Contacts of the helix formed by residues 2 - 25 (chain D) in PDB entry 6C4Z
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 2 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D SER* 1.3 76.8 + - - +
3D LEU* 1.3 68.0 + - - +
5D GLU* 3.3 17.2 - - - +
6D LEU* 3.2 16.5 + - - +
16F LYS* 5.5 2.6 - - - +
20F LEU* 3.9 24.3 - - + +
23F LYS* 5.0 15.7 - - + +
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Residues in contact with LEU 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 3.7 35.0 - - + +
4C LEU* 4.1 25.4 - - + -
7C LEU* 4.5 15.0 - - + -
1D SER 4.0 6.2 - - - +
2D LYS* 1.3 75.3 - - - +
4D LEU* 1.3 59.1 + - + +
6D LEU* 2.7 38.6 + - + +
7D LEU* 2.9 23.4 + - + -
20F LEU* 4.1 27.7 - - + +
24F TRP* 4.5 11.2 - - + -
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Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 4.3 13.0 - - + -
18B ILE* 4.7 4.6 - - + +
21B LEU* 4.3 20.2 - - + +
22B GLU* 3.9 29.0 - - + +
25B GLY* 4.2 28.3 - - - +
26B NH2 4.7 0.2 - - - +
3C LEU* 3.5 28.9 - - + -
1D SER* 3.7 26.1 + - - +
2D LYS 3.5 0.2 - - - -
3D LEU* 1.3 77.7 - - - +
5D GLU* 1.3 61.3 + - - +
7D LEU* 3.3 15.8 + - + +
8D ARG* 3.0 21.7 + - - +
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Residues in contact with GLU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 4.6 7.1 - - - +
1D SER 3.4 12.9 + - - +
2D LYS* 3.3 18.7 - - - +
3D LEU 3.1 0.6 - - - -
4D LEU* 1.3 75.5 - - - +
6D LEU* 1.3 64.1 + - - +
8D ARG* 2.8 44.8 + - - +
9D LYS* 3.0 16.4 + - - +
16F LYS* 3.1 40.3 + - + +
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Residues in contact with LEU 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.0 21.5 - - + -
2D LYS 3.2 7.8 + - - +
3D LEU* 2.7 17.2 + - + +
5D GLU* 1.3 74.6 - - - +
7D LEU* 1.3 62.6 + - - +
9D LYS* 3.3 5.0 + - - +
10D LEU* 3.0 33.9 + - + +
14E LEU* 5.0 2.0 - - + -
18E ILE* 5.5 1.3 - - + -
21E LEU* 3.5 31.6 - - + -
13F ALA* 3.3 31.6 - - - +
16F LYS* 4.3 12.4 - - + +
17F ALA* 3.9 17.3 - - + +
20F LEU* 4.2 11.0 - - + -
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Residues in contact with LEU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.8 16.2 - - + +
21B LEU* 5.7 1.6 - - + -
3C LEU* 3.8 34.5 - - + +
6C LEU* 4.0 19.1 - - + -
7C LEU* 3.7 36.1 - - + +
10C LEU* 3.6 27.8 - - + +
3D LEU* 2.9 16.7 + - + +
4D LEU* 3.4 21.3 - - + +
6D LEU* 1.3 74.3 - - - +
8D ARG* 1.3 63.1 + - - +
10D LEU* 3.1 7.1 + - - +
11D GLY* 2.9 20.4 + - - -
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Residues in contact with ARG 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B HIS* 4.8 2.9 + - + +
18B ILE* 3.6 16.1 - - + +
19B GLU* 4.2 29.6 - - + +
22B GLU* 2.8 46.6 + - + +
4D LEU 3.0 11.5 + - - +
5D GLU* 2.8 40.3 + - - +
7D LEU* 1.3 71.3 - - - +
9D LYS* 1.3 82.1 + - - +
11D GLY* 3.1 2.8 + - - -
12D GLU* 2.8 52.6 + - + +
16F LYS* 5.9 0.6 - - - +
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Residues in contact with LYS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLU 3.0 15.0 + - - +
6D LEU* 3.6 8.1 - - - +
8D ARG* 1.3 96.5 - - - +
10D LEU* 1.3 56.4 + - - +
12D GLU* 3.4 22.2 + - - +
13D ALA* 2.9 29.6 + - - +
9F LYS* 4.6 7.8 - - + +
12F GLU* 2.9 44.6 + - + +
13F ALA* 3.9 21.7 - - + +
16F LYS* 4.4 31.4 - - + +
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Residues in contact with LEU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.3 34.5 - - + +
10C LEU* 4.4 21.4 - - + +
11C GLY* 5.1 2.7 - - - +
14C LEU* 3.6 28.9 - - + +
6D LEU* 3.0 28.5 + - + +
7D LEU* 3.5 7.0 - - - +
9D LYS* 1.3 74.8 - - - +
11D GLY* 1.3 53.6 + - - +
13D ALA* 3.7 3.0 - - - +
14D LEU* 2.8 36.7 + - - +
14E LEU* 3.6 25.1 - - + -
18E ILE* 4.1 15.7 - - + -
13F ALA* 4.3 4.5 - - + -
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Residues in contact with GLY 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLY 5.2 0.3 - - - +
14B LEU* 5.9 1.6 - - - -
15B HIS* 4.2 12.7 + - - +
18B ILE* 4.2 19.2 - - - +
10C LEU* 4.7 5.3 - - - +
7D LEU 2.9 12.8 + - - -
8D ARG 3.1 4.0 + - - -
10D LEU* 1.3 75.5 - - - +
12D GLU* 1.3 52.2 + - - +
14D LEU* 3.7 5.4 - - - +
15D HIS* 2.8 36.8 + - - +
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B HIS* 3.4 28.5 + - + -
19B GLU* 5.6 1.0 - - - -
8D ARG* 2.8 40.1 + - + +
9D LYS* 3.6 30.7 + - - +
11D GLY* 1.3 69.8 - - - +
13D ALA* 1.3 59.2 + - - +
15D HIS* 3.6 5.1 - - - +
16D LYS* 2.9 37.8 + - + +
9F LYS* 3.4 32.8 + - + -
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Residues in contact with ALA 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.4 4.3 - - + -
9D LYS 2.9 17.2 + - - +
10D LEU* 3.7 7.0 - - - +
12D GLU* 1.3 72.9 - - - +
14D LEU* 1.3 55.7 + - - +
16D LYS* 3.2 5.0 + - - +
17D ALA* 2.8 34.9 + - - +
6F LEU* 3.6 6.0 - - + +
9F LYS* 4.0 25.9 - - + +
10F LEU* 4.0 27.8 - - + -
13F ALA* 5.3 1.3 - - + -
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.8 1.1 - - + -
10A LEU* 3.7 22.7 - - + -
11B GLY* 5.7 1.6 - - - -
14B LEU* 4.1 4.9 - - + -
10C LEU* 4.0 28.5 - - + +
13C ALA* 3.9 18.6 - - + +
14C LEU* 4.0 23.6 - - + +
17C ALA* 4.4 16.6 - - + -
10D LEU 2.8 21.7 + - - +
11D GLY* 3.7 3.6 - - - +
13D ALA* 1.3 70.3 - - - +
15D HIS* 1.3 65.6 + - - +
17D ALA* 2.8 15.1 + - - +
18D ILE* 3.0 37.8 + - + +
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Residues in contact with HIS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 5.0 3.1 - - + -
11B GLY* 4.2 17.7 - - - +
12B GLU* 3.5 35.9 + - + +
15B HIS* 4.1 26.8 + + + -
11D GLY 2.8 23.3 + - - +
12D GLU* 3.6 6.3 + - - +
14D LEU* 1.3 74.8 - - - +
16D LYS* 1.3 78.5 + - - +
18D ILE* 3.4 8.4 + - + +
19D GLU* 2.9 45.3 + - + +
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Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D GLU* 2.9 23.7 + - - +
13D ALA* 3.4 5.8 - - - +
15D HIS* 1.3 91.2 + - - +
17D ALA* 1.3 66.1 + - - +
19D GLU* 3.0 35.8 + - + +
20D LEU* 3.2 12.5 + - - +
2F LYS 5.8 1.3 - - - +
5F GLU* 3.4 42.0 - - + +
6F LEU* 4.6 17.0 - - + -
9F LYS* 4.7 20.1 - - + +
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Residues in contact with ALA 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.4 6.1 - - + -
17C ALA* 4.2 17.5 - - + -
18C ILE* 5.6 1.1 - - + +
21C LEU* 4.1 17.3 - - + +
13D ALA 2.8 15.6 + - - +
14D LEU* 2.8 16.0 + - - +
16D LYS* 1.3 72.1 - - - +
18D ILE* 1.3 61.0 + - - +
20D LEU* 3.2 5.1 + - - +
21D LEU* 3.1 21.5 + - - +
6F LEU* 4.0 23.0 - - + +
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Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.6 15.5 - - + -
10A LEU* 3.7 31.0 - - + -
4B LEU* 4.9 2.9 - - + +
7B LEU* 4.0 10.3 - - + +
8B ARG* 3.6 35.7 - - + +
11B GLY* 4.4 13.5 - - - -
17C ALA* 5.0 3.1 - - + -
14D LEU* 3.0 40.3 + - + +
15D HIS* 3.7 7.0 - - + +
17D ALA* 1.3 71.2 - - - +
19D GLU* 1.3 66.1 + - - +
21D LEU* 3.3 11.7 + - + +
22D GLU* 3.0 21.6 + - + +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 4.6 18.6 - - + +
12B GLU* 4.6 6.2 - - - +
15D HIS* 2.9 47.9 + - + +
16D LYS* 3.0 27.4 + - + +
18D ILE* 1.3 75.3 - - + +
20D LEU* 1.3 65.2 + - - +
22D GLU* 3.4 10.3 - - - +
23D LYS* 3.2 16.8 + - - +
2F LYS* 6.3 2.9 - - + -
5F GLU* 5.6 0.2 - - - +
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU* 3.9 18.2 - - + -
16D LYS 3.2 7.3 + - - +
17D ALA* 3.2 9.8 + - - +
19D GLU* 1.3 73.9 - - - +
21D LEU* 1.3 58.0 + - - +
22D GLU 3.0 1.1 - - - -
23D LYS* 2.5 32.2 + - + +
24D TRP* 2.9 49.3 + - + +
2F LYS* 3.4 43.5 - - + +
3F LEU* 4.1 27.8 - - + +
6F LEU* 4.3 10.3 - - + -
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 4.9 2.9 - - + -
6A LEU* 4.0 18.4 - - + -
4B LEU* 4.4 13.6 - - + +
7B LEU* 4.9 2.5 - - + -
17C ALA* 4.9 6.1 - - + +
20C LEU* 3.7 43.5 - - + -
21C LEU* 3.7 25.1 - - + +
24C TRP* 3.4 38.9 - - + -
17D ALA 3.1 9.8 + - - +
18D ILE* 3.3 16.1 + - + +
20D LEU* 1.3 76.2 - - - +
22D GLU* 1.3 56.5 + - - +
24D TRP* 4.7 3.1 - - - +
25D GLY* 2.8 28.1 + - - -
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B SER 5.7 1.0 - - - +
4B LEU* 4.0 36.4 - - + +
5B GLU* 4.9 1.6 - - - +
8B ARG* 2.6 49.2 + - + +
18D ILE 3.0 11.9 + - - +
19D GLU* 3.4 11.5 - - - +
20D LEU 2.8 4.2 + - - -
21D LEU* 1.3 71.2 - - - +
23D LYS* 1.3 65.3 + - - +
25D GLY 3.0 19.8 + - - +
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Residues in contact with LYS 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLU 3.2 9.1 + - - +
20D LEU* 2.5 20.1 + - + +
22D GLU* 1.3 78.3 - - - +
24D TRP* 1.3 69.5 + - + +
25D GLY 3.8 3.6 - - - +
2F LYS* 3.8 31.9 - - + +
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Residues in contact with TRP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 3.5 28.9 - - + -
24C TRP* 4.5 14.1 - - + +
25C GLY* 3.4 36.6 - - - -
20D LEU* 2.9 47.2 + - + +
21D LEU* 4.2 4.0 - - + +
23D LYS* 1.3 86.9 - - + +
25D GLY* 1.3 65.0 + - - +
4E LEU* 4.2 26.2 - - + -
3F LEU* 4.4 14.4 - - + -
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Residues in contact with GLY 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.2 5.9 - - - +
24C TRP* 3.4 29.3 - - - -
21D LEU 2.8 17.4 + - - -
22D GLU 3.0 14.5 + - - +
23D LYS 3.8 3.5 - - - +
24D TRP* 1.3 77.0 - - - +
26D NH2 1.3 47.1 + - - -
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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
------------------------------------------------------------
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