Contacts of the helix formed by residues 2 - 35 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 4.5 0.9 - - + +
25A ALA* 3.5 37.7 - - + +
28A ALA* 3.7 24.8 - - + +
29A ALA* 5.1 1.5 - - + +
1B ASP* 1.4 74.0 - - - +
3B ALA* 1.3 52.7 + - - +
5B ASP* 3.3 8.9 + - + +
6B ALA* 2.8 33.8 + - - +
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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
----------------------------------------------------------
1B ASP* 3.3 13.2 + - - +
2B THR* 1.3 76.3 - - - +
4B SER* 1.3 61.3 + - - +
6B ALA* 3.9 5.3 - - - +
7B ALA* 3.1 23.2 + - - +
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Residues in contact with SER 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ASP* 3.1 23.7 + - - -
3B ALA* 1.3 74.4 - - - +
5B ASP* 1.3 63.7 + - - +
7B ALA* 3.3 6.8 + - - +
8B ALA* 2.9 29.8 + - - +
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Residues in contact with ASP 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 3.9 14.2 - - + +
1B ASP 3.0 25.6 + - - +
2B THR* 3.7 7.4 - - - +
4B SER* 1.3 80.4 - - - +
6B ALA* 1.3 56.6 + - - +
8B ALA* 3.3 6.0 + - - +
9B ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 3.5 38.3 - - + +
24A THR* 3.8 11.2 - - - +
25A ALA* 4.3 14.4 - - + +
2B THR 2.8 22.5 + - - +
3B ALA* 3.9 5.6 - - - +
5B ASP* 1.3 72.5 - - - +
7B ALA* 1.3 57.6 + - - +
9B ALA* 3.3 1.7 + - - +
10B ALA* 3.0 23.7 + - - +
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Residues in contact with ALA 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 5.4 0.2 - - - -
3B ALA 3.1 17.7 + - - +
4B SER* 3.6 9.0 - - - +
5B ASP 3.3 0.2 - - - -
6B ALA* 1.3 77.0 - - - +
8B ALA* 1.3 61.4 + - - +
10B ALA* 3.3 7.2 + - - +
11B ALA* 3.0 24.5 + - - +
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Residues in contact with ALA 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B SER 2.9 17.7 + - - +
5B ASP* 3.3 6.7 + - - +
7B ALA* 1.3 74.8 - - - +
9B ALA* 1.4 57.2 + - - +
11B ALA* 3.8 5.9 - - - +
12B LEU* 2.9 33.1 + - - +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 4.0 11.4 - - + +
24A THR* 3.3 27.8 - - + +
5B ASP 2.9 16.2 + - - +
6B ALA 3.6 5.2 - - - +
7B ALA 3.3 0.2 - - - -
8B ALA* 1.4 75.7 - - - +
10B ALA* 1.3 54.5 + - - +
12B LEU* 3.9 4.7 - - - +
13B THR* 2.7 38.1 + - - +
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Residues in contact with ALA 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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17A ALA* 3.4 36.3 - - + +
18A LYS* 5.5 0.2 - - - -
20A ALA* 4.2 1.0 - - - +
21A ALA* 4.0 8.1 - - + -
6B ALA 3.0 14.2 + - - +
7B ALA* 3.3 11.4 + - - +
9B ALA* 1.3 76.5 - - - +
11B ALA* 1.3 56.7 + - - +
13B THR* 3.5 0.5 + - - -
14B ALA* 2.9 31.5 + - - +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ALA 3.0 17.3 + - - +
8B ALA* 3.8 5.8 - - - +
10B ALA* 1.3 75.7 - - - +
12B LEU* 1.3 58.1 + - - +
14B ALA* 3.4 6.1 + - - +
15B ALA* 3.0 29.7 + - - +
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Residues in contact with LEU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ALA 2.9 17.6 + - - +
9B ALA* 4.0 4.0 - - - +
11B ALA* 1.3 76.9 - - - +
13B THR* 1.3 63.2 + - - +
15B ALA* 3.3 8.4 + - + +
16B ASN* 2.9 51.4 + - - +
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Residues in contact with THR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN* 3.4 42.4 - - + +
17A ALA* 3.9 1.1 - - - +
20A ALA* 3.3 15.2 - - + +
9B ALA* 2.7 23.0 + - - +
10B ALA 3.7 3.4 - - - -
12B LEU* 1.3 77.3 - - - +
14B ALA* 1.3 56.2 + - - +
16B ASN* 3.3 9.2 + - - +
17B ALA* 2.9 28.3 + - + +
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Residues in contact with ALA 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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13A THR* 3.8 22.2 - - + +
17A ALA* 3.9 15.4 - - + +
10B ALA 2.9 22.6 + - - +
11B ALA* 3.7 6.1 - - - +
13B THR* 1.3 69.7 - - - +
15B ALA* 1.3 60.8 + - - +
17B ALA* 3.2 3.8 + - - +
18B LYS* 2.9 29.5 + - - +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 3.0 17.9 + - - +
12B LEU* 3.3 11.0 + - + +
14B ALA* 1.3 75.4 - - - +
16B ASN* 1.3 60.7 + - - +
18B LYS* 3.3 7.4 + - - +
19B ALA* 2.9 28.1 + - - +
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Residues in contact with ASN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 2.9 43.9 + - - +
13B THR* 3.7 7.1 - - - +
15B ALA* 1.3 77.6 - - - +
17B ALA* 1.3 58.3 + - - +
19B ALA* 3.3 8.2 + - - +
20B ALA* 3.0 27.4 + - - +
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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
----------------------------------------------------------
12A LEU* 5.3 1.8 - - + -
13A THR* 3.4 34.8 + - + +
16A ASN* 5.4 9.0 - - + +
13B THR* 2.9 16.8 + - + +
14B ALA* 3.5 4.3 - - - +
16B ASN* 1.3 77.0 - - - +
18B LYS* 1.3 55.2 + - - +
20B ALA* 3.2 10.0 + - - +
21B ALA* 3.0 26.7 + - - +
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Residues in contact with LYS 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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13A THR* 4.2 7.5 + - + +
14B ALA 2.9 16.3 + - - +
15B ALA* 3.6 7.9 - - - +
17B ALA* 1.3 71.2 - - - +
19B ALA* 1.3 65.1 + - - +
21B ALA* 3.1 14.8 + - + +
22B GLU* 2.9 48.1 + - - +
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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
----------------------------------------------------------
15B ALA 2.9 15.0 + - - +
16B ASN* 3.3 13.4 + - - +
18B LYS* 1.3 75.5 - - - +
20B ALA* 1.3 60.7 + - - +
22B GLU* 3.2 16.4 + - - +
23B LEU* 2.9 37.0 + - + +
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Residues in contact with ALA 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 ASN 3.0 13.3 + - - +
17B ALA* 3.2 11.9 + - - +
19B ALA* 1.3 74.8 - - - +
21B ALA* 1.3 56.8 + - - +
23B LEU* 3.4 8.3 + - - +
24B THR* 2.8 33.3 + - - +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ALA* 4.3 23.6 - - + -
13A THR* 5.7 1.6 - - - +
17B ALA 3.0 14.0 + - - +
18B LYS* 3.1 19.0 + - + +
20B ALA* 1.3 76.2 - - - +
22B GLU* 1.3 56.5 + - + +
24B THR* 3.3 7.6 + - - -
25B ALA* 2.9 30.0 + - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LYS* 2.9 37.5 + - - +
19B ALA* 3.5 24.5 + - - +
21B ALA* 1.3 74.9 - - - +
23B LEU* 1.3 61.7 + - + +
25B ALA* 3.3 6.2 + - - +
26B ALA* 2.9 29.5 + - - +
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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
----------------------------------------------------------
19B ALA* 2.9 32.7 + - + +
20B ALA* 3.6 10.8 - - - +
22B GLU* 1.3 83.1 - - + +
24B THR* 1.3 63.6 + - - +
26B ALA* 3.4 6.5 + - + +
27B ASN* 3.0 25.2 + - - +
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Residues in contact with THR 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ASP* 6.1 2.0 - - + +
20B ALA* 2.8 19.6 + - - +
21B ALA* 3.5 7.7 - - - -
22B GLU 3.3 0.2 - - - -
23B LEU* 1.3 76.3 - - - +
25B ALA* 1.3 57.6 + - - +
27B ASN* 3.2 6.2 + - - +
28B ALA* 2.9 33.0 + - + +
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Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 2.9 17.4 + - - +
22B GLU* 3.7 7.4 - - - +
24B THR* 1.3 74.9 - - - +
26B ALA* 1.3 66.0 + - - +
28B ALA* 3.4 5.5 + - - +
29B ALA* 2.9 26.3 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU 2.9 17.4 + - - +
23B LEU* 3.8 7.2 - - + +
25B ALA* 1.3 74.7 - - - +
27B ASN* 1.3 57.6 + - - +
29B ALA* 3.4 5.4 + - - +
30B ALA* 3.0 29.5 + - - +
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU 3.0 18.6 + - - +
24B THR* 3.5 6.3 - - - +
26B ALA* 1.3 78.7 - - - +
28B ALA* 1.3 56.3 + - - +
30B ALA* 3.3 8.6 + - - +
31B ALA* 3.0 27.7 + - - +
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Residues in contact with ALA 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 2.9 21.3 + - + +
25B ALA* 3.8 5.6 - - - +
27B ASN* 1.3 76.9 - - - +
29B ALA* 1.3 57.1 + - - +
31B ALA* 3.2 8.6 + - - +
32B ALA* 3.0 28.8 + - - +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 2.9 17.2 + - - +
26B ALA* 3.7 6.7 - - - +
28B ALA* 1.3 76.8 - - - +
30B ALA* 1.3 56.6 + - - +
32B ALA* 3.3 7.6 + - - +
33B ALA* 2.9 30.9 + - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 3.0 14.0 + - - +
27B ASN* 3.5 13.7 - - - +
29B ALA* 1.3 76.7 - - - +
31B ALA* 1.4 58.6 + - - +
33B ALA* 3.4 5.5 + - - +
34B ALA* 2.9 31.9 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASN 3.0 13.7 + - - +
28B ALA* 3.2 12.1 + - - +
30B ALA* 1.4 77.4 - - - +
32B ALA* 1.3 62.4 + - - +
34B ALA* 3.3 6.4 + - - +
35B THR* 3.1 30.5 + - + +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA 3.0 15.9 + - - +
29B ALA* 3.3 8.3 + - - +
31B ALA* 1.3 75.6 - - - +
33B ALA* 1.3 63.1 + - - +
35B THR* 2.7 25.7 + - - -
36B ALA* 3.5 7.1 + - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA 2.9 17.4 + - - +
30B ALA* 3.8 6.5 - - - +
32B ALA* 1.3 76.5 - - - +
34B ALA* 1.3 62.8 + - - +
36B ALA* 3.5 1.2 + - - -
37B ARG* 2.9 50.8 + - - +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ALA 2.9 17.8 + - - +
31B ALA* 3.3 7.2 + - - +
33B ALA* 1.3 76.6 - - - +
35B THR* 1.3 62.1 + - - +
37B ARG* 3.1 16.1 + - - +
38B NH2 3.2 9.4 + - - -
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ALA* 3.1 18.7 + - + +
32B ALA* 2.7 21.7 + - - -
34B ALA* 1.3 76.4 - - + +
36B ALA* 1.3 61.3 + - - +
37B ARG 3.3 0.9 + - - -
38B NH2 3.4 7.3 + - - -
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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