Contacts of the helix formed by residues 25 - 52 (chain C) in PDB entry 2Q9Q
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 ASN 25 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLU* 5.2 4.9 + - - +
9C LEU* 3.4 29.4 - - + +
12C GLU* 3.3 29.0 + - - +
23C ALA 3.3 1.5 + - - -
24C PHE* 1.3 75.2 - - - +
26C GLU* 1.3 61.1 + - - +
27C ASP* 3.8 5.7 + - - +
28C GLY* 2.7 30.0 + - - -
29C LEU* 2.9 21.1 + - - +
79C TYR* 2.9 17.4 + - - +
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C PHE* 3.1 36.0 + - + +
25C ASN* 1.3 70.4 - - - +
27C ASP* 1.3 59.7 + - - +
29C LEU* 3.0 5.8 + - - +
30C ARG* 2.8 30.4 + - - +
107C ALA* 5.7 3.5 - - - +
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Residues in contact with ASP 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN* 3.3 5.3 + - - +
26C GLU* 1.3 78.0 - - - +
28C GLY* 1.3 58.4 + - - +
30C ARG* 3.0 32.6 + - - +
31C GLN* 2.9 43.5 + - - +
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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
----------------------------------------------------------
5C LYS* 3.9 21.6 - - - +
9C LEU* 4.3 9.6 - - - -
25C ASN* 2.7 29.7 + - - -
27C ASP* 1.3 74.5 - - - +
29C LEU* 1.3 61.2 + - - +
31C GLN* 5.0 0.9 - - - +
32C VAL* 3.1 30.4 + - - +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL* 4.1 24.5 - - + +
145B ALA* 4.7 4.3 - - + -
9C LEU* 4.5 11.8 - - + +
24C PHE* 3.7 31.2 - - + -
25C ASN 2.9 13.6 + - - +
26C GLU* 3.5 8.3 - - - +
28C GLY* 1.3 73.2 - - - +
30C ARG* 1.3 66.8 + - - +
32C VAL* 3.3 3.7 + - - +
33C LEU* 3.0 43.1 + - + +
76C THR* 4.1 28.0 - - + +
79C TYR* 5.2 2.7 - - + -
80C LEU* 4.6 13.7 - - + -
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Residues in contact with ARG 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 GLU 2.8 12.5 + - - +
27C ASP* 3.0 39.4 + - - +
29C LEU* 1.3 75.4 - - - +
31C GLN* 1.3 78.5 + - - +
33C LEU* 3.1 11.7 + - - +
34C GLU* 2.9 60.0 + - + +
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Residues in contact with GLN 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS* 3.0 46.2 + - + +
27C ASP* 2.9 30.5 + - - +
28C GLY 5.0 0.2 - - - +
30C ARG* 1.3 92.9 - - - +
32C VAL* 1.3 58.4 + - - +
34C GLU* 3.7 12.2 - - - +
35C GLU* 3.1 26.2 + - - +
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS* 3.6 20.2 - - + -
6C ALA* 3.8 21.8 - - + +
9C LEU* 4.3 7.6 - - + -
28C GLY 3.1 20.4 + - - +
29C LEU* 3.7 5.2 - - - +
30C ARG 3.1 0.6 - - - -
31C GLN* 1.3 71.7 - - - +
33C LEU* 1.3 68.0 + - + +
34C GLU 3.1 1.6 - - - -
35C GLU* 3.2 6.5 + - - +
36C MET* 3.0 24.5 + - - +
72C ASN* 3.9 24.5 - - + +
76C THR* 3.5 31.2 - - + -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B VAL 4.7 4.7 - - - +
145B ALA* 4.1 11.9 - - + +
148B HIS* 3.7 42.3 - - + +
149B MET* 4.0 34.8 - - + -
150B PRO* 5.5 0.7 - - - +
29C LEU* 3.0 38.5 + - + +
30C ARG* 3.1 7.8 + - + +
32C VAL* 1.3 79.0 - - + +
34C GLU* 1.3 62.3 + - + +
36C MET* 3.6 10.6 + - - +
37C LYS* 3.2 20.1 + - - +
76C THR* 5.3 0.9 - - + -
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ARG* 2.9 54.7 + - + +
31C GLN* 3.7 10.8 - - - +
33C LEU* 1.3 75.6 - - + +
35C GLU* 1.3 60.9 + - - +
37C LYS* 2.9 16.1 + - + +
38C ALA* 2.8 29.3 + - - +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 4.6 3.3 - - - +
2C PHE* 4.1 20.0 - - + -
3C CYS* 3.3 23.2 + - - -
4C GLU 4.9 1.4 + - - -
5C LYS* 4.9 11.4 - - - +
31C GLN 3.1 12.7 + - - +
32C VAL* 3.2 10.3 + - - +
34C GLU* 1.3 76.7 - - - +
36C MET* 1.3 53.1 + - - +
38C ALA* 3.2 7.7 + - + +
39C LEU* 2.7 51.5 + - + +
72C ASN* 2.7 34.4 + - - +
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Residues in contact with MET 36 (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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149B MET* 3.5 48.9 - - + -
150B PRO* 4.1 17.5 - - + -
153B LEU* 4.1 11.7 - - + -
32C VAL* 3.0 23.6 + - - +
33C LEU* 3.6 13.5 - - - +
35C GLU* 1.3 76.0 - - - +
37C LYS* 1.3 52.7 + - - +
39C LEU* 3.3 2.2 + - - -
40C TYR* 2.8 33.8 + - - +
69C LEU* 3.2 35.7 - - + +
72C ASN* 3.6 29.8 - - + +
73C ARG* 3.9 8.1 - - + -
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Residues in contact with LYS 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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150B PRO* 4.4 6.7 - - + +
33C LEU 3.2 10.0 + - - +
34C GLU* 2.9 17.2 + - + +
36C MET* 1.3 79.6 - - - +
38C ALA* 1.3 57.5 + - + +
40C TYR* 3.6 7.6 - - + +
41C GLU* 2.8 65.8 + - + +
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Residues in contact with ALA 38 (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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34C GLU 2.8 16.7 + - - +
35C GLU* 3.5 11.0 - - + +
37C LYS* 1.3 74.4 - - + +
39C LEU* 1.3 57.8 + - + +
41C GLU* 3.1 11.2 + - - +
42C GLN* 2.8 48.4 + - + +
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Residues in contact with LEU 39 (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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2C PHE* 3.4 39.7 - - + -
35C GLU* 2.7 35.6 + - + +
36C MET 3.6 3.6 - - - +
38C ALA* 1.3 72.3 - - + +
40C TYR* 1.3 57.2 + - - +
42C GLN* 3.5 6.8 + - - +
43C ASN* 2.9 32.1 + - - +
65C ARG* 4.1 28.1 - - + +
68C SER* 3.7 22.4 - - - -
69C LEU* 3.8 15.0 - - + +
72C ASN* 3.6 27.4 - - - +
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Residues in contact with TYR 40 (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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150B PRO* 3.7 21.8 - - + -
151B PRO* 4.1 26.3 - - + +
152B ASN* 3.2 34.6 + - - -
36C MET 2.8 21.7 + - - +
37C LYS* 3.6 6.1 - - + +
39C LEU* 1.3 71.3 - - - +
41C GLU* 1.3 70.3 + - + +
43C ASN* 3.8 3.4 - - + +
44C GLN* 2.9 64.2 + - + +
69C LEU* 4.1 15.8 - - + +
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Residues in contact with GLU 41 (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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37C LYS* 2.8 57.9 + - + +
38C ALA* 3.1 8.9 + - - +
40C TYR* 1.3 81.9 - - + +
42C GLN* 1.3 67.2 + - + +
44C GLN* 3.2 7.6 + - - +
45C SER* 3.1 22.2 + - - -
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Residues in contact with GLN 42 (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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2C PHE* 4.5 14.0 - - - -
38C ALA* 2.8 39.8 + - + +
39C LEU* 3.8 6.7 - - - +
41C GLU* 1.3 72.0 - - + +
43C ASN* 1.3 64.1 + - - +
45C SER* 3.1 16.3 + - - -
46C ASP* 3.1 17.7 + - - +
65C ARG* 3.2 39.7 + - - +
47D PHE* 5.8 2.1 - - - -
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Residues in contact with ASN 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU 2.9 18.7 + - - +
40C TYR* 3.8 7.2 - - + +
42C GLN* 1.3 78.2 - - - +
44C GLN* 1.3 58.2 + - - +
45C SER 3.0 0.2 - - - -
46C ASP* 3.4 2.0 + - - +
47C VAL* 3.0 31.9 + - - +
62C ILE* 3.0 50.8 + - - +
65C ARG* 2.8 33.5 - - + +
66C HIS* 4.1 12.5 + - - +
69C LEU* 5.1 5.1 - - + +
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Residues in contact with GLN 44 (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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40C TYR* 2.9 53.7 + - + +
41C GLU* 3.2 7.8 + - - +
43C ASN* 1.3 77.6 - - - +
45C SER* 1.3 56.8 + - - +
47C VAL* 2.8 29.4 - - - +
48C ASN* 2.9 18.4 + - - +
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU 3.1 9.7 + - - -
42C GLN* 3.1 12.1 + - - -
43C ASN 3.0 0.6 - - - -
44C GLN* 1.3 76.6 - - - +
46C ASP* 1.3 69.5 + - - +
47C VAL 3.2 1.1 - - - -
48C ASN* 3.0 28.0 + - - +
49C GLU* 3.4 19.2 + - - +
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLN 3.1 13.1 + - - +
43C ASN* 4.0 4.0 - - - +
45C SER* 1.3 78.3 + - - +
47C VAL* 1.3 58.5 + - - +
49C GLU* 3.2 18.1 + - - +
50C ALA* 2.9 26.5 + - - +
58C LEU* 3.5 19.9 - - + +
61C THR* 4.4 6.1 - - - +
62C ILE* 4.3 14.1 - - + +
65C ARG* 3.5 28.8 + - - +
42D ARG* 3.8 28.2 + - - +
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Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ASN 3.0 11.7 + - - +
44C GLN* 2.8 52.0 - - - +
46C ASP* 1.3 76.6 - - - +
48C ASN* 1.3 66.8 + - - +
50C ALA* 3.3 3.6 + - + +
51C LYS* 2.9 48.1 + - + +
62C ILE* 4.2 21.0 - - + +
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLN* 2.9 24.1 + - - +
45C SER* 3.0 14.2 + - - +
47C VAL* 1.3 84.5 - - - +
49C GLU* 1.3 59.5 + - + +
51C LYS* 2.8 12.7 + - - +
52C SER* 2.8 30.8 + - - +
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C SER* 3.7 19.0 + - - +
46C ASP* 3.2 24.2 + - - +
48C ASN* 1.3 75.6 - - + +
50C ALA* 1.3 64.4 + - - +
52C SER* 3.2 13.2 + - - -
53C GLY 3.3 7.4 + - - +
54C GLY* 2.6 40.3 + - - +
58C LEU* 3.9 10.6 - - + +
42D ARG* 3.3 25.2 + - - -
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASP 2.9 13.8 + - - +
47C VAL* 3.4 13.9 - - + +
49C GLU* 1.3 77.4 - - - +
51C LYS* 1.3 66.0 + - + +
54C GLY 5.1 1.0 - - - +
55C ARG* 3.7 28.8 - - - +
56C SER* 4.8 7.8 + - - -
58C LEU* 4.4 2.8 - - + +
59C ILE* 5.1 5.4 - - + -
62C ILE* 4.2 14.8 - - + -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C VAL* 2.9 38.1 + - + +
48C ASN* 2.8 12.3 + - - +
50C ALA* 1.3 82.6 - - - +
52C SER* 1.3 70.3 + - - +
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ASN 2.8 17.3 + - - +
49C GLU* 3.2 7.0 + - - -
50C ALA 4.7 0.2 - - - -
51C LYS* 1.3 86.7 + - - +
53C GLY* 1.3 58.8 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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