Contacts of the helix formed by residues 3 - 31 (chain A) in PDB entry 4PBZ
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 ASP 3 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 1.3 76.2 - - - +
4A LYS* 1.3 66.1 + - - +
5A GLU 3.2 1.6 - - - -
6A ALA* 3.0 25.0 + - + +
7A ALA* 3.7 3.6 + - - +
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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 ALA* 3.2 12.2 - - + +
3A ASP* 1.3 77.1 - - - +
5A GLU* 1.3 63.5 + - + +
6A ALA 3.0 1.4 + - - -
7A ALA* 3.1 10.4 + - + +
8A PHE* 3.1 27.1 + - + +
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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
----------------------------------------------------------
2A ALA 4.1 17.2 + - - +
3A ASP 3.2 0.8 + - - -
4A LYS* 1.3 76.3 - - + +
6A ALA* 1.3 56.1 + - - +
8A PHE* 4.6 8.1 - - - -
9A ASP* 2.5 51.7 + - - +
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ASP* 3.0 15.2 + - + +
5A GLU* 1.3 76.5 - - - +
7A ALA* 1.3 60.1 + - - +
9A ASP* 3.3 5.0 + - - +
10A ASP* 2.9 38.9 + - - +
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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
----------------------------------------------------------
3A ASP 3.7 3.1 + - - +
4A LYS* 3.1 11.0 + - + +
6A ALA* 1.3 78.6 - - - +
8A PHE* 1.3 56.3 + - - +
10A ASP* 3.7 10.2 + - - +
11A ALA* 3.2 26.2 + - - +
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Residues in contact with PHE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 3.1 23.7 + - + +
5A GLU* 4.1 8.1 - - - +
7A ALA* 1.3 75.4 - - - +
9A ASP* 1.3 91.8 + - - +
11A ALA* 3.2 7.3 + - + +
12A VAL* 3.0 46.1 + - + +
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Residues in contact with ASP 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLU* 2.5 38.9 + - - +
6A ALA* 3.7 5.4 - - - +
8A PHE* 1.3 95.0 - - - +
10A ASP* 1.3 64.1 + - - +
12A VAL* 3.5 7.6 + - - +
13A GLU* 3.1 22.4 + - - +
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Residues in contact with ASP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA* 2.9 24.2 + - - +
7A ALA* 3.7 8.5 - - - +
9A ASP* 1.3 74.2 - - - +
11A ALA* 1.3 57.7 + - - +
13A GLU* 3.1 13.1 + - - +
14A GLU* 2.7 36.0 + - - +
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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
----------------------------------------------------------
7A ALA 3.2 14.5 + - - +
8A PHE* 3.2 7.8 + - + +
10A ASP* 1.3 81.8 - - - +
12A VAL* 1.3 59.8 + - - +
14A GLU* 3.5 17.3 + - - +
15A ARG* 3.1 22.2 + - - +
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Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.0 49.7 + - + +
9A ASP* 3.7 8.3 - - - +
11A ALA* 1.3 74.1 - - - +
13A GLU* 1.3 65.9 + - - +
15A ARG* 3.3 8.7 - - + +
16A VAL* 3.1 28.7 + - + +
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Residues in contact with GLU 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 ASP 3.1 11.5 + - - +
10A ASP* 3.1 16.6 + - - +
12A VAL* 1.3 80.2 - - - +
14A GLU* 1.3 56.4 + - - +
16A VAL* 3.0 11.6 + - + +
17A ILE* 2.9 50.1 + - + +
340A ARG* 4.1 10.4 + - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP 2.7 18.2 + - - +
11A ALA* 3.6 16.5 - - - +
13A GLU* 1.3 73.4 - - - +
15A ARG* 1.3 56.9 + - - +
17A ILE* 3.6 14.6 - - + +
18A ASN* 3.0 43.2 + - - +
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Residues in contact with ARG 15 (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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11A ALA 3.1 13.9 + - - +
12A VAL* 3.3 14.1 - - - +
13A GLU 3.1 0.2 - - - -
14A GLU* 1.3 76.4 - - - +
16A VAL* 1.3 64.7 + - + +
18A ASN* 3.5 7.0 + - - +
19A GLU* 3.2 50.3 + - + +
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Residues in contact with VAL 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 VAL* 3.1 19.9 + - + +
13A GLU* 3.0 13.0 + - + +
15A ARG* 1.3 75.6 - - + +
17A ILE* 1.3 66.5 + - + +
19A GLU* 3.3 7.5 + - + +
20A GLU* 3.1 45.7 + - + +
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Residues in contact with ILE 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 GLU* 2.9 37.6 + - + +
14A GLU* 3.6 11.7 - - + +
15A ARG 3.2 0.2 - - - -
16A VAL* 1.3 78.9 - - + +
18A ASN* 1.3 61.9 + - - +
20A GLU* 3.4 10.3 + - - +
21A TYR* 3.0 25.8 + - - +
340A ARG* 3.5 46.4 - - - +
373A HIS 5.5 0.4 - - - +
374A THR* 3.7 40.2 - - + +
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Residues in contact with ASN 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 GLU* 3.0 37.6 + - - +
15A ARG* 4.0 6.1 - - - +
17A ILE* 1.3 78.0 - - - +
19A GLU* 1.3 67.0 + - - +
21A TYR* 3.4 9.7 + - - +
22A LYS* 3.1 32.6 + - - +
374A THR* 4.6 13.2 - - - +
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Residues in contact with GLU 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 ARG* 3.2 38.4 + - + +
16A VAL* 3.3 10.5 + - + +
18A ASN* 1.3 79.0 - - - +
20A GLU* 1.3 64.0 + - + +
22A LYS* 3.1 43.6 + - - +
23A ILE* 3.2 24.1 + - + +
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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 VAL* 3.1 34.4 + - + +
17A ILE* 3.6 9.9 - - - +
19A GLU* 1.3 79.9 - - + +
21A TYR* 1.3 63.0 + - - +
23A ILE* 3.2 10.5 + - + +
24A TRP 2.9 18.5 + - - -
340A ARG* 4.7 10.4 + - - -
685B TYR* 3.5 61.3 - - + +
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Residues in contact with TYR 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 ILE 3.0 14.8 + - - +
18A ASN* 3.5 15.5 - - - +
19A GLU 3.2 0.4 - - - -
20A GLU* 1.3 76.1 - - - +
22A LYS* 1.3 64.6 + - + +
24A TRP* 3.2 30.1 + + - +
25A LYS* 2.9 47.7 + - + +
37A THR* 5.0 11.6 + - - +
371A GLY 4.7 2.0 - - - -
372A GLY 3.4 25.6 - - - -
374A THR* 3.6 28.9 - - + -
400A GLN* 4.9 2.0 + - - -
685B TYR* 4.7 3.1 - - - -
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Residues in contact with LYS 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 ASN* 3.1 22.6 + - - +
19A GLU* 3.1 36.5 + - - +
21A TYR* 1.3 83.2 - - + +
23A ILE* 1.3 64.8 + - + +
25A LYS* 3.5 4.3 + - - +
26A LYS* 3.1 24.3 + - - +
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Residues in contact with ILE 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 GLU* 3.2 22.3 + - + +
20A GLU* 3.6 9.6 - - + +
21A TYR 3.2 0.6 - - - -
22A LYS* 1.3 76.3 - - + +
24A TRP* 1.3 65.8 + - - +
26A LYS* 3.3 7.8 + - - +
27A ASN* 3.0 22.8 + - - +
685B TYR* 3.1 37.9 - - - +
686B LYS 3.7 2.5 - - - +
687B PRO* 3.5 39.7 - - + -
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Residues in contact with TRP 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 2.9 13.1 + - - +
21A TYR* 3.6 44.4 - + - +
23A ILE* 1.3 77.6 - - - +
25A LYS* 1.3 87.8 + - + +
27A ASN* 2.8 21.3 + - - +
28A THR* 3.2 29.3 + - + +
31A LEU* 5.2 5.4 - - + -
32A TYR* 2.8 37.9 + + - -
35A VAL* 4.0 15.9 - - + -
37A THR* 4.9 2.2 - - - -
369A ILE 5.7 0.2 - - - -
370A HIS* 4.0 6.5 - + - -
371A GLY* 3.7 23.6 - - - +
372A GLY* 3.3 27.5 - - - +
400A GLN* 3.8 11.2 - - - -
684B PRO* 3.8 25.9 + - + +
685B TYR* 4.3 3.8 - - + -
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A TYR* 2.9 36.3 + - + +
22A LYS* 3.7 6.5 - - - +
24A TRP* 1.3 99.7 - - + +
26A LYS* 1.3 61.9 + - - +
28A THR* 2.7 35.1 + - - +
29A PRO* 4.0 1.2 - - - +
35A VAL* 5.5 7.9 + - - +
37A THR* 5.3 6.9 + - - -
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Residues in contact with LYS 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 LYS 3.1 17.6 + - - +
23A ILE* 3.7 7.0 - - - +
24A TRP 3.2 0.2 - - - -
25A LYS* 1.3 78.4 - - - +
27A ASN* 1.3 62.7 + - - +
29A PRO* 3.4 13.8 - - - +
30A PHE* 4.6 6.9 - - - -
687B PRO* 6.5 0.4 - - + -
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Residues in contact with ASN 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ILE 3.0 13.3 + - - +
24A TRP* 2.8 13.5 + - + +
26A LYS* 1.3 77.2 - - - +
28A THR* 1.3 62.8 + - - +
29A PRO* 3.3 3.1 - - - -
30A PHE* 3.1 22.2 + - - +
31A LEU* 3.4 21.5 + - + +
680B ALA 5.7 0.2 + - - -
683B ARG 4.6 1.8 + - - -
684B PRO* 3.6 18.0 + - - +
686B LYS 2.9 28.1 + - - -
687B PRO* 3.8 2.4 - - - +
688B ILE* 3.0 42.6 + - + +
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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 TRP* 3.2 49.6 + - + +
25A LYS* 2.7 32.0 + - + +
27A ASN* 1.3 75.5 - - - +
29A PRO* 1.4 69.4 - - - +
30A PHE 3.0 1.2 + - - -
31A LEU 3.1 0.2 + - - -
32A TYR* 3.1 43.7 + - + +
35A VAL* 4.3 12.1 - - + -
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Residues in contact with PRO 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS 4.0 1.3 - - - +
26A LYS* 3.4 13.0 - - - +
27A ASN 3.3 5.4 - - - -
28A THR* 1.4 98.4 - - - +
30A PHE* 1.3 79.0 + - + +
32A TYR 3.9 10.8 - - - +
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Residues in contact with PHE 30 (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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26A LYS 4.6 9.0 - - - -
27A ASN* 3.1 13.8 + - - -
28A THR 3.0 0.8 - - - -
29A PRO* 1.3 95.3 - - + +
31A LEU* 1.3 61.9 + - + +
32A TYR 3.5 0.7 - - - -
405A ALA* 3.7 13.6 - - - +
407A ASN* 5.0 0.2 - - - +
672B LEU* 3.8 30.0 - - + +
677B THR* 3.7 14.1 - - + +
688B ILE* 3.7 28.7 - - + -
690B LEU* 4.3 28.9 - - + -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TRP* 5.2 3.8 - - + -
27A ASN* 3.4 28.4 + - + +
28A THR 3.1 1.6 + - - -
30A PHE* 1.3 83.0 - - - +
32A TYR* 1.3 78.3 + - + +
368A PHE* 3.8 9.1 - - + -
369A ILE 5.7 0.2 - - - +
404A MET* 3.4 7.6 - - - +
405A ALA* 2.7 26.7 + - - -
408A ILE* 3.5 14.1 - - + +
677B THR* 4.1 9.2 - - + +
680B ALA* 4.0 26.5 - - + +
681B ALA* 4.0 26.2 - - - +
684B PRO* 4.8 15.3 - - + -
688B ILE* 4.3 7.2 - - + -
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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