Contacts of the helix formed by residues 3 - 31 (chain A) in PDB entry 1CE9
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 VAL 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 74.0 - - - +
4A LYS* 1.3 68.0 + - + +
6A LEU* 3.2 5.5 + - - +
7A GLU* 2.8 51.2 + - - +
1B MET* 4.6 12.1 - - + +
3B VAL* 5.0 12.5 - - + +
6B LEU* 3.5 22.2 - - + -
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Residues in contact with LYS 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 3.2 8.9 + - - +
3A VAL* 1.3 85.8 - - + +
5A GLU* 1.3 66.9 + - + +
7A GLU* 3.1 15.5 + - + +
8A ASP* 2.9 49.6 + - - +
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.0 28.7 + - + +
2A SER* 2.6 43.5 + - - +
3A VAL 3.3 0.4 - - - -
4A LYS* 1.3 84.4 - - + +
6A LEU* 1.3 61.2 + - - +
8A ASP* 3.3 8.7 + - - +
9A LYS* 3.1 21.8 + - - +
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Residues in contact with LEU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.4 35.7 - - + +
2A SER 3.2 12.1 + - - +
3A VAL 3.2 6.0 + - - +
5A GLU* 1.3 76.0 - - - +
7A GLU* 1.3 64.4 + - - +
9A LYS* 3.4 5.3 + - + +
10A VAL* 3.1 28.6 + - - +
3B VAL* 3.8 36.8 - - + +
6B LEU* 3.9 18.6 - - + -
7B GLU* 3.9 17.0 - - + +
10B VAL* 4.1 12.8 - - + +
18D TYR* 3.4 25.4 - - + +
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Residues in contact with GLU 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 2.8 36.4 + - - +
4A LYS* 3.1 14.4 + - + +
6A LEU* 1.3 75.1 - - - +
8A ASP* 1.3 66.3 + - - +
10A VAL* 3.4 6.8 + - - +
11A GLU* 3.1 36.9 + - - +
1B MET* 4.1 16.2 - - - +
6B LEU* 3.9 20.2 - - + -
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Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 2.9 49.6 + - - +
5A GLU* 3.5 11.5 - - - +
7A GLU* 1.3 79.2 - - - +
9A LYS* 1.3 56.8 + - - +
11A GLU* 3.3 17.9 + - - +
12A GLU* 2.9 30.0 + - - +
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.5 3.6 - - + -
5A GLU 3.1 13.1 + - - +
6A LEU* 3.6 12.6 - - + +
8A ASP* 1.3 74.5 - - - +
10A VAL* 1.3 59.9 + - - +
12A GLU* 3.3 32.2 + - - +
13A LEU* 3.0 39.9 + - + +
10B VAL* 3.8 28.5 - - + -
14D LEU* 6.1 4.5 - - - -
18D TYR* 4.4 6.3 - - - +
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU 3.1 17.8 + - - +
7A GLU* 3.7 6.3 - - - +
8A ASP 3.3 0.2 - - - -
9A LYS* 1.3 75.5 - - - +
11A GLU* 1.3 66.4 + - + +
13A LEU* 3.5 1.1 + - - -
14A LEU* 3.1 24.6 + - + +
6B LEU* 4.1 15.5 - - + +
9B LYS* 3.7 33.2 - - + -
10B VAL* 3.6 21.8 - - + +
13B LEU* 3.7 14.0 - - + +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLU* 3.1 28.6 + - - +
8A ASP* 3.6 19.7 - - - +
9A LYS 3.2 0.2 - - - -
10A VAL* 1.3 80.5 - - + +
12A GLU* 1.3 61.8 + - - +
14A LEU* 3.4 8.4 + - + +
15A SER* 3.2 23.2 + - - -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP 2.9 16.9 + - - +
9A LYS* 3.4 39.1 + - - +
10A VAL 3.3 0.2 - - - -
11A GLU* 1.3 78.4 - - - +
13A LEU* 1.3 66.2 + - - +
15A SER* 3.4 6.9 + - - -
16A LYS* 3.0 54.2 + - - +
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Residues in contact with LEU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 3.0 39.8 + - + +
10A VAL* 4.1 3.4 - - - +
12A GLU* 1.3 81.6 - - - +
14A LEU* 1.3 60.9 + - - +
16A LYS* 3.4 10.5 + - + +
17A ASN* 2.8 35.8 + - - +
10B VAL* 4.0 34.5 - - + +
13B LEU* 4.1 17.3 - - + -
14B LEU* 4.2 29.8 - - + +
17B ASN* 4.6 15.9 - - + +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.1 20.2 + - + +
11A GLU* 3.7 8.3 - - + +
12A GLU 3.3 0.2 - - - -
13A LEU* 1.3 77.1 - - - +
15A SER* 1.3 58.4 + - - +
17A ASN* 3.3 7.5 + - + +
18A TYR* 3.0 63.8 + - + +
13B LEU* 4.2 22.8 - - + +
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Residues in contact with SER 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU 3.2 11.5 + - - -
12A GLU* 3.6 9.4 - - - -
14A LEU* 1.3 79.8 - - - +
16A LYS* 1.3 63.5 + - - +
18A TYR* 3.1 11.9 + - - +
19A HIS* 3.0 21.3 + - - +
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 3.0 46.6 + - + +
13A LEU* 3.7 13.9 - - + +
14A LEU 3.3 0.2 - - - -
15A SER* 1.3 76.6 - - - +
17A ASN* 1.3 64.4 + - - +
19A HIS* 3.1 10.8 + - - +
20A LEU* 3.0 27.1 + - + +
17B ASN* 4.1 13.0 - - - +
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LEU 2.8 19.9 + - - +
14A LEU* 3.6 10.1 - - + +
16A LYS* 1.3 77.2 - - - +
18A TYR* 1.3 63.8 + - + +
20A LEU* 3.3 5.1 + - - +
21A GLU* 3.0 29.2 + - + +
13B LEU* 3.2 34.7 + - - +
16B LYS* 3.4 21.4 - - + +
17B ASN* 2.8 38.1 - - - +
20B LEU* 3.7 11.9 - - + +
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Residues in contact with TYR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LEU* 3.0 48.9 + - + +
15A SER* 3.1 12.8 + - - +
17A ASN* 1.3 79.3 - - + +
19A HIS* 1.3 64.3 + - - +
21A GLU* 3.2 13.2 + - + +
22A ASN* 3.0 32.6 + - - +
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Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER 3.0 12.5 + - - +
16A LYS* 3.1 11.9 + - - +
18A TYR* 1.3 75.8 - - - +
20A LEU* 1.3 67.8 + - + +
22A ASN* 3.1 16.8 + - + +
23A GLU* 2.9 55.4 + - + +
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 3.0 14.2 + - + +
17A ASN* 3.5 7.2 - - - +
18A TYR 3.2 0.2 - - - -
19A HIS* 1.3 88.8 - - + +
21A GLU* 1.3 56.6 + - - +
23A GLU* 3.2 9.3 + - + +
24A VAL* 3.0 32.6 + - - +
17B ASN* 3.4 44.2 - - - +
20B LEU* 3.6 23.1 - - + -
21B GLU* 3.9 30.7 - - + +
24B VAL* 3.8 17.3 - - + +
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN* 3.0 21.7 + - + +
18A TYR* 3.2 17.4 + - + +
20A LEU* 1.3 75.9 - - - +
22A ASN* 1.3 66.2 + - - +
24A VAL* 3.4 10.4 + - - +
25A ALA* 3.1 22.2 + - - +
16B LYS* 4.3 11.4 + - - -
20B LEU* 3.9 27.6 - - + +
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Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 3.0 23.8 + - - +
19A HIS* 3.4 18.7 - - + +
21A GLU* 1.3 80.3 - - - +
23A GLU* 1.3 59.8 + - + +
25A ALA* 3.4 7.6 + - - +
26A ARG* 3.0 27.8 + - - +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A HIS* 2.9 43.7 + - + +
20A LEU* 3.5 13.7 - - + +
21A GLU 3.2 0.2 - - - -
22A ASN* 1.3 76.3 - - - +
24A VAL* 1.3 60.1 + - - +
26A ARG* 3.0 43.2 + - - +
27A LEU* 2.9 36.2 + - + +
24B VAL* 4.1 18.3 - - + +
28B LYS* 4.7 9.7 + - - -
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Residues in contact with VAL 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU 3.0 18.7 + - - +
21A GLU* 3.7 13.9 - - - +
23A GLU* 1.3 75.9 - - - +
25A ALA* 1.3 57.5 + - - +
27A LEU* 3.9 0.4 - - - -
28A LYS* 2.9 53.7 + - + +
20B LEU* 4.7 7.4 - - + +
23B GLU* 3.7 38.1 - - + +
24B VAL* 3.5 19.7 - - + -
27B LEU* 3.9 11.0 - - + +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU 3.1 13.8 + - - +
22A ASN* 3.5 11.7 - - - +
23A GLU 3.1 0.2 - - - -
24A VAL* 1.3 79.7 - - - +
26A ARG* 1.3 60.3 + - - +
28A LYS* 3.4 6.6 + - - +
29A LYS* 3.1 27.3 + - + +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ASN 3.0 16.4 + - - +
23A GLU* 3.0 41.5 + - - +
25A ALA* 1.3 77.6 - - - +
27A LEU* 1.3 82.6 + - - +
29A LYS* 3.2 19.6 + - - +
30A LEU* 3.5 21.4 + - + +
28B LYS* 4.4 2.6 - - - +
33B GLU* 2.8 42.8 + - - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU* 2.9 21.7 + - + +
24A VAL 4.0 2.9 - - - +
26A ARG* 1.3 98.7 - - - +
28A LYS* 1.3 64.1 + - - +
29A LYS 3.1 1.6 - - - -
30A LEU* 3.1 17.3 + - + +
31A VAL* 3.2 11.7 + - - +
24B VAL* 3.7 40.8 - - + +
27B LEU* 3.9 22.2 - - + -
28B LYS* 3.9 9.4 - - + -
31B VAL* 3.7 38.8 - - + +
33B GLU* 3.8 10.3 - - - +
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Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 2.9 43.8 + - + +
25A ALA* 3.7 7.9 - - - +
26A ARG 3.3 0.2 - - - -
27A LEU* 1.3 76.7 - - - +
29A LYS* 1.3 60.1 + - - +
30A LEU 3.2 0.4 + - - -
31A VAL* 3.7 9.7 + - - +
32A GLY 3.6 20.4 + - - +
34A ARG* 4.1 52.1 - - + +
23B GLU* 3.9 15.6 + - - -
27B LEU* 3.9 16.2 - - + -
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.1 14.1 + - + +
26A ARG* 3.3 13.9 - - - +
27A LEU 3.1 0.2 - - - -
28A LYS* 1.3 77.5 - - - +
30A LEU* 1.3 62.9 + - + +
31A VAL 3.5 0.2 - - - -
32A GLY* 4.9 4.9 + - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 3.5 32.2 + - + +
27A LEU* 3.1 12.2 + - + +
29A LYS* 1.3 81.5 - - - +
31A VAL* 1.3 63.8 + - - +
31B VAL* 4.3 19.9 - - + +
33B GLU* 4.2 8.7 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 3.2 9.6 + - - +
28A LYS* 3.7 6.7 + - - +
29A LYS 3.5 0.4 - - - -
30A LEU* 1.3 79.5 - - - +
32A GLY* 1.3 64.3 + - - +
34A ARG* 4.5 22.0 - - - +
27B LEU* 4.8 5.6 - - + +
30B LEU* 3.6 38.4 - - + -
31B VAL* 3.4 28.5 - - + +
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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