Contacts of the helix formed by residues 4 - 36 (chain A) in PDB entry 2JR8
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 PRO 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY 4.9 0.2 - - - +
2A LYS 2.9 12.3 - - - +
3A ILE* 1.3 83.3 - - + +
5A VAL* 1.3 64.2 + - - +
6A LYS* 3.1 4.0 - - + +
7A ALA* 3.0 30.3 + - + +
8A ILE* 3.3 15.3 - - + +
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Residues in contact with VAL 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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3A ILE* 2.7 40.6 + - + +
4A PRO* 1.3 71.4 - - - +
6A LYS* 1.3 76.1 + - - +
8A ILE* 3.3 16.7 + - + +
9A LYS* 3.0 34.2 + - + +
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 5.0 1.3 - - + -
5A VAL* 1.3 92.8 - - - +
7A ALA* 1.3 52.7 + - - +
9A LYS* 3.6 12.7 - - + +
10A GLN* 2.7 47.7 + - + +
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Residues in contact with ALA 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 3.0 25.6 + - + +
6A LYS* 1.3 79.7 - - - +
8A ILE* 1.3 63.7 + - + +
10A GLN* 3.2 7.6 + - - +
11A ALA* 3.1 21.0 + - - +
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Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 5.5 4.3 - - + -
4A PRO* 3.3 26.9 - - + +
5A VAL* 3.3 20.3 + - + +
7A ALA* 1.3 76.2 - - + +
9A LYS* 1.3 63.0 + - - +
11A ALA* 3.2 17.9 + - + +
12A GLY* 3.4 8.5 + - - -
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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
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5A VAL* 3.0 28.5 + - + +
6A LYS* 3.8 12.8 - - + +
8A ILE* 1.3 76.5 - - - +
10A GLN* 1.3 62.0 + - - +
12A GLY* 3.3 10.9 + - - +
13A LYS* 3.4 32.8 + - + +
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Residues in contact with GLN 10 (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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6A LYS* 2.7 32.8 + - + +
7A ALA* 3.4 8.5 - - - +
8A ILE 3.2 0.2 - - - -
9A LYS* 1.3 72.0 - - - +
11A ALA* 1.3 61.5 + - - +
13A LYS* 3.2 35.3 + - - +
14A VAL* 3.0 28.3 + - + +
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Residues in contact with ALA 11 (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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7A ALA 3.1 11.3 + - - +
8A ILE* 3.2 13.2 + - + +
10A GLN* 1.3 79.5 - - - +
12A GLY* 1.3 60.7 + - - +
13A LYS 3.4 0.5 + - - -
14A VAL* 3.4 16.3 + - - +
15A ILE* 3.3 21.4 + - + +
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Residues in contact with GLY 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE 3.4 5.3 + - - -
9A LYS 3.3 8.2 + - - -
10A GLN 3.2 1.0 - - - -
11A ALA* 1.3 79.5 - - - +
13A LYS* 1.3 61.6 + - - +
15A ILE* 3.5 26.7 + - - +
16A GLY* 3.7 4.5 + - - -
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Residues in contact with LYS 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 LYS* 3.4 30.5 + - + +
10A GLN* 3.2 32.2 + - - +
11A ALA 3.2 0.4 - - - -
12A GLY* 1.3 75.8 - - - +
14A VAL* 1.3 55.9 + - + +
15A ILE 3.1 0.2 - - - -
16A GLY* 3.0 3.0 + - - +
17A LYS* 2.7 40.6 + - + +
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Residues in contact with VAL 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 GLN* 3.0 26.2 + - - +
11A ALA* 3.7 11.4 - - - +
12A GLY 3.4 0.4 - - - -
13A LYS* 1.3 76.2 - - + +
15A ILE* 1.3 57.9 + - + +
17A LYS* 4.4 6.3 - - + -
18A GLY* 2.8 29.5 + - - +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA 3.3 18.4 - - - +
12A GLY* 3.6 16.2 - - - +
13A LYS 3.1 0.4 - - - -
14A VAL* 1.3 78.9 - - + +
16A GLY* 1.3 59.2 + - - +
19A LEU* 3.4 27.9 + - + +
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Residues in contact with GLY 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 GLY 3.7 4.7 + - - -
13A LYS* 3.0 6.0 + - - -
15A ILE* 1.3 77.8 - - - +
17A LYS* 1.3 64.6 + - - +
18A GLY 3.1 1.8 - - - -
19A LEU* 3.1 6.8 + - - +
20A ARG* 3.0 28.7 + - - +
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Residues in contact with LYS 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 LYS* 2.7 25.5 + - + +
14A VAL* 4.3 4.5 - - + +
16A GLY* 1.3 71.4 - - - -
18A GLY* 1.3 57.5 + - - +
20A ARG* 3.5 7.8 + - + +
21A ALA* 3.1 44.4 + - - +
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 2.8 21.1 + - - +
15A ILE 4.4 0.2 - - - -
17A LYS* 1.3 77.5 - - - +
19A LEU* 1.3 58.6 + - - +
21A ALA* 3.3 6.1 + - - +
22A ILE* 3.0 40.6 + - - +
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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 ILE* 3.4 24.4 + - + +
16A GLY* 3.1 7.9 + - - +
18A GLY* 1.3 78.1 - - - +
20A ARG* 1.3 62.0 + - + +
22A ILE* 3.5 13.7 + - + +
23A ASN* 3.3 28.8 + - - +
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Residues in contact with ARG 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 GLY 3.0 19.0 + - - +
17A LYS* 3.9 7.6 - - + +
19A LEU* 1.3 78.1 - - + +
21A ALA* 1.3 58.7 + - - +
23A ASN* 3.6 8.2 + - + +
24A ILE* 3.1 37.1 + - + +
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Residues in contact with ALA 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 LYS* 3.1 35.1 + - - +
18A GLY* 3.5 8.5 - - - +
19A LEU 3.2 0.4 - - - -
20A ARG* 1.3 76.9 - - - +
22A ILE* 1.3 54.6 + - + +
23A ASN 3.2 0.2 - - - -
24A ILE* 3.2 8.9 + - - +
25A ALA* 2.8 35.9 + - - +
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Residues in contact with ILE 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 GLY 3.0 25.5 + - - +
19A LEU* 3.9 13.7 - - + +
20A ARG 3.4 0.2 - - - -
21A ALA* 1.3 78.1 - - + +
23A ASN* 1.3 63.5 + - - +
25A ALA* 3.4 19.2 + - + +
26A GLY* 3.7 5.0 + - - -
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Residues in contact with ASN 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* 3.3 19.3 + - - +
20A ARG* 3.7 13.9 - - + +
21A ALA 3.2 0.2 - - - -
22A ILE* 1.3 81.5 - - - +
24A ILE* 1.3 61.9 + - + +
26A GLY* 3.8 7.8 + - - -
27A THR* 4.5 3.5 + - - +
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Residues in contact with ILE 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 ARG* 3.1 26.2 - - + +
21A ALA* 3.2 8.6 + - - +
23A ASN* 1.3 76.8 - - + +
25A ALA* 1.3 58.5 + - - +
26A GLY 3.0 3.1 - - - -
27A THR* 2.7 33.3 - - + +
28A THR* 2.5 29.6 + - + +
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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 ALA 2.8 17.1 + - - +
22A ILE* 3.5 15.5 - - + +
23A ASN 3.4 0.2 - - - -
24A ILE* 1.3 78.0 - - - +
26A GLY* 1.3 56.4 + - - +
28A THR* 3.6 8.1 - - - -
29A HIS* 3.0 29.5 + - - +
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Residues in contact with GLY 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 ILE 3.7 7.7 + - - -
23A ASN 3.8 5.0 + - - -
24A ILE 3.0 1.2 - - - -
25A ALA* 1.3 80.4 - - - +
27A THR* 1.3 60.3 + - - +
29A HIS* 3.5 17.3 - - - +
30A ASP* 3.7 7.4 + - - +
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Residues in contact with THR 27 (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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23A ASN 4.5 3.8 + - - +
24A ILE* 2.7 44.8 - - + +
26A GLY* 1.3 73.1 - - - +
28A THR* 1.3 67.5 + - - +
30A ASP* 3.1 14.6 + - - +
31A VAL* 3.1 25.2 + - + +
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Residues in contact with THR 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 ILE* 2.5 37.4 + - + +
25A ALA* 3.6 7.3 - - - -
27A THR* 1.3 77.0 - - - +
29A HIS* 1.3 62.6 + - - +
31A VAL* 3.4 12.2 + - + +
32A VAL* 3.0 35.5 + - + +
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Residues in contact with HIS 29 (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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25A ALA 3.0 19.1 + - - +
26A GLY* 3.5 9.9 - - - +
27A THR 3.2 0.4 - - - -
28A THR* 1.3 77.4 - - - +
30A ASP* 1.3 62.2 + - - +
32A VAL* 3.9 15.0 - - - +
33A SER* 3.9 5.7 + - - -
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLY 3.7 5.6 + - - +
27A THR* 3.1 13.1 + - - +
29A HIS* 1.3 77.8 - - - +
31A VAL* 1.3 57.8 + - + +
32A VAL 3.1 2.0 - - - -
33A SER* 2.6 38.9 + - - -
34A PHE* 3.5 2.4 + - - +
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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 THR* 3.1 23.8 - - - +
28A THR* 3.7 15.7 - - + +
30A ASP* 1.3 74.7 - - + +
32A VAL* 1.3 58.6 + - + +
34A PHE* 2.9 33.4 + - + +
35A PHE* 3.5 4.7 + - - +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A THR* 3.0 24.9 - - + +
29A HIS* 3.9 12.1 - - - +
30A ASP 3.0 0.8 + - - -
31A VAL* 1.3 77.7 - - + +
33A SER* 1.3 57.0 + - - +
35A PHE* 3.3 5.8 + - + +
36A ARG* 2.8 28.5 + - - +
37A PRO* 5.1 11.9 - - + -
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A HIS 3.9 5.5 + - - -
30A ASP* 2.6 27.0 + - - -
32A VAL* 1.3 75.5 - - - +
34A PHE* 1.3 59.6 + - - +
35A PHE 3.5 0.2 + - - -
36A ARG* 3.9 17.1 - - - +
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP 3.5 1.8 + - - +
31A VAL* 2.9 19.5 + - + +
33A SER* 1.3 82.0 - - - +
35A PHE* 1.3 62.8 + + - +
36A ARG* 4.8 0.5 - - - +
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Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL 3.5 4.6 + - - +
32A VAL* 3.3 9.0 + - + +
33A SER 3.3 0.4 - - - -
34A PHE* 1.3 82.3 - + - +
36A ARG* 1.3 83.3 - - - +
37A PRO* 5.9 1.8 - - + -
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 2.8 19.3 + - - +
33A SER* 3.9 14.6 - - - +
34A PHE 4.8 0.4 - - - +
35A PHE* 1.3 94.4 - - - +
37A PRO* 1.3 82.1 - - + +
38A LYS* 3.5 19.2 + - + +
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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