Contacts of the helix formed by residues 0 - 25 (chain B) in PDB entry 3N93
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 ALA 0 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-4B THR 3.3 2.6 + - - -
-3B ASN 3.0 16.7 + - - +
-2B ALA 3.3 2.6 - - - +
-1B ALA* 1.3 78.3 - - - +
1B GLU* 1.3 59.4 + - - +
2B PHE* 3.4 2.2 - - - -
3B ALA* 3.4 16.8 + - + +
4B ALA* 2.9 25.8 + - - +
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Residues in contact with GLU 1 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.6 38.6 - - + +
25A ASP* 2.8 29.1 - - - +
26A GLY* 4.2 10.2 - - - -
27A TRP* 3.9 12.1 - - + -
-5B GLN* 4.7 7.8 + - - +
-4B THR* 3.1 37.2 + - + +
-1B ALA* 3.2 12.6 + - + +
0B ALA* 1.3 73.8 - - - +
2B PHE* 1.3 60.7 + - - +
4B ALA* 3.7 5.5 - - - -
5B LEU* 2.9 29.6 + - - +
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Residues in contact with PHE 2 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TRP* 3.7 28.8 - + + -
-4B THR* 4.6 4.6 + - + +
0B ALA 3.4 0.4 - - - -
1B GLU* 1.3 77.5 - - - +
3B ALA* 1.3 58.4 + - - +
5B LEU* 3.2 6.8 + - + +
6B LEU* 3.0 36.8 + - + +
67B TYR* 3.6 50.3 - + + +
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Residues in contact with ALA 3 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B ALA* 3.4 21.1 + - + +
1B GLU 3.3 0.2 - - - -
2B PHE* 1.3 83.8 - - - +
4B ALA* 1.3 58.0 + - - +
6B LEU* 3.5 5.6 + - - +
7B HIS* 3.0 28.8 + - - +
67B TYR* 4.9 16.3 + - + +
69B ASN* 5.7 6.3 - - - +
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Residues in contact with ALA 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.5 0.2 - - - +
22A LEU* 3.6 18.1 - - + +
-191B LYS* 5.6 11.2 - - + -
-1B ALA 5.1 2.7 - - - +
0B ALA 2.9 17.8 + - - +
1B GLU* 3.8 9.0 - - - +
2B PHE 3.2 0.4 - - - -
3B ALA* 1.3 77.2 - - - +
5B LEU* 1.3 61.0 + - - +
7B HIS* 3.7 7.8 + - - +
8B SER* 3.3 23.2 + - - -
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Residues in contact with LEU 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 3.2 39.3 - - + +
22A LEU* 3.8 12.3 - - + +
23A LEU* 3.8 27.1 - - + +
27A TRP* 3.6 28.3 - - + -
1B GLU 2.9 15.8 + - - +
2B PHE* 3.6 7.4 - - + +
4B ALA* 1.3 74.5 - - - +
6B LEU* 1.3 64.4 + - - +
7B HIS 3.2 0.2 - - - -
8B SER* 3.2 3.7 + - - -
9B LEU* 3.2 30.6 + - + +
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Residues in contact with LEU 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PHE* 3.0 26.7 + - + +
3B ALA* 3.9 5.8 - - - +
5B LEU* 1.3 77.7 - - - +
7B HIS* 1.3 64.5 + - - +
9B LEU* 3.1 20.0 + - + +
10B LEU* 2.9 45.7 + - + +
67B TYR* 3.5 45.8 - - + +
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Residues in contact with HIS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ALA 3.0 19.2 + - - +
4B ALA* 3.7 10.1 - - - +
5B LEU 3.2 0.2 - - - -
6B LEU* 1.3 77.1 - - - +
8B SER* 1.3 58.4 + - - +
10B LEU* 3.1 10.0 + - - +
11B GLU* 2.8 59.1 + - - +
44B LEU* 3.7 24.2 - - + +
45B ASP 5.4 4.3 - - - -
46B GLN* 6.4 1.6 - - - -
48B GLY* 5.6 5.2 - - - -
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Residues in contact with SER 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 3.4 30.6 - - - +
18A LEU* 3.3 31.4 - - - +
19A ALA* 4.1 12.1 - - - -
22A LEU* 4.2 0.7 - - - +
4B ALA 3.3 10.9 + - - -
5B LEU* 3.2 11.1 + - - -
7B HIS* 1.3 79.8 - - - +
9B LEU* 1.3 58.4 + - - +
11B GLU* 4.3 9.1 + - - -
12B ALA* 3.0 24.9 + - - +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.8 13.5 - - + -
19A ALA* 3.8 22.0 - - + -
5B LEU* 3.2 24.2 + - + +
6B LEU* 3.1 23.0 + - + +
8B SER* 1.3 78.1 - - - +
10B LEU* 1.3 58.6 + - + +
12B ALA* 3.4 4.5 + - - +
13B ASN* 2.9 29.7 + - - +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 2.9 46.2 + - + +
7B HIS* 3.1 9.2 + - - +
9B LEU* 1.3 73.7 - - + +
11B GLU* 1.3 67.7 + - - +
13B ASN* 3.2 11.2 + - + +
14B CYS* 2.9 26.0 + - - +
44B LEU* 4.1 18.2 - - + +
47B ILE 5.2 0.7 - - - +
48B GLY* 3.6 32.8 - - - +
50B CYS* 5.5 0.5 - - - +
67B TYR 6.0 0.9 - - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 3.4 21.0 + - - +
18A LEU* 5.4 4.7 - - - +
7B HIS* 2.8 45.3 + - - +
8B SER* 3.7 7.2 + - - +
10B LEU* 1.3 72.0 - - - +
12B ALA* 1.3 62.5 + - - +
14B CYS* 3.2 3.6 + - - +
15B SER* 3.1 27.9 + - - +
44B LEU* 3.7 21.7 - - + +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 3.8 23.5 - - + +
15A SER* 3.8 16.3 - - - -
16A LEU* 4.5 15.0 - - + +
8B SER 3.0 17.8 + - - +
9B LEU* 3.7 6.7 - - - +
11B GLU* 1.3 76.2 - - - +
13B ASN* 1.3 63.3 + - - +
15B SER* 3.4 2.4 + - - -
16B LEU* 3.1 29.9 + - + +
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Residues in contact with ASN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU 2.9 18.7 + - - +
10B LEU* 3.2 13.0 + - + +
12B ALA* 1.3 75.4 - - - +
14B CYS* 1.3 62.0 + - - +
16B LEU* 3.3 13.0 + - - +
17B ALA* 3.1 31.3 + - - +
50B CYS* 5.2 7.7 - - - +
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Residues in contact with CYS 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU 2.9 17.1 + - - +
11B GLU* 3.6 5.8 - - - +
13B ASN* 1.3 78.3 - - - +
15B SER* 1.3 61.1 + - - +
17B ALA* 3.6 3.8 + - - +
18B LEU* 3.3 19.8 + - - +
42B THR* 3.2 22.3 - - - +
43B THR 4.0 9.4 - - - -
44B LEU* 4.5 9.0 - - + -
50B CYS* 2.1 56.4 - - + -
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Residues in contact with SER 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 3.3 42.1 - - - -
11A GLU* 3.6 23.8 + - - +
12A ALA* 4.0 6.6 + - - -
11B GLU* 3.1 14.3 + - - +
12B ALA 3.7 7.6 - - - -
14B CYS* 1.3 73.4 - - - +
16B LEU* 1.3 60.8 + - - +
18B LEU* 3.4 5.7 + - - +
19B ALA* 2.8 23.9 + - - +
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.5 19.1 - - + -
12A ALA* 3.9 19.5 - - + -
16A LEU* 6.3 3.1 - - + -
12B ALA* 3.1 21.5 + - + +
13B ASN* 3.3 13.7 + - - +
15B SER* 1.3 75.1 - - - +
17B ALA* 1.3 55.3 + - - +
19B ALA* 2.9 6.2 + - + +
20B GLU* 2.7 44.5 + - - +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASN* 3.1 18.0 + - - +
14B CYS* 3.9 7.6 - - - +
15B SER 3.4 0.2 - - - -
16B LEU* 1.3 76.7 - - - +
18B LEU* 1.3 61.8 + - - +
20B GLU* 3.5 15.8 + - - +
21B GLU* 3.2 24.3 + - - +
42B THR* 6.4 0.2 - - + -
50B CYS* 5.1 7.2 - - - -
52B PRO* 6.2 4.5 - - + -
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ALA* 4.7 8.5 - - + +
8A SER* 4.3 14.6 - - - +
14B CYS 3.3 10.3 + - - +
15B SER* 3.4 10.3 - - - +
16B LEU 3.2 0.2 - - - -
17B ALA* 1.3 75.8 - - - +
19B ALA* 1.3 65.1 + - - +
21B GLU* 3.3 5.5 + - + +
22B LEU* 3.0 52.8 + - + +
42B THR* 4.1 23.0 + - - +
53B ARG* 4.1 23.6 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A LEU* 3.6 19.2 - - + +
8A SER* 4.0 9.4 + - - +
9A LEU* 3.7 30.7 - - + -
15B SER 2.8 17.1 + - - +
16B LEU* 2.9 12.9 + - + +
18B LEU* 1.3 73.8 - - - +
20B GLU* 1.3 63.8 + - - +
22B LEU* 3.3 1.5 + - - +
23B LEU* 3.0 25.8 + - - +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 2.7 24.4 + - - +
17B ALA* 3.6 18.6 - - - +
19B ALA* 1.3 72.6 - - - +
21B GLU* 1.3 61.9 + - - +
23B LEU* 3.5 9.4 + - + +
24B LEU* 3.3 36.9 + - + +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA 3.2 14.7 + - - +
18B LEU* 3.8 7.5 - - + +
19B ALA 3.3 0.2 - - - -
20B GLU* 1.3 77.1 - - - +
22B LEU* 1.3 66.3 + - + +
24B LEU* 3.1 15.9 + - - +
25B ASP* 3.1 16.3 + - - +
52B PRO* 5.2 4.9 - - - +
53B ARG* 3.9 52.6 + - + +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLU* 3.7 26.8 - - + +
4A ALA* 3.9 11.9 - - + -
5A LEU* 3.7 40.5 - - + +
8A SER* 4.8 0.2 - - - +
18B LEU* 3.0 47.9 + - + +
19B ALA 3.8 3.8 - - - +
21B GLU* 1.3 76.2 - - + +
23B LEU* 1.3 61.7 + - - +
25B ASP* 3.4 23.0 - - - +
53B ARG* 3.4 34.3 - - - +
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 4.2 24.2 - - + +
19B ALA 3.0 18.5 + - - +
20B GLU* 3.7 10.1 - - + +
21B GLU 3.2 0.2 - - - -
22B LEU* 1.3 78.5 - - - +
24B LEU* 1.3 70.3 + - + +
25B ASP 3.7 5.0 + - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU* 3.3 25.8 + - + +
21B GLU* 3.1 7.8 + - - +
23B LEU* 1.3 86.6 - - + +
25B ASP* 1.3 67.8 + - - +
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Residues in contact with ASP 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLU* 3.1 27.6 - - - +
21B GLU* 3.1 20.7 + - - +
22B LEU* 3.4 15.9 - - - +
23B LEU 3.4 6.5 - - - +
24B LEU* 1.3 82.2 - - - +
39B TYR* 5.4 2.4 + - - -
53B ARG* 2.9 32.4 + - - -
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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
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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) + - + + + + + -
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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