Contacts of the helix formed by residues 9 - 37 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250K ARG* 5.6 1.0 - - - +
10L THR* 1.3 59.3 + - - -
11L ARG* 3.2 25.4 + - - +
12L ARG* 3.6 42.0 + - - +
13L ASP* 3.9 5.7 - - - +
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Residues in contact with THR 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L GLY* 1.3 71.8 - - - -
11L ARG* 1.3 59.4 + - - +
12L ARG 3.5 0.9 - - - -
13L ASP* 3.7 15.7 + - + +
14L PHE* 3.1 35.7 - - + +
17L TYR* 6.3 0.4 - - + -
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Residues in contact with ARG 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K ARG* 4.5 18.0 + - - +
9L GLY* 3.2 17.6 - - - +
10L THR* 1.3 81.7 - - - +
12L ARG* 1.3 63.0 + - - +
14L PHE* 3.6 7.0 + - - +
15L LEU* 3.6 15.6 + - - +
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Residues in contact with ARG 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250K ARG* 2.7 50.5 - - - +
9L GLY* 3.6 33.8 + - - +
11L ARG* 1.3 78.1 - - - +
13L ASP* 1.3 70.3 + - + +
15L LEU* 3.1 6.0 + - - +
16L TYR* 2.9 45.2 + - + -
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Residues in contact with ASP 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L GLY 3.9 5.6 - - - +
10L THR* 3.7 25.8 + - + +
11L ARG 3.4 0.2 - - - -
12L ARG* 1.3 81.6 - - + +
14L PHE* 1.3 65.1 + - - +
16L TYR* 3.4 13.2 + - - +
17L TYR* 3.0 58.7 + - - -
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Residues in contact with PHE 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243K LEU* 6.4 0.7 - - + -
10L THR* 3.1 31.4 + - + +
11L ARG* 3.7 7.9 - - - +
12L ARG 3.1 0.6 - - - -
13L ASP* 1.3 75.4 - - - +
15L LEU* 1.3 70.8 + - + +
17L TYR* 2.8 9.1 + - + +
18L ALA* 2.7 55.9 + - + -
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Residues in contact with LEU 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243K LEU* 4.2 19.3 - - + +
246K LEU* 3.8 32.5 - - + +
247K THR* 3.6 38.6 - - - +
250K ARG* 4.4 17.3 - - + +
11L ARG 3.6 7.3 + - - +
12L ARG* 3.1 9.8 + - - +
14L PHE* 1.3 91.7 - - + +
16L TYR* 1.3 54.6 + - + +
18L ALA* 2.9 4.7 + - + +
19L THR* 2.7 37.4 + - - +
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Residues in contact with TYR 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250J ILE* 6.1 0.7 - - + -
247K THR* 4.3 25.1 - - + -
250K ARG* 4.1 24.4 + - - +
251K LEU* 4.4 25.9 - - + +
12L ARG* 2.9 38.4 + - + +
13L ASP* 3.6 17.0 - - - +
14L PHE 3.2 0.2 - - - -
15L LEU* 1.3 79.2 - - + +
17L TYR* 1.3 62.8 + - + +
19L THR* 3.7 7.3 - - - +
20L ALA* 3.1 28.8 + - - +
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Residues in contact with TYR 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L THR* 6.3 0.7 - - + -
13L ASP* 3.0 52.1 + - - +
14L PHE* 2.8 8.9 + - + +
16L TYR* 1.3 78.0 - - + +
18L ALA* 1.3 64.1 + - - +
19L THR 3.2 1.8 - - - -
20L ALA* 4.2 7.5 - - + +
21L GLY* 3.3 17.2 + - - -
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Residues in contact with ALA 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K LEU* 3.7 23.2 - - + +
14L PHE* 2.7 43.9 + - + +
15L LEU* 3.5 8.3 - - - +
17L TYR* 1.3 74.2 - - - +
19L THR* 1.3 62.6 + - - +
21L GLY* 3.5 1.8 + - - -
22L ALA* 3.2 17.0 + - - +
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Residues in contact with THR 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240K LEU* 4.5 4.0 - - + +
243K LEU* 3.4 26.5 - - - +
244K LEU* 4.0 20.8 + - + -
247K THR* 2.9 32.3 + - + +
15L LEU* 2.7 15.5 + - - +
16L TYR* 3.7 6.7 - - - +
18L ALA* 1.3 73.2 - - - +
20L ALA* 1.3 71.3 + - + +
21L GLY 2.7 4.9 + - - -
22L ALA* 2.8 15.5 + - - +
23L GLY* 3.0 9.5 + - - -
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Residues in contact with ALA 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L TYR 3.1 14.5 + - - +
17L TYR* 4.5 9.4 - - + +
19L THR* 1.3 84.2 - - + +
21L GLY* 1.3 60.7 + - - +
23L GLY* 3.4 2.9 + - - +
24L ALA* 3.0 24.1 + - - +
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Residues in contact with GLY 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L TYR 3.3 13.3 + - - -
18L ALA 3.7 4.3 - - - -
19L THR 2.7 3.2 + - - -
20L ALA* 1.3 76.5 - - - +
22L ALA* 1.3 65.0 + - - -
23L GLY 3.2 0.2 + - - -
24L ALA* 3.2 8.3 + - - +
25L VAL* 3.0 26.0 + - - +
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Residues in contact with ALA 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K PHE* 5.7 2.1 - - + +
239K VAL* 5.2 5.2 - - + -
240K LEU* 3.8 24.6 - - + +
243K LEU* 4.1 13.2 - - + -
18L ALA 3.2 10.6 + - - +
19L THR 2.8 10.6 + - - +
21L GLY* 1.3 70.5 - - - -
23L GLY* 1.3 68.9 + - - +
25L VAL* 3.1 12.7 + - - +
26L ALA* 3.0 20.4 + - - +
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Residues in contact with GLY 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240K LEU* 4.0 16.0 - - - +
19L THR 3.0 12.1 + - - -
20L ALA* 3.7 5.8 - - - -
22L ALA* 1.3 79.1 - - - +
24L ALA* 1.3 64.0 + - - +
26L ALA* 3.0 3.3 + - - +
27L THR* 2.9 26.5 + - - -
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Residues in contact with ALA 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20L ALA 3.0 12.7 + - - +
21L GLY* 3.2 9.8 + - - +
23L GLY* 1.3 72.4 - - - +
25L VAL* 1.3 64.7 + - - +
27L THR* 3.1 10.9 + - - -
28L GLY* 3.0 21.0 + - - -
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Residues in contact with VAL 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K PHE* 3.7 29.8 - - + -
21L GLY 3.0 17.5 - - - +
22L ALA* 3.2 13.9 - - - +
24L ALA* 1.3 76.2 - - + +
26L ALA* 1.3 64.6 + - - +
28L GLY* 3.2 1.9 + - - -
29L ALA* 3.0 19.1 + - - +
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Residues in contact with ALA 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K PHE* 5.0 18.4 - - + -
237K LEU* 6.1 2.2 - - + -
240K LEU* 4.4 17.5 - - + -
22L ALA 3.0 6.4 + - - +
23L GLY 3.0 8.4 + - - +
25L VAL* 1.3 77.3 - - - +
27L THR* 1.3 60.4 + - - +
29L ALA* 2.5 35.3 + - - +
30L ALA* 3.0 10.3 + - - +
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Residues in contact with THR 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L GLY 2.9 17.0 + - - -
24L ALA* 3.3 13.9 - - - +
26L ALA* 1.3 75.3 - - - +
28L GLY* 1.3 63.4 + - - +
30L ALA* 3.2 9.7 - - - +
31L VAL* 3.1 34.5 + - + +
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Residues in contact with GLY 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L ALA 3.0 13.7 + - - -
25L VAL 3.7 2.7 - - - -
26L ALA 2.8 1.0 + - - -
27L THR* 1.3 72.3 - - - +
29L ALA* 1.3 58.4 + - - +
30L ALA 2.9 6.1 + - - -
31L VAL* 3.0 9.2 + - - +
32L TRP* 2.8 33.7 + - - +
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Residues in contact with ALA 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K PHE* 4.1 28.0 - - + -
25L VAL* 3.0 12.4 + - + +
26L ALA* 2.5 18.4 + - - +
28L GLY* 1.3 71.1 - - - +
30L ALA* 1.3 53.8 + - - -
32L TRP* 4.5 3.1 - - - +
33L PRO* 2.9 23.7 - - - +
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Residues in contact with ALA 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L ALA 3.0 7.2 + - - +
27L THR* 3.2 13.7 - - - +
28L GLY 2.9 0.2 - - - -
29L ALA* 1.3 76.2 - - - +
31L VAL* 1.3 69.7 + - + +
33L PRO* 2.8 20.6 - - - +
34L LEU* 3.4 17.3 + - + +
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Residues in contact with VAL 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L THR* 3.2 25.1 - - + +
28L GLY* 3.5 10.3 - - - +
30L ALA* 1.3 76.7 - - + +
32L TRP* 1.3 67.8 + - - +
34L LEU* 3.0 24.4 + - + +
35L ILE* 3.0 34.2 + - + +
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Residues in contact with TRP 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L GLY 2.8 18.4 + - - +
29L ALA* 4.5 2.9 - - - +
31L VAL* 1.3 73.0 - - - +
33L PRO* 1.3 63.9 - - + +
35L ILE* 2.7 37.0 + - + +
36L ASN* 2.6 71.4 + - + +
39L ASN* 4.3 5.8 - - - -
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Residues in contact with PRO 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ASN 4.7 4.5 - - - +
89J GLY* 6.2 3.6 - - - -
93J LEU* 4.9 10.8 - - + +
29L ALA 2.9 23.3 - - - +
30L ALA* 2.8 26.0 - - - +
32L TRP* 1.3 92.4 - - + +
34L LEU* 1.3 60.7 + - + +
36L ASN* 3.8 9.0 - - + +
37L GLN* 3.0 26.2 + - - +
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J VAL* 3.9 35.0 - - + -
61J THR* 5.0 2.7 - - + +
64J VAL* 4.0 20.9 - - + +
93J LEU* 4.6 16.6 - - + -
30L ALA* 3.6 17.0 - - + +
31L VAL* 3.0 18.7 + - + +
33L PRO* 1.3 80.2 - - + +
35L ILE* 1.3 59.6 + - + +
37L GLN* 3.0 28.6 + - - +
38L MET* 5.1 0.5 - - - +
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Residues in contact with ILE 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G TRP* 3.3 44.9 + - + +
31L VAL* 3.3 33.0 - - + +
32L TRP* 2.7 28.2 + - + +
34L LEU* 1.3 79.5 - - + +
36L ASN* 1.3 67.9 + - - +
37L GLN 3.1 1.8 - - - -
38L MET* 3.0 15.2 + - - +
39L ASN* 5.8 0.4 - - - +
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Residues in contact with ASN 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88J ASN* 3.3 25.1 + - + +
32L TRP* 2.6 54.9 + - + +
33L PRO* 3.6 6.5 + - + -
35L ILE* 1.3 74.4 - - - +
37L GLN* 1.3 53.9 + - - +
38L MET 2.9 0.2 - - - -
39L ASN* 2.6 63.1 + - - +
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Residues in contact with GLN 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J VAL* 3.5 25.3 - - + +
67J MET* 3.6 16.1 - - - +
68J HIS* 2.8 40.5 + - - -
87J VAL* 3.8 11.1 - - + +
88J ASN* 3.7 25.1 + - - +
93J LEU* 4.1 12.8 - - + -
33L PRO 3.0 15.0 + - - +
34L LEU* 3.0 31.0 + - - +
36L ASN* 1.3 74.7 - - - +
38L MET* 1.3 89.8 + - - +
39L ASN 3.5 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) + - + + + + + -
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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