Contacts of the helix formed by residues 1 - 30 (chain F) in PDB entry 2O7H
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 1 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D SER* 4.6 5.3 + - - -
2D MET* 3.6 28.0 - - + +
3D LYS* 3.6 25.1 - - - +
6D GLU* 2.6 47.6 + - - +
2F MET* 1.3 62.5 + - - +
3F LYS* 3.4 4.1 - - - +
4F GLN* 3.4 15.9 + - - +
5F LEU* 2.9 31.6 + - - +
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Residues in contact with MET 2 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D MET* 3.4 41.8 - - + +
1E ARG* 3.7 39.7 - - + +
2E MET* 4.1 36.1 - - + +
5E LEU* 2.9 34.5 - - + +
1F ARG* 1.3 77.7 - - - +
3F LYS* 1.3 57.5 + - - +
5F LEU* 3.4 4.6 + - + +
6F GLU* 2.9 28.8 + - - +
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Residues in contact with LYS 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 6.3 1.1 - - - +
1E ARG* 4.0 15.1 - - - +
1F ARG 3.4 1.9 - - - +
2F MET* 1.3 76.0 - - - +
4F GLN* 1.3 61.0 + - - +
6F GLU* 3.3 22.9 + - - +
7F ASP* 2.9 61.7 + - - +
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Residues in contact with GLN 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1F ARG* 3.4 19.5 + - - +
2F MET 3.4 0.2 - - - -
3F LYS* 1.3 74.6 - - - +
5F LEU* 1.3 66.1 + - - +
7F ASP* 3.3 9.1 + - - +
8F LYS* 3.0 65.3 + - - +
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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
----------------------------------------------------------
2D MET* 3.6 30.1 - - - -
5D LEU* 3.7 27.4 - - + -
6D GLU* 3.7 34.5 - - + +
9D VAL* 3.7 32.5 - - + -
5E LEU* 3.6 14.1 - - + -
1F ARG 2.9 14.1 + - - +
2F MET 3.5 5.8 - - - +
4F GLN* 1.3 75.5 - - - +
6F GLU* 1.3 57.1 + - - +
8F LYS* 3.3 7.1 + - + +
9F VAL* 2.9 34.2 + - + +
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Residues in contact with GLU 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E ARG* 3.0 40.2 + - - +
5E LEU* 4.2 19.4 - - + +
2F MET* 2.9 15.0 + - - +
3F LYS* 3.4 19.1 - - - +
5F LEU* 1.3 76.7 - - - +
7F ASP* 1.3 63.5 + - - +
9F VAL* 3.4 5.3 + - - +
10F GLU* 3.0 37.1 + - + +
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Residues in contact with ASP 7 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 5.2 10.1 + - - -
3F LYS* 2.9 49.3 + - - +
4F GLN* 3.3 8.5 + - - +
6F GLU* 1.3 76.7 - - - +
8F LYS* 1.3 57.4 + - + +
10F GLU* 3.3 8.0 + - - +
11F GLU* 2.9 39.7 + - - +
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Residues in contact with LYS 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 5.5 2.7 - - - +
9D VAL* 3.6 20.9 - - + -
10D GLU* 3.4 27.0 + - - +
13D LEU* 4.2 10.9 - - + +
4F GLN* 3.0 57.5 + - - +
5F LEU* 3.8 6.3 - - + +
7F ASP* 1.3 75.3 - - + +
9F VAL* 1.3 61.8 + - - +
11F GLU* 3.1 22.8 + - - +
12F LEU* 2.9 32.8 + - - +
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 3.7 24.7 - - + -
5E LEU* 4.9 12.1 - - + +
8E LYS* 3.7 39.9 - - + -
9E VAL* 3.8 15.0 - - + -
12E LEU* 4.0 10.8 - - + -
5F LEU* 2.9 22.8 + - + +
6F GLU* 3.8 5.2 - - - +
8F LYS* 1.3 71.2 - - - +
10F GLU* 1.3 63.2 + - - +
12F LEU* 3.2 7.9 + - - +
13F LEU* 2.9 32.7 + - + +
----------------------------------------------------------
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Residues in contact with GLU 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 4.2 21.8 + - - -
8E LYS* 2.6 34.4 + - - +
6F GLU* 3.0 29.7 + - + +
7F ASP* 3.6 7.6 - - - +
9F VAL* 1.3 74.9 - - - +
11F GLU* 1.3 63.2 + - - +
13F LEU* 3.3 19.0 + - - +
14F SER* 3.1 23.2 + - - -
----------------------------------------------------------
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Residues in contact with GLU 11 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 2.6 37.9 + - - -
21B ASN* 3.2 32.2 + - - +
24B ALA* 6.2 1.6 - - - -
13D LEU* 4.3 11.9 - - + +
7F ASP* 2.9 27.9 + - + +
8F LYS* 3.1 22.5 + - - +
10F GLU* 1.3 75.4 - - - +
12F LEU* 1.3 58.4 + - + +
14F SER* 3.3 7.3 + - - -
15F LYS* 2.8 46.2 + - + +
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D VAL* 4.0 23.8 - - + +
12D LEU* 3.7 46.4 - - + +
13D LEU* 3.5 24.9 - - + +
16D ASN* 4.5 12.3 - - + +
12E LEU* 3.6 24.6 - - + +
8F LYS 2.9 17.7 + - - +
9F VAL* 3.5 9.2 - - - +
11F GLU* 1.3 73.6 - - - +
13F LEU* 1.3 60.5 + - - +
15F LYS* 4.0 4.4 - - + +
16F ASN* 2.8 32.7 + - - +
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Residues in contact with LEU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 6.0 4.9 - - - +
8E LYS* 3.9 26.9 - - + +
11E GLU* 3.8 24.7 - - - +
12E LEU* 3.6 26.2 - - + -
15E LYS* 6.1 1.1 - - + -
9F VAL* 2.9 20.5 + - + +
10F GLU* 3.3 35.4 + - - +
12F LEU* 1.3 76.5 - - - +
14F SER* 1.3 62.4 + - - +
16F ASN* 3.8 4.9 + - - +
17F TYR* 3.1 23.0 + - - +
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Residues in contact with SER 14 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.7 12.5 + - - -
20B GLU* 5.0 0.9 + - - +
24B ALA* 3.7 18.3 - - - +
27B GLU* 4.2 1.2 + - - -
28B LYS* 6.3 3.4 - - - -
10F GLU 3.1 13.7 + - - -
11F GLU* 3.6 9.9 - - - -
13F LEU* 1.3 76.9 - - - +
15F LYS* 1.3 66.1 + - - +
17F TYR* 3.3 6.0 + - - +
18F HIS* 3.0 43.2 + - - -
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Residues in contact with LYS 15 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LYS* 5.8 4.4 - - - +
17B TYR* 3.9 31.1 + - - +
20B GLU* 3.5 41.4 + - - +
21B ASN* 4.5 7.0 + - - -
13D LEU* 5.7 5.9 - - + +
16D ASN* 3.8 35.0 - - - +
20D GLU* 6.0 0.4 - - - +
11F GLU* 2.8 37.2 + - + +
12F LEU* 4.0 8.3 - - + +
14F SER* 1.3 75.3 - - - +
16F ASN* 1.3 57.4 + - - +
18F HIS* 3.8 4.7 - - - +
19F LEU* 2.8 33.8 + - - +
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Residues in contact with ASN 16 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASN* 4.8 2.8 + - - -
12E LEU* 4.3 12.0 - - + +
15E LYS* 3.5 48.8 - - - +
16E ASN* 4.7 1.7 + - - -
19E LEU* 3.9 17.4 - - - +
12F LEU 2.8 17.4 + - - +
13F LEU* 3.8 6.1 + - - +
15F LYS* 1.3 77.4 - - - +
17F TYR* 1.3 56.7 + - - +
19F LEU* 3.9 4.2 - - - +
20F GLU* 2.8 43.7 + - - +
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Residues in contact with TYR 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 5.4 6.6 + - - -
13F LEU 3.1 13.8 + - - +
14F SER* 3.3 9.6 + - - +
16F ASN* 1.3 81.0 - - - +
18F HIS* 1.3 97.0 + + - +
20F GLU* 3.4 6.1 + - - +
21F ASN* 3.1 50.2 + - - +
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Residues in contact with HIS 18 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 3.2 42.1 + - + +
20B GLU* 5.7 0.2 - - - +
27B GLU* 2.8 38.9 + - - +
14F SER* 3.0 31.4 + - - +
15F LYS* 4.1 4.3 - - - +
17F TYR* 1.3 105.3 - + - +
19F LEU* 1.3 66.3 + - - +
21F ASN* 3.3 10.2 + - - +
22F ARG* 3.1 28.8 + - - +
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Residues in contact with LEU 19 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ASN* 3.9 16.8 - - - +
19D LEU* 4.0 25.1 - - + -
20D GLU* 3.8 31.6 - - + +
23D VAL* 3.7 34.8 - - + -
19E LEU* 4.2 8.5 - - + -
15F LYS 2.8 22.7 + - - +
16F ASN* 3.9 3.8 - - - +
18F HIS* 1.3 73.1 - - - +
20F GLU* 1.3 64.5 + - - +
22F ARG* 3.0 24.6 + - - +
23F VAL* 2.9 25.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 20 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E LYS* 5.5 4.0 + - - +
19E LEU* 3.9 19.8 - - + +
22E ARG* 2.8 34.7 + - - +
16F ASN* 2.8 34.3 + - - +
17F TYR* 3.7 7.0 - - - +
19F LEU* 1.3 72.8 - - - +
21F ASN* 1.3 55.6 + - - +
23F VAL* 3.1 3.1 + - - +
24F ALA* 2.7 34.3 + - + +
----------------------------------------------------------
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Residues in contact with ASN 21 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR* 3.1 53.8 + - - +
18F HIS* 3.7 11.6 + - - +
19F LEU 3.3 0.4 - - - -
20F GLU* 1.3 78.0 - - - +
22F ARG* 1.3 59.6 + - + +
24F ALA* 3.3 9.0 + - - +
25F ARG* 2.9 27.4 + - - +
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Residues in contact with ARG 22 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 3.8 7.5 + - - -
18A HIS* 3.2 42.3 + - + +
20D GLU* 2.9 38.6 + - - +
23D VAL* 3.8 12.8 - - + +
24D ALA* 3.9 10.1 - - - +
27D GLU* 2.8 43.0 + - - +
18F HIS* 3.1 16.6 + - - +
19F LEU* 3.0 23.0 + - - +
21F ASN* 1.3 75.9 - - + +
23F VAL* 1.3 64.7 + - - +
25F ARG* 3.2 10.1 + - - +
26F LEU* 3.1 28.5 + - - +
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Residues in contact with VAL 23 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 3.8 15.0 - - + -
19E LEU* 3.7 27.4 - - + -
22E ARG* 3.9 14.6 - - + +
23E VAL* 3.6 24.0 - - + -
26E LEU* 4.1 11.4 - - + -
19F LEU 2.9 18.8 + - - +
20F GLU 3.4 6.7 - - - +
22F ARG* 1.3 75.7 - - - +
24F ALA* 1.3 56.7 + - - +
26F LEU* 3.2 11.2 + - + +
27F GLU* 2.9 45.0 + - - +
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Residues in contact with ALA 24 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ARG* 3.9 11.0 - - - +
20F GLU* 2.7 20.5 + - + +
21F ASN* 3.6 11.0 - - - +
23F VAL* 1.3 72.9 - - - +
25F ARG* 1.3 63.5 + - - +
27F GLU* 3.3 14.0 + - - +
28F LYS* 3.0 23.4 + - - +
----------------------------------------------------------
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Residues in contact with ARG 25 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 5.9 1.2 + - - -
31D GLY 4.8 5.5 + - - -
21F ASN 2.9 14.4 + - - +
22F ARG* 3.4 13.7 - - - +
23F VAL 3.2 0.2 - - - -
24F ALA* 1.3 76.1 - - - +
26F LEU* 1.3 56.8 + - + +
28F LYS* 3.2 10.4 + - + +
29F LEU* 2.9 54.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 3.9 25.4 - - + +
26D LEU* 3.7 35.7 - - + +
27D GLU* 3.8 34.1 - - + +
30D VAL* 4.1 17.0 - - + -
26E LEU* 3.8 17.9 - - + -
22F ARG 3.1 18.5 + - - +
23F VAL* 3.2 8.9 + - - +
25F ARG* 1.3 75.5 - - + +
27F GLU* 1.3 58.7 + - - +
29F LEU* 3.1 9.3 + - + -
30F VAL* 2.7 35.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU 27 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ARG* 2.9 60.9 + - - +
26E LEU* 3.9 21.5 - - + -
23F VAL* 2.9 18.0 + - - +
24F ALA* 3.3 11.9 + - - +
26F LEU* 1.3 75.1 - - - +
28F LYS* 1.3 58.5 + - - +
30F VAL* 3.6 0.9 + - - +
31F GLY* 3.0 30.8 + - - -
----------------------------------------------------------
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Residues in contact with LYS 28 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ALA 3.0 12.8 + - - +
25F ARG* 3.4 12.1 - - + +
27F GLU* 1.3 76.9 - - - +
29F LEU* 1.3 56.5 + - + +
31F GLY* 3.1 17.1 + - - -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D VAL* 3.6 27.0 - - + +
31D GLY 3.8 22.0 - - - +
25F ARG* 2.9 47.4 + - + +
26F LEU* 3.1 11.0 + - + +
28F LYS* 1.3 75.0 - - + +
30F VAL* 1.3 59.7 + - - +
31F GLY 3.1 5.0 + - - -
----------------------------------------------------------
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Residues in contact with VAL 30 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LEU* 6.5 0.2 - - + -
30D VAL* 3.9 27.8 - - + -
26E LEU* 3.9 17.5 - - + -
29E LEU* 4.1 35.4 - - + +
30E VAL* 4.5 14.1 - - + -
26F LEU* 2.7 25.4 + - + +
27F GLU 4.4 1.3 - - - +
29F LEU* 1.3 72.6 - - - +
31F GLY* 1.3 62.1 + - - +
----------------------------------------------------------
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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