Contacts of the helix formed by residues 3 - 29 (chain E) in PDB entry 4DZL
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 ILE 3 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.2 30.5 - - + +
6D ILE* 4.0 21.3 - - + +
2E GLU* 1.3 76.9 - - + +
4E ALA* 1.3 60.3 + - - +
6E ILE* 3.6 6.2 + - - +
7E LYS* 3.2 33.5 + - + +
3F ILE* 4.7 18.4 - - + -
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Residues in contact with ALA 4 (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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2E GLU 3.3 4.6 - - - +
3E ILE* 1.3 76.5 - - - +
5E ALA* 1.3 63.6 + - - +
7E LYS* 3.6 12.1 + - - +
8E GLN* 3.4 26.6 + - - +
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Residues in contact with ALA 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E GLU* 3.2 21.2 + - + +
4E ALA* 1.3 77.8 - - - +
6E ILE* 1.3 69.6 + - + +
8E GLN* 3.2 9.5 + - - +
9E GLU* 3.1 26.4 + - - +
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Residues in contact with ILE 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.9 33.7 - - + -
2E GLU* 3.0 21.6 + - + +
3E ILE* 3.6 6.0 + - - +
5E ALA* 1.3 80.6 - - + +
7E LYS* 1.3 59.1 + - - +
9E GLU* 3.3 18.6 + - - +
10E ILE* 3.0 27.5 + - + +
3F ILE* 5.4 5.6 - - + -
6F ILE* 4.4 9.0 - - + -
7F LYS* 4.5 29.6 - - + -
10F ILE* 3.6 26.0 - - + +
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Residues in contact with LYS 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.1 20.9 - - + -
9D GLU* 5.5 5.8 - - - +
3E ILE* 3.2 31.4 + - + +
4E ALA* 3.8 10.5 - - - +
5E ALA 3.3 0.2 - - - -
6E ILE* 1.3 78.6 - - - +
8E GLN* 1.3 58.4 + - + +
10E ILE* 3.6 8.5 + - - +
11E ALA* 3.0 26.7 + - - +
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Residues in contact with GLN 8 (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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4E ALA 3.4 14.1 + - - +
5E ALA* 3.2 11.7 + - - +
7E LYS* 1.3 78.6 - - + +
9E GLU* 1.3 59.7 + - + +
11E ALA* 3.5 11.6 + - - +
12E ALA* 3.1 26.9 + - - +
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Residues in contact with GLU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E ALA* 3.1 15.1 + - - +
6E ILE* 3.3 33.6 + - - +
8E GLN* 1.3 75.8 - - + +
10E ILE* 1.3 57.4 + - - +
12E ALA* 3.3 7.0 + - - +
13E ILE* 2.9 36.5 + - + +
10F ILE* 4.0 26.8 - - + +
14F LYS* 3.2 29.4 + - + +
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Residues in contact with ILE 10 (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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6D ILE* 4.7 6.3 - - + +
9D GLU* 3.6 35.7 - - + +
10D ILE* 3.6 32.3 - - + +
13D ILE* 3.5 25.1 - - + +
6E ILE* 3.0 25.9 + - + +
7E LYS* 3.6 8.5 - - - +
9E GLU* 1.3 74.1 - - - +
11E ALA* 1.3 65.9 + - - +
13E ILE* 3.4 8.0 + - + +
14E LYS* 3.0 32.9 + - + +
10F ILE* 4.5 12.5 - - + +
13F ILE* 6.0 0.7 - - + -
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Residues in contact with ALA 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E LYS 3.0 18.7 + - - +
8E GLN* 3.6 16.8 - - - +
9E GLU 3.3 0.4 - - - -
10E ILE* 1.3 78.1 - - - +
12E ALA* 1.3 62.7 + - - +
14E LYS* 3.5 10.3 + - - +
15E LYS* 3.3 30.9 + - + +
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Residues in contact with ALA 12 (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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8E GLN 3.1 17.4 + - - +
9E GLU* 3.6 7.6 - - - +
10E ILE 3.3 0.2 - - - -
11E ALA* 1.3 74.9 - - - +
13E ILE* 1.3 65.2 + - + +
15E LYS* 3.2 13.7 + - - +
16E GLU* 3.1 28.3 + - + +
29G GLN* 6.1 0.7 - - - +
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Residues in contact with ILE 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ILE* 3.8 37.0 - - + -
9E GLU* 2.9 27.1 + - + +
10E ILE* 3.8 8.5 - - + +
12E ALA* 1.3 74.8 - - + +
14E LYS* 1.3 59.5 + - - +
16E GLU* 3.1 18.0 + - - +
17E ILE* 2.9 31.9 + - + +
10F ILE* 4.5 16.6 - - + -
13F ILE* 4.0 24.7 - - + -
14F LYS* 4.1 23.1 - - + -
17F ILE* 4.5 9.6 - - + -
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Residues in contact with LYS 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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9D GLU* 3.6 27.7 + - + +
13D ILE* 4.3 17.7 - - + -
16D GLU* 5.8 3.6 - - - +
10E ILE* 3.0 26.2 + - + +
11E ALA* 3.6 9.4 - - - +
13E ILE* 1.3 77.5 - - - +
15E LYS* 1.3 55.8 + - + +
17E ILE* 3.3 10.8 + - - +
18E ALA* 3.0 27.5 + - - +
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Residues in contact with LYS 15 (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 ALA* 3.3 17.2 + - + +
12E ALA* 3.2 15.0 + - - +
14E LYS* 1.3 77.3 - - + +
16E GLU* 1.3 58.4 + - + +
18E ALA* 3.3 7.9 + - - +
19E ALA* 3.0 27.5 + - - +
26G ALA* 5.8 1.7 - - - +
29G GLN* 3.2 55.8 + - + +
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Residues in contact with GLU 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E ALA* 3.1 18.0 + - - +
13E ILE* 3.1 15.5 + - - +
15E LYS* 1.3 73.8 - - + +
17E ILE* 1.3 59.2 + - - +
19E ALA* 3.4 6.1 + - - +
20E ILE* 3.0 36.6 + - + +
14F LYS* 6.0 1.9 - - - +
17F ILE* 3.5 30.9 - - + +
21F LYS* 2.7 36.2 + - + +
28I LYS* 5.7 1.2 + - - +
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Residues in contact with ILE 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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13D ILE* 5.0 5.6 - - + +
16D GLU* 3.4 36.6 - - + +
17D ILE* 4.2 13.7 - - + -
20D ILE* 3.8 19.5 - - + -
13E ILE* 2.9 29.0 + - + +
14E LYS* 3.5 9.9 - - - +
15E LYS 3.3 0.2 - - - -
16E GLU* 1.3 73.9 - - - +
18E ALA* 1.3 66.2 + - - +
20E ILE* 3.3 5.8 + - + +
21E LYS* 2.9 40.9 + - + +
17F ILE* 3.5 26.2 - - + -
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Residues in contact with ALA 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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14E LYS 3.0 14.2 + - - +
15E LYS* 3.6 11.2 - - - +
17E ILE* 1.3 78.1 - - - +
19E ALA* 1.3 62.3 + - - +
21E LYS* 3.2 11.7 + - - +
22E PHI 3.1 18.2 + - - -
22G PHI 3.9 24.2 - - + +
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Residues in contact with ALA 19 (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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15E LYS 3.0 16.8 + - - +
16E GLU* 3.8 7.0 - - - +
17E ILE 3.3 0.2 - - - -
18E ALA* 1.3 76.6 - - - +
20E ILE* 1.3 58.5 + - + +
22E PHI 3.4 2.8 + - - +
23E GLU* 3.0 36.6 + - - +
22G PHI 4.4 14.2 - - + -
23G GLU* 5.4 2.2 - - - +
26G ALA* 4.4 22.4 - - + -
28I LYS* 4.4 18.2 - - - +
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Residues in contact with ILE 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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20D ILE* 3.5 33.0 - - + -
16E GLU 3.0 26.7 + - - +
17E ILE* 3.3 4.5 + - - +
19E ALA* 1.3 75.7 - - + +
21E LYS* 1.3 56.3 + - - +
23E GLU* 3.1 14.0 + - - +
24E ILE* 2.8 33.6 + - + +
17F ILE* 4.3 18.6 - - + -
20F ILE* 3.7 17.7 - - + -
21F LYS* 4.3 23.1 - - + -
24F ILE* 2.9 29.2 - - + -
28I LYS* 6.1 1.3 - - - +
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Residues in contact with LYS 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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16D GLU* 2.9 29.5 + - + +
20D ILE* 4.9 13.5 - - + -
17E ILE* 2.9 33.3 + - + +
18E ALA* 3.5 11.4 - - - +
20E ILE* 1.3 76.4 - - - +
22E PHI 1.3 56.7 + - - +
24E ILE* 3.3 11.1 + - + +
25E ALA* 2.9 28.1 + - - +
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Residues in contact with PHI 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 ALA 3.1 9.6 + - - +
19E ALA 3.7 4.5 - - - +
21E LYS* 1.3 74.9 + - - +
23E GLU* 1.3 70.7 + - + +
25E ALA* 3.1 11.3 + - + +
26E ALA* 2.9 30.1 + - + +
18G ALA* 3.9 37.4 - - + +
19G ALA* 4.3 17.5 - - + +
22G PHI 3.3 69.4 - + + -
23G GLU* 5.3 1.3 - - - -
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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
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19E ALA* 3.0 23.2 + - - +
20E ILE* 3.5 16.6 - - - +
22E PHI 1.3 80.8 + - + -
24E ILE* 1.3 58.2 + - - +
26E ALA* 3.4 4.8 + - - +
27E ILE* 2.9 37.6 + - + +
32E GLY* 5.0 0.8 - - - -
24F ILE* 3.2 33.9 - - + +
28F LYS* 3.8 18.9 - - + +
22G PHI 6.3 0.2 - - + -
23G GLU* 2.6 39.7 - - - +
28I LYS* 3.5 17.7 + - - -
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Residues in contact with ILE 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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20D ILE* 4.3 8.7 - - + -
23D GLU* 3.6 34.5 - - + -
24D ILE* 3.7 27.8 - - + -
27D ILE* 4.2 16.5 - - + +
20E ILE* 2.8 32.8 + - + +
21E LYS* 3.6 9.2 - - + +
23E GLU* 1.3 76.3 - - - +
25E ALA* 1.3 61.9 + - - +
27E ILE* 3.4 8.6 + - + +
28E LYS* 3.0 40.0 + - - +
24F ILE* 4.6 5.6 - - + -
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Residues in contact with ALA 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 LYS 2.9 13.6 + - - +
22E PHI 3.3 15.7 - - + +
24E ILE* 1.3 80.3 - - - +
26E ALA* 1.3 61.8 + - - +
28E LYS* 3.3 16.9 + - - +
29E GLN* 3.4 18.0 + - - +
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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
----------------------------------------------------------
22E PHI 2.9 30.7 + - + +
23E GLU* 3.9 6.1 - - - +
25E ALA* 1.3 73.5 - - - +
27E ILE* 1.3 65.9 + - - +
29E GLN* 3.0 18.3 + - - +
30E GLY 3.2 0.5 + - - -
31E TYR* 3.1 23.5 + - + +
32E GLY* 3.8 16.6 - - - +
19G ALA* 5.4 6.5 - - + -
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Residues in contact with ILE 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.8 35.4 - - + -
23E GLU* 2.9 29.4 + - + +
24E ILE* 3.7 10.3 - - + +
26E ALA* 1.3 75.9 - - - +
28E LYS* 1.3 57.4 + - - +
30E GLY* 2.8 24.4 + - - -
31E TYR 4.3 0.7 - - - +
32E GLY* 3.9 21.5 - - - +
24F ILE* 4.7 8.5 - - + +
27F ILE* 3.9 28.9 - - + -
28F LYS* 4.2 15.3 - - + -
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Residues in contact with LYS 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU* 3.2 30.2 + - - +
27D ILE* 4.9 13.2 - - + -
24E ILE* 3.0 35.1 + - + +
25E ALA* 3.5 12.2 - - - +
26E ALA 3.3 0.4 - - - -
27E ILE* 1.3 76.4 - - - +
29E GLN* 1.3 69.7 + - - +
30E GLY 3.7 0.2 + - - -
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Residues in contact with GLN 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 ALA 3.4 15.1 + - - +
26E ALA* 3.0 10.6 + - - +
28E LYS* 1.3 88.8 + - - +
30E GLY* 1.3 58.3 + - - +
31E TYR* 3.4 28.6 - - + -
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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