Contacts of the helix formed by residues 10 - 38 (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 SER 10 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ARG* 4.0 4.4 + - - +
8E TYR 3.7 2.0 + - - -
9E HIS* 1.3 83.9 + - - +
11E ASP* 1.3 65.3 + - - +
13E GLU* 3.4 18.8 + - - +
14E ALA* 3.1 22.7 + - - +
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Residues in contact with ASP 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E HIS* 2.8 23.7 + - - +
10E SER* 1.3 72.6 - - - +
12E CYS* 1.3 62.7 + - - +
14E ALA* 3.4 7.7 + - - +
15E ALA* 2.9 29.5 + - - +
18E ARG* 4.6 2.1 + - - -
116E LEU* 3.6 22.0 - - + +
120E LYS* 3.1 22.1 + - - +
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Residues in contact with CYS 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR* 4.1 9.4 - - + -
9E HIS* 3.1 25.0 + - + +
11E ASP* 1.3 79.8 - - - +
13E GLU* 1.3 57.8 - - - +
15E ALA* 3.1 3.3 + - - +
16E VAL* 2.9 35.1 + - - +
113E LEU* 4.3 1.0 - - - +
116E LEU* 4.0 25.1 - - - -
117E ALA* 4.3 7.2 - - - -
120E LYS* 4.1 15.7 - - - -
122E ASP* 5.0 5.4 - - - -
125E LEU* 4.0 26.7 - - + -
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Residues in contact with GLU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ARG* 2.7 35.0 + - - -
8E TYR* 3.7 20.1 + - + -
9E HIS 3.1 8.3 + - - +
10E SER* 3.5 17.2 + - - +
12E CYS* 1.3 79.2 - - - +
14E ALA* 1.3 62.5 + - - +
16E VAL 3.3 0.5 + - - -
17E ASN* 3.1 22.9 + - - +
69E GLN* 3.2 27.5 + - - +
74E GLY* 3.8 2.9 - - - -
75E ARG* 2.9 33.6 + - - +
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Residues in contact with ALA 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E SER 3.1 16.5 + - - +
11E ASP* 3.7 7.2 - - - +
13E GLU* 1.3 78.9 - - - +
15E ALA* 1.3 61.8 + - - +
17E ASN* 3.5 9.7 + - - +
18E ARG* 3.1 39.1 + - - +
79E GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP 2.9 18.0 + - - +
12E CYS 3.1 1.8 + - - +
14E ALA* 1.3 75.3 - - - +
16E VAL* 1.3 60.3 + - - +
18E ARG* 3.3 24.3 + - - +
19E MET* 2.9 29.3 + - - +
113E LEU* 3.5 27.1 - - + +
116E LEU* 3.7 11.0 - - + -
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Residues in contact with VAL 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR* 3.6 15.0 - - - +
12E CYS 2.9 19.2 + - - +
13E GLU 3.6 5.6 - - - +
15E ALA* 1.3 76.7 - - - +
17E ASN* 1.3 56.9 + - - +
19E MET* 3.2 6.7 + - - +
20E LEU* 2.9 28.7 + - + +
65E PHE* 3.9 34.0 - - + +
68E TYR* 4.6 4.9 - - + -
69E GLN* 3.5 21.5 - - + +
113E LEU* 4.3 13.9 - - + -
125E LEU* 4.3 22.9 - - + -
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Residues in contact with ASN 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E GLU* 3.1 15.0 + - - +
14E ALA* 3.6 11.8 - - - +
16E VAL* 1.3 76.2 - - - +
18E ARG* 1.3 60.9 + - - +
20E LEU* 3.5 17.2 - - - +
21E ASN* 3.4 19.8 + - - +
69E GLN* 3.4 12.5 + - - +
75E ARG 3.2 19.2 + - - -
76E VAL* 3.3 10.2 - - - -
77E VAL* 3.1 47.6 + - - +
79E GLN* 4.6 9.6 + - - +
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Residues in contact with ARG 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E ASP 4.6 2.6 + - - -
14E ALA* 3.1 22.0 + - - +
15E ALA* 3.4 34.1 - - - +
17E ASN* 1.3 79.5 - - - +
19E MET* 1.3 65.0 + - - +
21E ASN* 3.4 7.5 + - - +
22E LEU* 3.1 20.6 + - - +
79E GLN* 4.8 17.0 - - - +
116E LEU* 5.4 2.2 - - - +
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Residues in contact with MET 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ALA 2.9 16.2 + - - +
16E VAL* 3.2 6.0 + - - +
18E ARG* 1.3 76.0 - - - +
20E LEU* 1.3 65.4 + - - +
22E LEU* 3.2 13.7 + - - +
23E GLU* 2.9 27.5 + - - +
65E PHE* 3.4 31.2 - - + -
106E VAL* 4.6 3.4 - - - +
109E ALA* 3.1 51.4 - - + +
110E LEU* 3.5 21.8 - - + +
113E LEU* 3.7 19.5 - - + -
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Residues in contact with LEU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E VAL* 2.9 16.6 + - + +
17E ASN* 3.5 19.7 - - - +
19E MET* 1.3 76.3 - - - +
21E ASN* 1.3 62.8 + - + +
23E GLU* 3.4 8.6 + - - +
24E LEU* 3.1 42.5 + - + +
62E ALA* 3.7 16.8 - - - +
65E PHE* 4.2 13.8 - - + +
66E MET* 3.8 35.0 - - + +
69E GLN* 5.8 0.7 - - - +
76E VAL* 4.0 18.8 - - + -
77E VAL 5.6 0.7 - - - +
78E LEU* 3.7 17.3 - - + -
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Residues in contact with ASN 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E ASN 3.4 7.8 + - - +
18E ARG 3.6 8.9 - - - +
20E LEU* 1.3 83.4 - - + +
22E LEU* 1.3 61.0 + - - +
24E LEU* 3.1 8.1 + - - +
25E TYR* 2.8 30.1 + - - +
79E GLN* 3.5 43.2 + - - +
80E ASP 3.2 27.3 + - - +
81E ILE* 4.3 7.7 - - - +
82E LYS 5.6 0.7 + - - -
28I TYR* 4.4 5.6 + - - +
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Residues in contact with LEU 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E ARG 3.1 14.1 + - - +
19E MET* 3.2 15.0 + - - +
21E ASN* 1.3 77.4 + - - +
23E GLU* 1.3 57.6 + - - +
25E TYR* 3.2 23.5 + - + -
26E ALA* 2.9 26.9 + - - +
102E LEU* 5.4 1.3 - - + -
105E THR* 4.4 17.3 - - + +
106E VAL* 3.9 30.2 - - + +
109E ALA* 3.7 30.7 - - + -
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Residues in contact with GLU 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E MET* 2.9 18.7 + - + +
20E LEU 3.4 9.4 - - - +
21E ASN 3.2 0.2 - - - -
22E LEU* 1.3 76.9 - - - +
24E LEU* 1.3 58.9 + - - +
26E ALA* 3.3 5.9 + - - +
27E SER* 2.9 28.1 + - - -
58E GLU* 2.7 20.7 - - - +
61E HIS* 3.4 19.1 - - + +
62E ALA* 3.8 13.7 - - + -
65E PHE* 4.1 18.2 - - + -
106E VAL* 4.0 15.4 - - - +
110E LEU* 4.9 2.6 - - - +
133E TYR* 3.7 15.1 - - - -
176E MG 2.4 30.5 - - - -
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LEU* 3.1 31.0 + - + +
21E ASN* 3.1 9.6 + - - +
23E GLU* 1.3 74.9 - - - +
25E TYR* 1.3 56.5 + - - +
27E SER* 3.5 6.7 - - - -
28E TYR* 3.0 27.2 + - - +
59E ARG* 4.9 16.8 - - + +
62E ALA* 3.7 19.3 - - + -
63E GLU* 6.4 0.4 - - + -
66E MET* 5.1 6.5 - - + -
81E ILE* 3.7 23.1 - - + +
28I TYR* 3.5 40.4 - - + +
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Residues in contact with TYR 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ASN* 2.8 17.0 + - - +
22E LEU* 3.4 27.4 - - + +
23E GLU 3.2 0.2 - - - -
24E LEU* 1.3 73.8 - - - +
26E ALA* 1.3 63.7 + - - +
28E TYR* 3.2 4.3 + - + +
29E THR* 2.9 48.4 + - + -
81E ILE* 4.0 10.0 - - + +
82E LYS* 3.4 38.6 - - + +
83E LYS 3.8 11.4 + - - -
84E PRO* 4.1 1.3 - - + -
85E GLU* 3.8 25.1 + - - +
102E LEU* 4.1 16.6 - - + -
105E THR* 6.5 0.4 - - + -
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E LEU 2.9 14.0 + - - +
23E GLU* 3.5 10.1 - - - +
25E TYR* 1.3 76.8 - - - +
27E SER* 1.3 61.9 + - - +
29E THR* 3.3 2.8 + - - -
30E TYR* 3.1 31.9 + - + -
58E GLU* 4.2 15.3 - - + -
102E LEU* 3.9 26.0 - - + +
103E GLU* 6.2 0.4 - - - +
106E VAL* 4.2 19.1 - - + -
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Residues in contact with SER 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLU 2.9 16.8 + - - -
24E LEU* 3.5 11.3 - - - +
26E ALA* 1.3 76.5 - - - +
28E TYR* 1.3 61.9 + - - +
30E TYR 3.1 2.8 + - - -
31E SER* 3.0 18.8 + - - -
55E SER* 2.9 40.1 + - - +
58E GLU* 3.8 12.0 - - - +
59E ARG* 3.6 17.5 - - - +
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Residues in contact with TYR 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E LEU 3.0 18.6 + - - +
25E TYR* 3.2 5.6 + - - +
27E SER* 1.3 77.4 + - - +
29E THR* 1.3 60.1 + - - +
31E SER* 3.2 15.7 - - - -
32E SER* 3.2 18.5 + - - -
81E ILE* 4.0 9.0 - - + -
82E LYS 3.6 18.4 - - - +
83E LYS* 4.0 3.6 - - - -
84E PRO* 3.7 18.0 - - + +
20I LEU* 5.1 0.2 - - - +
21I ASN* 4.4 2.8 + - - +
24I LEU* 3.6 28.6 - - + +
66I MET* 5.5 0.4 - - + -
78I LEU* 3.4 36.4 - - + +
79I GLN 3.0 30.6 + - - -
81I ILE* 3.7 27.9 - - + +
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Residues in contact with THR 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E TYR* 2.9 30.2 + - - +
26E ALA 3.6 7.9 - - - -
27E SER 3.2 0.2 - - - -
28E TYR* 1.3 75.2 - - - +
30E TYR* 1.3 61.7 + - - +
32E SER* 3.2 6.6 + - - -
33E MET* 3.2 39.4 + - + +
84E PRO* 3.4 21.6 - - + +
85E GLU* 5.0 0.8 + - - +
89E TRP* 4.0 15.0 - - + -
102E LEU* 3.7 25.8 - - + -
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Residues in contact with TYR 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ALA* 3.1 23.4 + - + -
27E SER 3.1 6.3 + - - +
29E THR* 1.3 73.4 - - - +
31E SER* 1.3 59.7 + - - +
33E MET* 3.2 12.6 + - + +
34E TYR* 2.8 29.1 + - - +
50E PHE* 5.9 0.2 - + - -
51E PHE* 3.6 46.3 - + - +
54E HIS* 3.9 27.8 + + + -
55E SER* 3.7 7.6 - - - -
58E GLU* 4.0 13.2 - - + -
99E ALA* 3.9 24.9 + - + +
102E LEU* 3.9 16.8 - - + +
103E GLU* 2.8 41.5 + - - +
144E ILE* 4.3 4.0 - - + +
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Residues in contact with SER 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E SER 3.0 12.7 + - - -
28E TYR* 3.2 24.4 - - - -
30E TYR* 1.3 75.1 - - - +
32E SER* 1.3 62.1 + - - +
34E TYR* 3.4 11.9 + - - +
35E ALA* 3.1 22.9 + - - +
55E SER* 3.8 12.3 + - - -
24I LEU* 6.1 0.7 - - - +
63I GLU* 4.9 5.7 + - - -
66I MET* 3.3 30.1 - - - +
78I LEU* 4.8 3.1 - - - -
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Residues in contact with SER 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E TYR 3.2 5.5 + - - -
29E THR 3.2 11.3 + - - -
30E TYR 3.2 0.4 - - - -
31E SER* 1.3 73.9 - - - +
33E MET* 1.3 59.8 + - - +
35E ALA* 3.2 7.1 + - - +
36E PHE* 2.9 28.8 + - - +
84E PRO* 3.2 29.3 - - - +
86E ARG 4.0 6.2 + - - -
87E ASP* 5.1 7.9 + - - +
89E TRP* 3.4 17.9 + - - -
76I VAL* 6.4 0.2 - - - -
78I LEU* 3.3 17.9 - - - +
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Residues in contact with MET 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E THR* 3.2 33.0 + - + +
30E TYR* 3.2 16.1 + - + +
32E SER* 1.3 76.4 - - - +
34E TYR* 1.3 65.8 + - - +
36E PHE* 3.3 1.1 + - - +
37E PHE* 3.0 32.8 + - + -
51E PHE* 3.8 42.2 - - + -
89E TRP* 3.7 43.7 - - + +
95E ALA* 3.8 22.9 - - + +
98E ALA* 4.0 7.6 - - + +
99E ALA* 4.2 9.4 - - - +
102E LEU* 5.2 0.2 - - + -
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Residues in contact with TYR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E TYR 2.8 13.3 + - - +
31E SER* 3.4 15.0 - - - +
32E SER 3.2 0.2 - - - -
33E MET* 1.3 76.3 - - - +
35E ALA* 1.3 72.4 + - - +
37E PHE 3.4 0.5 + - - -
38E ASP* 3.2 30.3 + - + +
48E ALA* 3.2 37.8 - - + +
49E GLU* 3.6 20.1 + - - -
51E PHE* 4.0 2.8 - - - +
52E LYS* 3.7 40.9 + - + +
63I GLU* 5.1 13.0 + - + -
66I MET* 4.5 22.7 - - + -
67I LYS* 3.4 35.6 - - + +
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Residues in contact with ALA 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E SER 3.1 11.1 + - - +
32E SER* 3.2 9.2 + - - +
34E TYR* 1.3 84.7 - - - +
36E PHE* 1.3 63.1 + - - +
38E ASP* 4.4 1.1 - - - -
39E ARG* 3.5 9.8 + - - +
66I MET* 4.3 14.8 - - + -
70I ASN* 3.1 27.8 + - - +
76I VAL* 4.2 32.0 - - + +
78I LEU* 6.3 0.2 - - + -
----------------------------------------------------------
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Residues in contact with PHE 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E SER 2.9 16.5 + - - +
33E MET 3.5 4.9 - - - +
34E TYR 3.1 0.4 - - - -
35E ALA* 1.3 78.1 - - - +
37E PHE* 1.3 85.5 + + - +
39E ARG* 3.3 52.5 - - - +
42E VAL* 3.3 35.1 - - + +
87E ASP 4.5 3.4 - - - +
88E GLU* 3.8 13.0 - - + -
89E TRP* 3.6 34.1 - - + -
90E GLY* 3.5 42.8 - - - -
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Residues in contact with PHE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E MET* 3.0 27.6 + - + +
36E PHE* 1.3 90.2 - + - +
38E ASP* 1.3 61.5 + - - +
39E ARG 3.2 0.7 - - - -
42E VAL* 3.5 23.1 - - + -
43E ALA* 3.5 7.8 + - - -
44E LEU* 3.2 50.6 + - + +
45E HIS* 4.3 0.7 + - - -
47E VAL* 3.9 12.6 - - + -
48E ALA* 3.7 14.1 - - + -
51E PHE* 3.7 19.7 - + - -
89E TRP* 4.8 0.2 - - + -
91E ASN* 3.5 23.6 - - - -
92E THR* 3.6 27.6 - - - -
95E ALA* 3.7 22.4 - - + -
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Residues in contact with ASP 38 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR* 3.2 28.5 + - + +
35E ALA* 4.3 1.8 - - - -
36E PHE 3.2 0.2 - - - -
37E PHE* 1.3 74.4 - - - +
39E ARG* 1.3 60.6 + - - +
45E HIS* 3.4 23.5 + - - -
48E ALA* 4.5 2.3 - - + +
67I LYS* 3.2 43.9 + - - +
70I ASN* 3.2 31.7 + - - +
142W LYS* 2.9 31.2 + - - -
----------------------------------------------------------
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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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