Contacts of the helix formed by residues 19 - 45 (chain B) in PDB entry 3DXR
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 ILE 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.0 29.6 + - + +
15B SER 3.3 15.3 - - - +
16B GLN* 2.7 26.0 - - + +
18B LYS* 1.3 71.3 - - - +
20B GLN* 1.3 56.4 + - + +
21B ALA* 2.6 6.9 + - - -
22B ALA* 2.6 37.2 + - + +
23B GLU* 3.7 1.0 + - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B GLN 4.5 1.1 - - - +
17B GLN* 2.7 47.5 + - - +
19B ILE* 1.3 83.9 - - + +
21B ALA* 1.3 49.4 + - - +
23B GLU* 3.0 13.5 + - + +
24B ALA* 2.7 36.6 + - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LYS 2.8 17.1 + - - +
19B ILE* 2.6 4.8 + - - +
20B GLN* 1.3 75.2 - - - +
22B ALA* 1.3 52.1 + - - +
24B ALA* 3.6 6.9 - - - +
25B GLU* 2.5 40.9 + - + +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE 4.4 21.3 - - - +
15A VAL* 5.1 3.6 - - + -
19B ILE* 2.6 20.4 + - + +
21B ALA* 1.3 72.5 - - - +
23B GLU* 1.3 57.3 + - - +
25B GLU* 4.5 3.4 - - - -
26B LEU* 2.8 51.0 + - + +
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Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 5.4 16.1 - - + +
19B ILE 3.7 0.6 + - - +
20B GLN* 3.0 16.1 + - + +
22B ALA* 1.3 78.6 - - - +
24B ALA* 1.3 51.9 + - - +
26B LEU* 3.9 2.6 - - - -
27B ASP* 2.8 37.2 + - - +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN 2.7 20.2 + - - +
21B ALA* 3.6 9.6 - - - +
23B GLU* 1.3 72.4 - - - +
25B GLU* 1.3 60.7 + - - +
27B ASP* 3.0 21.3 - - - +
28B LEU* 3.1 10.9 + - - +
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 2.5 23.5 + - + +
22B ALA* 4.2 2.9 - - - +
24B ALA* 1.3 69.8 - - - +
26B LEU* 1.3 60.4 + - + +
27B ASP 2.8 4.5 - - - -
28B LEU* 2.9 9.2 + - - +
29B VAL* 2.8 36.7 + - + +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 5.0 6.1 - - + -
16A VAL* 3.9 30.7 - - + -
19A LYS* 5.7 9.4 - - + -
22B ALA* 2.8 41.6 + - + +
23B GLU* 3.9 2.7 - - - +
25B GLU* 1.3 77.6 - - + +
27B ASP* 1.3 57.2 + - - +
29B VAL* 3.8 15.8 - - + +
30B THR* 2.7 32.8 + - - +
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Residues in contact with ASP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU 2.8 21.8 + - - +
24B ALA* 3.0 14.8 - - - +
25B GLU 2.8 0.2 - - - -
26B LEU* 1.3 79.5 - - - +
28B LEU* 1.3 54.4 + - - +
30B THR* 3.9 3.1 - - - -
31B ASP* 3.1 29.3 + - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 3.1 7.1 + - - +
25B GLU* 2.9 9.9 + - - +
27B ASP* 1.3 77.0 - - - +
29B VAL* 1.3 61.3 + - + +
31B ASP* 4.3 12.8 - - + +
32B MET* 2.9 37.9 + - + +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.8 23.6 - - + -
78A ASN* 5.0 11.4 - - - +
25B GLU* 2.8 37.5 + - + +
26B LEU* 3.8 17.0 - - + +
28B LEU* 1.3 77.0 - - + +
30B THR* 1.3 63.8 - - - +
32B MET* 3.9 3.5 - - - +
33B PHE* 3.1 23.7 + - - +
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Residues in contact with THR 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LYS* 5.7 6.1 - - - +
23A ASP* 5.1 17.9 - - + +
26B LEU* 2.7 23.8 + - - +
27B ASP* 3.9 4.0 - - - -
29B VAL* 1.3 75.9 - - - +
31B ASP* 1.3 60.3 + - - +
33B PHE* 3.2 9.4 + - + +
34B ASN* 2.5 46.2 + - - +
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASP 3.1 19.1 + - - +
28B LEU* 4.0 12.9 - - + +
30B THR* 1.3 77.9 - - - +
32B MET* 1.3 62.2 + - - +
34B ASN* 3.2 12.3 + - - +
35B LYS* 2.9 62.2 + - - +
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Residues in contact with MET 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PHE* 3.9 13.0 - - + -
28B LEU* 2.9 29.5 + - + +
29B VAL* 3.9 5.6 - - - +
31B ASP* 1.3 78.0 - - - +
33B PHE* 1.3 58.8 + - - +
35B LYS* 3.0 9.6 + - + +
36B LEU* 2.8 32.6 + - + +
69B TYR* 3.8 22.6 - - + +
70B PHE* 3.6 40.8 - - + -
73B ASN* 3.5 36.6 - - - +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 4.4 13.2 - - - -
70A VAL* 4.4 2.2 - - + -
71A GLY* 3.7 31.0 - - - -
74A PHE* 3.4 41.0 - + + -
75A GLN* 5.3 1.1 - - - -
29B VAL 3.1 17.1 + - - +
30B THR* 3.5 7.9 - - + +
32B MET* 1.3 79.1 - - - +
34B ASN* 1.3 72.6 + - - +
36B LEU* 3.3 8.8 - - + +
37B VAL* 2.9 57.7 + - + +
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Residues in contact with ASN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 5.2 9.8 - - - +
30A ASN* 5.1 10.5 + - - +
30B THR* 2.5 43.1 + - - +
31B ASP* 3.5 9.7 + - - +
32B MET 3.1 0.4 - - - -
33B PHE* 1.3 90.1 - - - +
35B LYS* 1.3 65.2 + - + +
37B VAL* 3.4 5.6 + - - +
38B ASN* 2.9 36.7 + - - +
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Residues in contact with LYS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ASP* 2.9 47.2 + - - +
32B MET* 3.0 8.0 + - + +
34B ASN* 1.3 76.5 - - + +
36B LEU* 1.3 55.0 + - - +
38B ASN* 3.3 4.8 + - - +
39B ASN* 2.6 48.9 + - - +
69B TYR* 3.4 18.6 - - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.6 25.8 - - + -
74A PHE* 3.3 36.3 - - + -
32B MET* 2.8 13.4 + - + +
33B PHE* 3.3 9.6 - - + +
35B LYS* 1.3 76.2 - - - +
37B VAL* 1.3 56.0 + - - +
39B ASN* 4.4 1.6 - - - -
40B CYS* 2.9 39.2 + - - +
66B VAL* 4.0 25.1 - - + +
69B TYR* 3.4 49.7 + - + -
70B PHE* 4.4 2.9 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 4.2 20.4 - - + -
66A HIS* 2.9 43.6 + - + +
67A SER* 4.3 12.3 - - - +
70A VAL* 4.0 14.4 - - + -
33B PHE* 2.9 60.5 + - + +
34B ASN* 3.7 7.6 - - - +
36B LEU* 1.3 76.3 - - - +
38B ASN* 1.3 62.8 + - - +
41B TYR* 3.2 9.9 + - - +
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Residues in contact with ASN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASN* 5.5 12.6 - - - +
63A PHE* 4.9 10.4 - - - -
34B ASN* 2.9 29.8 + - - +
35B LYS* 3.9 4.4 - - - +
37B VAL* 1.3 80.0 - - - +
39B ASN* 1.3 67.7 + - - +
41B TYR* 3.4 7.4 + - - +
42B LYS* 3.3 32.3 + - - +
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Residues in contact with ASN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 2.6 39.2 + - - +
36B LEU 3.8 2.2 - - - +
38B ASN* 1.3 74.2 - - - +
40B CYS* 1.3 59.9 + - - +
42B LYS* 3.1 14.0 + - - +
43B LYS* 3.1 41.7 + - + +
65B CYS* 5.7 0.2 - - - -
69B TYR* 3.7 31.1 + - + -
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Residues in contact with CYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 4.0 12.8 - - + -
70A VAL* 4.6 5.6 - - + -
36B LEU* 2.9 27.1 + - - +
39B ASN* 1.3 76.1 - - - +
41B TYR* 1.3 58.9 + - - +
43B LYS* 3.8 1.3 - - - -
44B CYS* 3.0 32.1 + - - +
62B LEU* 3.9 7.3 - - + +
65B CYS* 2.0 61.7 - - + -
66B VAL* 3.8 10.3 - - + -
69B TYR* 5.1 2.5 - - - -
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Residues in contact with TYR 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 3.3 31.7 + - + +
38A ASP* 3.7 12.1 + - - -
59A CYS* 5.9 0.9 - - - -
62A LYS* 5.1 7.2 - - + -
63A PHE* 4.2 30.1 - + + -
66A HIS* 3.7 15.0 - + + +
37B VAL 3.2 19.6 + - - +
38B ASN* 3.5 8.7 - - - +
39B ASN 3.1 0.4 - - - -
40B CYS* 1.3 78.3 - - - +
42B LYS* 1.3 68.4 + - + +
45B ILE* 2.7 71.2 + - + +
47B THR* 2.9 28.8 - - + +
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ARG* 6.3 0.7 - - - +
38B ASN* 3.5 20.2 - - - +
39B ASN* 3.1 12.9 + - - +
41B TYR* 1.3 91.7 - - + +
43B LYS* 1.3 62.5 + - + +
45B ILE 4.7 6.1 + - - +
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASN* 3.1 29.0 + - + +
40B CYS 4.0 4.0 - - - +
41B TYR 3.3 0.2 - - - -
42B LYS* 1.3 80.7 - - + +
44B CYS* 1.3 62.2 + - - +
61B CYS* 4.1 4.0 - - - -
65B CYS* 4.2 18.6 - - - -
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Residues in contact with CYS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B CYS 3.0 17.0 + - - +
43B LYS* 1.3 83.4 - - - +
45B ILE* 1.3 61.0 + - + +
46B ASN* 3.9 1.6 + - - +
58B GLU* 3.7 22.2 - - - +
61B CYS* 2.0 65.9 - - + -
62B LEU* 3.7 15.5 - - + -
65B CYS* 3.9 13.2 - - - -
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LYS* 4.3 20.0 - - + -
66A HIS* 4.1 18.8 - - + +
41B TYR* 2.7 70.5 + - + +
42B LYS* 4.7 5.6 + - - +
43B LYS 4.0 0.2 - - - -
44B CYS* 1.3 78.4 - - + +
46B ASN* 1.3 64.9 + - - +
47B THR* 4.0 14.8 + - + +
54B LEU* 5.1 10.5 - - + -
58B GLU* 4.4 7.0 - - + +
62B LEU* 4.9 1.8 - - + -
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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