Contacts of the helix formed by residues 10 - 38 (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 SER 10 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ARG* 4.0 3.7 + - - +
8F TYR 3.7 2.0 + - - -
9F HIS* 1.3 83.1 + - - +
11F ASP* 1.3 64.5 + - - +
13F GLU* 3.4 19.7 + - - +
14F ALA* 3.1 22.9 + - - +
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Residues in contact with ASP 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F HIS* 2.8 23.2 + - - +
10F SER* 1.3 75.4 - - - +
12F CYS* 1.3 62.6 + - - +
14F ALA* 3.4 6.5 + - - +
15F ALA* 2.9 28.4 + - - +
18F ARG* 4.6 1.9 + - - -
116F LEU* 3.6 22.0 - - + +
120F LYS* 3.1 22.3 + - - +
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Residues in contact with CYS 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F TYR* 4.1 10.8 - - + -
9F HIS* 3.1 25.4 + - + +
11F ASP* 1.3 79.1 - - - +
13F GLU* 1.3 57.9 + - - +
15F ALA* 3.1 3.7 + - - +
16F VAL* 2.9 34.9 + - - +
113F LEU* 4.3 0.6 - - - +
116F LEU* 4.0 25.4 - - - -
117F ALA* 4.3 7.6 - - - -
120F LYS* 4.1 15.5 - - - -
122F ASP* 5.0 5.4 - - - -
125F LEU* 4.0 26.0 - - + -
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Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ARG* 2.7 34.3 + - - -
8F TYR* 3.7 20.8 + - + -
9F HIS 3.1 8.3 + - - +
10F SER* 3.5 17.1 + - - +
12F CYS* 1.3 79.5 - - - +
14F ALA* 1.3 62.5 + - - +
16F VAL 3.3 0.5 + - - -
17F ASN* 3.1 21.8 + - - +
69F GLN* 3.2 27.1 + - - +
74F GLY* 3.8 2.5 - - - -
75F ARG* 2.9 32.9 + - - +
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Residues in contact with ALA 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F SER 3.1 16.7 + - - +
11F ASP* 3.7 7.4 - - - +
13F GLU* 1.3 77.6 - - - +
15F ALA* 1.3 61.9 + - - +
17F ASN* 3.5 10.2 + - - +
18F ARG* 3.1 39.1 + - - +
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Residues in contact with ALA 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ASP 2.9 17.7 + - - +
12F CYS 3.5 1.3 - - - +
14F ALA* 1.3 74.9 - - - +
16F VAL* 1.3 61.1 + - - +
18F ARG* 3.3 24.2 + - - +
19F MET* 2.9 29.1 + - - +
113F LEU* 3.5 27.4 - - + +
116F LEU* 3.7 11.7 - - + -
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Residues in contact with VAL 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F TYR* 3.6 15.7 - - - +
12F CYS 2.9 19.6 + - - +
13F GLU 3.6 5.2 - - - +
15F ALA* 1.3 77.0 - - - +
17F ASN* 1.3 56.6 + - - +
19F MET* 3.2 7.0 + - - +
20F LEU* 2.9 29.9 + - + +
65F PHE* 3.9 33.8 - - + +
68F TYR* 4.6 5.2 - - + -
69F GLN* 3.5 20.9 - - + +
113F LEU* 4.3 12.1 - - + -
125F LEU* 4.3 22.9 - - + -
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Residues in contact with ASN 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 3.1 15.5 + - - +
14F ALA* 3.6 12.2 - - - +
16F VAL* 1.3 76.1 - - - +
18F ARG* 1.3 60.0 + - - +
20F LEU* 3.5 17.3 - - - +
21F ASN* 3.4 19.8 + - - +
69F GLN* 3.4 12.5 + - - +
75F ARG 3.2 19.0 + - - -
76F VAL* 3.3 10.2 - - - -
77F VAL* 3.1 45.9 + - + +
79F GLN* 4.6 10.5 + - - +
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Residues in contact with ARG 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ASP 4.6 2.6 + - - -
14F ALA* 3.1 21.6 + - - +
15F ALA* 3.4 33.5 - - - +
17F ASN* 1.3 79.9 - - - +
19F MET* 1.3 63.5 + - - +
21F ASN* 3.4 7.5 + - - +
22F LEU* 3.1 20.4 + - - +
79F GLN* 4.8 17.0 - - - +
116F LEU* 5.4 2.2 - - - +
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Residues in contact with MET 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ALA 2.9 17.3 + - - +
16F VAL* 3.5 5.6 - - - +
18F ARG* 1.3 75.8 - - - +
20F LEU* 1.3 63.9 + - - +
22F LEU* 3.2 12.7 + - - +
23F GLU* 2.9 27.9 + - - +
65F PHE* 3.4 30.1 - - + -
106F VAL* 4.6 3.4 - - - +
109F ALA* 3.1 50.7 - - + +
110F LEU* 3.5 21.1 - - + +
113F LEU* 3.7 20.2 - - + -
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F VAL* 2.9 17.1 + - + +
17F ASN* 3.5 18.8 - - - +
19F MET* 1.3 75.9 - - - +
21F ASN* 1.3 64.1 + - + +
23F GLU* 3.4 8.8 + - - +
24F LEU* 3.1 42.4 + - + +
62F ALA* 3.7 17.5 - - + +
65F PHE* 4.2 13.4 - - + +
66F MET* 3.8 35.7 - - + +
69F GLN* 5.8 0.7 - - - +
76F VAL* 4.0 19.1 - - + -
77F VAL 5.6 0.2 - - - +
78F LEU* 3.7 17.0 - - + -
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Residues in contact with ASN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B TYR* 4.4 4.4 + - - +
17F ASN 3.4 8.0 + - - +
18F ARG 3.6 8.7 - - - +
19F MET 3.2 0.2 - - - -
20F LEU* 1.3 82.3 - - + +
22F LEU* 1.3 61.4 + - - +
24F LEU* 3.1 8.6 + - - +
25F TYR* 2.8 30.0 + - - +
79F GLN* 3.5 43.0 + - - +
80F ASP 3.2 27.7 + - - +
81F ILE* 4.3 7.8 - - - +
82F LYS 5.6 0.9 + - - -
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Residues in contact with LEU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F ARG 3.1 14.0 + - - +
19F MET* 3.2 15.2 + - - +
21F ASN* 1.3 77.9 + - - +
23F GLU* 1.3 57.3 + - - +
25F TYR* 3.2 24.3 + - + -
26F ALA* 2.9 26.3 + - - +
102F LEU* 5.4 1.3 - - + -
105F THR* 4.4 16.6 - - + +
106F VAL* 3.9 30.7 - - + +
109F ALA* 3.7 31.0 - - + -
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Residues in contact with GLU 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F MET* 2.9 19.3 + - + +
20F LEU 3.4 9.4 - - - +
21F ASN 3.2 0.2 - - - -
22F LEU* 1.3 76.5 - - - +
24F LEU* 1.3 58.6 + - - +
26F ALA* 3.3 4.7 + - - +
27F SER* 2.9 28.1 + - - -
58F GLU* 2.7 20.1 - - - +
61F HIS* 3.4 18.8 - - + +
62F ALA* 3.8 13.7 - - + +
65F PHE* 4.1 19.4 - - + -
106F VAL* 4.0 15.1 - - - +
110F LEU* 4.9 2.4 - - - +
133F TYR* 3.7 14.7 - - - -
176F MG 2.4 30.0 - - - -
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Residues in contact with LEU 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 3.6 39.7 - - + +
20F LEU* 3.1 30.6 + - + +
21F ASN* 3.1 9.6 + - - +
23F GLU* 1.3 76.2 - - - +
25F TYR* 1.3 56.4 + - - +
27F SER* 3.5 6.1 - - - -
28F TYR* 3.0 27.4 + - - +
59F ARG* 4.9 17.7 - - + +
62F ALA* 3.7 17.9 - - + -
63F GLU* 6.4 0.2 - - + -
66F MET* 5.1 6.1 - - + -
81F ILE* 3.7 24.5 - - + +
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Residues in contact with TYR 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ASN* 2.8 18.1 + - - +
22F LEU* 3.4 26.7 - - + +
23F GLU 3.2 0.4 - - - -
24F LEU* 1.3 72.3 - - - +
26F ALA* 1.3 64.1 + - - +
28F TYR* 3.2 3.3 + - - +
29F THR* 2.9 48.1 + - - +
81F ILE* 4.0 9.8 - - + +
82F LYS* 3.4 37.9 - - + +
83F LYS 3.8 12.1 + - - -
84F PRO* 4.1 1.6 - - + -
85F GLU* 3.8 26.0 + - - +
102F LEU* 4.1 17.3 - - + -
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Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU 2.9 13.1 + - - +
23F GLU* 3.5 10.5 - - - +
25F TYR* 1.3 77.3 - - - +
27F SER* 1.3 63.3 + - - +
29F THR* 3.3 3.5 + - - -
30F TYR* 3.1 30.4 + - + -
58F GLU* 4.2 15.3 - - + -
102F LEU* 4.0 26.5 - - + -
103F GLU* 6.2 0.7 - - - +
106F VAL* 4.2 19.1 - - + -
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Residues in contact with SER 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLU 2.9 16.8 + - - -
24F LEU* 3.5 11.3 - - - +
26F ALA* 1.3 75.9 - - - +
28F TYR* 1.3 62.3 + - - +
30F TYR 3.1 2.4 + - - -
31F SER* 3.0 19.3 + - - -
55F SER* 2.9 39.6 + - - +
58F GLU* 3.8 13.3 - - - +
59F ARG* 3.6 17.3 - - - +
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Residues in contact with TYR 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 5.1 0.2 - - - +
21B ASN* 4.4 2.9 + - - +
24B LEU* 3.6 28.8 - - + +
78B LEU* 3.4 37.7 - - + +
79B GLN 3.0 31.2 + - - -
81B ILE* 3.7 22.9 - - + +
24F LEU 3.0 18.6 + - - +
25F TYR* 3.2 6.3 + - - +
27F SER* 1.3 77.6 + - - +
29F THR* 1.3 61.1 + - - +
31F SER* 3.2 16.8 - - - -
32F SER* 3.2 18.7 + - - -
81F ILE* 4.0 13.7 - - + -
82F LYS 3.6 17.9 - - - +
83F LYS* 4.0 3.4 - - - -
84F PRO* 3.7 18.9 - - + +
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Residues in contact with THR 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F TYR* 2.9 30.3 + - - +
26F ALA* 3.6 7.9 - - - -
27F SER 3.2 0.2 - - - -
28F TYR* 1.3 76.8 - - - +
30F TYR* 1.3 61.7 + - - +
32F SER* 3.2 6.2 + - - -
33F MET* 3.2 39.5 + - + +
84F PRO* 3.4 21.0 - - + +
85F GLU* 5.8 0.4 - - - +
89F TRP* 4.0 15.5 - - + -
102F LEU* 3.7 26.0 - - + -
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Residues in contact with TYR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F ALA* 3.1 23.4 + - + -
27F SER 3.1 6.9 + - - +
29F THR* 1.3 72.8 - - - +
31F SER* 1.3 61.0 + - - +
33F MET* 3.2 14.2 + - + +
34F TYR* 2.8 29.1 + - - +
50F PHE* 5.9 0.2 - + - -
51F PHE* 3.6 46.0 - + - +
54F HIS* 3.9 28.0 + + + -
55F SER* 3.7 7.0 - - - -
58F GLU* 4.0 13.5 - - + -
99F ALA* 3.9 24.4 + - + +
102F LEU* 3.9 17.6 - - + +
103F GLU* 2.8 42.0 + - - +
144F ILE* 4.3 3.3 - - + +
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Residues in contact with SER 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 6.1 0.3 - - - +
63B GLU* 4.8 6.6 + - - +
66B MET* 3.3 31.6 - - - +
78B LEU* 4.8 1.3 - - - -
27F SER 3.0 12.0 + - - -
28F TYR* 3.2 24.6 - - - -
30F TYR* 1.3 74.7 - - - +
32F SER* 1.3 62.3 + - - +
34F TYR* 3.4 12.1 + - - +
35F ALA* 3.1 23.0 + - - +
55F SER* 3.8 11.6 + - - -
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Residues in contact with SER 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 6.4 0.2 - - - -
78B LEU* 3.3 18.0 - - - +
28F TYR 3.2 4.9 + - - -
29F THR 3.2 12.0 + - - -
30F TYR 3.2 0.2 - - - -
31F SER* 1.3 73.7 - - - +
33F MET* 1.3 60.9 + - - +
35F ALA* 3.2 7.0 + - - +
36F PHE* 2.9 28.2 + - - +
84F PRO* 3.2 30.1 - - - +
86F ARG 4.0 6.1 + - - -
87F ASP* 5.1 7.3 + - - +
89F TRP* 3.4 17.2 + - - -
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Residues in contact with MET 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F THR* 3.5 32.8 - - + +
30F TYR* 3.2 15.7 + - + +
32F SER* 1.3 77.2 - - - +
34F TYR* 1.3 64.7 + - - +
36F PHE* 3.3 0.7 + - - +
37F PHE* 3.0 33.2 + - + -
51F PHE* 3.8 42.6 - - + -
89F TRP* 3.7 44.0 - - + -
95F ALA* 3.8 22.4 - - + +
98F ALA* 4.0 7.9 - - + +
99F ALA* 4.2 9.6 - - - +
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Residues in contact with TYR 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 5.1 12.5 - - + +
66B MET* 4.5 24.2 - - + -
67B LYS* 3.3 36.5 - - + +
70B ASN* 6.3 0.2 - - - -
30F TYR 2.8 13.1 + - - +
31F SER* 3.4 15.5 - - - +
33F MET* 1.3 76.1 - - - +
35F ALA* 1.3 72.9 + - - +
36F PHE 3.3 0.2 + - - -
37F PHE 3.4 0.7 + - - -
38F ASP* 3.2 29.4 + - + +
48F ALA* 3.2 38.5 - - + +
49F GLU* 3.6 20.1 + - - -
51F PHE* 4.0 2.0 - - - +
52F LYS* 3.7 42.0 + - + +
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Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B MET* 4.3 15.3 - - + -
70B ASN* 3.0 28.3 + - - +
76B VAL* 4.1 32.5 - - + +
78B LEU* 6.3 0.2 - - + -
31F SER 3.1 10.2 + - - +
32F SER* 3.2 9.4 + - - +
34F TYR* 1.3 84.7 - - - +
36F PHE* 1.3 63.1 + - - +
38F ASP* 4.4 1.1 - - - -
39F ARG* 3.5 9.7 + - - +
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Residues in contact with PHE 36 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F SER 2.9 15.7 + - - +
33F MET 3.5 5.2 - - - +
34F TYR 3.1 0.4 - - - -
35F ALA* 1.3 77.9 - - - +
37F PHE* 1.3 86.0 + + - +
39F ARG* 3.3 52.6 - - - +
42F VAL* 3.3 35.7 - - + +
87F ASP 4.5 3.6 - - - +
88F GLU* 3.8 12.3 - - + -
89F TRP* 3.6 33.7 - - + -
90F GLY* 3.5 41.5 - - - -
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Residues in contact with PHE 37 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F MET* 3.0 26.7 + - + -
34F TYR 3.4 0.2 + - - -
36F PHE* 1.3 90.5 - + - +
38F ASP* 1.3 61.5 + - - +
39F ARG 3.2 0.2 - - - -
42F VAL* 3.5 22.7 - - + -
43F ALA* 3.5 7.5 + - - -
44F LEU* 3.2 50.2 + - + +
45F HIS* 4.3 0.3 + - - -
47F VAL* 3.9 11.0 - - + -
48F ALA* 3.7 14.8 - - + +
51F PHE* 3.7 20.9 - + - -
89F TRP* 4.8 0.9 - - + -
91F ASN* 3.5 24.9 - - - -
92F THR* 3.6 27.6 - - - -
95F ALA* 3.7 21.5 - - + -
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Residues in contact with ASP 38 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LYS* 3.1 45.4 + - - +
70B ASN* 3.2 31.9 + - - +
34F TYR* 3.2 28.5 + - + +
35F ALA* 4.3 1.3 - - - -
36F PHE 3.2 0.2 - - - -
37F PHE* 1.3 74.0 - - - +
39F ARG* 1.3 62.1 + - - +
45F HIS* 3.4 23.4 + - - -
48F ALA* 4.1 3.0 - - + +
142V LYS* 2.9 31.8 + - - -
----------------------------------------------------------
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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).
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