Contacts of the helix formed by residues 1 - 34 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C VAL* 3.7 30.1 - - + -
6C GLU* 5.6 5.6 - - - -
0D ACE 1.3 69.0 - - - +
2D VAL* 1.3 64.7 + - + +
4D GLN* 3.1 25.6 + - - +
5D LEU* 2.8 52.9 + - + +
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Residues in contact with VAL 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLU* 3.7 34.3 - - + -
2C VAL* 3.9 14.4 - - + -
5C LEU* 3.8 9.0 - - + +
0D ACE 5.8 0.2 - - + -
1D LYS* 1.3 77.7 - - + +
3D LYS* 1.3 63.9 + - - +
6D LYS* 2.9 55.4 + - + +
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Residues in contact with LYS 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D ACE 3.7 17.3 + - + +
1D LYS 3.3 0.2 - - - -
2D VAL* 1.3 79.8 - - - +
4D GLN* 1.3 60.9 + - - +
6D LYS* 3.8 7.8 - - - +
7D ALA* 3.3 20.1 + - - +
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Residues in contact with GLN 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D ACE 2.8 21.1 + - - +
1D LYS* 3.5 23.5 + - - +
2D VAL 3.1 0.2 - - - -
3D LYS* 1.3 73.0 - - - +
5D LEU* 1.3 88.6 + - - +
6D LYS 3.1 1.3 - - - -
7D ALA* 2.8 11.6 + - + +
8D LYS* 2.8 27.5 + - + +
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Residues in contact with LEU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C VAL* 3.9 28.0 - - + +
5C LEU* 3.9 24.2 - - + +
6C GLU* 3.9 18.8 - - + +
9C VAL* 4.6 15.0 - - + -
1D LYS* 2.8 44.0 + - + +
4D GLN* 1.3 91.1 - - - +
6D LYS* 1.3 62.0 + - - +
8D LYS* 3.1 10.2 + - + +
9D VAL* 2.9 28.8 + - - +
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Residues in contact with LYS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C GLU* 5.5 2.5 - - - -
5C LEU* 3.7 26.5 - - + -
2D VAL* 2.9 41.6 + - + +
3D LYS* 3.8 8.3 - - - +
5D LEU* 1.3 78.0 - - - +
7D ALA* 1.3 60.8 + - - +
9D VAL* 3.4 4.1 + - - +
10D GLU* 3.1 29.0 + - + +
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Residues in contact with ALA 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS 3.3 10.6 + - - +
4D GLN* 2.8 11.9 + - + +
6D LYS* 1.3 76.9 - - - +
8D LYS* 1.3 60.1 + - - +
10D GLU* 3.4 8.0 + - - +
11D GLU* 2.8 31.8 + - - +
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.7 21.8 - - + -
13C GLU* 4.3 14.6 + - - -
4D GLN* 2.8 14.5 + - + +
5D LEU* 3.1 21.3 + - + +
7D ALA* 1.3 75.8 - - - +
9D VAL* 1.3 59.8 + - - +
11D GLU* 3.3 16.9 + - + +
12D LEU* 2.9 58.1 + - + +
15D LYS* 5.4 4.6 - - - +
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 4.3 10.3 - - + +
8C GLU* 3.3 51.4 - - + +
9C VAL* 3.8 18.2 - - + -
12C LEU* 3.7 12.2 - - + +
5D LEU 2.9 15.5 + - - +
6D LYS* 3.6 8.7 - - - +
8D LYS* 1.3 73.6 - - - +
10D GLU* 1.3 61.8 + - - +
12D LEU* 3.0 4.4 + - - +
13D LYS* 2.7 50.1 + - + +
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Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LYS* 3.1 16.1 + - + +
7D ALA* 3.7 10.1 - - - +
9D VAL* 1.3 82.7 - - - +
11D GLU* 1.3 62.3 + - - +
13D LYS* 3.2 32.3 + - - +
14D SER* 2.9 23.7 + - - -
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ALA 2.8 18.1 + - - +
8D LYS* 3.6 18.7 + - + +
10D GLU* 1.3 75.6 - - - +
12D LEU* 1.3 62.5 + - + +
14D SER* 2.7 26.1 + - - +
15D LYS* 3.4 22.6 + - + +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 3.9 31.4 - - + +
12C LEU* 4.0 20.9 - - + -
13C GLU* 4.0 15.5 - - + +
16C LEU* 3.4 29.0 - - + +
8D LYS* 2.9 49.6 + - + +
9D VAL 3.0 3.6 + - - +
11D GLU* 1.3 74.3 - - + +
13D LYS* 1.3 70.0 + - - +
15D LYS* 3.1 32.3 + - - +
16D LEU* 3.6 10.3 + - - +
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Residues in contact with LYS 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLU* 3.0 26.5 + - - -
12C LEU* 4.1 18.9 - - + +
9D VAL* 2.7 25.9 + - + +
10D GLU* 3.4 36.7 + - - +
12D LEU* 1.3 71.6 - - - +
14D SER* 1.3 64.5 + - - +
16D LEU* 2.8 36.7 + - + +
17D TRP 4.1 0.7 + - - -
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU 2.9 11.9 + - - -
11D GLU* 2.7 28.2 + - - +
13D LYS* 1.3 76.6 - - - +
15D LYS* 1.3 59.5 + - - +
16D LEU 2.9 6.2 + - - -
17D TRP* 3.3 16.3 + - - +
18D HIS* 4.3 2.3 + - - +
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Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.6 28.6 - - + +
20C GLU* 6.1 0.4 - - - +
8D LYS* 5.4 5.1 - - - +
11D GLU* 3.4 22.6 + - + +
12D LEU* 3.1 22.8 + - + +
14D SER* 1.3 77.1 + - - +
16D LEU* 1.3 62.1 + - - +
17D TRP 3.5 0.2 - - - -
18D HIS* 3.8 7.6 + - - +
19D LEU* 3.4 26.9 + - + +
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Residues in contact with LEU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.0 18.2 - - + -
15C GLU* 3.7 35.7 - - + +
16C LEU* 4.1 17.9 - - + -
19C LEU* 4.1 9.1 - - + +
12D LEU 3.8 7.0 - - - +
13D LYS* 2.8 34.1 + - + +
14D SER 2.9 0.8 + - - -
15D LYS* 1.3 76.4 - - - +
17D TRP* 1.3 64.6 + - - +
19D LEU* 3.2 3.4 + - - +
20D LYS* 2.9 46.4 + - + +
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Residues in contact with TRP 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D LYS 4.1 0.6 + - - -
14D SER 3.3 10.1 + - - +
16D LEU* 1.3 77.5 - - - +
18D HIS* 1.3 103.5 - + + +
20D LYS* 3.8 4.6 - - + +
21D ASN* 2.8 65.2 + - + +
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Residues in contact with HIS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D SER 4.3 2.4 + - - +
15D LYS* 3.8 10.3 + - - +
16D LEU 3.2 0.6 - - - -
17D TRP* 1.3 109.7 - + + +
19D LEU* 1.3 62.9 + - + +
21D ASN* 3.4 1.6 + - + +
22D LYS* 3.0 50.6 + - + +
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 3.6 33.7 - - + +
19C LEU* 3.9 21.1 - - + -
20C GLU* 3.9 33.7 - - + +
23C VAL* 4.3 18.4 - - + -
15D LYS* 3.4 13.1 + - + +
16D LEU 3.2 2.0 + - - +
18D HIS* 1.3 80.9 - - + +
20D LYS* 1.3 58.1 + - - +
22D LYS* 3.2 11.8 + - + +
23D VAL* 2.9 33.1 + - - +
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLU* 4.4 14.1 + - - -
19C LEU* 3.8 31.2 - - + -
16D LEU* 2.9 43.4 + - + +
17D TRP* 4.0 3.8 - - + +
19D LEU* 1.3 72.3 - - - +
21D ASN* 1.3 61.3 + - - +
23D VAL* 3.3 4.2 + - - +
24D ALA* 2.8 29.2 + - - +
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Residues in contact with ASN 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D TRP* 2.8 61.3 + - + +
18D HIS 3.9 3.1 - - - +
20D LYS* 1.3 73.8 - - - +
22D LYS* 1.3 58.6 + - - +
24D ALA* 3.6 8.4 - - - +
25D ARG* 3.0 49.0 + - - +
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Residues in contact with LYS 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C VAL* 3.7 35.2 - - + +
27C GLU* 3.8 16.8 + - - -
18D HIS* 3.0 37.1 + - + +
19D LEU* 3.4 12.5 - - + +
21D ASN* 1.3 77.1 - - - +
23D VAL* 1.3 61.0 + - - +
25D ARG* 3.3 7.8 + - - +
26D LEU* 2.8 41.0 + - + +
----------------------------------------------------------
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.9 20.2 - - + +
22C GLU* 4.0 17.0 - - + -
23C VAL* 3.6 22.7 - - + +
26C LEU* 3.8 15.7 - - + -
19D LEU 2.9 19.7 + - - +
20D LYS* 3.6 7.2 - - - +
22D LYS* 1.3 77.8 - - - +
24D ALA* 1.3 58.4 + - - +
26D LEU* 3.2 3.5 + - - +
27D LYS* 2.9 55.3 + - + +
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Residues in contact with ALA 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LYS 2.8 17.6 + - - +
21D ASN* 3.6 11.4 - - - +
22D LYS 3.2 0.2 - - - -
23D VAL* 1.3 78.1 - - - +
25D ARG* 1.3 62.1 + - + +
27D LYS* 3.3 7.3 + - - +
28D LYS* 3.0 25.7 + - - +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ASN* 3.0 40.9 + - - +
22D LYS* 3.7 6.5 - - - +
24D ALA* 1.3 76.6 - - + +
26D LEU* 1.3 64.6 + - + +
28D LYS* 3.4 9.8 + - - +
29D LYS* 3.1 54.7 + - - +
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Residues in contact with LEU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C VAL* 3.8 27.4 - - + +
26C LEU* 3.8 21.0 - - + +
27C GLU* 3.8 37.7 - - + +
30C ASN* 2.9 24.8 + - + +
22D LYS* 2.8 30.9 + - + +
23D VAL 3.2 4.5 + - - +
25D ARG* 1.3 78.5 - - + +
27D LYS* 1.3 56.8 + - - +
29D LYS* 4.6 10.1 - - + +
30D ASN* 2.9 25.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU* 3.5 23.9 + - - -
25C ARG* 4.5 7.2 - - - +
26C LEU* 3.7 17.9 - - + -
23D VAL* 2.9 36.0 + - + +
24D ALA* 3.3 7.8 + - - +
26D LEU* 1.3 73.8 - - - +
28D LYS* 1.3 55.5 + - - +
30D ASN* 3.3 7.9 + - - +
31D ALA* 2.7 35.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ALA 3.0 16.6 + - - +
25D ARG* 3.7 10.3 - - - +
27D LYS* 1.3 73.3 - - - +
29D LYS* 1.3 63.8 - - + +
31D ALA* 3.1 9.8 + - + +
32D GLU* 2.9 52.9 + - + +
----------------------------------------------------------
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Residues in contact with LYS 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASN* 3.7 16.6 - - - +
25D ARG* 3.1 44.6 + - - +
26D LEU* 5.0 8.1 - - + +
28D LYS* 1.3 79.5 - - + +
30D ASN* 1.3 64.7 + - - +
32D GLU* 2.9 19.0 + - - +
33D CYS* 2.8 24.7 + - - +
----------------------------------------------------------
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Residues in contact with ASN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 4.3 9.9 - - + +
29C GLU* 2.8 36.0 - - - +
30C ASN* 2.7 19.2 + - - +
33C CYS* 5.2 3.1 - - - +
26D LEU 2.9 15.3 + - - +
27D LYS* 3.4 9.9 - - - +
28D LYS 3.2 0.2 - - - -
29D LYS* 1.3 77.6 - - - +
31D ALA* 1.3 58.5 + - - +
33D CYS* 3.3 4.2 + - - +
34D LYS* 2.9 38.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS 2.7 17.0 + - - +
28D LYS* 3.3 13.2 - - + +
30D ASN* 1.3 76.3 + - - +
32D GLU* 1.3 61.3 + - + +
34D LYS* 3.3 17.0 - - - +
----------------------------------------------------------
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Residues in contact with GLU 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LYS* 2.9 40.4 + - + +
29D LYS* 2.9 20.2 + - - +
31D ALA* 1.3 77.5 - - + +
33D CYS* 1.3 68.1 + - - +
34D LYS 2.7 11.6 - - - +
----------------------------------------------------------
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Residues in contact with CYS 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ASN* 4.9 4.3 - - + +
33C CYS* 2.0 62.0 - - + -
34C GLU* 3.4 21.5 - - + -
29D LYS 2.8 16.7 + - - +
30D ASN* 4.0 4.7 - - - +
32D GLU* 1.3 73.6 - - - +
34D LYS* 1.3 65.4 + - - +
----------------------------------------------------------
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C CYS* 3.6 11.4 - - + -
30D ASN* 2.9 28.4 + - - +
31D ALA* 3.3 13.4 - - - +
32D GLU 2.7 22.0 - - - +
33D CYS* 1.3 79.8 - - - +
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il