +
57F GLU* 3.4 17.3 + - - +
58F GLU* 3.2 32.2 + - - +
103F GLU* 3.6 18.1 + - - -
140F ASP* 3.7 26.0 - - + -
143F ARG* 3.1 27.8 + - - -
144F ILE* 4.9 4.5 - - + -
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Residues in contact with SER 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 4.4 5.9 + - - -
27F SER* 2.9 47.5 + - - +
30F TYR* 3.7 15.0 - - - +
31F SER* 3.8 14.8 - - - -
51F PHE 2.9 10.0 + - - -
52F LYS* 3.2 15.9 + - - +
53F GLU 3.3 0.4 - - - -
54F HIS* 1.3 74.3 - - - +
56F HIS* 1.3 76.3 + - - +
58F GLU 3.4 1.0 + - - -
59F ARG* 3.1 11.4 + - - +
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Residues in contact with HIS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG* 6.0 2.9 - - + +
63B GLU* 3.0 35.4 + - - -
52F LYS* 3.3 28.8 + - + +
53F GLU* 3.3 11.9 + - - +
54F HIS 3.2 0.2 - - - -
55F SER* 1.3 91.6 + - - +
57F GLU* 1.3 55.4 + - - +
59F ARG* 3.5 8.0 + - + +
60F GLU* 3.1 26.2 + - - +
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53F GLU* 3.1 20.5 + - - +
54F HIS* 3.6 26.4 + - - +
55F SER 3.2 0.2 - - - -
56F HIS* 1.3 76.1 - - + +
58F GLU* 1.3 64.7 + - + +
60F GLU* 3.2 6.9 + - - +
61F HIS* 2.9 44.7 + - + +
140F ASP* 4.1 17.5 - - - +
143F ARG* 5.8 1.4 + - - -
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Residues in contact with GLU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLU* 2.7 31.4 - - - +
26F ALA* 4.2 9.4 - - + +
27F SER* 3.8 12.6 - - - +
30F TYR* 4.0 17.5 - - + -
54F HIS* 3.2 20.8 + - - +
57F GLU* 1.3 80.7 - - - +
59F ARG* 1.3 57.6 + - - +
61F HIS* 3.1 11.6 + - - +
62F ALA* 3.0 26.0 + - - +
103F GLU* 3.4 15.1 - - - +
106F VAL* 4.9 0.8 - - - +
176F MG 2.0 32.3 - - - -
177F MG 2.6 24.8 - - - -
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B HIS* 6.0 2.9 - - + +
59B ARG* 5.7 9.6 - - + -
24F LEU* 4.9 11.7 - - + -
27F SER* 3.6 14.1 + - - +
55F SER 3.1 18.0 + - - +
56F HIS* 3.6 9.9 - - + +
58F GLU* 1.3 73.9 - - - +
60F GLU* 1.3 63.7 + - - +
62F ALA* 3.2 8.6 + - - +
63F GLU* 3.1 36.8 + - + +
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Residues in contact with GLU 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F HIS 3.1 15.5 + - - +
57F GLU* 3.2 11.2 + - + +
59F ARG* 1.3 76.0 - - - +
61F HIS* 1.3 60.5 + - + +
63F GLU* 3.5 11.9 + - - +
64F LYS* 3.1 32.5 + - - +
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Residues in contact with HIS 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLU* 3.4 16.1 + - - +
57F GLU* 2.9 30.1 + - + +
58F GLU* 3.1 17.5 + - - +
59F ARG 3.2 0.2 - - - -
60F GLU* 1.3 77.9 - - + +
62F ALA* 1.3 64.5 + - - +
64F LYS* 3.4 19.3 + - - +
65F PHE* 3.3 13.0 + - - -
132F GLU 4.6 6.4 + - - -
133F TYR* 3.0 40.3 + + + -
136F GLU* 5.1 14.6 - - + +
137F GLN* 5.1 1.1 - - - -
140F ASP* 5.6 0.4 - - - -
176F MG 2.7 24.1 - - - -
177F MG 4.3 10.3 - - - -
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Residues in contact with ALA 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F LEU* 3.7 17.0 - - + +
23F GLU* 3.8 10.5 - - + +
24F LEU* 3.7 35.2 - - + -
58F GLU 3.0 12.0 + - - +
59F ARG 3.2 8.7 + - - +
61F HIS* 1.3 76.3 - - - +
63F GLU* 1.3 63.7 + - + +
65F PHE* 3.3 8.5 + - - +
66F MET* 3.1 26.8 + - + +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 4.9 5.6 + - - +
34B TYR* 5.1 10.5 + - + -
52B LYS* 3.6 21.5 - - - +
55B SER* 4.4 5.5 + - - -
56B HIS* 3.0 35.6 + - - -
24F LEU* 6.4 0.2 - - + -
59F ARG* 3.1 24.3 + - + +
60F GLU* 3.8 11.7 - - - +
62F ALA* 1.3 75.7 - - + +
64F LYS* 1.3 63.4 + - - +
66F MET* 3.2 24.7 + - + +
67F LYS* 3.1 24.8 + - - +
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Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F GLU* 3.1 19.7 + - - +
61F HIS* 3.6 17.1 + - - +
62F ALA 3.3 0.4 - - - -
63F GLU* 1.3 76.8 - - - +
65F PHE* 1.3 57.2 + - - +
67F LYS* 3.5 7.8 + - - +
68F TYR* 2.9 27.7 + - - +
128F PHE* 3.7 10.4 - - + -
132F GLU* 2.9 53.3 + - + +
133F TYR* 3.2 21.8 - - + +
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Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16F VAL* 3.9 30.3 - - + +
19F MET* 3.4 32.8 - - + -
20F LEU* 4.2 18.8 - - + +
23F GLU* 4.1 14.8 - - + -
61F HIS 3.3 16.7 + - - -
62F ALA 3.3 8.4 + - - +
63F GLU 3.2 0.4 - - - -
64F LYS* 1.3 78.0 - - - +
66F MET* 1.3 64.4 + - - +
68F TYR* 3.5 3.0 - - + +
69F GLN* 3.0 25.1 + - - +
110F LEU* 4.0 10.5 - - + -
113F LEU* 4.5 7.4 - - + -
125F LEU* 5.3 0.2 - - + -
128F PHE* 3.5 25.1 - + - -
129F LEU* 4.0 12.3 - - + -
133F TYR* 3.4 31.2 - + - -
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Residues in contact with MET 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 3.3 41.7 - - - +
34B TYR* 4.5 15.3 - - + -
35B ALA* 4.3 12.8 - - + -
20F LEU* 3.8 30.9 - - + +
24F LEU* 5.1 7.6 - - + -
62F ALA* 3.1 20.4 + - + +
63F GLU* 3.5 22.7 - - + +
65F PHE* 1.3 76.4 - - - +
67F LYS* 1.3 61.5 + - - +
69F GLN* 3.4 4.2 - - - +
70F ASN* 3.3 27.0 + - - -
76F VAL* 3.9 20.1 - - + +
78F LEU* 4.7 7.9 - - + -
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Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 3.3 30.3 - - - +
38B ASP* 3.1 33.4 + - - +
45B HIS* 5.0 5.1 + - - -
49B GLU* 5.7 1.8 - - - -
63F GLU 3.1 9.7 + - - +
64F LYS* 3.6 10.5 - - - +
66F MET* 1.3 79.0 - - - +
68F TYR* 1.3 59.1 + - - +
70F ASN* 3.5 3.5 + - - +
71F LYS* 3.0 43.8 + - + +
142G LYS* 6.0 0.4 - - - +
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Residues in contact with TYR 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 3.9 18.2 - + - -
16F VAL* 4.6 8.3 - - + -
64F LYS 2.9 18.3 + - - +
65F PHE* 3.5 6.5 - - - +
66F MET 3.2 0.2 - - - -
67F LYS* 1.3 74.5 - - - +
69F GLN* 1.3 68.3 - - - +
71F LYS* 3.1 17.4 + - + +
72F ARG* 2.8 52.4 + - + +
124F HIS* 2.8 42.8 + + - -
125F LEU* 3.2 35.5 - - + -
128F PHE* 3.6 42.8 - + + -
135G GLU* 5.6 0.2 - - - -
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Residues in contact with GLN 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 3.0 36.6 + - - -
13F GLU* 3.2 27.8 + - - +
16F VAL* 3.5 14.6 - - + +
17F ASN* 3.4 19.0 + - - -
20F LEU* 6.0 0.7 - - + -
65F PHE 3.0 13.3 + - - +
66F MET 3.4 6.5 - - - +
68F TYR* 1.3 84.0 - - - +
70F ASN* 1.3 61.6 + - - +
72F ARG* 3.2 4.9 + - - +
73F GLY 3.1 3.3 + - - -
74F GLY* 2.9 43.8 + - - -
75F ARG 4.0 7.4 - - - -
76F VAL* 3.7 23.3 - - + +
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Residues in contact with ASN 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR* 6.3 0.2 - - - -
35B ALA* 3.0 30.8 + - - +
38B ASP* 3.1 40.1 + - - +
39B ARG* 3.2 27.7 - - - +
40B ASP* 4.8 3.6 + - - +
4F VAL* 4.5 0.9 - - - +
66F MET 3.3 12.7 + - - -
67F LYS 3.9 2.9 - - - +
69F GLN* 1.3 76.2 - - - +
71F LYS* 1.3 65.9 + - - +
73F GLY* 3.2 10.6 + - - +
74F GLY 3.9 11.8 - - - +
75F ARG* 4.0 1.7 + - - +
76F VAL* 4.6 9.1 + - - +
142G LYS* 3.3 16.3 - - - +
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Residues in contact with LYS 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F VAL* 3.4 17.3 - - - +
67F LYS* 3.0 29.4 + - + +
68F TYR* 3.1 22.1 + - + +
70F ASN* 1.3 76.9 - - - +
72F ARG* 1.3 63.5 + - + +
128F PHE* 6.2 2.6 - - - -
135G GLU* 2.8 36.0 + - - +
138G VAL* 4.3 26.0 - - + +
139G LYS* 4.6 11.8 - - - +
142G LYS* 4.1 27.6 - - + +
----------------------------------------------------------
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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