Contacts of the helix formed by residues 10 - 35 (chain B) in PDB entry 2WCD
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 VAL 10 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS 5.8 2.0 - - - +
9B THR* 1.3 78.4 - - + +
11B GLU* 1.3 61.5 + - - +
12B VAL 2.9 5.4 - - - -
13B VAL* 2.8 35.3 + - + +
14B LYS* 3.3 6.5 + - - +
12C VAL* 4.8 11.2 - - + +
15C ASN* 4.4 12.8 - - - +
16C ALA* 4.3 29.6 - - + +
19C THR* 4.3 21.5 - - + +
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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
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8A LYS* 3.8 26.1 + - - -
8B LYS* 4.5 30.7 - - - +
9B THR 3.3 1.4 - - - +
10B VAL* 1.3 81.5 - - - +
12B VAL* 1.3 57.4 + - - +
14B LYS* 3.9 25.2 - - - -
15B ASN* 2.9 30.8 + - + +
15C ASN* 4.1 18.8 - - - +
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Residues in contact with VAL 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 4.8 21.1 - - - +
10A VAL* 5.0 8.2 - - + +
8B LYS 5.8 1.6 - - - +
9B THR* 3.8 13.8 + - - +
10B VAL 2.8 0.8 + - - -
11B GLU* 1.3 76.7 - - + +
13B VAL* 1.3 65.4 + - + +
15B ASN* 3.4 5.4 + - - +
16B ALA* 2.9 32.2 + - + +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR 5.2 1.6 - - - +
10B VAL* 2.8 26.7 + - + +
12B VAL* 1.3 81.6 - - + +
14B LYS* 1.3 52.4 + - - +
16B ALA* 3.0 7.4 + - + +
17B ILE* 2.7 49.4 + - + +
19C THR* 4.4 10.8 - - + -
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Residues in contact with LYS 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 VAL 3.3 2.8 + - - -
11B GLU* 3.7 28.9 - - + +
13B VAL* 1.3 78.3 - - - +
15B ASN* 1.3 69.3 + - - +
17B ILE* 3.0 21.6 + - + +
18B GLU* 3.1 38.6 + - + +
15C ASN* 4.2 20.2 - - - +
18C GLU* 5.6 3.4 - - + -
19C THR* 3.1 40.2 - - + +
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Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 5.1 12.9 - - - +
10A VAL* 4.2 13.3 - - + +
11A GLU* 4.2 27.3 - - - +
14A LYS* 4.3 15.9 - - - +
11B GLU* 2.9 27.0 + - + +
12B VAL* 3.8 5.2 - - - +
14B LYS* 1.3 81.5 + - + +
16B ALA* 1.3 57.1 + - - +
18B GLU* 3.4 11.8 + - - +
19B THR* 3.0 31.5 + - - -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.5 17.9 - - + -
12B VAL* 2.9 22.4 + - + +
13B VAL* 3.4 6.5 - - + +
15B ASN* 1.3 74.2 - - - +
17B ILE* 1.3 63.5 + - + +
19B THR* 3.1 10.3 + - - +
20B ALA* 2.8 30.8 + - - +
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B VAL* 2.7 32.0 + - + +
14B LYS* 3.1 17.5 - - + +
16B ALA* 1.3 72.3 - - + +
18B GLU* 1.3 70.1 + - + +
20B ALA* 3.2 8.6 + - + +
21B ASP* 3.0 25.5 + - - +
19C THR* 5.0 5.8 - - + +
22C GLY* 4.4 19.3 - - - +
23C ALA* 4.1 27.6 - - + +
26C LEU* 3.9 22.9 - - + +
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 5.7 4.3 - - + -
14B LYS* 3.1 40.0 + - + +
15B ASN* 3.7 12.4 - - - +
17B ILE* 1.3 86.9 - - + +
19B THR* 1.3 67.8 + - - +
21B ASP* 3.2 16.2 + - - +
22B GLY* 3.3 10.6 + - - -
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 4.3 21.8 - - + +
13A VAL* 4.4 11.0 - - + -
14A LYS* 3.2 50.2 - - + +
17A ILE* 5.1 6.8 - - + +
15B ASN* 3.0 16.5 + - - -
16B ALA* 3.3 12.8 - - - +
18B GLU* 1.3 78.4 - - - +
20B ALA* 1.3 63.6 + - - +
22B GLY* 3.5 1.9 + - - -
23B ALA* 3.0 21.8 + - + +
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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 ALA 2.8 12.7 + - - +
17B ILE* 3.2 10.1 + - + +
19B THR* 1.3 74.4 - - - +
21B ASP* 1.3 66.5 + - - +
23B ALA* 3.0 23.5 - - + +
24B LEU* 3.2 8.5 + - - +
26C LEU* 3.9 20.5 - - + +
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Residues in contact with ASP 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 ILE 3.0 12.5 + - - +
18B GLU* 3.4 13.7 - - - +
19B THR 3.2 0.2 - - - -
20B ALA* 1.3 71.4 - - - +
22B GLY* 1.3 64.8 + - - +
23B ALA 2.9 5.4 + - - -
24B LEU* 3.0 15.4 + - - +
25B ASP* 3.2 11.6 + - - +
25C ASP* 6.1 1.2 - - - +
26C LEU* 3.6 20.6 + - + +
29C LYS* 2.8 42.3 + - - +
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ILE* 4.4 15.3 - - - +
18B GLU 3.3 8.9 + - - -
19B THR 3.8 2.9 - - - -
21B ASP* 1.3 78.8 - - - +
23B ALA* 1.3 61.0 + - - +
25B ASP* 3.5 14.6 - - - +
26B LEU* 3.1 24.3 + - - +
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Residues in contact with ALA 23 (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 ILE* 4.2 19.7 - - + -
19B THR* 3.0 14.4 + - + +
20B ALA* 3.0 18.4 - - - +
21B ASP 2.9 1.2 + - - -
22B GLY* 1.3 76.5 - - - +
24B LEU* 1.3 67.8 + - - +
26B LEU* 3.2 2.9 + - - +
27B TYR* 2.8 23.5 + - - +
186C VAL* 6.1 6.5 - - + -
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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
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20B ALA 3.2 5.4 + - - +
21B ASP 3.0 9.9 + - - +
23B ALA* 1.3 76.0 - - - +
25B ASP* 1.3 70.4 + - - +
27B TYR* 2.8 34.5 + - + +
28B ASN* 2.8 19.5 + - - +
26C LEU* 4.5 12.3 - - + -
29C LYS* 4.3 13.7 - - + -
30C TYR* 4.1 39.5 - - + -
33C GLN* 3.5 38.8 - - - +
183C ALA* 4.8 7.0 - - + -
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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
----------------------------------------------------------
21A ASP* 6.0 1.3 - - - +
21B ASP* 3.2 9.7 + - - +
22B GLY* 3.5 16.2 + - - +
23B ALA 3.2 0.4 + - - -
24B LEU* 1.3 74.1 - - - +
26B LEU* 1.3 58.8 + - - +
28B ASN* 3.3 6.0 + - - +
29B LYS* 2.8 32.6 + - - +
29C LYS* 2.9 36.7 + - - -
33C GLN* 5.6 0.2 + - - -
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Residues in contact with LEU 26 (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 ILE* 4.0 27.6 - - + +
20A ALA* 4.0 23.8 - - + +
21A ASP* 3.5 44.3 + - + +
24A LEU* 4.6 14.1 - - + -
22B GLY 3.1 13.9 + - - +
23B ALA 3.7 3.8 - - - +
25B ASP* 1.3 78.2 - - - +
27B TYR* 1.3 64.7 + - - +
29B LYS* 3.6 7.0 - - + +
30B TYR* 3.0 25.7 + - + +
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Residues in contact with TYR 27 (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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23B ALA 2.8 13.7 + - - +
24B LEU* 2.8 32.9 + - + +
26B LEU* 1.3 74.6 - - - +
28B ASN* 1.3 79.1 + - - -
30B TYR* 3.4 6.4 + + - +
31B LEU* 2.8 53.7 + - + +
198B ILE* 6.0 1.2 - - - +
33C GLN* 5.2 1.1 - - - -
179C ALA* 2.8 31.3 + - - -
182C ALA* 4.4 6.2 - - - +
183C ALA* 3.4 26.2 + - + +
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Residues in contact with ASN 28 (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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24B LEU* 2.8 21.8 + - - +
25B ASP* 3.9 4.8 + - - +
27B TYR* 1.3 84.9 - - - +
29B LYS* 1.3 69.3 + - - +
30B TYR 3.0 2.0 - - - -
31B LEU* 2.6 14.4 + - - +
32B ASP* 2.6 38.7 + - - +
33C GLN* 2.9 42.6 + - - -
179C ALA* 5.6 0.6 + - - +
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Residues in contact with LYS 29 (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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21A ASP* 2.8 36.5 + - - +
24A LEU* 4.2 14.8 - - + -
25A ASP* 2.9 30.6 + - - -
25B ASP 2.8 23.7 + - - +
26B LEU* 3.6 8.1 - - + +
28B ASN* 1.3 72.9 - - - +
30B TYR* 1.3 58.0 + - - +
32B ASP* 3.8 7.4 + - - +
33B GLN* 3.2 35.0 + - - +
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Residues in contact with TYR 30 (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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24A LEU* 4.0 29.4 - - + -
26B LEU* 3.0 18.3 + - + +
27B TYR* 3.7 5.2 - + - +
28B ASN 2.8 3.0 + - - -
29B LYS* 1.3 72.7 - - - +
31B LEU* 1.3 63.8 + - + +
32B ASP 3.0 2.0 - - - -
33B GLN* 2.9 8.8 + - + +
34B VAL* 2.8 47.9 + - + +
180B GLY* 3.1 30.1 + - - -
181B ALA* 3.9 1.9 + - - -
183B ALA* 4.5 10.1 - - + -
184B GLY* 4.5 5.2 + - - -
195B SER* 3.2 30.3 + - - -
198B ILE* 6.5 0.4 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 2.8 54.5 + - + +
28B ASN* 2.6 19.3 + - - +
30B TYR* 1.3 76.8 - - + +
32B ASP* 1.3 54.0 + - - +
34B VAL* 3.3 6.7 + - + +
35B ILE* 2.7 44.6 + - + +
198B ILE* 4.0 30.7 - - + -
175C LYS* 5.5 7.4 - - - +
179C ALA* 3.7 30.5 - - + -
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ASN* 2.6 32.6 + - - +
29B LYS* 3.9 7.8 + - - +
31B LEU* 1.3 72.8 - - - +
33B GLN* 1.3 66.4 + - - +
34B VAL 2.9 2.4 + - - -
35B ILE 3.1 25.7 + - - +
36B PRO* 3.6 5.7 - - - +
37B TRP* 5.9 1.0 - - - +
175C LYS* 4.5 14.9 + - - -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.5 32.1 - - - +
25A ASP* 5.5 0.2 + - - -
27A TYR* 5.0 1.6 - - - -
28A ASN* 2.8 42.9 + - - -
29B LYS* 3.2 23.5 + - - +
30B TYR* 2.9 14.9 + - + +
32B ASP* 1.3 79.8 - - + +
34B VAL* 1.3 59.7 + - - +
36B PRO* 4.8 0.9 - - - +
176B GLU* 2.8 31.7 - - - +
177B ALA* 3.8 0.5 - - - -
179B ALA 6.0 0.3 - - - -
180B GLY* 4.2 10.3 - - - -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 2.8 58.9 + - + +
31B LEU* 3.4 5.8 - - - +
32B ASP 2.9 0.2 - - - -
33B GLN* 1.3 81.1 - - - +
35B ILE* 1.3 65.3 + - + +
36B PRO* 3.5 1.0 - - - +
177B ALA* 3.3 27.1 - - - +
180B GLY 4.2 8.7 - - - -
181B ALA* 4.4 1.8 - - - +
195B SER* 4.4 2.9 - - - +
198B ILE* 3.6 31.4 - - + -
199B ALA* 3.6 20.5 - - + +
203B VAL* 4.6 0.5 - - - +
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Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 2.7 27.1 + - + +
32B ASP* 3.1 17.7 - - - +
34B VAL* 1.3 89.2 - - + +
36B PRO* 1.3 56.6 - - + +
37B TRP* 2.6 39.7 + - + +
198B ILE* 3.7 31.0 - - + +
199B ALA* 4.8 0.4 - - - -
202B VAL* 3.6 35.4 - - + -
203B VAL* 5.2 1.6 - - + -
207B LEU* 4.4 2.9 - - + -
175C LYS* 4.5 17.2 - - + -
179C ALA* 6.4 1.3 - - + -
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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