Contacts of the helix formed by residues 2 - 29 (chain F) 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 SER 2 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 1.3 77.4 + - - +
3F GLY* 1.3 66.4 + - - +
4F GLU 3.3 3.0 - - - +
5F LEU* 3.8 19.7 - - - +
6F LEU* 3.3 26.5 + - - +
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Residues in contact with GLY 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET* 4.6 0.4 - - - +
2F SER* 1.3 81.8 + - - +
4F GLU* 1.3 56.2 + - - +
6F LEU* 4.0 4.1 - - - +
7F ASN* 3.1 27.4 + - - +
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Residues in contact with GLU 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN* 4.6 15.9 - - - +
1F MET* 5.1 9.1 - - + +
2F SER 3.3 2.4 - - - +
3F GLY* 1.3 76.5 - - - +
5F LEU* 1.3 64.4 + - - +
7F ASN* 3.3 8.6 + - + +
8F ALA* 3.0 22.5 + - - +
4G PRO* 3.2 31.7 - - + +
5G LEU* 4.0 17.8 + - - +
30H OPC 3.8 25.8 - - - +
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Residues in contact with LEU 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F MET 5.2 2.5 - - - +
2F SER* 3.8 23.8 - - - +
3F GLY 3.4 0.4 - - - -
4F GLU* 1.3 77.5 - - - +
6F LEU* 1.3 66.7 + - + +
8F ALA 3.1 3.5 + - - -
9F ALA* 2.8 29.2 + - + +
2G VAL* 5.6 6.7 - - + -
4G PRO* 3.4 31.9 - - + +
7G SER* 3.9 19.7 - - - -
8G GLY* 3.4 17.7 - - - +
11G LEU* 3.8 26.7 - - + -
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Residues in contact with LEU 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F SER 3.3 15.6 + - - +
3F GLY* 4.2 5.2 - - - +
4F GLU 3.4 0.2 - - - -
5F LEU* 1.3 82.8 - - + +
7F ASN* 1.3 58.7 + - - +
9F ALA* 3.8 9.2 - - + -
10F LEU* 2.9 61.9 + - + +
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Residues in contact with ASN 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F GLY 3.1 20.0 + - - +
4F GLU* 3.3 13.3 - - + +
6F LEU* 1.3 77.5 - - - +
8F ALA* 1.3 58.2 + - - +
10F LEU* 3.9 6.5 - - - +
11F LEU* 3.1 47.2 + - - +
30H OPC 4.7 17.5 + - + +
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Residues in contact with ALA 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F GLU* 3.0 12.6 + - + +
5F LEU 3.5 7.6 - - - +
7F ASN* 1.3 75.4 - - - +
9F ALA* 1.3 59.1 + - - +
11F LEU* 3.5 1.0 + - - +
12F SER* 3.0 34.7 + - - -
5G LEU* 3.7 41.7 - - + +
8G GLY* 3.8 5.8 - - - -
9G ILE* 4.1 2.9 + - + +
30H OPC 4.1 17.4 - - + +
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Residues in contact with ALA 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F LEU* 2.8 20.8 + - + +
6F LEU* 3.8 12.1 - - + +
8F ALA* 1.3 73.8 - - - +
10F LEU* 1.3 70.0 + - + +
11F LEU 3.2 0.2 + - - -
12F SER* 3.4 1.4 + - - -
13F PHE* 2.9 28.1 + - - +
8G GLY* 3.5 19.9 + - - +
11G LEU* 4.9 4.7 - - + -
12G GLY* 3.8 14.2 - - - +
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Residues in contact with LEU 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 2.9 51.8 + - + +
7F ASN* 3.9 5.8 - - - +
9F ALA* 1.3 75.0 - - + +
11F LEU* 1.3 57.7 + - + +
13F PHE* 3.7 7.0 - - - +
14F GLY* 2.8 27.2 + - - -
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F ASN* 3.1 35.6 + - - +
8F ALA 3.9 2.7 - - - +
10F LEU* 1.3 78.2 - - + +
12F SER* 1.3 59.0 + - - +
14F GLY* 4.4 0.7 - - - +
15F LEU* 2.7 60.6 + - + +
12H LEU* 4.4 9.0 - - + -
30H OPC 3.8 76.9 - - + -
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Residues in contact with SER 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ALA 3.0 20.4 + - - -
9F ALA 3.4 3.6 + - - -
11F LEU* 1.3 73.6 - - - +
13F PHE* 1.3 65.8 + - - +
16F ILE* 3.4 23.7 + - - +
9G ILE* 4.0 10.9 + - - -
12G GLY* 3.5 16.5 - - - -
13G LEU* 3.7 18.9 + - - +
16G VAL* 3.9 3.3 - - - +
15H PHE* 3.9 8.4 - - - -
30H OPC 3.7 27.8 - - - -
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Residues in contact with PHE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ALA 2.9 18.6 + - - +
10F LEU* 3.7 6.1 - - - +
12F SER* 1.3 78.7 + - - +
14F GLY* 1.3 68.1 + - - +
15F LEU 3.6 0.2 + - - -
16F ILE* 3.7 4.5 - - - +
17F PHE* 3.3 35.8 - + - -
12G GLY* 4.4 4.7 - - - +
15G VAL* 3.7 32.1 - - + -
16G VAL* 3.4 45.0 - - + +
19G ALA* 5.1 7.6 - - + -
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Residues in contact with GLY 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F LEU 2.8 20.6 + - - -
11F LEU* 3.2 0.9 + - - -
13F PHE* 1.3 78.2 - - - +
15F LEU* 1.3 63.3 + - - +
16F ILE 3.2 2.5 - - - -
17F PHE* 3.3 18.8 + - - +
18F VAL* 3.4 16.4 + - - +
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Residues in contact with LEU 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E TYR* 3.0 42.8 - - + +
11F LEU* 2.7 52.2 + - + +
14F GLY* 1.3 69.7 - - - +
16F ILE* 1.3 60.9 + - - +
18F VAL* 3.3 9.2 + - + +
19F GLY* 2.9 24.6 + - - -
12H LEU* 3.7 32.3 - - + +
15H PHE* 4.0 23.8 - - + -
16H THR* 3.5 17.1 + - - +
30H OPC 4.4 8.7 - - + -
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Residues in contact with ILE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F SER 3.4 21.0 + - - +
13F PHE 3.7 7.5 + - - +
14F GLY 3.2 0.4 - - - -
15F LEU* 1.3 76.9 - - - +
17F PHE* 1.3 57.4 + - + +
19F GLY* 2.9 3.6 + - - -
20F TRP* 2.6 38.7 + - + +
13G LEU* 3.8 16.4 - - + -
16G VAL* 3.8 16.6 - - + -
101G BCR 3.5 61.0 - - + -
15H PHE* 4.1 9.2 - - + -
19H ILE* 3.5 26.2 - - + +
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Residues in contact with PHE 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PHE* 3.3 54.3 - + - -
14F GLY* 3.3 10.5 + - - +
16F ILE* 1.3 74.4 - - + +
18F VAL* 1.3 54.2 + - + +
20F TRP* 3.6 22.5 - + - +
21F ALA* 2.8 36.4 + - - +
16G VAL* 4.0 7.6 - - + -
101G BCR 3.7 49.4 - - + -
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Residues in contact with VAL 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E TYR* 3.5 23.8 - - + +
11E LEU* 4.5 2.7 - - + -
14F GLY 3.4 17.7 - - - +
15F LEU* 3.5 11.7 - - + +
16F ILE 3.2 0.6 - - - -
17F PHE* 1.3 75.1 - - + +
19F GLY* 1.3 57.1 + - - +
21F ALA* 3.9 5.1 - - - +
22F LEU* 3.0 32.2 + - + +
16H THR* 4.0 5.6 - - + -
30H OPC 4.2 51.1 - - + -
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Residues in contact with GLY 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15F LEU 2.9 12.9 + - - -
16F ILE 2.9 3.6 + - - -
18F VAL* 1.3 73.4 - - - +
20F TRP* 1.3 58.1 + - - +
22F LEU* 3.2 2.5 + - - -
23F GLY* 2.8 24.6 + - - -
16H THR* 3.5 30.7 - - - +
19H ILE* 3.7 10.8 - - - -
20H ALA* 3.3 12.2 - - - +
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Residues in contact with TRP 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 2.6 21.9 + - + +
17F PHE* 3.6 27.1 - + - +
19F GLY* 1.3 70.2 - - - +
21F ALA* 1.3 52.7 + - - +
23F GLY* 2.9 3.6 + - - -
24F ALA* 2.8 39.8 + - + +
23G TYR* 3.9 28.3 - + - -
27G LYS* 5.1 4.0 - - - -
101G BCR 3.2 51.1 - - + -
19H ILE* 3.6 9.9 - - + +
23H VAL* 4.2 18.5 - - + +
28H GLY* 5.4 0.6 - - - -
29H LEU* 3.8 29.9 + - - +
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Residues in contact with ALA 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F PHE 2.8 22.3 + - - +
18F VAL* 3.9 5.8 - - - +
20F TRP* 1.3 71.7 - - - +
22F LEU* 1.3 52.7 + - - +
24F ALA* 3.2 8.3 + - - +
25F LEU* 2.7 35.7 + - - +
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Residues in contact with LEU 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 4.0 39.9 - - + -
15E THR* 3.1 29.6 - - + +
18F VAL* 3.0 25.3 + - + +
19F GLY* 3.6 5.2 - - - +
20F TRP 3.2 0.2 - - - -
21F ALA* 1.3 76.1 - - - +
23F GLY* 1.3 60.6 + - - +
25F LEU* 3.7 12.5 - - + +
26F LEU* 3.1 46.2 + - + +
16H THR* 4.5 4.3 - - + -
17H TRP* 4.3 10.3 - - + -
20H ALA* 4.2 9.1 - - + +
30H OPC 4.7 9.9 - - + -
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Residues in contact with GLY 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F GLY 2.8 14.2 + - - -
20F TRP 2.9 4.0 + - - -
22F LEU* 1.3 76.2 - - - +
24F ALA* 1.3 63.8 + - - +
26F LEU* 3.3 5.6 + - - +
27F LEU* 3.1 25.1 + - - +
20H ALA* 3.7 23.3 - - - -
23H VAL* 3.8 13.9 - - - -
24H TRP* 4.3 4.4 - - - +
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F TRP* 2.8 20.8 + - + +
21F ALA* 3.4 12.8 - - - +
23F GLY* 1.3 72.1 - - - +
25F LEU* 1.3 68.6 + - - +
27F LEU* 3.0 14.6 + - - +
28F LYS* 3.0 24.6 + - + +
23H VAL* 3.9 3.6 - - + +
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Residues in contact with LEU 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR* 5.1 15.7 - - + -
21F ALA 2.7 20.1 + - - +
22F LEU* 3.7 16.6 - - + +
24F ALA* 1.3 70.9 - - - +
26F LEU* 1.3 66.3 + - + +
28F LYS* 2.9 22.3 + - + +
29F ILE* 2.9 29.9 + - + +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR* 3.7 27.8 - - + -
18E ALA* 4.0 24.7 - - + -
19E ALA* 4.5 8.1 - - - +
22E LEU* 5.8 1.1 - - + -
22F LEU* 3.1 33.0 + - + +
23F GLY* 3.3 8.5 + - - +
25F LEU* 1.3 81.4 - - + +
27F LEU* 1.3 61.2 + - - +
29F ILE* 3.5 20.3 + - + +
30F GLN* 3.2 23.4 + - - +
17H TRP* 5.3 4.7 - - + -
20H ALA* 5.9 1.8 - - + -
21H MET* 6.0 1.3 - - - -
24H TRP* 3.6 44.6 + - + -
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F GLY 3.1 15.1 + - - +
24F ALA* 3.0 13.1 + - - +
25F LEU 3.0 0.2 + - - -
26F LEU* 1.3 75.0 - - - +
28F LYS* 1.3 64.8 + - + +
30F GLN* 3.3 18.8 - - - +
31F GLY 3.2 16.6 + - - -
32F ALA* 3.4 25.8 + - + -
23H VAL* 3.7 24.2 - - + +
24H TRP* 3.6 32.1 - - + +
27H ASN* 3.6 32.8 - - - +
28H GLY* 3.9 3.6 - - - +
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Residues in contact with LYS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ALA* 3.0 18.5 + - + +
25F LEU* 2.9 13.6 + - + +
27F LEU* 1.3 75.5 - - + +
29F ILE* 1.3 57.9 + - + +
30F GLN 3.0 5.4 + - - -
31F GLY* 3.1 14.0 + - - -
32F ALA* 5.2 1.3 - - - +
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Residues in contact with ILE 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E THR* 6.0 3.4 - - + -
19E ALA* 3.6 33.0 - - + -
22E LEU* 4.2 5.1 - - + +
23E PHE* 3.5 35.1 - - + -
26E ARG* 4.6 0.2 + - - -
25F LEU* 2.9 40.8 + - + +
26F LEU* 3.5 17.9 - - + +
28F LYS* 1.3 73.1 - - - +
30F GLN* 1.3 57.1 + - - +
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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