Contacts of the helix formed by residues 2 - 35 (chain A) in PDB entry 1WFB
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 THR 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASP* 1.3 75.1 + - - +
3A ALA* 1.3 57.9 - - - +
5A ASP* 3.2 4.6 + - - +
6A ALA* 2.8 35.3 + - + +
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Residues in contact with ALA 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASP* 3.5 9.6 + - - +
2A THR* 1.3 78.8 - - - +
4A SER* 1.3 57.2 + - - +
6A ALA* 3.3 6.6 + - - +
7A ALA* 3.0 29.3 + - - +
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Residues in contact with SER 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASP* 2.8 34.5 + - - +
3A ALA* 1.3 76.4 - - - +
5A ASP* 1.3 61.4 + - - +
7A ALA* 3.3 7.6 + - - +
8A ALA* 2.9 28.5 + - - +
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Residues in contact with ASP 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ASP 2.9 30.4 + - - +
2A THR* 3.8 4.5 - - - +
4A SER* 1.3 80.6 - - - +
6A ALA* 1.3 58.8 + - - +
8A ALA* 3.7 8.2 - - - +
9A ALA* 2.9 30.8 + - - +
24B THR* 6.1 1.7 - - + +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A THR* 2.8 20.8 + - + +
3A ALA* 3.7 7.9 - - - +
5A ASP* 1.3 77.5 - - - +
7A ALA* 1.3 57.0 + - - +
9A ALA* 3.4 6.9 + - - +
10A ALA* 3.0 28.2 + - - +
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Residues in contact with ALA 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ALA 3.0 16.6 + - - +
4A SER* 3.6 7.4 - - - +
6A ALA* 1.3 74.5 - - - +
8A ALA* 1.4 59.7 + - - +
10A ALA* 3.3 7.2 + - - +
11A ALA* 2.9 30.0 + - - +
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Residues in contact with ALA 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER 2.9 17.4 + - - +
5A ASP* 3.7 10.1 - - - +
7A ALA* 1.4 75.4 - - - +
9A ALA* 1.3 58.1 + - - +
11A ALA* 3.3 6.1 + - - +
12A LEU* 2.9 42.5 + - + +
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Residues in contact with ALA 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP 2.9 18.8 + - - +
6A ALA* 3.8 7.9 - - - +
8A ALA* 1.3 76.2 - - - +
10A ALA* 1.3 56.6 + - - +
12A LEU* 3.5 9.8 + - - +
13A THR* 2.8 36.2 + - - +
21B ALA* 4.3 24.2 - - + -
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Residues in contact with ALA 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA 3.0 18.1 + - - +
7A ALA* 3.3 7.4 + - - +
9A ALA* 1.3 76.2 - - - +
11A ALA* 1.4 56.2 + - - +
13A THR* 3.4 6.2 + - - -
14A ALA* 3.0 30.6 + - - +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA 2.9 17.1 + - - +
8A ALA* 3.3 6.5 + - - +
10A ALA* 1.4 75.8 - - - +
12A LEU* 1.3 59.0 + - + +
14A ALA* 3.4 5.2 + - - +
15A ALA* 2.8 32.0 + - - +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ALA* 2.9 30.9 + - + +
9A ALA* 3.8 7.2 - - - +
11A ALA* 1.3 74.6 - - + +
13A THR* 1.3 56.9 + - - +
15A ALA* 3.8 5.3 - - + +
16A ASN* 2.9 47.3 + - - +
17B ALA* 5.3 1.3 - - + -
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Residues in contact with THR 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ALA* 2.8 23.1 + - - +
10A ALA* 3.6 7.4 - - - +
12A LEU* 1.3 74.2 - - - +
14A ALA* 1.3 58.3 + - - +
16A ASN* 3.9 0.7 - - - +
17A ALA* 2.9 33.2 + - + +
14B ALA* 3.8 35.1 - - + +
17B ALA* 3.4 27.9 + - - +
18B LYS* 4.2 6.0 + - + +
21B ALA* 5.7 1.4 - - - +
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA 3.0 17.9 + - - +
11A ALA* 3.8 5.8 - - - +
13A THR* 1.3 76.1 - - - +
15A ALA* 1.3 64.2 + - - +
17A ALA* 3.8 4.1 - - - +
18A LYS* 3.0 27.0 + - - +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 2.8 19.5 + - - +
12A LEU* 3.8 7.2 - - + +
14A ALA* 1.3 76.6 - - - +
16A ASN* 1.3 60.8 + - - +
18A LYS* 3.8 3.6 - - - +
19A ALA* 2.9 32.3 + - - +
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Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 2.9 32.9 + - - +
13A THR* 4.1 4.2 - - - +
15A ALA* 1.3 80.5 - - - +
17A ALA* 1.3 58.3 + - - +
19A ALA* 3.8 5.4 - - - +
20A ALA* 2.9 29.8 + - - +
13B THR* 3.4 19.7 - - + +
17B ALA* 5.4 7.6 - - + +
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR 2.9 19.2 + - - +
14A ALA* 3.8 4.9 - - - +
16A ASN* 1.3 73.9 - - - +
18A LYS* 1.3 64.1 + - - +
20A ALA* 3.3 2.3 + - - +
21A ALA* 3.1 17.8 + - - +
10B ALA* 3.4 41.0 - - + +
13B THR* 3.9 6.4 - - - +
14B ALA* 3.9 13.5 - - + +
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Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA 3.0 18.2 + - - +
15A ALA* 3.9 4.5 - - - +
17A ALA* 1.3 75.8 - - - +
19A ALA* 1.3 64.5 + - - +
21A ALA* 3.1 7.6 + - + +
22A GLU* 2.9 51.4 + - + +
10B ALA* 5.5 0.2 - - - -
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA 2.9 19.4 + - - +
16A ASN* 3.9 6.7 - - - +
18A LYS* 1.3 77.6 - - - +
20A ALA* 1.3 62.6 + - - +
22A GLU* 3.2 12.4 + - - +
23A LEU* 2.8 43.1 + - + +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASN 2.9 19.2 + - - +
17A ALA 3.5 5.4 - - - +
18A LYS 3.3 0.2 - - - -
19A ALA* 1.3 77.0 - - - +
21A ALA* 1.3 56.8 + - - +
23A LEU* 4.3 4.2 - - - +
24A THR* 2.7 36.1 + - - +
9B ALA* 3.8 15.0 - - + +
13B THR* 3.3 25.6 - - + +
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 3.1 13.0 + - - +
18A LYS* 3.6 8.5 - - + +
20A ALA* 1.3 75.2 - - - +
22A GLU* 1.3 64.5 + - + +
24A THR 3.3 0.7 + - - -
25A ALA* 2.9 27.0 + - - +
6B ALA* 3.5 36.9 + - + +
7B ALA* 5.4 0.4 - - - -
10B ALA* 4.0 7.6 - - + +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LYS* 2.9 51.2 + - + +
19A ALA* 3.6 13.1 + - - +
21A ALA* 1.3 79.8 - - + +
23A LEU* 1.3 62.9 + - + +
25A ALA* 3.8 5.0 - - - +
26A ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 23 (chain A).
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* 2.8 35.8 + - + +
20A ALA* 4.3 3.4 - - - +
22A GLU* 1.3 74.4 - - + +
24A THR* 1.3 61.1 + - - +
26A ALA* 4.4 7.0 - - + +
27A ASN* 2.8 48.8 + - - +
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Residues in contact with THR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ALA 2.7 23.3 + - - -
21A ALA 3.6 3.1 - - - -
23A LEU* 1.3 76.9 - - - +
25A ALA* 1.3 57.7 + - - +
27A ASN* 3.9 4.8 - - - +
28A ALA* 2.9 34.8 + - + +
2B THR* 5.2 0.9 - - + +
5B ASP* 3.9 18.4 - - + +
6B ALA* 3.8 21.8 - - + +
9B ALA* 3.3 17.2 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA 2.9 16.8 + - - +
22A GLU* 3.8 4.7 - - - +
24A THR* 1.3 78.2 - - - +
26A ALA* 1.3 62.8 + - - +
28A ALA* 3.8 1.2 - - - +
29A ALA* 3.0 24.7 + - - +
2B THR* 3.5 24.0 - - + +
6B ALA* 4.3 8.5 - - + +
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU 2.9 18.0 + - - +
23A LEU* 3.9 9.2 - - + +
25A ALA* 1.3 75.6 - - - +
27A ASN* 1.3 61.8 + - - +
29A ALA* 3.3 5.1 + - - +
30A ALA* 2.9 31.4 + - - +
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 2.8 34.5 + - - +
24A THR* 3.9 4.8 - - - +
26A ALA* 1.3 77.5 - - - +
28A ALA* 1.3 60.1 + - - +
30A ALA* 3.8 4.8 - - - +
31A ALA* 2.9 33.1 + - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 2.9 20.8 + - + +
27A ASN* 1.3 74.3 - - - +
29A ALA* 1.3 63.0 + - - +
31A ALA* 3.9 3.7 - - - +
32A ALA* 3.0 27.8 + - - +
2B THR* 3.7 31.2 - - + +
5B ASP* 6.0 2.5 - - + +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA 3.0 18.1 + - - +
26A ALA* 3.6 5.8 - - - +
28A ALA* 1.3 76.8 - - - +
30A ALA* 1.3 62.5 + - - +
32A ALA* 3.8 4.7 - - - +
33A ALA* 3.0 25.7 + - - +
2B THR* 5.1 2.4 - - + +
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 2.9 18.1 + - - +
27A ASN* 4.0 5.2 - - - +
29A ALA* 1.3 76.2 - - - +
31A ALA* 1.3 58.3 + - - +
33A ALA* 3.4 5.9 + - - +
34A ALA* 2.9 31.2 + - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASN 2.9 19.7 + - - +
28A ALA* 3.9 4.7 - - - +
30A ALA* 1.3 78.1 - - - +
32A ALA* 1.3 57.4 + - - +
34A ALA* 3.4 5.2 + - - +
35A THR* 2.9 36.8 + - - +
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA 3.0 19.1 + - - +
29A ALA* 3.8 5.2 - - - +
31A ALA* 1.3 74.0 - - - +
33A ALA* 1.3 56.4 + - - +
35A THR* 3.3 7.0 + - - +
36A ALA* 2.9 30.5 + - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 3.0 18.9 + - - +
30A ALA* 3.7 7.0 - - - +
32A ALA* 1.3 77.5 - - - +
34A ALA* 1.4 61.3 + - - +
36A ALA* 3.3 5.3 + - - -
37A ARG* 2.9 39.4 + - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 2.9 18.2 + - - +
31A ALA* 3.8 5.8 - - - +
33A ALA* 1.4 74.8 - - - +
35A THR* 1.4 64.5 + - - +
37A ARG* 3.1 23.5 + - - +
38A NH2 4.1 1.4 + - - -
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 2.9 20.9 + - - +
32A ALA* 3.6 6.3 - - - +
34A ALA* 1.4 77.4 - - - +
36A ALA* 1.3 61.4 + - - +
38A NH2 3.1 11.4 + - - -
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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
------------------------------------------------------------
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