Contacts of the helix formed by residues 1 - 28 (chain E) in PDB entry 2ZT9
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 MET 1 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E LEU* 1.3 62.0 + - - +
3E ALA* 3.2 8.2 - - - +
4E ILE* 3.8 30.5 - - + +
5E VAL* 2.9 42.5 + - - +
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Residues in contact with LEU 2 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 1.3 75.8 - - - +
3E ALA* 1.3 57.0 + - - +
5E VAL* 3.8 7.1 - - + -
6E ALA* 2.8 48.2 + - + +
2H ALA* 4.2 32.1 - - + +
5H THR* 4.4 16.8 - - + +
6H LEU* 5.3 8.7 - - + -
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Residues in contact with ALA 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 3.9 8.3 - - - +
2E LEU* 1.3 79.4 - - - +
4E ILE* 1.3 58.4 + - - +
6E ALA* 3.7 1.6 - - - +
7E TYR* 2.9 31.9 + - - +
5H THR* 4.0 22.4 - - + +
9H VAL* 3.9 8.4 - - + +
30H OPC 3.9 39.3 - - + +
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Residues in contact with ILE 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.4 24.1 + - - +
3E ALA* 1.3 78.1 - - - +
5E VAL* 1.3 65.0 + - + +
7E TYR* 3.4 4.6 + - - +
8E ILE* 2.8 47.1 + - + +
30H OPC 4.1 33.6 - - + +
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Residues in contact with VAL 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 2.9 32.3 + - - +
2E LEU* 3.9 8.3 - - + +
4E ILE* 1.3 76.4 - - + +
6E ALA* 1.3 54.5 + - - +
8E ILE* 3.3 6.1 + - - +
9E GLY* 2.8 33.5 + - - -
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Residues in contact with ALA 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E LEU* 2.8 28.8 + - + +
3E ALA 3.7 2.7 - - - +
5E VAL* 1.3 73.8 - - - +
7E TYR* 1.3 53.8 + - - +
9E GLY* 4.9 1.1 - - - -
10E PHE* 2.8 38.2 + - + +
6H LEU* 3.7 30.1 - - + -
9H VAL* 4.0 13.5 - - + -
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Residues in contact with TYR 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ALA 2.9 17.1 + - - +
4E ILE 3.6 3.4 - - - +
6E ALA* 1.3 74.0 - - - +
8E ILE* 1.3 70.5 + - + +
10E PHE* 3.7 1.7 - - - +
11E LEU* 3.1 46.9 + - + +
15F LEU* 3.0 26.3 - - + +
18F VAL* 3.5 18.7 - - + +
9H VAL* 3.8 13.7 - - + +
12H LEU* 3.7 28.5 - - + -
13H VAL* 3.8 14.6 - - + -
16H THR* 2.8 19.4 + - - -
30H OPC 3.7 53.6 - - + -
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Residues in contact with ILE 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 2.8 39.7 + - + +
5E VAL* 3.7 4.9 - - - +
7E TYR* 1.3 78.4 - - + +
9E GLY* 1.3 52.9 + - - +
11E LEU* 3.7 3.9 - - - +
12E ALA* 2.8 40.0 + - + +
30H OPC 3.6 49.3 - - + +
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Residues in contact with GLY 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E VAL* 2.8 21.0 + - - -
6E ALA* 3.7 1.8 - - - -
8E ILE* 1.3 71.7 - - - +
10E PHE* 1.3 53.7 + - - +
12E ALA* 3.6 5.9 - - - +
13E LEU* 2.8 36.4 + - - +
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Residues in contact with PHE 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ILE* 4.3 22.2 - - + -
262C VAL* 5.0 1.1 - - + -
263C ALA* 4.8 7.4 - - + -
266C MET* 3.6 18.2 - - + -
6E ALA* 2.8 20.4 + - + +
7E TYR 3.2 3.6 + - - +
9E GLY* 1.3 72.9 - - - +
11E LEU* 1.3 60.1 + - - +
13E LEU* 3.5 11.8 + - + +
14E PHE* 3.1 58.4 + + - +
6H LEU* 5.5 4.7 - - + -
9H VAL* 4.3 11.7 - - + -
10H SER* 4.2 21.8 - - - -
13H VAL* 3.7 25.6 - - + -
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Residues in contact with LEU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E TYR* 3.1 59.2 + - + +
8E ILE* 3.9 3.1 - - - +
10E PHE* 1.3 74.5 - - - +
12E ALA* 1.3 53.2 + - - +
14E PHE* 3.6 2.5 - - + +
15E THR* 2.7 42.5 + - - -
18F VAL* 4.5 2.7 - - + -
22F LEU* 4.0 18.8 - - + -
13H VAL* 3.8 30.1 - - + +
16H THR* 3.9 21.1 - - + -
17H TRP* 4.0 22.7 - - + -
30H OPC 5.0 6.7 - - + -
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Residues in contact with ALA 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 2.8 26.9 + - + +
9E GLY* 3.6 8.1 - - - +
11E LEU* 1.3 72.2 - - - +
13E LEU* 1.3 53.4 + - - +
15E THR* 3.6 6.3 - - - -
16E GLY* 2.7 34.3 + - - -
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Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLY 2.8 20.8 + - - +
10E PHE* 3.7 11.0 - - + +
11E LEU 3.3 0.2 - - - -
12E ALA* 1.3 72.5 - - - +
14E PHE* 1.3 74.1 + - + +
16E GLY* 3.3 4.4 + - - -
17E ILE* 2.9 50.2 + - + +
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Residues in contact with PHE 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C ALA* 3.8 24.0 - - + -
266C MET* 3.7 33.0 - - + -
267C LEU* 3.8 22.2 - - + -
270C VAL* 4.7 4.3 - - + -
10E PHE* 3.1 54.2 + + - +
11E LEU* 4.0 1.8 - - + +
13E LEU* 1.3 86.9 - - + +
15E THR* 1.3 62.3 + - - +
16E GLY 3.2 0.9 - - - -
17E ILE* 3.3 20.9 + - + +
18E ALA* 2.8 23.9 + - - +
17H TRP* 3.3 35.7 - + + -
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Residues in contact with THR 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU 2.7 29.5 + - - -
12E ALA* 3.6 6.0 - - - -
14E PHE* 1.3 67.9 - - - +
16E GLY* 1.3 67.1 + - - +
18E ALA* 3.5 1.7 - - - +
19E ALA* 2.9 27.8 + - + +
22F LEU* 3.1 25.9 - - + +
25F LEU* 5.1 10.8 - - + -
26F LEU* 3.7 26.0 - - + -
29F ILE* 6.0 2.5 - - + -
17H TRP* 3.7 9.3 - - - -
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Residues in contact with GLY 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ALA 2.7 18.9 + - - -
13E LEU* 3.4 6.7 - - - -
15E THR* 1.3 72.9 - - - +
17E ILE* 1.3 52.0 + - - +
19E ALA* 3.7 3.1 - - - +
20E GLY* 2.7 34.1 + - - -
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Residues in contact with ILE 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C LEU* 4.9 13.0 - - + -
270C VAL* 5.7 4.0 - - + -
13E LEU* 2.9 47.7 + - + +
14E PHE* 3.3 29.1 + - + +
16E GLY* 1.3 73.4 - - - +
18E ALA* 1.3 55.9 - - - +
20E GLY* 4.9 1.1 - - - -
21E LEU* 2.8 55.9 + - + +
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Residues in contact with ALA 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C VAL* 3.9 15.8 - - + +
274C LEU* 4.6 1.6 - - - +
14E PHE 2.8 18.4 + - - +
15E THR 3.5 5.2 - - - +
17E ILE* 1.3 76.7 - - - +
19E ALA* 1.3 58.4 + - - +
21E LEU* 3.7 1.7 - - - +
22E LEU* 2.9 28.3 + - - +
26F LEU* 4.0 19.5 - - + -
17H TRP* 4.0 14.1 - - + -
24H TRP* 4.0 20.1 - - + -
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Residues in contact with ALA 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E THR* 2.9 21.3 + - + +
16E GLY* 3.7 3.1 - - - +
18E ALA* 1.3 69.3 - - - +
20E GLY* 1.3 68.6 + - - +
22E LEU* 2.8 20.0 + - - +
23E PHE* 3.1 24.7 + - + -
26F LEU* 4.5 4.6 - - + +
29F ILE* 3.6 31.4 - - + -
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Residues in contact with GLY 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E GLY 2.7 20.8 + - - -
17E ILE* 4.0 1.8 - - - -
19E ALA* 1.3 72.2 - - - +
21E LEU* 1.3 56.0 + - - +
23E PHE* 4.5 3.3 - - - +
24E GLY* 2.8 28.9 + - - -
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Residues in contact with LEU 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C LEU* 4.7 14.6 - - + -
270C VAL* 5.1 3.8 - - + -
271C MET* 4.8 13.2 - - + -
274C LEU* 3.8 19.3 - - + -
17E ILE* 2.8 40.4 + - + +
18E ALA* 3.7 3.6 - - - +
20E GLY* 1.3 75.6 - - - +
22E LEU* 1.3 66.9 + - - +
24E GLY* 5.8 2.0 - - - -
25E LEU* 3.0 48.5 + - + +
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Residues in contact with LEU 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C LEU* 4.2 17.4 - - + +
277C LYS* 5.5 1.6 - - + -
281C LYS* 5.3 1.3 - - - +
18E ALA 2.9 12.6 + - - +
19E ALA* 2.8 18.3 + - - +
21E LEU* 1.3 73.2 - - - +
23E PHE* 1.3 67.1 + - + +
25E LEU* 3.7 1.7 - - - +
26E ARG* 2.9 59.1 + - - +
31E LEU* 3.7 24.3 - - + +
26F LEU* 5.3 1.1 - - + +
29F ILE* 4.2 12.3 - - + +
30F GLN* 3.8 39.9 - - + +
24H TRP* 4.4 10.1 - - + -
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Residues in contact with PHE 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E ALA* 3.1 24.9 + - + +
20E GLY* 4.5 2.9 - - - +
22E LEU* 1.3 83.4 - - + +
24E GLY* 1.3 53.1 + - - +
26E ARG* 3.1 37.3 + - - +
27E SER* 2.7 37.5 + - - -
29F ILE* 3.5 46.0 - - + -
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Residues in contact with GLY 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLY 2.8 20.6 + - - -
21E LEU* 4.1 2.5 - - - -
23E PHE* 1.3 78.0 - - - +
25E LEU* 1.3 60.6 + - - +
27E SER* 3.4 8.2 - - - -
28E ALA* 3.3 20.6 + - - +
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C MET* 4.8 7.6 - - + -
274C LEU* 4.0 11.7 - - + -
18D PHE* 5.4 5.4 - - + -
19D MET* 3.7 28.0 - - + -
22D LEU* 6.1 3.8 - - + -
21E LEU* 3.0 43.2 + - + +
22E LEU 3.8 2.0 - - - +
24E GLY* 1.3 74.3 - - - +
26E ARG* 1.3 59.7 + - - +
28E ALA* 3.6 3.7 + - + +
29E LYS 3.3 2.9 + - - -
30E ILE* 2.8 65.9 + - + +
31E LEU* 3.3 14.3 + - + -
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Residues in contact with ARG 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C LYS* 4.1 13.5 - - - +
22E LEU* 2.9 34.9 + - + +
23E PHE* 3.3 42.8 - - + +
25E LEU* 1.3 75.1 - - - +
27E SER* 1.3 57.2 + - - +
29E LYS* 2.7 30.7 + - - +
31E LEU* 4.0 28.7 - - + +
29F ILE 4.6 0.4 + - - -
30F GLN* 2.8 44.5 + - - +
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Residues in contact with SER 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E PHE 2.7 20.2 + - - -
24E GLY* 3.4 9.9 - - - -
25E LEU 3.3 0.2 - - - -
26E ARG* 1.3 73.9 - - - +
28E ALA* 1.3 56.8 + - - +
29E LYS* 3.1 10.4 + - - +
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Residues in contact with ALA 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D ARG* 2.4 34.8 + - - -
24E GLY 3.3 11.5 + - - +
25E LEU* 4.2 5.2 - - + +
26E ARG 3.3 0.4 - - - -
27E SER* 1.3 75.7 - - - +
29E LYS* 1.3 53.1 + - - +
30E ILE* 3.3 16.8 + - + +
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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