Contacts of the helix formed by residues 9 - 37 (chain O) in PDB entry 2QJK
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 GLY 9 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250N ARG* 5.9 1.0 - - - +
10O THR* 1.3 60.3 + - - -
11O ARG* 3.2 27.4 + - - +
12O ARG* 3.5 38.1 + - - +
13O ASP* 3.9 9.2 + - - +
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Residues in contact with THR 10 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O GLY* 1.3 70.9 - - - -
11O ARG* 1.3 59.2 + - - +
12O ARG 3.6 0.9 - - - -
13O ASP* 3.8 16.1 + - + +
14O PHE* 3.1 36.2 - - + +
17O TYR* 6.3 0.2 - - + -
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Residues in contact with ARG 11 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250N ARG* 4.7 13.7 - - - +
9O GLY* 3.2 20.2 - - - +
10O THR* 1.3 81.4 - - - +
12O ARG* 1.3 62.9 + - - +
14O PHE* 3.6 6.2 - - - +
15O LEU* 3.6 16.1 + - - +
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Residues in contact with ARG 12 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250N ARG* 2.8 50.2 - - - +
9O GLY* 3.5 35.8 + - - +
11O ARG* 1.3 77.1 - - - +
13O ASP* 1.3 70.9 + - + +
14O PHE 3.2 0.4 - - - -
15O LEU* 3.1 7.8 + - - +
16O TYR* 2.9 49.4 + - + -
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Residues in contact with ASP 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9O GLY 3.9 5.8 - - - +
10O THR* 3.8 27.6 + - + +
11O ARG 3.4 0.2 - - - -
12O ARG* 1.3 83.0 - - + +
14O PHE* 1.3 65.4 + - - +
16O TYR* 3.4 10.7 + - - +
17O TYR* 3.0 60.1 + - - -
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Residues in contact with PHE 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O THR* 3.1 30.1 + - + +
11O ARG* 3.6 7.4 - - - +
12O ARG 3.2 0.8 - - - -
13O ASP* 1.3 75.2 - - - +
15O LEU* 1.3 61.3 + - + +
17O TYR* 2.9 8.8 + - + +
18O ALA* 2.7 50.5 + - + +
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Residues in contact with LEU 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243N LEU* 3.9 28.5 - - + +
246N LEU* 3.8 26.0 - - + -
247N THR* 3.7 37.9 - - - +
250N ARG* 4.8 13.5 - - + +
11O ARG 3.6 7.7 + - - +
12O ARG* 3.1 10.7 + - - +
14O PHE* 1.3 88.1 - - + +
16O TYR* 1.3 58.6 + - + +
18O ALA* 2.9 5.3 + - + +
19O THR* 2.7 36.3 + - - +
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Residues in contact with TYR 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247N THR* 4.2 25.5 + - + -
250N ARG* 4.0 28.5 + - - +
251N LEU* 4.7 18.8 - - + +
12O ARG* 2.9 41.8 + - + +
13O ASP* 3.5 17.9 - - - +
15O LEU* 1.3 82.4 - - + +
17O TYR* 1.3 65.0 + - + +
19O THR* 3.6 7.2 + - - +
20O ALA* 3.1 28.2 + - - +
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Residues in contact with TYR 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O THR* 6.3 0.2 - - + -
13O ASP* 3.0 55.9 + - - +
14O PHE* 2.9 8.2 + - + +
16O TYR* 1.3 79.1 - - + +
18O ALA* 1.3 64.3 + - - +
19O THR 3.2 1.3 - - - -
20O ALA* 4.5 7.7 - - + +
21O GLY* 3.3 18.1 + - - -
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Residues in contact with ALA 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243N LEU* 3.7 23.2 - - + +
14O PHE* 2.7 37.4 + - + +
15O LEU* 3.5 11.0 - - + +
17O TYR* 1.3 72.8 - - - +
19O THR* 1.3 64.7 + - - +
21O GLY* 3.5 1.6 + - - -
22O ALA* 3.2 16.5 + - - +
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Residues in contact with THR 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240N LEU* 4.4 4.9 - - + +
243N LEU* 3.3 32.7 - - - +
244N LEU* 4.7 19.7 - - + -
247N THR* 3.3 24.0 + - + +
15O LEU* 2.7 15.3 + - - +
16O TYR* 3.7 8.1 - - - +
18O ALA* 1.3 74.1 - - - +
20O ALA* 1.3 70.4 + - + +
21O GLY 2.7 5.9 + - - -
22O ALA* 2.8 14.7 + - - +
23O GLY* 3.0 9.5 + - - -
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Residues in contact with ALA 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O TYR 3.1 15.4 + - - +
17O TYR* 4.5 10.8 - - + +
19O THR* 1.3 84.6 - - + +
21O GLY* 1.3 60.6 + - - +
23O GLY* 3.4 3.2 + - - +
24O ALA* 3.1 23.7 + - - +
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Residues in contact with GLY 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O TYR 3.3 13.9 + - - -
18O ALA* 3.7 5.2 - - - -
19O THR 2.7 3.0 + - - -
20O ALA* 1.3 78.6 - - - +
22O ALA* 1.3 63.7 + - - -
24O ALA* 3.2 5.9 + - - +
25O VAL* 3.0 26.9 + - - +
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Residues in contact with ALA 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N PHE* 5.6 2.6 - - - +
239N VAL* 5.2 5.6 - - + -
240N LEU* 3.9 24.1 - - + +
243N LEU* 4.3 11.4 - - + -
18O ALA 3.2 11.1 + - - +
19O THR 2.8 11.1 + - - +
21O GLY* 1.3 68.0 - - - -
23O GLY* 1.3 70.0 + - - +
25O VAL* 3.1 13.0 + - - +
26O ALA* 3.0 20.1 + - - +
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Residues in contact with GLY 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240N LEU* 4.2 15.6 - - - +
19O THR 3.0 11.9 + - - -
20O ALA* 3.7 4.9 - - - -
22O ALA* 1.3 79.0 - - - +
24O ALA* 1.3 63.4 + - - +
26O ALA* 3.0 3.3 + - - +
27O THR* 2.9 27.0 + - - -
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Residues in contact with ALA 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O ALA 3.1 13.1 + - - +
21O GLY* 3.5 9.4 - - - +
23O GLY* 1.3 73.2 - - - +
25O VAL* 1.3 65.2 + - + +
27O THR* 3.1 10.0 + - - -
28O GLY* 3.0 19.8 + - - -
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Residues in contact with VAL 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N PHE* 3.8 29.6 - - + -
21O GLY 3.0 18.1 + - - +
22O ALA* 3.1 13.7 + - - +
24O ALA* 1.3 77.3 - - + +
26O ALA* 1.3 65.7 + - - +
28O GLY* 3.3 1.7 + - - -
29O ALA* 3.0 16.6 + - - +
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Residues in contact with ALA 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N PHE* 4.4 21.3 - - + -
237N LEU* 6.2 2.0 - - + -
240N LEU* 4.7 15.3 - - + -
22O ALA 3.0 7.9 + - - +
23O GLY 3.0 8.4 + - - +
25O VAL* 1.3 76.8 - - - +
27O THR* 1.3 58.3 + - - +
29O ALA* 2.6 34.6 + - - +
30O ALA* 3.0 10.1 + - - +
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Residues in contact with THR 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O GLY 2.9 20.5 + - - -
24O ALA* 3.2 13.4 - - - -
26O ALA* 1.3 72.0 - - - +
28O GLY* 1.3 63.1 + - - +
30O ALA* 3.1 10.1 - - - +
31O VAL* 3.0 33.1 + - + +
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Residues in contact with GLY 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O ALA 3.0 12.0 + - - -
25O VAL 3.8 3.1 - - - -
26O ALA 2.8 1.0 + - - -
27O THR* 1.3 71.9 - - - +
29O ALA* 1.3 57.9 + - - +
30O ALA 2.9 5.1 + - - -
31O VAL* 3.0 9.2 + - - +
32O TRP* 2.8 33.0 + - - +
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Residues in contact with ALA 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236N PHE* 3.7 29.2 - - + -
25O VAL* 3.0 12.8 + - + +
26O ALA* 2.6 16.7 + - - +
28O GLY* 1.3 71.6 - - - +
30O ALA* 1.3 53.9 + - - -
32O TRP* 4.4 3.3 - - - +
33O PRO* 2.9 22.7 - - - +
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Residues in contact with ALA 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O ALA 3.0 6.6 + - - +
27O THR* 3.1 13.5 - - - +
28O GLY 2.9 0.4 - - - -
29O ALA* 1.3 76.7 - - - +
31O VAL* 1.3 63.4 - - + +
33O PRO* 2.8 26.4 - - - +
34O LEU* 3.4 17.0 + - + +
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Residues in contact with VAL 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O THR* 3.2 25.6 - - + +
28O GLY* 3.5 9.6 - - - +
30O ALA* 1.3 77.3 - - + +
32O TRP* 1.3 69.1 + - - +
34O LEU* 3.0 23.2 + - + +
35O ILE* 3.1 35.7 + - + +
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Residues in contact with TRP 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O GLY 2.8 17.6 + - - +
29O ALA* 4.4 3.1 - - - +
31O VAL* 1.3 73.5 - - - +
33O PRO* 1.3 63.6 - - + +
35O ILE* 2.7 34.7 + - + +
36O ASN* 2.7 72.1 + - + +
39O ASN* 4.2 6.3 - - - -
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Residues in contact with PRO 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ASN 4.6 5.4 - - - +
89M GLY* 6.1 3.8 - - - -
93M LEU* 4.9 12.0 - - + +
29O ALA 2.9 23.3 - - - +
30O ALA* 2.8 27.1 - - - +
32O TRP* 1.3 92.4 - - + +
34O LEU* 1.3 61.8 + - + +
36O ASN* 4.2 9.0 - - + +
37O GLN* 3.0 26.3 + - - +
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Residues in contact with LEU 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M VAL* 4.0 34.5 - - + -
61M THR* 5.1 1.6 - - + +
64M VAL* 4.0 21.0 - - + +
93M LEU* 4.7 16.8 - - + -
30O ALA* 3.5 18.4 - - + +
31O VAL* 3.0 17.6 + - + +
33O PRO* 1.3 81.1 - - + +
35O ILE* 1.3 59.8 + - + +
37O GLN* 3.0 28.3 + - - +
38O MET* 5.1 0.7 - - - +
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Residues in contact with ILE 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O VAL* 3.2 34.8 - - + +
32O TRP* 2.7 27.9 + - + +
34O LEU* 1.3 80.1 - - + +
36O ASN* 1.3 66.4 + - - +
37O GLN 3.1 2.0 - - - -
38O MET* 2.9 15.3 + - - +
39O ASN* 5.8 0.4 - - - +
179P TRP* 3.2 44.4 + - + +
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Residues in contact with ASN 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M ASN* 3.1 28.2 + - + +
32O TRP* 2.7 55.4 + - + +
33O PRO* 4.2 6.5 - - + -
35O ILE* 1.3 74.2 - - - +
37O GLN* 1.3 53.8 + - - +
39O ASN* 2.6 62.1 + - - +
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Residues in contact with GLN 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M VAL* 3.6 25.1 - - + +
67M MET* 3.7 15.1 - - - +
68M HIS* 2.8 39.8 + - - -
87M VAL* 3.8 14.8 - - + +
88M ASN* 3.7 23.2 + - - +
93M LEU* 4.2 9.9 - - + -
33O PRO 3.0 15.0 + - - +
34O LEU* 3.0 26.4 + - - +
36O ASN* 1.3 75.3 - - - +
38O MET* 1.3 86.6 + - - +
39O ASN 3.4 7.6 + - - +
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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) + - + + + + + -
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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