Contacts of the helix formed by residues 9 - 37 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10F THR* 1.3 60.2 + - - -
11F ARG* 3.2 23.9 + - - +
12F ARG* 4.3 5.5 + - - +
13F ASP* 3.9 13.7 + - - +
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Residues in contact with THR 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F GLY* 1.3 71.2 - - - -
11F ARG* 1.3 60.4 + - - +
12F ARG 3.5 0.9 - - - -
13F ASP* 3.7 16.3 + - + +
14F PHE* 3.1 34.5 + - + +
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Residues in contact with ARG 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ARG* 3.9 8.3 + - - -
9F GLY* 3.2 17.7 - - - +
10F THR* 1.3 82.0 - - - +
12F ARG* 1.3 87.0 + - + +
14F PHE* 3.6 7.9 - - - +
15F LEU 3.6 12.3 + - - -
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Residues in contact with ARG 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E ARG* 2.9 74.8 - - - +
9F GLY 4.3 6.8 + - - +
11F ARG* 1.3 102.5 - - + +
13F ASP* 1.3 59.0 + - - +
15F LEU* 3.1 4.5 + - - +
16F TYR* 2.9 48.9 + - + +
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Residues in contact with ASP 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F GLY 3.9 7.4 + - - +
10F THR* 3.7 27.4 + - + +
11F ARG 3.4 0.4 - - - -
12F ARG* 1.3 76.8 - - - +
14F PHE* 1.3 65.1 + - - +
16F TYR* 3.4 13.1 + - - +
17F TYR* 3.0 50.0 + - - +
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Residues in contact with PHE 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E LEU* 5.8 2.7 - - + -
250E ARG* 6.0 0.4 - - - -
10F THR* 3.1 29.6 + - + +
11F ARG* 3.6 9.0 - - - +
12F ARG 3.2 0.2 - - - -
13F ASP* 1.3 76.2 - - - +
15F LEU* 1.3 80.7 + - + +
17F TYR* 2.9 9.1 + - + +
18F ALA* 2.7 54.5 + - + -
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E LEU* 4.1 21.5 - - + +
246E LEU* 3.8 27.1 - - + -
247E THR* 3.6 36.8 - - - +
250E ARG* 3.6 42.2 - - - +
11F ARG 3.6 2.3 + - - +
12F ARG 3.1 8.4 + - - +
14F PHE* 1.3 94.9 - - + +
16F TYR* 1.3 60.5 + - + +
18F ALA* 2.9 2.5 + - - +
19F THR* 2.8 37.0 + - - +
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Residues in contact with TYR 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D ILE* 6.1 0.9 - - + -
247E THR* 4.2 28.3 - - + -
250E ARG* 5.2 3.6 - - + +
251E LEU* 4.4 25.9 + - + +
12F ARG* 2.9 45.4 + - + +
13F ASP* 3.6 17.5 - - - +
15F LEU* 1.3 83.4 - - + +
17F TYR* 1.3 68.6 + + + +
19F THR* 3.7 7.6 - - - +
20F ALA* 3.1 28.1 + - - +
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Residues in contact with TYR 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ASP* 3.0 39.0 + - - +
14F PHE* 2.9 6.9 + - + +
16F TYR* 1.3 84.2 - - + +
18F ALA* 1.3 64.7 + - - +
19F THR 3.2 1.3 - - - -
20F ALA* 4.1 5.7 - - + +
21F GLY* 3.3 17.3 + - - -
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Residues in contact with ALA 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243E LEU* 3.6 20.6 - - + +
14F PHE* 2.7 47.7 + - + +
15F LEU* 3.5 7.2 - - - +
17F TYR* 1.3 73.6 - - - +
19F THR* 1.3 62.4 + - - +
21F GLY* 3.5 1.7 + - - -
22F ALA* 3.2 16.8 + - - +
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Residues in contact with THR 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LEU* 4.4 4.8 - - + +
243E LEU* 3.3 27.5 - - - +
244E LEU* 4.6 20.0 - - + -
247E THR* 3.1 30.4 + - + +
15F LEU* 2.8 16.0 + - - +
16F TYR* 3.7 7.2 - - - +
18F ALA* 1.3 73.3 - - - +
20F ALA* 1.3 70.1 + - + +
21F GLY 2.7 5.3 + - - -
22F ALA* 2.8 14.7 + - - +
23F GLY* 3.0 9.7 + - - -
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Residues in contact with ALA 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F TYR 3.1 14.9 + - - +
17F TYR* 4.4 7.2 - - + +
19F THR* 1.3 85.1 - - + +
21F GLY* 1.3 61.8 + - - +
23F GLY* 3.4 3.0 + - - +
24F ALA* 3.1 23.2 + - - +
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Residues in contact with GLY 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F TYR 3.3 14.3 + - - -
18F ALA* 3.7 4.5 - - - -
19F THR 2.7 3.0 + - - -
20F ALA* 1.3 75.5 - - - +
22F ALA* 1.3 65.7 + - - -
23F GLY 3.2 0.3 + - - -
24F ALA* 3.2 8.5 + - - +
25F VAL* 3.0 25.5 + - - +
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Residues in contact with ALA 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E PHE* 4.9 6.4 - - + +
239E VAL* 5.2 5.6 - - + -
240E LEU* 3.9 24.6 - - + +
243E LEU* 4.2 12.3 - - + -
18F ALA 3.2 10.6 + - - +
19F THR 2.8 10.6 + - - +
21F GLY* 1.3 71.4 - - - +
23F GLY* 1.3 68.1 + - - +
25F VAL* 3.1 12.4 + - - +
26F ALA* 3.0 19.8 + - - +
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Residues in contact with GLY 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E LEU* 4.1 16.6 - - - +
19F THR 3.0 12.1 + - - -
20F ALA* 3.7 5.4 - - - -
21F GLY 3.1 0.2 - - - -
22F ALA* 1.3 80.2 - - - +
24F ALA* 1.3 63.6 + - - +
26F ALA* 3.0 3.3 + - - +
27F THR* 2.9 25.7 + - - -
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F ALA 3.1 12.1 + - - +
21F GLY* 3.2 9.2 + - - +
23F GLY* 1.3 73.4 - - - +
25F VAL* 1.3 64.6 + - + +
27F THR* 3.1 11.4 + - - -
28F GLY* 3.0 21.0 + - - -
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Residues in contact with VAL 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E PHE* 3.1 29.2 - - + -
21F GLY 3.0 18.6 + - - +
22F ALA* 3.2 13.9 - - - +
24F ALA* 1.3 78.0 - - + +
26F ALA* 1.3 65.3 + - - +
28F GLY* 3.3 1.6 + - - -
29F ALA* 3.0 17.5 + - - +
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Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E PHE* 4.0 21.3 - - + -
237E LEU* 6.2 2.0 - - + -
240E LEU* 4.6 15.7 - - + -
22F ALA 3.0 6.4 + - - +
23F GLY 3.0 9.0 + - - +
25F VAL* 1.3 76.0 - - - +
27F THR* 1.3 58.6 + - - +
29F ALA* 2.5 35.5 + - - +
30F ALA* 3.0 10.5 + - - +
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Residues in contact with THR 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F GLY 2.9 15.2 + - - -
24F ALA* 3.2 14.6 - - - +
26F ALA* 1.3 75.4 - - - +
28F GLY* 1.3 62.3 + - - +
30F ALA* 3.1 9.7 - - - +
31F VAL* 3.1 33.5 + - + +
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Residues in contact with GLY 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ALA 3.0 12.7 + - - -
25F VAL 3.7 2.9 - - - -
26F ALA 2.8 1.0 + - - -
27F THR* 1.3 71.1 - - - +
29F ALA* 1.3 58.9 + - - +
30F ALA 2.9 5.5 + - - -
31F VAL* 3.0 9.8 + - - +
32F TRP* 2.8 33.0 + - - +
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Residues in contact with ALA 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E PHE* 4.3 20.4 - - + -
25F VAL 3.0 12.0 + - - +
26F ALA* 2.5 21.8 + - - +
28F GLY* 1.3 71.6 - - - +
30F ALA* 1.3 53.7 + - - -
32F TRP* 5.0 2.7 - - - -
33F PRO* 2.9 24.1 - - - +
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ALA 3.0 6.6 + - - +
27F THR* 3.1 14.1 - - - +
28F GLY 2.9 0.2 - - - -
29F ALA* 1.3 76.4 - - - +
31F VAL* 1.3 63.8 + - + +
33F PRO* 2.8 25.1 - - - +
34F LEU* 3.4 17.1 + - + +
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Residues in contact with VAL 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F THR* 3.2 25.8 - - + +
28F GLY* 3.0 10.1 + - - +
30F ALA* 1.3 77.2 - - + +
32F TRP* 1.3 69.4 + - - +
34F LEU* 3.0 23.0 + - + +
35F ILE* 3.1 34.3 + - + +
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Residues in contact with TRP 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F GLY 2.8 17.9 + - - +
29F ALA* 4.5 3.6 - - - +
31F VAL* 1.3 73.5 - - - +
33F PRO* 1.3 64.1 - - + +
35F ILE* 2.7 34.5 + - + +
36F ASN* 2.6 71.5 + - + +
39F ASN* 4.3 6.1 - - - -
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Residues in contact with PRO 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ASN 4.6 4.5 - - - +
89D GLY* 6.1 4.5 - - - -
93D LEU* 4.8 10.3 - - + +
29F ALA 2.9 23.3 - - - +
30F ALA* 2.8 26.5 - - - +
32F TRP* 1.3 92.7 - - + +
34F LEU* 1.3 61.9 + - + +
36F ASN* 3.8 8.7 - - + +
37F GLN* 3.0 27.2 + - - +
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 3.9 35.9 - - + -
61D THR* 4.9 2.5 - - + -
64D VAL* 4.0 20.4 - - + +
93D LEU* 4.5 17.5 - - + -
30F ALA* 3.5 17.3 - - + +
31F VAL* 3.0 18.9 + - + +
33F PRO* 1.3 79.1 - - + +
35F ILE* 1.3 60.4 + - + +
37F GLN* 3.0 28.2 + - - +
38F MET* 5.4 1.0 - - - +
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Residues in contact with ILE 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A TRP* 3.1 49.9 + - + +
31F VAL* 3.2 33.7 - - + +
32F TRP* 2.7 28.0 + - + +
34F LEU* 1.3 79.1 - - + +
36F ASN* 1.3 68.0 + - - +
37F GLN 3.1 1.6 - - - -
38F MET* 3.0 15.1 + - - +
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Residues in contact with ASN 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ASN* 3.1 27.6 + - + +
32F TRP* 2.6 54.9 + - + +
33F PRO* 4.2 6.3 - - + -
35F ILE* 1.3 73.7 - - - +
37F GLN* 1.3 54.3 + - - +
38F MET 2.9 0.2 - - - -
39F ASN* 2.6 60.5 + - - +
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Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D VAL* 3.5 25.5 - - + +
67D MET* 3.6 15.2 - - - +
68D HIS* 2.7 38.8 + - - -
87D VAL* 3.7 18.4 - - + +
88D ASN* 3.6 24.5 + - - +
93D LEU* 4.1 12.8 - - + -
33F PRO 3.0 15.7 + - - +
34F LEU* 3.0 27.1 + - - +
36F ASN* 1.3 75.3 - - - +
38F MET* 1.3 85.2 + - - +
39F ASN 3.2 7.2 + - - +
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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