Contacts of the helix formed by residues 1 - 27 (chain A) in PDB entry 1IJ3
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A ACE 1.3 74.4 - - - +
2A MET* 1.3 65.1 + - - +
3A LYS* 4.1 12.8 - - + +
4A GLN* 3.1 51.5 + - + +
5A LEU* 3.7 6.1 + - - +
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Residues in contact with MET 2 (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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0A ACE 3.7 1.0 + - - -
1A ARG* 1.3 71.2 - - - +
3A LYS* 1.3 61.2 + - - +
5A LEU* 3.0 29.0 + - + +
6A GLU* 2.9 37.1 + - + +
2B MET* 3.3 27.0 - - + +
5B LEU* 4.7 0.9 - - + -
1C ARG* 3.6 35.2 - - + +
2C MET* 4.4 23.1 - - - -
5C LEU* 3.1 32.8 - - + -
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Residues in contact with LYS 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ARG* 4.1 14.1 - - + +
2A MET* 1.3 78.4 - - - +
4A GLN* 1.3 61.6 + - - +
6A GLU* 3.0 26.2 + - + +
7A ASP* 2.9 43.5 + - - +
1C ARG* 4.0 9.9 - - - +
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Residues in contact with GLN 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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0A ACE 3.5 24.0 - - - +
1A ARG* 3.1 39.7 + - + +
3A LYS* 1.3 78.1 - - - +
5A LEU* 1.3 65.9 + - + +
7A ASP* 3.4 8.6 + - - +
8A LYS* 3.3 44.6 + - - +
6B GLU* 4.5 7.7 + - - -
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Residues in contact with LEU 5 (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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1A ARG 3.7 4.9 + - - +
2A MET* 3.0 31.0 + - + +
4A GLN* 1.3 84.7 - - + +
6A GLU* 1.3 66.3 + - - +
8A LYS* 3.3 11.1 + - + +
9A VAL* 2.9 27.7 + - - +
2B MET* 3.7 15.5 - - + -
5B LEU* 3.9 17.3 - - + -
6B GLU* 3.9 33.4 - - + +
9B VAL* 4.0 29.8 - - + -
5C LEU* 3.5 13.7 - - + -
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Residues in contact with GLU 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A MET* 2.9 22.9 + - + +
3A LYS* 3.0 25.0 + - + +
5A LEU* 1.3 76.7 - - - +
7A ASP* 1.3 57.1 + - - +
9A VAL* 3.3 1.9 + - - +
10A GLU* 2.9 44.6 + - + +
1C ARG* 2.7 52.6 + - - +
4C GLN* 4.7 6.4 - - - +
5C LEU* 4.2 20.5 - - + +
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Residues in contact with ASP 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 2.9 35.7 + - - +
4A GLN* 3.8 8.3 - - - +
6A GLU* 1.3 74.5 - - - +
8A LYS* 1.3 64.2 + - + +
10A GLU* 3.3 19.6 + - - +
11A GLU* 3.0 23.2 + - - +
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Residues in contact with LYS 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 3.3 34.3 + - - +
5A LEU* 3.3 16.9 + - + +
7A ASP* 1.3 78.9 - - + +
9A VAL* 1.3 57.7 + - - +
11A GLU* 3.3 7.9 + - - +
12A LEU* 3.0 31.5 + - - +
9B VAL* 3.8 26.9 - - + -
13B LEU* 4.2 20.3 - - + +
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU 2.9 21.6 + - - +
6A GLU* 3.8 4.0 - - - +
8A LYS* 1.3 74.4 - - - +
10A GLU* 1.3 65.3 - - + +
12A LEU* 3.1 7.7 + - + +
13A LEU* 2.9 30.2 + - + +
9B VAL* 3.9 25.1 - - + -
5C LEU* 3.3 23.1 - - + -
8C LYS* 3.9 28.5 - - + -
9C VAL* 4.0 6.3 - - + -
12C LEU* 3.8 18.4 - - + -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLU* 2.9 36.9 + - + +
7A ASP* 3.4 24.2 - - - +
9A VAL* 1.3 76.5 - - + +
11A GLU* 1.3 61.6 + - - +
13A LEU* 3.3 13.5 + - + +
14A SER* 3.1 26.4 + - - -
8C LYS* 5.8 7.0 - - + +
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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 ASP 3.0 13.4 + - - +
8A LYS* 3.6 10.8 - - - +
9A VAL 3.2 0.2 - - - -
10A GLU* 1.3 78.1 - - - +
12A LEU* 1.3 57.2 + - - +
14A SER* 3.2 9.8 + - - +
15A LYS* 2.9 61.8 + - + +
13B LEU* 5.3 6.3 - - + -
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Residues in contact with LEU 12 (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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8A LYS 3.0 19.8 + - - +
9A VAL* 3.1 8.3 + - + +
11A GLU* 1.3 76.0 - - - +
13A LEU* 1.3 57.8 + - - +
15A LYS* 3.5 16.8 + - - +
16A SER* 3.0 29.5 + - - -
9B VAL* 3.9 22.9 - - + -
12B LEU* 3.7 44.9 - - + +
13B LEU* 3.5 29.2 - - + -
16B SER* 4.1 4.3 - - - -
12C LEU* 3.7 22.4 - - + +
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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
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9A VAL* 2.9 31.9 + - + +
10A GLU* 3.8 10.8 - - + +
11A GLU 3.3 0.2 - - - -
12A LEU* 1.3 72.9 - - - +
14A SER* 1.3 66.9 + - - +
16A SER* 3.3 3.9 + - - -
17A TYR* 3.0 22.7 + - - +
8C LYS* 4.5 23.3 - - + +
11C GLU* 6.0 2.7 - - + -
12C LEU* 3.2 30.3 - - + +
15C LYS* 4.4 20.1 + - + +
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Residues in contact with SER 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 GLU 3.1 14.3 + - - -
11A GLU* 3.2 15.0 + - - -
13A LEU* 1.3 79.1 - - - +
15A LYS* 1.3 62.3 + - - +
17A TYR* 3.3 9.2 + - - +
18A HIS* 3.0 23.6 + - - +
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Residues in contact with LYS 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 2.9 56.1 + - + +
12A LEU* 3.8 16.8 - - + +
13A LEU 3.3 0.2 - - - -
14A SER* 1.3 75.6 - - - +
16A SER* 1.3 57.7 + - - +
18A HIS* 3.4 6.8 + - - +
19A LEU* 2.9 39.7 + - + +
13B LEU* 4.4 5.4 - - - +
16B SER* 3.2 33.9 + - - -
17B TYR* 3.4 24.9 + - - -
20B GLU* 3.7 23.9 + - - +
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Residues in contact with SER 16 (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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12A LEU 3.0 19.1 + - - -
13A LEU* 3.6 7.9 - - - -
15A LYS* 1.3 75.6 - - - +
17A TYR* 1.3 59.8 + - - +
19A LEU* 3.3 11.1 + - - +
20A GLU* 2.9 46.2 + - - +
12C LEU* 4.4 9.5 - - - +
15C LYS* 3.9 20.9 - - - +
16C SER* 5.3 0.5 + - - -
19C LEU* 3.8 10.6 - - - +
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Residues in contact with TYR 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 3.0 13.4 + - - +
14A SER* 3.5 11.9 - - - +
16A SER* 1.3 77.0 - - - +
18A HIS* 1.3 66.3 + - + +
20A GLU* 3.3 15.8 + - + +
21A ASN* 3.1 54.8 + - - -
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Residues in contact with HIS 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 SER 3.0 13.8 + - - +
15A LYS* 3.7 8.5 - - - +
17A TYR* 1.3 81.3 - - + +
19A LEU* 1.3 66.0 + - + +
21A ASN* 3.2 12.2 + - + +
22A GLU* 3.0 51.3 + - + +
20B GLU* 4.6 14.8 - - - -
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Residues in contact with LEU 19 (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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15A LYS* 2.9 29.5 + - + +
16A SER* 3.7 8.5 - - - +
18A HIS* 1.3 77.7 - - + +
20A GLU* 1.3 60.8 + - - +
22A GLU* 3.1 6.9 + - + +
23A VAL* 2.9 38.5 + - + +
16B SER* 4.3 18.6 - - - +
19B LEU* 4.4 20.9 - - + +
20B GLU* 3.3 51.8 - - + +
23B VAL* 4.7 11.7 - - + -
19C LEU* 4.2 10.8 - - + -
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Residues in contact with GLU 20 (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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16A SER* 2.9 21.8 + - - +
17A TYR* 3.4 20.1 - - + +
18A HIS 3.3 0.2 - - - -
19A LEU* 1.3 77.3 - - - +
21A ASN* 1.3 63.4 + - - +
23A VAL* 3.4 3.9 + - - +
24A ALA* 3.1 21.8 + - - +
15C LYS* 4.2 21.2 + - - +
18C HIS* 5.5 4.1 + - + +
19C LEU* 3.4 39.9 - - + +
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Residues in contact with ASN 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 TYR* 3.1 58.3 + - - +
18A HIS* 3.2 11.0 + - + +
20A GLU* 1.3 76.6 - - - +
22A GLU* 1.3 60.0 + - + +
24A ALA* 3.3 8.0 + - - +
25A ARG* 3.0 40.9 + - - +
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Residues in contact with GLU 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 HIS* 3.0 45.0 + - + +
19A LEU* 3.1 12.8 + - + +
21A ASN* 1.3 76.9 - - - +
23A VAL* 1.3 56.8 + - - +
25A ARG* 3.2 18.0 + - - +
26A LEU* 2.9 38.6 + - - +
23B VAL* 3.4 24.5 - - + +
27B LYS* 2.7 34.5 + - - +
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Residues in contact with VAL 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 LEU* 2.9 25.3 + - + +
20A GLU* 3.6 7.6 - - - +
22A GLU* 1.3 75.7 - - - +
24A ALA* 1.3 56.4 + - - +
26A LEU* 3.4 4.0 + - - +
27A LYS* 3.0 31.3 + - + +
23B VAL* 4.4 11.7 - - + -
19C LEU* 4.5 12.6 - - + -
22C GLU* 3.8 32.5 - - + +
23C VAL* 4.2 21.5 - - + -
26C LEU* 3.9 23.5 - - + +
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Residues in contact with ALA 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 GLU 3.1 13.5 + - - +
21A ASN* 3.5 13.5 - - - +
22A GLU 3.2 0.2 - - - -
23A VAL* 1.3 74.7 - - - +
25A ARG* 1.3 64.6 + - + +
27A LYS* 3.3 24.0 - - - +
28A LYS* 3.2 31.5 + - - +
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ASN* 3.0 27.1 + - - +
22A GLU* 3.6 20.6 - - - +
24A ALA* 1.3 76.0 - - + +
26A LEU* 1.3 60.4 + - + +
28A LYS* 3.3 9.6 + - - +
29A LEU* 2.8 49.2 + - + +
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 2.9 20.4 + - - +
23A VAL* 3.7 4.5 - - - +
25A ARG* 1.3 78.2 - - + +
27A LYS* 1.3 52.6 + - - +
28A LYS 3.1 5.0 + - - -
29A LEU* 3.7 6.5 + - + +
31A GLY* 2.3 41.7 + - - -
23B VAL* 3.5 40.2 - - + +
26B LEU* 4.2 16.6 - - + +
27B LYS* 3.8 26.0 - - + -
30B VAL* 4.8 14.8 - - + -
26C LEU* 3.8 18.6 - - + -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.0 19.5 + - + +
24A ALA* 3.3 29.4 - - - +
26A LEU* 1.3 76.3 - - - +
28A LYS* 1.3 59.2 + - + +
30A VAL* 4.5 1.4 + - - -
31A GLY 4.2 2.5 - - - -
32A GLU* 3.4 34.3 + - - +
22C GLU* 4.3 18.6 + - - +
26C LEU* 4.5 14.6 - - + +
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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) + - + + + + + -
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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