Contacts of the helix formed by residues 10 - 35 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D LYS 5.8 1.8 - - - +
9D THR* 1.3 79.0 - - + +
11D GLU* 1.3 61.0 + - - +
12D VAL 3.0 5.8 - - - -
13D VAL* 2.8 35.4 + - + -
14D LYS* 3.2 6.8 + - - +
12E VAL* 4.8 10.8 - - + +
15E ASN* 4.4 12.1 - - + +
16E ALA* 4.2 31.0 - - + +
19E THR* 4.3 21.8 - - + +
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Residues in contact with GLU 11 (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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8C LYS* 3.6 29.3 + - - +
8D LYS* 4.5 30.1 - - + +
9D THR 3.2 1.8 - - - +
10D VAL* 1.3 83.4 - - - +
12D VAL* 1.3 56.4 + - - +
14D LYS* 3.8 22.9 - - + -
15D ASN* 2.9 32.3 + - + +
15E ASN* 4.0 21.1 - - - +
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Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LYS* 4.7 22.2 - - - +
10C VAL* 4.9 8.7 - - + +
8D LYS 5.8 2.2 - - - +
9D THR 3.8 13.8 + - - +
10D VAL 2.9 0.6 + - - -
11D GLU* 1.3 75.9 - - - +
13D VAL* 1.3 64.8 + - + +
15D ASN* 3.4 5.7 + - - +
16D ALA* 2.8 33.3 + - + +
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Residues in contact with VAL 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D THR 5.2 1.3 - - - +
10D VAL* 2.8 30.9 + - + +
12D VAL* 1.3 76.5 - - + +
14D LYS* 1.3 53.9 + - - +
16D ALA* 3.1 6.7 + - + +
17D ILE* 2.6 52.4 + - + +
19E THR* 4.4 9.6 - - + -
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Residues in contact with LYS 14 (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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10D VAL 3.2 2.8 + - - -
11D GLU* 3.7 27.8 - - + +
13D VAL* 1.3 79.0 - - - +
15D ASN* 1.3 69.0 + - - +
17D ILE* 3.0 21.0 + - + +
18D GLU* 3.1 39.1 + - - +
15E ASN* 4.2 20.4 - - - +
18E GLU* 5.5 4.7 - - + -
19E THR* 3.1 42.7 - - + +
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Residues in contact with ASN 15 (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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8C LYS* 5.1 14.0 - - - +
10C VAL* 4.2 11.9 - - + +
11C GLU* 4.0 28.9 - - - +
14C LYS* 4.3 16.7 - - - +
11D GLU* 2.9 24.2 + - + +
12D VAL* 3.8 5.6 - - - +
14D LYS* 1.3 81.1 + - + +
16D ALA* 1.3 57.0 + - - +
18D GLU* 3.4 11.1 + - - +
19D THR* 3.0 30.6 + - - -
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Residues in contact with ALA 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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10C VAL* 4.4 18.1 - - + +
12D VAL* 2.8 21.6 + - + +
13D VAL* 3.4 6.5 - - - +
15D ASN* 1.3 74.4 - - - +
17D ILE* 1.3 62.2 + - + +
19D THR* 3.1 9.8 + - - -
20D ALA* 2.8 31.0 + - - +
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Residues in contact with ILE 17 (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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13D VAL* 2.6 31.0 + - + +
14D LYS* 3.1 18.6 - - + +
16D ALA* 1.3 75.9 - - + +
18D GLU* 1.3 70.9 + - + +
20D ALA* 3.2 6.8 + - + +
21D ASP* 3.0 25.3 + - - +
19E THR* 5.0 6.1 - - + +
22E GLY* 4.3 19.1 - - - +
23E ALA* 4.1 27.4 - - + +
26E LEU* 4.0 24.0 - - + +
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Residues in contact with GLU 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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14C LYS* 5.6 5.9 - - + -
14D LYS* 3.1 39.5 + - + +
15D ASN* 3.7 12.6 - - - +
17D ILE* 1.3 86.9 - - + +
19D THR* 1.3 65.4 + - - +
21D ASP* 3.2 15.9 + - - +
22D GLY* 3.3 11.8 + - - -
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Residues in contact with THR 19 (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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10C VAL* 4.3 19.9 - - + +
13C VAL* 4.4 10.5 - - + -
14C LYS* 3.1 50.5 - - + +
17C ILE* 5.0 6.5 - - + +
15D ASN* 3.0 17.6 + - - -
16D ALA* 3.3 13.4 - - - -
18D GLU* 1.3 77.2 - - - +
20D ALA* 1.3 63.6 + - - +
22D GLY* 3.5 2.1 + - - -
23D ALA* 3.0 21.1 + - + +
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Residues in contact with ALA 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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16D ALA 2.8 12.4 + - - +
17D ILE* 3.2 10.5 + - + +
19D THR* 1.3 75.9 - - - +
21D ASP* 1.3 66.7 + - - +
23D ALA* 3.0 22.3 - - + +
24D LEU* 3.2 8.7 + - - +
26E LEU* 4.0 19.2 - - + +
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Residues in contact with ASP 21 (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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17D ILE* 3.0 12.9 + - + +
18D GLU* 3.4 13.5 - - - +
19D THR 3.2 0.4 - - - -
20D ALA* 1.3 71.8 - - - +
22D GLY* 1.3 60.0 + - - +
23D ALA 2.8 9.2 + - - -
24D LEU* 3.0 15.2 + - - +
25D ASP* 3.2 10.9 + - - +
25E ASP* 6.0 1.0 - - - +
26E LEU* 3.5 19.9 + - + +
29E LYS* 2.7 45.7 + - - +
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Residues in contact with GLY 22 (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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17C ILE* 4.3 16.2 - - - +
18D GLU 3.3 8.7 + - - -
19D THR 3.8 3.4 - - - -
21D ASP* 1.3 77.8 - - - +
23D ALA* 1.3 60.9 + - - +
25D ASP* 3.6 15.1 - - - +
26D LEU* 3.1 23.4 + - - +
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Residues in contact with ALA 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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17C ILE* 4.1 20.4 - - + +
19D THR* 3.0 15.0 + - + +
20D ALA* 3.0 17.7 - - - +
21D ASP 2.8 1.6 + - - -
22D GLY* 1.3 76.4 - - - +
24D LEU* 1.3 67.7 + - - +
26D LEU* 3.2 2.9 + - - +
27D TYR* 2.8 23.3 + - - +
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Residues in contact with LEU 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 ALA 3.2 6.2 + - - +
21D ASP* 3.0 9.9 + - - +
23D ALA* 1.3 76.0 - - - +
25D ASP* 1.3 59.4 + - - +
27D TYR* 2.7 49.7 + - + +
28D ASN* 2.8 12.6 + - - +
26E LEU* 4.5 11.0 - - + -
29E LYS* 4.3 13.5 - - + -
30E TYR* 4.1 39.9 - - + -
33E GLN* 3.4 40.4 - - - +
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Residues in contact with ASP 25 (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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21C ASP* 5.9 2.0 - - - +
21D ASP* 3.2 9.8 + - - +
22D GLY* 3.6 14.8 - - - +
23D ALA 3.2 0.2 - - - -
24D LEU* 1.3 73.3 - - - +
26D LEU* 1.3 58.0 + - - +
28D ASN* 3.3 5.6 + - - +
29D LYS* 2.8 32.5 + - - +
29E LYS* 3.0 37.1 + - - -
33E GLN* 5.5 0.2 + - - -
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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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17C ILE* 4.0 26.9 - - + +
20C ALA* 3.9 25.1 - - + +
21C ASP* 3.5 43.3 + - + +
24C LEU* 4.5 15.0 - - + -
22D GLY 3.1 15.2 + - - +
23D ALA 3.7 2.9 - - - +
25D ASP* 1.3 77.1 - - - +
27D TYR* 1.3 65.3 + - - +
29D LYS* 3.6 7.2 - - + +
30D TYR* 3.0 25.3 + - + +
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Residues in contact with TYR 27 (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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23D ALA 2.8 13.5 + - - +
24D LEU* 2.7 35.3 + - + +
26D LEU* 1.3 74.4 - - - +
28D ASN* 1.3 68.1 + - - -
30D TYR* 3.3 7.2 + + - +
31D LEU* 2.7 69.5 + - + +
198D ILE* 5.8 2.3 - - - +
33E GLN* 5.2 1.1 - - - -
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Residues in contact with ASN 28 (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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24D LEU 2.8 20.0 + - - +
25D ASP* 3.9 6.4 + - - +
27D TYR* 1.3 85.6 - - - +
29D LYS* 1.3 69.4 + - - +
30D TYR 2.9 1.8 - - - -
31D LEU* 2.6 16.0 + - - +
32D ASP* 2.6 39.3 + - - +
33E GLN* 2.9 43.1 + - - -
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Residues in contact with LYS 29 (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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21C ASP* 2.9 29.9 + - - +
24C LEU* 4.3 12.1 - - + -
25C ASP* 2.8 36.7 + - - -
25D ASP 2.8 23.0 + - - +
26D LEU* 3.6 7.9 - - + +
28D ASN* 1.3 72.5 - - - +
30D TYR* 1.3 59.0 + - - +
32D ASP* 3.9 8.4 + - - +
33D GLN* 3.2 37.2 + - - +
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Residues in contact with TYR 30 (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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24C LEU* 3.9 29.2 - - + -
26D LEU* 3.0 18.9 + - + +
27D TYR* 3.7 6.1 - + - +
28D ASN 2.7 3.4 + - - -
29D LYS* 1.3 71.5 - - - +
31D LEU* 1.3 63.3 + - + +
32D ASP 3.0 2.0 - - - -
33D GLN* 2.9 8.8 + - + +
34D VAL* 2.8 47.3 + - + +
180D GLY* 3.1 29.7 + - - -
181D ALA* 3.9 2.3 + - - -
183D ALA* 4.4 10.5 - - + -
184D GLY* 4.4 5.7 + - - -
195D SER* 3.2 31.0 + - - -
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Residues in contact with LEU 31 (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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27D TYR* 2.7 60.0 + - + +
28D ASN* 2.6 20.2 + - - +
30D TYR* 1.3 76.8 - - + +
32D ASP* 1.3 53.3 + - - +
34D VAL* 3.3 5.7 + - + +
35D ILE* 2.7 47.2 + - + +
198D ILE* 4.0 31.4 - - + -
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Residues in contact with ASP 32 (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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28D ASN* 2.6 32.3 + - - +
29D LYS* 3.9 7.8 + - - +
31D LEU* 1.3 73.5 - - - +
33D GLN* 1.3 61.9 + - + +
34D VAL 2.9 5.7 + - - -
35D ILE 3.0 27.4 + - - +
36D PRO* 3.6 5.4 - - - +
37D TRP* 6.0 1.7 - - - +
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Residues in contact with GLN 33 (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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24C LEU* 3.5 32.8 - - - +
27C TYR* 5.0 1.4 - - - -
28C ASN* 2.8 43.9 + - - -
29D LYS* 3.2 24.1 + - - +
30D TYR* 2.9 14.3 + - + +
32D ASP* 1.3 79.7 - - + +
34D VAL* 1.3 59.7 + - - +
36D PRO* 4.9 0.9 - - - +
176D GLU* 2.8 31.5 - - - +
177D ALA* 3.8 0.3 - - - -
179D ALA 6.0 0.2 - - - -
180D GLY* 4.2 10.8 - - - -
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Residues in contact with VAL 34 (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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30D TYR* 2.8 58.3 + - + +
31D LEU* 3.5 6.3 - - + +
33D GLN* 1.3 80.5 - - - +
35D ILE* 1.3 62.0 + - + +
36D PRO* 3.5 0.8 - - - +
177D ALA* 3.3 27.5 - - - +
180D GLY 4.2 9.2 - - - -
181D ALA* 4.4 1.8 - - - +
195D SER* 4.4 3.6 - - - +
198D ILE* 3.6 31.6 - - + -
199D ALA* 3.6 21.7 - - + +
203D VAL* 4.6 0.7 - - - +
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Residues in contact with ILE 35 (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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31D LEU* 2.7 26.1 + - + +
32D ASP* 3.0 18.0 - - - +
34D VAL* 1.3 90.0 - - + +
36D PRO* 1.3 56.3 - - + +
37D TRP* 2.7 40.2 + - + +
198D ILE* 3.7 30.1 - - + +
199D ALA* 4.8 0.4 - - - -
202D VAL* 3.6 35.4 - - + -
203D VAL* 5.2 0.7 - - + -
207D LEU* 4.5 2.9 - - + -
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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