Contacts of the helix formed by residues 15 - 39 (chain P) in PDB entry 1TQE
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 ARG 15 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D T 3.4 44.5 + - + +
13P ASP* 2.9 21.8 + - - +
14P GLN* 1.3 85.0 + - + +
16P ASN* 1.3 59.4 + - - +
18P GLN* 3.1 19.3 + - - +
19P VAL* 3.1 19.9 + - + +
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Residues in contact with ASN 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C A 5.2 14.3 - - - +
14C A 5.5 8.1 + - - -
11P ILE* 2.9 33.4 - - + +
13P ASP* 2.7 28.5 + - + +
15P ARG* 1.3 68.3 - - - +
17P ARG* 1.3 57.3 + - - +
18P GLN 3.0 5.2 - - - -
19P VAL* 3.9 10.0 - - - +
20P THR* 3.0 40.9 + - - -
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Residues in contact with ARG 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P ARG* 2.8 45.9 - - - +
11P ILE* 2.9 44.8 + - + +
12P LEU 3.3 20.8 + - - -
13P ASP 2.8 15.4 + - - +
14P GLN* 3.6 33.1 - - - +
16P ASN* 1.3 72.3 - - - +
18P GLN* 1.3 57.8 + - - +
21P PHE* 3.6 20.9 + - - +
50P SER* 5.1 8.7 + - - -
38Q LEU 4.1 7.9 - - - -
39Q CYS* 4.0 27.5 + - + +
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Residues in contact with GLN 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D T 5.8 8.5 - - + +
14P GLN* 3.4 18.0 + - + +
15P ARG* 3.1 6.4 + - - +
16P ASN 3.0 0.4 - - - -
17P ARG* 1.3 80.6 - - - +
19P VAL* 1.3 64.5 + - + +
20P THR 3.3 1.6 - - - -
21P PHE* 3.9 14.2 - - - +
22P THR* 3.4 30.8 + - - -
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Residues in contact with VAL 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C A 6.3 0.9 - - - +
1D T 5.2 12.6 - - + +
2D T 6.1 4.9 - - + -
3D G 6.3 0.9 - - - +
4D C 6.3 0.2 - - - +
15P ARG 3.1 19.3 + - - +
16P ASN* 3.9 11.0 - - - +
18P GLN* 1.3 78.2 - - + +
20P THR* 1.3 60.8 + - - +
22P THR* 3.5 4.6 + - - +
23P LYS* 3.1 50.4 + - + +
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Residues in contact with THR 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C A 3.7 25.2 + - - +
6P ILE* 6.0 0.2 - - + -
11P ILE* 3.6 26.4 - - + +
16P ASN* 3.0 25.6 + - - -
17P ARG 4.7 0.2 - - - -
19P VAL* 1.3 78.8 - - - +
21P PHE* 1.3 66.2 + - - +
23P LYS* 4.4 7.0 - - + -
24P ARG* 2.8 45.5 + - + +
38Q LEU* 4.6 3.8 - - + -
39Q CYS* 4.2 7.2 - - - -
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Residues in contact with PHE 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ARG 3.6 13.0 + - - +
18P GLN* 3.7 16.0 + - - +
19P VAL 3.4 0.6 - - - -
20P THR* 1.3 76.2 - - - +
22P THR* 1.3 67.2 + - - +
25P LYS* 2.9 65.0 + - + +
47P ILE* 4.1 15.7 - - + -
49P ASN* 4.4 18.2 - - + -
55P PHE* 3.9 28.7 - + - -
35Q LEU* 3.9 11.3 - - + +
39Q CYS* 3.4 37.3 - - + -
41Q CYS* 3.8 21.5 - - + -
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Residues in contact with THR 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P GLN* 3.4 25.5 + - - -
19P VAL* 3.8 8.3 - - - +
20P THR 3.2 0.6 - - - -
21P PHE* 1.3 85.8 - - - +
23P LYS* 1.3 69.2 + - + +
25P LYS* 4.0 14.9 + - - +
26P PHE* 3.3 19.8 + - + +
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Residues in contact with LYS 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C T 4.4 22.7 + - + +
13C A 2.9 40.4 + - + +
14C A 3.1 24.9 + - - +
15C G 5.0 0.2 + - - -
4D C 4.8 8.5 - - - +
5D T 4.5 1.8 + - - -
19P VAL* 3.1 38.4 + - + +
20P THR* 3.7 6.5 - - + +
22P THR* 1.3 82.4 - - + +
24P ARG* 1.3 67.6 + - + +
26P PHE* 3.2 11.5 + - - +
27P GLY* 3.2 8.8 + - - -
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Residues in contact with ARG 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C T 3.6 34.0 + - - +
13C A 3.0 32.6 + - - +
6P ILE* 4.6 6.9 - - - +
8P ILE* 6.0 1.0 - - - +
20P THR* 2.8 29.7 + - + +
23P LYS* 1.3 71.9 - - + +
25P LYS* 1.3 69.1 + - - +
26P PHE 2.9 1.8 - - - -
27P GLY* 2.6 15.5 + - - +
28P LEU* 2.8 13.2 + - - -
31Q LYS* 4.3 11.3 + - - +
34Q GLU* 2.8 41.0 + - - +
35Q LEU* 4.2 20.2 - - + +
38Q LEU* 3.3 27.7 - - - +
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Residues in contact with LYS 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P PHE* 2.9 44.6 + - + +
22P THR* 4.0 17.0 + - - +
24P ARG* 1.3 71.9 - - - +
26P PHE* 1.3 75.3 + - - +
28P LEU* 3.4 2.8 + - - +
29P MET* 3.0 36.0 + - - +
47P ILE* 3.6 16.8 - - + -
55P PHE* 3.6 34.1 - - + -
35Q LEU* 3.6 19.3 - - + +
77Q GLU* 3.5 30.4 + - - +
79Q ARG* 5.1 2.6 - - - +
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Residues in contact with PHE 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22P THR 3.3 9.0 + - - +
23P LYS* 3.2 11.8 + - - +
24P ARG 2.6 4.6 + - - -
25P LYS* 1.3 80.5 - - - +
27P GLY* 1.3 57.5 + - - +
29P MET* 3.1 7.9 + - + +
30P LYS* 2.7 43.1 + - + +
79Q ARG* 3.4 31.0 - - - -
84Q ILE* 3.6 23.8 - - + -
87Q THR* 3.9 20.9 - - + -
88Q LEU* 3.5 35.7 - - + -
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Residues in contact with GLY 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C A 5.3 5.6 + - - -
12C T 4.1 19.3 - - - -
23P LYS 3.2 4.6 + - - -
24P ARG 2.6 11.4 + - - -
26P PHE* 1.3 79.2 - - - +
28P LEU* 1.3 60.7 + - - -
30P LYS* 3.0 14.0 + - - +
31P LYS* 2.9 28.4 + - - +
31Q LYS* 5.3 2.5 - - - -
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Residues in contact with LEU 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C T 5.2 0.4 + - - -
24P ARG 2.8 14.1 + - - +
25P LYS* 3.5 9.6 - - - +
27P GLY* 1.3 73.1 - - - +
29P MET* 1.3 63.9 + - - +
31P LYS* 3.0 5.5 + - - +
32P ALA* 2.9 19.6 + - - +
45P LEU* 3.8 30.3 - - + -
47P ILE* 4.4 6.1 - - + -
28Q LEU* 3.6 20.8 - - + +
31Q LYS* 3.4 22.7 - - + +
32Q ALA* 3.2 40.4 - - + +
35Q LEU* 3.7 24.7 - - + -
43Q ILE* 4.6 2.7 - - + -
45Q LEU* 6.1 0.2 - - + -
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Residues in contact with MET 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P LYS* 3.0 25.8 - - + +
26P PHE* 3.1 8.2 + - - +
28P LEU* 1.3 76.2 - - - +
30P LYS* 1.3 63.6 + - - +
32P ALA* 3.4 9.2 - - - +
33P TYR* 2.8 25.3 + - - +
45P LEU* 4.0 16.4 - - + +
47P ILE* 4.8 8.5 - - + -
55P PHE 4.7 1.6 - - - -
56P GLN* 2.9 45.5 - - - +
57P TYR* 3.2 20.3 - - + -
77Q GLU* 4.2 10.5 - - - +
79Q ARG* 3.8 26.2 - - + -
84Q ILE* 4.1 14.3 - - + +
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Residues in contact with LYS 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C T 4.2 1.8 + - - -
11C A 2.5 43.8 + - - +
26P PHE* 2.7 29.2 + - + +
27P GLY* 3.2 14.4 - - - +
29P MET* 1.3 75.4 - - - +
31P LYS* 1.3 58.0 + - - +
33P TYR* 3.2 13.6 - - + -
34P GLU* 2.8 43.9 + - + +
84Q ILE* 4.5 7.1 - - - +
88Q LEU* 4.3 38.2 - - + +
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Residues in contact with LYS 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C T 4.6 3.0 + - - -
11C A 4.0 36.3 + - - +
11D A 3.5 19.5 + - - -
12D T 3.1 31.9 + - - +
27P GLY 2.9 15.1 + - - +
28P LEU* 3.5 7.9 - - - +
30P LYS* 1.3 73.6 - - - +
32P ALA* 1.3 70.5 + - - +
34P GLU* 2.9 21.5 + - - +
35P LEU* 2.7 22.2 + - - +
24Q ARG* 4.4 6.6 + - - +
27Q GLY 5.3 0.9 - - - -
28Q LEU* 3.5 21.8 - - + +
31Q LYS* 4.2 21.8 - - + +
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Residues in contact with ALA 32 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P LEU 2.9 12.8 + - - +
29P MET* 3.4 12.1 - - - +
31P LYS* 1.3 79.6 - - - +
33P TYR* 1.3 64.4 + - - +
35P LEU* 2.9 2.6 + - - +
36P SER* 2.7 21.0 + - - -
43P ILE* 3.6 8.8 - - + +
45P LEU* 4.6 7.0 - - + -
57P TYR* 3.5 28.0 - - + -
28Q LEU* 3.1 24.7 - - + +
45Q LEU* 5.6 0.2 - - + -
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Residues in contact with TYR 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P MET 2.8 16.1 + - - +
30P LYS* 3.2 15.0 - - + +
32P ALA* 1.3 72.6 - - - +
34P GLU* 1.3 88.4 + - + +
36P SER* 3.0 3.5 - - - -
37P VAL* 3.0 37.0 + - + +
57P TYR* 3.0 7.2 + - + +
8Q ILE* 3.9 25.4 + - + +
81Q ASN* 2.8 56.5 - - + +
84Q ILE* 4.1 19.7 - - + -
85Q LEU* 3.9 28.5 - - + +
88Q LEU* 4.3 15.5 - - + -
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Residues in contact with GLU 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C T 5.1 1.8 - - - +
11C A 4.3 5.2 + - - -
30P LYS* 2.8 45.9 + - + +
31P LYS* 2.9 19.1 + - - +
33P TYR* 1.3 88.3 - - + +
35P LEU* 1.3 68.0 + - - +
37P VAL* 2.9 3.6 + - - +
38P LEU* 2.8 33.1 + - + +
8Q ILE* 4.3 23.4 - - + +
24Q ARG* 2.8 34.4 + - - +
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Residues in contact with LEU 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31P LYS 2.7 15.7 + - - +
32P ALA* 3.4 7.4 - - - +
34P GLU* 1.3 71.8 - - - +
36P SER* 1.3 62.6 + - - +
38P LEU* 4.5 6.7 - - - -
39P CYS* 3.1 43.7 + - - +
41P CYS* 3.7 5.9 - - - -
43P ILE* 4.0 8.1 - - + -
21Q PHE* 3.9 19.1 - - + +
24Q ARG* 4.0 25.1 - - + +
25Q LYS* 3.5 31.2 - - + +
28Q LEU* 3.8 21.3 - - + -
47Q ILE* 4.1 11.4 - - + -
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Residues in contact with SER 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P ALA 2.7 11.9 + - - -
33P TYR 3.0 10.1 - - - -
34P GLU 2.9 0.6 + - - -
35P LEU* 1.3 76.7 - - - +
37P VAL* 1.3 58.0 - - - +
40P ASP* 3.1 9.0 + - - -
41P CYS* 3.0 39.7 + - - +
43P ILE* 3.8 8.7 - - - +
57P TYR* 3.7 7.9 - - - -
59P SER* 3.0 25.7 - - - -
81Q ASN* 3.0 14.4 + - - -
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Residues in contact with VAL 37 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P TYR* 3.0 34.6 + - + +
34P GLU 2.9 6.7 + - - -
36P SER* 1.3 71.1 - - - +
38P LEU* 1.3 67.2 + - - +
40P ASP* 3.2 10.1 + - - +
8Q ILE* 3.5 37.0 - - + +
9Q SER* 3.6 10.3 - - - -
10Q ARG* 3.3 13.5 + - - +
81Q ASN* 4.3 9.9 - - + +
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Residues in contact with LEU 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P GLU* 2.8 24.0 + - + +
35P LEU 4.2 0.7 - - - +
37P VAL* 1.3 74.5 - - - +
39P CYS* 1.3 66.9 + - - +
40P ASP 3.5 0.5 + - - -
6Q ILE* 4.1 15.7 - - + -
7Q GLN 4.0 20.4 - - - +
8Q ILE* 4.2 15.5 - - + -
9Q SER 4.2 8.3 - - - +
10Q ARG* 3.3 1.9 - - - -
11Q ILE* 2.8 50.4 + - + +
17Q ARG* 3.9 1.0 - - - +
20Q THR* 4.6 3.6 - - + -
24Q ARG* 3.2 51.8 - - - +
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Residues in contact with CYS 39 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P LEU* 3.1 23.3 + - - +
36P SER 4.0 0.4 - - - -
38P LEU* 1.3 80.6 - - - +
40P ASP* 1.3 71.7 + - - +
41P CYS* 3.3 5.2 + - - +
11Q ILE* 4.8 0.2 - - - -
17Q ARG* 3.9 26.0 + - + +
20Q THR* 4.0 14.1 - - - -
21Q PHE* 3.3 57.7 - - + -
49Q ASN* 5.7 0.9 - - - +
50Q SER* 4.8 2.8 + - - -
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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