Contacts of the helix formed by residues 9 - 37 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B ARG* 5.7 2.2 - - - +
10C THR* 1.3 59.0 + - - -
11C ARG* 3.2 26.6 + - - +
12C ARG* 3.5 39.7 + - - +
13C ASP* 3.9 8.3 + - - +
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Residues in contact with THR 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY* 1.3 70.4 - - - -
11C ARG* 1.3 60.2 + - - +
12C ARG 3.5 0.4 - - - -
13C ASP* 3.7 17.0 + - + +
14C PHE* 3.1 35.7 - - + +
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Residues in contact with ARG 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ARG* 5.1 9.0 - - - +
9C GLY* 3.2 17.1 - - - +
10C THR* 1.3 82.1 - - - +
12C ARG* 1.3 64.1 + - + +
14C PHE* 3.6 7.3 - - - +
15C LEU* 3.6 15.4 + - - +
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Residues in contact with ARG 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ARG* 2.7 52.7 - - - +
9C GLY* 3.5 33.5 + - - +
11C ARG* 1.3 77.0 - - - +
13C ASP* 1.3 80.7 + - + +
15C LEU* 3.1 7.3 + - - +
16C TYR* 2.9 46.5 + - + -
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Residues in contact with ASP 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY 3.9 5.8 - - - +
10C THR* 3.7 27.2 + - + +
12C ARG* 1.3 88.8 + - + +
14C PHE* 1.3 61.4 + - - +
16C TYR* 3.3 11.1 + - - +
17C TYR* 3.0 58.4 + - - -
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Residues in contact with PHE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 3.1 29.5 + - + +
11C ARG* 3.6 7.6 - - - +
12C ARG 3.1 0.2 - - - -
13C ASP* 1.3 74.5 - - - +
15C LEU* 1.3 61.1 + - + +
17C TYR* 2.8 9.0 + - + +
18C ALA* 2.7 51.7 + - + +
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU* 3.9 22.7 - - + +
246B LEU* 3.7 46.7 - - + -
247B THR* 3.8 23.8 - - - +
250B ARG* 4.7 14.8 - - - -
11C ARG 3.6 7.9 + - - +
12C ARG* 3.1 9.4 + - - +
14C PHE* 1.3 89.3 - - + +
16C TYR* 1.3 56.0 + - + +
18C ALA* 2.9 5.2 + - + +
19C THR* 2.8 36.9 + - - +
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Residues in contact with TYR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B THR* 4.3 27.1 + - + -
250B ARG* 4.0 28.0 + - - +
251B LEU* 4.6 20.2 + - + +
12C ARG* 2.9 40.6 + - + -
13C ASP* 3.5 17.7 - - - +
15C LEU* 1.3 81.2 - - + +
17C TYR* 1.3 65.5 + - + +
19C THR* 3.7 7.0 - - - +
20C ALA* 3.1 27.5 + - - +
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Residues in contact with TYR 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASP* 3.0 53.4 + - - +
14C PHE* 2.8 8.2 + - + +
16C TYR* 1.3 80.2 - - + +
18C ALA* 1.3 64.3 + - - +
19C THR 3.2 1.6 - - - -
20C ALA* 4.5 7.2 - - + +
21C GLY* 3.3 17.2 + - - -
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Residues in contact with ALA 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LEU* 3.6 22.0 - - + +
14C PHE* 2.7 37.1 + - + +
15C LEU* 3.5 11.4 - - - +
17C TYR* 1.3 73.0 - - - +
19C THR* 1.3 62.7 + - - +
21C GLY* 3.5 1.6 + - - -
22C ALA* 3.2 17.5 + - - +
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Residues in contact with THR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 4.5 4.6 - - + +
243B LEU* 3.1 34.1 - - + +
244B LEU* 4.8 18.6 - - + -
247B THR* 3.3 26.1 + - + +
15C LEU* 2.8 15.2 + - - +
16C TYR* 3.7 7.4 - - - +
18C ALA* 1.3 73.4 - - - +
20C ALA* 1.3 72.0 + - + +
21C GLY 2.7 5.2 + - - -
22C ALA* 2.8 15.4 + - - +
23C GLY* 3.0 9.2 + - - -
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C TYR 3.1 14.7 + - - +
17C TYR* 4.5 11.2 - - + +
19C THR* 1.3 83.9 - - + +
21C GLY* 1.3 62.5 + - - +
23C GLY* 3.7 3.2 - - - +
24C ALA* 3.1 23.6 + - - +
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR 3.3 13.5 + - - -
18C ALA 3.7 4.9 - - - -
19C THR 2.7 2.8 + - - -
20C ALA* 1.3 76.2 - - - +
22C ALA* 1.3 63.3 + - - -
23C GLY 3.2 0.3 + - - -
24C ALA* 3.2 8.3 + - - +
25C VAL* 3.1 26.0 + - - +
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Residues in contact with ALA 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 5.5 5.0 - - + +
239B VAL* 5.0 6.7 - - + -
240B LEU* 4.1 22.1 - - + +
243B LEU* 4.2 11.7 - - + -
18C ALA 3.2 11.2 + - - +
19C THR 2.8 10.2 + - - +
21C GLY* 1.3 71.1 - - - +
23C GLY* 1.3 68.4 + - - +
25C VAL* 3.1 12.4 + - - +
26C ALA* 3.0 20.3 + - - +
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Residues in contact with GLY 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 4.1 18.7 - - - +
19C THR 3.0 11.5 + - - -
20C ALA* 3.7 5.6 - - - -
22C ALA* 1.3 79.5 - - - +
24C ALA* 1.3 64.4 + - - +
26C ALA* 3.0 2.8 + - - +
27C THR* 2.9 25.9 + - - -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA 3.1 12.0 + - - +
21C GLY* 3.5 9.4 - - - +
23C GLY* 1.3 74.6 - - - +
25C VAL* 1.3 64.2 + - + +
27C THR* 3.2 10.4 + - - +
28C GLY* 3.0 20.4 + - - -
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Residues in contact with VAL 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE* 3.6 27.4 - - + -
21C GLY 3.1 18.6 + - - +
22C ALA* 3.1 13.2 + - - +
24C ALA* 1.3 75.9 - - + +
26C ALA* 1.3 64.3 + - - +
28C GLY* 3.3 2.1 + - - -
29C ALA* 3.0 18.5 + - - +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE* 4.7 21.9 - - + -
237B LEU* 6.2 1.6 - - + -
240B LEU* 4.7 16.8 - - + -
22C ALA 3.0 7.4 + - - +
23C GLY* 3.4 7.9 - - - +
25C VAL* 1.3 76.8 - - - +
27C THR* 1.3 59.8 + - - +
29C ALA* 2.5 34.7 + - - +
30C ALA* 3.0 10.3 + - - +
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C GLY 2.9 19.9 + - - -
24C ALA* 3.3 13.5 - - - -
26C ALA* 1.3 73.0 - - - +
28C GLY* 1.3 63.1 + - - +
30C ALA* 3.2 9.0 + - - +
31C VAL* 3.1 35.0 + - + +
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Residues in contact with GLY 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA 3.0 13.7 + - - -
25C VAL 3.8 2.7 - - - -
26C ALA 2.8 1.0 + - - -
27C THR* 1.3 71.9 - - - +
29C ALA* 1.3 57.4 + - - +
30C ALA 2.9 5.5 + - - -
31C VAL* 3.0 9.2 + - - +
32C TRP* 2.8 33.6 + - - +
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE* 3.9 30.3 - - + -
25C VAL 3.0 12.6 + - - +
26C ALA* 2.5 16.5 + - - +
28C GLY* 1.3 71.8 - - - +
30C ALA* 1.3 54.0 + - - -
32C TRP* 4.5 2.6 - - - +
33C PRO* 2.9 23.3 - - - +
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Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA 3.0 7.2 + - - +
27C THR* 3.2 13.5 - - - +
28C GLY 2.9 0.4 - - - -
29C ALA* 1.3 76.0 - - - +
31C VAL* 1.3 68.9 - - + +
33C PRO* 2.8 21.0 - - - +
34C LEU* 3.4 16.7 + - + +
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Residues in contact with VAL 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C THR* 3.2 24.9 - - + +
28C GLY* 3.5 9.9 - - - +
30C ALA* 1.3 76.9 - - + +
32C TRP* 1.3 67.9 + - - +
34C LEU* 3.0 22.0 + - + +
35C ILE* 3.1 34.4 + - + +
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Residues in contact with TRP 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLY 2.8 16.9 + - - +
29C ALA* 4.5 3.4 - - - +
31C VAL* 1.3 73.9 - - - +
33C PRO* 1.3 63.2 - - + +
35C ILE* 2.7 35.3 + - + +
36C ASN* 2.6 69.2 + - + +
39C ASN* 4.3 6.5 - - - -
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Residues in contact with PRO 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ASN 4.6 5.2 - - - +
89A GLY* 6.0 4.5 - - - -
93A LEU* 5.0 10.1 - - + +
29C ALA 2.9 23.3 - - - +
30C ALA* 2.8 26.7 - - - +
32C TRP* 1.3 92.4 - - + +
34C LEU* 1.3 60.8 + - + +
36C ASN* 4.1 9.2 - - + +
37C GLN* 3.1 25.8 + - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 4.1 29.2 - - + -
61A THR* 5.1 1.8 - - + -
64A VAL* 4.0 23.6 - - + +
93A LEU* 4.5 18.2 - - + -
30C ALA* 3.7 17.7 - - + +
31C VAL* 3.0 18.2 + - + +
33C PRO* 1.3 79.0 - - + +
35C ILE* 1.3 60.1 + - + +
37C GLN* 3.0 29.3 + - - +
38C MET* 5.1 0.7 - - - +
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Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C VAL* 3.2 34.3 - - + +
32C TRP* 2.7 28.5 + - + +
34C LEU* 1.3 79.0 - - + +
36C ASN* 1.3 66.9 + - - +
37C GLN 3.1 1.3 - - - -
38C MET* 3.0 14.4 + - - +
39C ASN* 5.8 0.2 - - - +
179D TRP* 3.2 46.9 + - + +
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Residues in contact with ASN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 3.1 27.5 + - + +
32C TRP* 2.6 53.4 + - + +
33C PRO* 3.5 6.9 + - + -
35C ILE* 1.3 75.1 - - - +
37C GLN* 1.3 52.1 + - - +
38C MET 2.9 0.2 - - - -
39C ASN* 2.7 61.2 + - - +
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 3.6 26.0 - - + +
67A MET* 3.7 16.1 - - - +
68A HIS* 2.8 37.4 + - - -
87A VAL* 3.8 21.1 - - + +
88A ASN* 3.6 25.7 + - - +
93A LEU* 4.2 9.0 - - + -
33C PRO 3.1 14.9 + - - +
34C LEU* 3.0 29.9 + - - +
36C ASN* 1.3 76.5 - - - +
38C MET* 1.3 90.5 + - - +
39C ASN 3.4 7.4 + - - +
41C SER* 6.2 0.2 - - - -
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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