Contacts of the helix formed by residues 12 - 39 (chain E) in PDB entry 2FMM
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 12 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ASP 4.2 0.8 + - - -
11E LEU* 1.3 76.6 - - - +
13E ARG* 1.3 86.6 + - - +
14E ASP* 3.6 9.3 + - - +
15E GLU* 2.9 32.8 + - - +
16E CYS* 2.9 21.6 + - - -
18E ARG* 4.6 0.2 + - - -
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Residues in contact with ARG 13 (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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11E LEU 3.9 2.0 + - - -
12E SER* 1.3 98.7 - - - +
14E ASP* 1.3 65.7 + - - +
16E CYS* 3.2 10.3 + - - +
17E LYS* 3.0 29.9 + - + +
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Residues in contact with ASP 14 (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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12E SER* 3.1 7.4 + - - +
13E ARG* 1.3 78.1 - - - +
15E GLU* 1.3 63.4 + - - +
17E LYS* 3.1 31.3 + - - +
18E ARG* 3.0 49.8 + - - +
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Residues in contact with GLU 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 4.5 16.8 - - + +
12E SER* 2.9 32.4 + - - +
14E ASP* 1.3 75.1 - - - +
16E CYS* 1.3 58.2 + - - +
18E ARG* 2.8 38.1 + - - +
19E ILE* 2.9 46.1 + - + +
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Residues in contact with CYS 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 3.7 31.0 - - - -
12E SER 2.9 17.0 + - - -
13E ARG* 3.4 11.9 - - - +
15E GLU* 1.3 77.0 - - - +
17E LYS* 1.3 58.8 + - + +
19E ILE* 3.3 7.6 + - - +
20E LEU* 2.9 31.2 + - - +
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Residues in contact with LYS 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 ARG* 3.0 18.1 + - + +
14E ASP* 3.1 33.4 + - - +
16E CYS* 1.3 77.8 - - + +
18E ARG* 1.3 59.3 + - + +
20E LEU* 3.7 8.3 - - + +
21E ARG* 3.0 30.4 + - - +
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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
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12E SER* 4.6 0.2 + - - -
14E ASP* 3.0 56.3 + - - +
15E GLU* 2.8 44.1 + - - +
17E LYS* 1.3 75.5 - - + +
19E ILE* 1.3 66.1 + - + +
21E ARG* 3.3 6.9 + - - +
22E LYS* 3.0 23.2 + - - +
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Residues in contact with ILE 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 5.4 15.5 - - + -
15E GLU* 2.9 35.3 + - + +
16E CYS* 3.7 6.7 - - - +
18E ARG* 1.3 79.3 - - + +
20E LEU* 1.3 58.6 + - - +
22E LYS* 3.1 15.5 + - + +
23E LEU* 2.8 45.2 + - + +
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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 CYS 2.9 17.7 + - - +
17E LYS* 3.7 7.9 - - + +
19E ILE* 1.3 77.0 - - - +
21E ARG* 1.3 63.1 + - - +
23E LEU* 3.0 18.3 + - + +
24E GLU* 2.9 55.7 + - + +
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Residues in contact with ARG 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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143D GLU* 2.6 51.3 + - + +
17E LYS 3.0 18.1 + - - +
18E ARG* 3.7 7.2 - - - +
20E LEU* 1.3 75.7 - - - +
22E LYS* 1.3 62.0 + - - +
24E GLU* 3.0 34.5 + - - +
25E LEU* 3.0 37.8 + - - +
56E LEU 3.3 7.7 + - - -
57E SER* 2.6 35.7 + - - -
58E ILE* 4.2 7.5 - - - +
59E SER* 4.9 2.2 - - - +
62E ARG* 4.9 7.3 - - - +
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Residues in contact with LYS 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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142D ASP* 4.6 26.6 + - + +
18E ARG 3.0 13.6 + - - +
19E ILE* 3.4 18.4 - - + +
21E ARG* 1.3 77.4 - - - +
23E LEU* 1.3 58.8 + - + +
25E LEU* 3.4 9.2 + - - +
26E GLU* 3.0 63.4 + - + +
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Residues in contact with LEU 23 (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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19E ILE* 2.8 32.0 + - + +
20E LEU* 3.0 21.7 + - + +
22E LYS* 1.3 77.1 - - + +
24E GLU* 1.3 58.7 + - - +
26E GLU* 3.9 15.0 - - + +
27E ALA* 2.9 31.6 + - - +
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Residues in contact with GLU 24 (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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20E LEU* 2.9 45.0 + - + +
21E ARG* 3.0 35.5 + - - +
22E LYS 3.2 0.2 - - - -
23E LEU* 1.3 77.0 - - + +
25E LEU* 1.3 61.5 + - - +
27E ALA* 3.4 6.6 + - - +
28E TYR* 3.0 24.1 + - - +
55E VAL 4.6 3.6 - - - +
56E LEU* 3.6 47.2 - - + +
57E SER* 4.7 4.4 - - - -
58E ILE* 4.1 3.0 - - - +
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Residues in contact with LEU 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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142D ASP* 3.5 32.1 - - + +
143D GLU* 3.9 6.5 - - - +
21E ARG* 3.0 32.8 + - - +
22E LYS* 3.9 5.8 - - - +
23E LEU 3.4 0.2 - - - -
24E GLU* 1.3 77.5 - - - +
26E GLU* 1.3 58.6 + - + +
28E TYR* 3.3 2.6 + - - +
29E ALA* 2.9 30.6 + - - +
58E ILE* 3.6 24.9 - - + -
62E ARG* 3.8 38.8 - - + +
66E GLU* 5.5 1.4 - - - +
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Residues in contact with GLU 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 LYS* 3.0 54.2 + - + +
23E LEU* 4.0 16.7 - - - +
25E LEU* 1.3 76.3 - - + +
27E ALA* 1.3 57.3 + - - +
29E ALA* 3.8 6.0 - - - +
30E GLY* 2.9 26.5 + - - -
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Residues in contact with ALA 27 (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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23E LEU 2.9 19.5 + - - +
24E GLU* 3.6 6.3 - - - +
25E LEU 3.2 0.2 - - - -
26E GLU* 1.3 76.6 - - - +
28E TYR* 1.3 62.1 + - - +
30E GLY* 3.3 3.0 + - - -
31E VAL* 3.2 27.9 + - + +
56E LEU* 3.9 17.0 - - + -
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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
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24E GLU 3.0 16.5 + - - +
25E LEU 3.8 3.8 - - - +
27E ALA* 1.3 77.4 - - - +
29E ALA* 1.3 62.5 + - - +
31E VAL* 3.2 3.8 + - - +
32E ILE* 3.0 46.2 + - + +
49E LEU* 3.6 34.3 + - + +
52E LEU* 3.7 26.7 - - + -
53E SER* 3.7 18.2 - - - -
56E LEU* 3.9 5.5 - - + +
58E ILE* 3.8 31.4 - - + -
63E HIS* 2.6 50.4 + + - +
66E GLU* 4.4 11.2 - - + -
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Residues in contact with ALA 29 (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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25E LEU 2.9 19.0 + - - +
26E GLU* 3.8 7.4 - - - +
28E TYR* 1.3 76.6 - - - +
30E GLY* 1.3 58.4 + - - +
32E ILE* 3.3 6.8 + - - +
33E SER* 2.9 33.1 + - - -
66E GLU* 3.5 29.3 - - - +
69E ARG* 4.3 4.7 + - - +
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Residues in contact with GLY 30 (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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26E GLU 2.9 17.9 + - - -
27E ALA* 3.3 2.2 + - - -
28E TYR 3.2 0.4 - - - -
29E ALA* 1.3 77.8 - - - +
31E VAL* 1.3 61.4 + - - +
33E SER* 3.4 7.3 + - - -
34E ALA* 3.1 23.0 + - - +
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Residues in contact with VAL 31 (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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27E ALA* 3.2 14.0 + - + +
28E TYR 3.2 7.5 + - - +
30E GLY* 1.3 72.0 - - - +
32E ILE* 1.3 68.9 + - - +
34E ALA* 3.2 6.1 + - + +
35E LEU* 2.9 46.9 + - + +
48E LEU* 5.2 8.1 - - + -
49E LEU* 4.0 5.6 - - + -
52E LEU* 3.6 30.1 - - + -
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Residues in contact with ILE 32 (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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28E TYR* 3.0 43.2 + - + +
29E ALA* 3.5 8.7 - - - +
31E VAL* 1.3 77.4 - - - +
33E SER* 1.3 57.0 + - - +
35E LEU* 3.4 4.8 + - - +
36E ARG* 2.9 28.6 + - - +
49E LEU* 3.6 36.6 - - + -
66E GLU* 3.8 23.6 - - + +
67E VAL* 4.2 18.6 - - + -
69E ARG* 4.5 2.0 - - - +
70E ALA* 3.7 22.9 - - + -
92E TRP* 4.5 8.5 - - + -
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Residues in contact with SER 33 (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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29E ALA 2.9 15.5 + - - -
30E GLY* 3.7 7.9 - - - -
32E ILE* 1.3 77.5 - - - +
34E ALA* 1.3 62.9 + - - +
36E ARG* 3.3 2.5 + - - +
37E ALA* 3.0 24.1 + - - +
69E ARG* 2.7 27.8 + - - +
76E LEU* 4.0 26.3 - - - +
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Residues in contact with ALA 34 (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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30E GLY 3.1 17.2 + - - +
31E VAL* 3.7 6.7 - - + +
33E SER* 1.3 75.2 - - - +
35E LEU* 1.3 66.4 + - + +
37E ALA* 3.3 9.1 + - - +
38E GLN* 3.2 29.7 + - - +
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Residues in contact with LEU 35 (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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31E VAL* 2.9 29.0 + - + +
32E ILE 3.9 1.6 - - - +
34E ALA* 1.3 74.6 - - + +
36E ARG* 1.3 66.0 + - - +
38E GLN* 3.1 37.0 + - - +
39E GLY 3.3 12.6 + - - +
45E LYS* 4.1 33.4 + - + +
48E LEU* 4.8 13.0 - - + -
49E LEU* 3.8 40.6 - - + -
92E TRP* 3.7 15.6 - - + -
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Residues in contact with ARG 36 (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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32E ILE 2.9 18.5 + - - +
33E SER* 3.7 3.8 - - - +
35E LEU* 1.3 76.4 - - - +
37E ALA* 1.3 61.5 + - - +
39E GLY 3.2 11.3 + - - +
70E ALA* 3.5 38.8 + - + +
71E VAL* 4.1 10.0 + - + +
76E LEU* 3.6 17.7 - - + -
77E THR* 3.5 41.3 + - - +
80E ALA* 3.5 10.3 - - - +
81E HIS* 5.6 0.6 + - - -
88E SER* 2.8 25.4 + - - -
89E SER* 3.4 27.0 - - - -
92E TRP* 3.6 27.4 - - + +
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Residues in contact with ALA 37 (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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33E SER 3.0 16.5 + - - +
34E ALA* 3.5 8.3 - - - +
35E LEU 3.2 0.2 - - - -
36E ARG* 1.3 79.5 - - - +
38E GLN* 1.3 60.8 + - + +
76E LEU* 3.9 26.4 - - + +
79E ILE* 3.7 23.9 - - + +
80E ALA* 3.1 20.3 + - - -
83E MET* 3.9 4.2 - - - +
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Residues in contact with GLN 38 (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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34E ALA* 3.2 18.9 + - - +
35E LEU* 3.1 21.3 + - - +
37E ALA* 1.3 77.7 - - - +
39E GLY* 1.3 57.6 + - - +
45E LYS* 2.8 43.2 + - - +
80E ALA* 4.7 0.2 - - - -
83E MET* 4.0 11.8 - - - +
84E SER* 2.9 18.4 + - - -
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Residues in contact with GLY 39 (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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35E LEU 3.3 4.9 - - - +
36E ARG 3.2 12.0 + - - +
37E ALA 3.3 0.2 - - - -
38E GLN* 1.3 81.7 - - - +
40E ASP* 1.3 65.7 + - - +
45E LYS* 5.5 1.6 - - - -
80E ALA* 4.1 3.8 - - - -
84E SER* 3.2 14.4 - - - -
88E SER* 3.7 13.0 - - - -
92E TRP* 2.8 19.1 + - - -
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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
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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