Contacts of the helix formed by residues 1 - 28 (chain D) in PDB entry 1D7G
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 1 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D GLU* 1.3 73.8 + - - +
3D ARG* 3.2 11.3 - - - +
4D ARG* 3.3 17.3 + - - +
5D LYS* 3.3 21.5 + - - +
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Residues in contact with GLU 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D SER* 1.3 83.9 + - - +
3D ARG* 1.3 88.2 + - - +
5D LYS* 3.4 5.5 + - - +
6D GLU* 2.9 46.1 + - - +
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Residues in contact with ARG 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A G 3.3 50.5 + - - +
1D SER 3.2 5.7 - - - +
2D GLU* 1.3 96.9 + - - +
4D ARG* 1.3 96.9 + - - +
6D GLU* 3.6 6.6 + - - +
7D LYS* 3.1 30.3 + - - +
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Residues in contact with ARG 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A G 3.0 34.4 + - - -
6A C 3.3 14.4 - - - +
7A C 5.0 0.8 - - - +
15B G 5.4 4.2 + - - -
16B G 3.4 33.1 + - - -
17B G 3.9 3.6 + - - -
1D SER* 3.3 18.0 + - - +
3D ARG* 1.3 108.2 - - - +
5D LYS* 1.3 62.8 + - - +
7D LYS* 3.3 15.0 + - - +
8D SER* 3.3 14.6 + - - -
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Residues in contact with LYS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B T 3.2 34.2 - - - +
14B A 3.0 74.0 + - + +
15B G 5.6 1.6 - - + +
1D SER 3.3 10.1 + - - +
2D GLU* 3.6 10.1 - - - +
3D ARG 3.3 0.2 - - - -
4D ARG* 1.3 72.8 - - - +
6D GLU* 1.3 70.4 + - - +
7D LYS 3.0 3.8 - - - -
8D SER* 2.9 31.3 + - - +
9D ARG* 3.0 13.0 + - - +
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Residues in contact with GLU 6 (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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13B T 4.4 15.2 + - - +
14B A 5.7 0.2 + - - -
2D GLU* 2.9 42.4 + - - +
3D ARG* 3.7 6.3 - - - +
5D LYS* 1.3 82.7 - - - +
7D LYS* 1.3 56.8 + - - +
9D ARG* 3.6 23.9 - - + +
10D ASP* 3.1 14.9 + - - +
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Residues in contact with LYS 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A G 3.8 3.8 - - + +
6A C 2.9 84.3 + - + +
7A C 3.6 17.5 - - + +
3D ARG* 3.1 24.8 + - - +
4D ARG* 3.3 14.8 - - - +
5D LYS 2.9 1.4 + - - -
6D GLU* 1.3 72.4 - - - +
8D SER* 1.3 59.1 + - - +
9D ARG 2.9 9.8 + - - -
10D ASP* 2.9 41.1 + - - +
11D ALA* 3.4 6.0 + - - -
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Residues in contact with SER 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A C 4.0 4.0 - - - -
8A C 3.4 20.0 + - - +
13B T 4.6 0.7 - - - +
14B A 4.2 9.0 + - - -
15B G 3.2 41.9 + - - -
16B G 5.1 0.2 - - - -
4D ARG* 3.3 9.0 + - - -
5D LYS* 2.9 33.5 + - - +
7D LYS* 1.3 77.1 - - - +
9D ARG* 1.3 60.1 + - - +
12D ALA* 3.5 13.1 + - - +
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Residues in contact with ARG 9 (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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12B G 3.2 51.3 + - - +
13B T 3.5 33.1 + - + +
5D LYS* 3.0 13.6 + - - +
6D GLU* 3.6 28.7 - - + +
7D LYS 2.9 0.2 + - - -
8D SER* 1.3 75.4 - - - +
10D ASP* 1.3 67.8 + - + +
12D ALA* 3.2 17.5 + - - +
13D ARG* 3.4 26.9 + - - +
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Residues in contact with ASP 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A C 5.5 0.5 + - - -
6D GLU 3.1 14.6 - - - +
7D LYS* 2.9 38.7 + - - +
9D ARG* 1.3 80.7 - - + +
11D ALA* 1.3 73.8 + - - +
13D ARG* 3.2 26.2 + - - +
14D SER* 3.3 6.8 + - - -
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A C 4.9 0.4 - - + -
7A C 3.3 51.6 + - + +
8A C 3.9 11.3 - - + +
7D LYS* 3.4 9.5 + - - +
9D ARG 3.4 0.6 - - - -
10D ASP* 1.3 83.1 + - - +
12D ALA* 1.3 63.0 + - - +
14D SER* 3.3 18.0 + - - -
15D ARG* 3.4 13.2 + - - +
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Residues in contact with ALA 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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8A C 4.2 1.4 - - - +
9A T 4.5 9.9 - - + -
13B T 3.8 11.9 - - - +
14B A 5.0 0.2 - - - +
8D SER 3.5 15.1 + - - +
9D ARG 3.2 9.0 + - - +
11D ALA* 1.3 74.8 - - - +
13D ARG* 1.3 84.4 + - - +
15D ARG* 3.4 24.5 - - - +
16D ARG* 3.0 27.0 + - - -
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Residues in contact with ARG 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B C 5.0 13.6 + - - -
12B G 2.7 44.0 + - - -
13B T 3.3 25.9 + - - +
9D ARG* 3.6 30.9 - - - +
10D ASP* 3.2 11.4 + - - +
12D ALA* 1.3 98.7 - - - +
14D SER* 1.3 60.2 + - - +
15D ARG 3.3 0.2 + - - -
16D ARG* 2.9 43.6 + - - +
17D SER* 3.0 29.6 + - - +
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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
----------------------------------------------------------
7A C 5.2 9.0 + - - -
8A C 5.6 2.9 + - - -
10D ASP 3.3 5.6 + - - -
11D ALA* 3.3 18.0 + - - -
13D ARG* 1.3 78.2 - - - +
15D ARG* 1.3 58.9 + - - +
17D SER* 3.6 7.6 - - - -
18D LYS* 3.4 20.0 + - - +
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Residues in contact with ARG 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A C 4.7 15.5 + - + +
9A T 2.7 78.5 + - + +
10A A 3.4 17.2 + - - +
42C LYS* 5.1 1.3 - - - +
11D ALA 3.4 5.2 + - - +
12D ALA* 3.4 19.0 + - - +
13D ARG 3.3 0.2 - - - -
14D SER* 1.3 76.5 - - - +
16D ARG* 1.4 115.9 + - - +
17D SER 3.2 0.2 - - - -
18D LYS* 3.0 26.3 + - + +
19D GLU* 3.0 45.7 + - + +
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Residues in contact with ARG 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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10A A 3.3 16.7 + - - +
11A C 3.7 9.5 - - - +
10B A 5.8 3.6 - - + -
11B C 3.2 37.8 - - + +
12B G 2.7 43.8 + - - -
12D ALA 3.0 25.9 + - - +
13D ARG* 2.9 26.1 - - - +
15D ARG* 1.4 110.7 - - - +
17D SER* 1.3 56.2 + - - +
19D GLU* 3.3 12.6 + - - +
20D SER* 3.0 36.9 + - - +
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Residues in contact with SER 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ARG* 3.0 14.2 + - - +
14D SER* 3.6 12.7 - - - -
16D ARG* 1.3 76.5 - - - +
18D LYS* 1.3 60.7 + - - +
20D SER* 3.4 5.8 + - - -
21D GLU* 3.0 43.7 + - - +
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Residues in contact with LYS 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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8A C 3.0 40.1 + - - -
42C LYS* 3.5 22.5 - - + +
46C LEU* 4.5 13.7 - - + -
47C ARG* 3.3 42.0 - - + +
14D SER 3.4 8.6 + - - +
15D ARG* 3.0 21.0 + - + +
17D SER* 1.3 76.8 - - - +
19D GLU* 1.3 69.3 + - + +
21D GLU* 3.3 13.6 + - - +
22D VAL* 3.0 32.3 + - + +
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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
----------------------------------------------------------
9A T 4.9 8.9 + - - +
46C LEU* 4.0 25.7 - - + +
15D ARG* 3.0 45.3 + - + +
16D ARG* 3.6 14.8 + - - +
18D LYS* 1.3 77.0 - - + +
20D SER* 1.3 58.3 + - - +
22D VAL* 3.3 4.7 + - - +
23D PHE* 2.9 53.9 + - + -
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Residues in contact with SER 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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10B A 3.8 27.2 + - - -
16D ARG* 3.0 18.7 + - - +
17D SER* 3.7 6.7 - - - -
19D GLU* 1.3 74.6 - - - +
21D GLU* 1.3 56.4 + - - +
23D PHE* 3.3 12.2 + - - +
24D TYR* 2.9 29.6 + - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D SER* 3.0 39.0 + - - +
18D LYS* 3.5 10.1 - - - +
20D SER* 1.3 73.3 - - - +
22D VAL* 1.3 56.8 + - + +
24D TYR* 3.2 11.2 + - + +
25D GLU* 2.9 44.8 + - - +
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Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 4.3 46.7 - - + +
47C ARG* 6.0 2.0 - - + -
49C ALA* 5.4 4.7 - - + -
50C VAL* 4.4 18.0 - - + +
18D LYS* 3.0 26.1 + - + +
19D GLU* 3.6 7.0 - - - +
21D GLU* 1.3 72.2 - - + +
23D PHE* 1.3 62.6 + - + +
25D GLU* 3.5 14.8 + - - +
26D LEU* 2.9 33.7 + - + +
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Residues in contact with PHE 23 (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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10B A 5.7 4.9 - - - -
19C MET* 5.4 4.9 - - - -
23C ILE* 6.1 4.5 - - + -
46C LEU* 6.0 7.9 - - + -
19D GLU* 2.9 45.4 + - + -
20D SER* 3.6 10.8 - - - +
22D VAL* 1.3 78.6 - - + +
24D TYR* 1.3 55.7 + - - +
26D LEU* 3.5 16.6 - - + +
27D ALA* 3.0 27.4 + - - +
45D VAL* 4.0 28.9 - - + +
46D MET* 3.6 33.7 - - + -
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Residues in contact with TYR 24 (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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20D SER 2.9 17.3 + - - +
21D GLU* 3.2 10.9 + - + +
23D PHE* 1.3 73.8 - - - +
25D GLU* 1.3 58.5 - - + +
27D ALA* 3.2 10.7 + - + +
28D HIS* 2.9 72.9 + + - -
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C VAL* 3.8 27.1 - - + +
53C MET* 5.7 0.2 - - - -
21D GLU* 2.9 34.8 + - - +
22D VAL* 3.7 12.7 + - - +
24D TYR* 1.3 72.3 - - + +
26D LEU* 1.3 59.7 + - - +
28D HIS* 3.0 35.4 + - + +
29D GLN* 3.4 19.2 - - - +
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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
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50C VAL* 6.1 0.2 - - - +
53C MET* 3.5 30.0 - - + -
22D VAL* 2.9 20.9 + - + +
23D PHE* 3.5 25.8 - - + +
25D GLU* 1.3 73.4 - - - +
27D ALA* 1.3 59.8 + - - +
29D GLN* 3.4 20.1 + - - +
30D LEU* 3.7 11.4 - - - +
45D VAL* 4.5 11.9 - - + +
46D MET* 5.5 3.1 - - + +
49D THR* 3.3 40.4 - - + +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE 3.0 17.9 + - - +
24D TYR* 3.2 16.5 + - + +
26D LEU* 1.3 73.0 - - - +
28D HIS* 1.3 58.2 + - + +
29D GLN 3.3 3.6 - - - -
30D LEU* 3.2 32.4 - - + +
31D PRO* 3.4 10.2 - - - +
45D VAL* 4.3 19.5 - - + +
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Residues in contact with HIS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR* 2.9 76.2 + + - -
25D GLU* 3.0 22.4 + - + +
27D ALA* 1.3 77.0 - - + +
29D GLN* 1.3 61.7 + - + +
31D PRO* 3.3 23.8 - - + +
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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