Contacts of the helix formed by residues 1 - 34 (chain E) in PDB entry 1KD9
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 LYS 1 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E ACE 1.3 70.2 - - - +
2E VAL* 1.3 61.4 + - + +
4E GLN* 3.3 7.7 + - + +
5E LEU* 2.9 60.3 + - + +
2F VAL* 3.6 29.4 - - + -
6F GLU* 4.0 16.4 + - - -
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Residues in contact with VAL 2 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E ACE 3.3 1.0 - - + +
1E LYS* 1.3 78.2 - - + +
3E LYS* 1.3 62.2 + - - +
5E LEU* 3.3 1.7 + - - -
6E LYS* 3.0 52.2 + - + +
1F GLU* 3.0 45.1 - - + +
2F VAL* 4.2 16.4 - - + -
5F LEU* 3.6 11.5 - - + +
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Residues in contact with LYS 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E ACE 3.6 14.3 + - + +
1E LYS 3.3 0.4 - - - -
2E VAL* 1.3 79.7 - - - +
4E GLN* 1.3 64.1 + - - +
6E LYS* 3.4 11.6 + - - +
7E ALA* 3.1 22.0 + - - +
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Residues in contact with GLN 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0E ACE 3.2 15.4 + - - +
1E LYS* 3.3 10.3 + - + +
3E LYS* 1.3 79.8 - - - +
5E LEU* 1.3 63.4 + - + +
7E ALA* 3.3 8.8 + - - +
8E LYS* 3.0 21.5 + - - +
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Residues in contact with LEU 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E LYS* 2.9 55.4 + - + +
3E LYS 3.3 0.4 - - - -
4E GLN* 1.3 78.9 - - + +
6E LYS* 1.3 51.8 + - - +
8E LYS* 3.1 9.2 + - + +
9E VAL* 2.8 38.4 + - - +
2F VAL* 3.8 22.4 - - + +
5F LEU* 3.6 34.3 - - + -
6F GLU* 3.8 15.0 - - + -
9F VAL* 4.0 22.8 - - + +
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Residues in contact with LYS 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 4.8 14.3 + - - +
32A GLU* 5.6 3.4 + - - -
2E VAL* 3.0 44.9 + - + +
3E LYS* 3.7 8.5 - - - +
5E LEU* 1.3 71.6 - - - +
7E ALA* 1.3 64.6 + - - +
9E VAL* 3.2 11.0 + - - +
10E GLU* 3.0 28.7 + - + +
1F GLU* 3.7 14.3 + - - -
5F LEU* 4.0 17.5 - - + -
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Residues in contact with ALA 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E LYS 3.1 12.9 + - - +
4E GLN* 3.4 12.6 - - - +
6E LYS* 1.3 76.2 - - - +
8E LYS* 1.3 58.2 + - - +
10E GLU* 3.1 10.1 + - - +
11E GLU* 2.9 29.1 + - - +
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Residues in contact with LYS 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E GLN 3.0 14.3 + - - +
5E LEU* 3.2 15.5 - - + +
7E ALA* 1.3 74.2 - - - +
9E VAL* 1.3 66.6 + - - +
11E GLU* 3.3 29.7 + - - +
12E LEU* 2.9 54.6 + - + +
9F VAL* 3.8 17.0 - - + -
13F GLU* 4.2 13.1 + - - -
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Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E LEU 2.8 20.8 + - - +
6E LYS* 3.2 11.6 + - - +
8E LYS* 1.3 77.5 - - - +
10E GLU* 1.3 57.9 + - - +
12E LEU* 3.3 1.4 + - - -
13E LYS* 2.8 60.3 + - - +
5F LEU* 4.3 15.7 - - + -
8F GLU* 3.7 26.2 - - + +
9F VAL* 4.0 16.2 - - + -
12F LEU* 3.8 14.6 - - + +
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Residues in contact with GLU 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 5.1 1.0 - - - +
6E LYS* 3.0 20.2 + - + +
7E ALA* 3.1 9.8 + - - +
9E VAL* 1.3 78.9 - - - +
11E GLU* 1.3 62.4 + - - +
13E LYS* 3.1 36.0 + - - +
14E SER* 3.0 25.7 + - - -
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Residues in contact with GLU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E ALA 2.9 14.6 + - - +
8E LYS* 3.7 36.6 + - - +
10E GLU* 1.3 78.3 - - - +
12E LEU* 1.3 62.7 + - - +
14E SER* 3.3 6.9 + - - -
15E LYS* 3.0 30.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LYS* 2.9 53.9 + - + +
9E VAL 4.0 2.9 - - - +
11E GLU* 1.3 80.0 - - - +
13E LYS* 1.3 61.6 + - - +
15E LYS* 3.7 8.4 - - + +
16E LEU* 2.8 30.5 + - - +
9F VAL* 3.9 17.9 - - + +
12F LEU* 4.0 21.2 - - + +
13F GLU* 3.9 28.9 - - + +
16F LEU* 3.9 26.9 - - + +
----------------------------------------------------------
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Residues in contact with LYS 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 5.6 12.3 - - + -
22A GLU* 3.3 36.3 + - - +
9E VAL* 2.8 41.3 + - + +
10E GLU* 3.1 33.3 + - - +
12E LEU* 1.3 78.7 - - - +
14E SER* 1.3 56.6 + - - +
16E LEU* 3.3 8.6 + - + +
17E TRP* 3.0 26.2 + - - +
8F GLU* 4.4 8.7 + - - -
12F LEU* 4.3 15.3 - - + -
----------------------------------------------------------
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Residues in contact with SER 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E GLU 3.0 13.5 + - - -
11E GLU* 3.8 7.9 - - - -
13E LYS* 1.3 73.9 - - - +
15E LYS* 1.3 68.5 + - - +
17E TRP* 3.2 10.9 + - - +
18E HIS* 3.1 37.5 + - - -
----------------------------------------------------------
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Residues in contact with LYS 15 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E GLU* 3.0 21.4 + - + +
12E LEU* 3.8 10.1 - - + +
14E SER* 1.3 77.8 - - - +
16E LEU* 1.3 62.9 + - - +
18E HIS* 3.2 11.3 + - + +
19E LEU* 3.1 28.5 + - + +
16F LEU* 3.5 30.7 - - + -
20F GLU* 4.4 14.8 - - - -
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Residues in contact with LEU 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 3.0 39.3 - - + +
12E LEU 2.8 16.8 + - - +
13E LYS* 3.5 8.3 - - + +
14E SER 3.1 0.2 - - - -
15E LYS* 1.3 79.7 - - - +
17E TRP* 1.3 64.7 + - - +
19E LEU* 3.3 3.3 + - - +
20E LYS* 3.0 46.2 + - - +
12F LEU* 4.2 12.3 - - + +
15F GLU* 3.6 9.9 - - + +
16F LEU* 3.4 34.2 - - + +
19F LEU* 3.6 18.8 - - + -
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Residues in contact with TRP 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LYS 3.0 13.5 + - - +
14E SER* 3.2 11.4 + - - +
16E LEU* 1.3 76.1 - - - +
18E HIS* 1.3 101.8 + + - +
20E LYS* 3.3 10.0 + - + +
21E ASN* 3.0 49.9 + - - +
----------------------------------------------------------
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Residues in contact with HIS 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E SER* 3.1 34.2 + - - -
15E LYS* 3.7 9.4 - - + +
16E LEU 3.2 0.2 - - - -
17E TRP* 1.3 106.6 - + - +
19E LEU* 1.3 56.7 + - + +
21E ASN* 2.8 32.7 + - - +
22E LYS* 2.9 13.0 + - - +
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Residues in contact with LEU 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LYS* 3.1 18.7 + - + +
16E LEU 3.8 5.6 - - - +
18E HIS* 1.3 76.7 - - + +
20E LYS* 1.3 58.1 + - - +
22E LYS* 3.3 13.7 + - + +
23E VAL* 2.9 31.7 + - - +
16F LEU* 3.5 48.9 - - + +
19F LEU* 4.0 15.5 - - + -
20F GLU* 4.0 23.6 - - + +
23F VAL* 3.9 26.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 20 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU 5.2 2.0 + - - -
14A SER* 4.2 11.4 - - - -
15A GLU* 4.5 13.7 - - - +
18A HIS* 4.0 10.5 + - - -
16E LEU* 3.0 50.5 + - + +
17E TRP* 3.7 10.5 - - + +
19E LEU* 1.3 74.0 - - - +
21E ASN* 1.3 67.8 + - - +
23E VAL* 3.9 6.4 - - - +
24E ALA* 3.0 23.6 + - - +
15F GLU* 3.7 18.7 + - - -
19F LEU* 3.8 17.9 - - + -
----------------------------------------------------------
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Residues in contact with ASN 21 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E TRP* 3.0 57.0 + - - +
18E HIS* 2.8 16.4 + - - +
20E LYS* 1.3 79.9 - - - +
22E LYS* 1.3 56.4 + - - +
24E ALA* 3.3 7.9 + - - +
25E ARG* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 22 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E HIS 2.9 11.0 + - - +
19E LEU* 3.6 18.4 - - + +
20E LYS 3.3 0.2 - - - -
21E ASN* 1.3 73.3 - - - +
23E VAL* 1.3 66.5 + - - +
25E ARG* 3.3 11.5 + - - +
26E LEU* 2.9 36.7 + - + +
23F VAL* 3.8 26.6 - - + +
27F GLU* 3.8 20.9 + - - -
----------------------------------------------------------
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Residues in contact with VAL 23 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E LEU 2.9 19.3 + - - +
20E LYS* 3.9 7.0 - - - +
21E ASN 3.3 0.2 - - - -
22E LYS* 1.3 79.1 - - - +
24E ALA* 1.3 64.1 + - - +
26E LEU* 3.3 3.8 + - - +
27E LYS* 3.0 43.1 + - + +
19F LEU* 4.2 17.7 - - + +
22F GLU* 4.1 25.4 - - + +
23F VAL* 4.0 20.2 - - + +
26F LEU* 4.1 11.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 24 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E LYS 3.0 17.8 + - - +
21E ASN* 3.6 7.9 - - - +
23E VAL* 1.3 78.1 - - - +
25E ARG* 1.3 62.5 + - - +
27E LYS* 3.5 10.2 + - - +
28E LYS* 3.1 22.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASN 2.9 14.5 + - - +
22E LYS* 3.5 13.5 - - - +
24E ALA* 1.3 76.3 - - - +
26E LEU* 1.3 70.4 + - - +
28E LYS* 2.9 10.8 + - + +
29E LYS* 2.8 60.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E LYS* 2.9 30.8 + - + +
23E VAL* 3.9 4.3 - - - +
25E ARG* 1.3 90.7 - - + +
27E LYS* 1.3 56.6 + - - +
29E LYS* 3.2 13.2 + - + +
30E ASN* 2.7 34.0 + - - +
23F VAL* 3.9 30.3 - - + +
26F LEU* 3.7 19.7 - - + +
27F GLU* 3.7 42.2 - - + +
30F ASN* 5.1 6.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 27 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 5.1 15.3 - - - -
23E VAL* 3.0 38.4 + - + +
24E ALA* 3.8 8.0 + - - +
26E LEU* 1.3 72.1 - - - +
28E LYS* 1.3 62.4 + - - +
30E ASN* 3.7 7.3 - - - +
31E ALA* 2.8 30.4 + - - +
22F GLU* 6.0 0.7 - - - +
26F LEU* 3.7 23.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 28 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ALA 3.1 13.7 + - - +
25E ARG* 2.9 14.0 + - + +
27E LYS* 1.3 76.7 - - - +
29E LYS* 1.3 57.7 - - - +
31E ALA* 3.0 7.2 + - - +
32E GLU* 2.9 30.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 29 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ARG* 2.8 49.7 + - + +
26E LEU* 3.4 15.7 - - + +
28E LYS* 1.3 77.3 - - - +
30E ASN* 1.3 62.7 + - - +
32E GLU* 3.4 7.0 + - - +
33E CYS* 2.9 24.3 + - - +
30F ASN* 3.4 30.8 + - - +
----------------------------------------------------------
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Residues in contact with ASN 30 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU 2.7 25.3 + - - +
27E LYS* 3.7 7.6 - - - +
29E LYS* 1.3 74.2 - - - +
31E ALA* 1.3 63.7 + - - +
33E CYS* 3.2 4.8 + - - +
34E LYS* 3.0 24.4 + - - +
26F LEU* 3.2 22.3 + - + +
29F GLU* 3.5 25.1 - - - +
30F ASN* 3.1 36.7 - - - +
33F CYS* 4.9 5.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 31 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LYS 2.8 17.9 + - - +
28E LYS* 3.4 7.4 - - - +
30E ASN* 1.3 78.7 - - - +
32E GLU* 1.3 64.3 + - - +
33E CYS 3.2 0.2 + - - -
34E LYS* 3.2 20.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 32 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E LYS 2.9 15.2 + - - +
29E LYS* 3.6 7.9 - - - +
31E ALA* 1.3 76.7 - - - +
33E CYS* 1.3 65.2 + - - +
34E LYS 4.2 2.4 - - - +
----------------------------------------------------------
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Residues in contact with CYS 33 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LYS 2.9 16.7 + - - +
30E ASN* 3.6 5.2 - - - +
32E GLU* 1.3 80.6 - - - +
34E LYS* 1.3 66.8 + - - +
30F ASN* 4.7 7.2 - - - +
33F CYS* 2.0 61.5 - - + -
34F GLU* 3.7 7.4 - - - -
----------------------------------------------------------
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Residues in contact with LYS 34 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ASN 3.0 16.7 + - - +
31E ALA* 3.2 14.8 + - - +
32E GLU 4.2 2.3 - - - +
33E CYS* 1.3 84.3 - - - +
33F CYS* 3.5 10.7 - - - -
----------------------------------------------------------
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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