Contacts of the helix formed by residues 11 - 39 (chain I) in PDB entry 2DYS
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 GLY 11 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PSC 4.8 5.9 - - - -
40E ASP* 2.8 32.3 + - - -
8I GLN* 4.7 0.3 - - - +
10I ARG* 1.3 73.2 - - - +
12I LEU* 1.3 58.0 + - - +
13I LEU 3.3 2.7 - - - -
14I ALA* 4.1 5.2 - - - +
15I ARG* 2.9 31.4 + - - +
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Residues in contact with LEU 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.9 27.3 - - + +
40E ASP* 3.3 5.6 + - - +
41E LEU* 5.8 1.6 - - - -
42E VAL* 4.4 8.3 - - + +
74E LYS 4.7 0.9 - - - +
75E ALA 4.3 2.0 - - - +
78E HIS* 3.5 35.2 + - + +
81E ILE* 3.6 21.3 - - + -
8I GLN* 3.7 25.1 - - + +
9I MET 4.4 11.7 - - - +
10I ARG 4.4 6.3 - - - +
11I GLY* 1.3 75.1 - - - +
13I LEU* 1.3 65.5 + - - +
15I ARG* 3.6 24.5 - - - +
16I ARG* 3.1 22.9 + - - +
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Residues in contact with LEU 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 3.6 29.3 - - + +
329A GLY* 3.4 29.6 - - - +
48B THR* 3.8 22.4 - - + +
50B LEU* 3.7 37.1 - - + +
51B THR 4.9 1.8 - - - +
52B HIS* 3.7 20.9 - - + +
40E ASP* 2.9 17.8 + - - +
12I LEU* 1.3 76.4 - - - +
14I ALA* 1.3 59.5 + - - +
16I ARG* 3.1 11.1 + - - +
17I LEU* 3.0 25.5 + - - +
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Residues in contact with ALA 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 5.3 3.4 - - - +
52B HIS* 6.2 0.2 - - - +
303B PSC 3.5 40.2 - - + +
40E ASP* 2.9 10.5 + - - +
11I GLY* 4.1 5.4 - - - +
12I LEU 3.4 0.2 - - - -
13I LEU* 1.3 73.9 - - - +
15I ARG* 1.3 59.5 + - - +
17I LEU* 3.3 12.6 + - + +
18I ARG* 2.9 31.2 + - - +
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Residues in contact with ARG 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E HIS* 4.6 16.1 - - - -
8I GLN* 4.9 17.6 + - - +
11I GLY 2.9 21.7 + - - +
12I LEU* 3.6 29.2 - - - +
14I ALA* 1.3 77.7 - - - +
16I ARG* 1.3 68.2 + - - +
18I ARG* 3.5 8.6 + - - +
19I PHE* 3.2 26.0 + - - +
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Residues in contact with ARG 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 6.4 0.2 - - - -
44B LEU* 3.1 36.8 + - + +
45B MET* 5.2 3.2 - - - +
47B THR* 3.0 41.8 + - - -
48B THR* 3.3 33.1 + - - +
50B LEU* 4.7 8.3 - - + -
201D TGL 3.3 26.2 - - - +
78E HIS* 6.2 0.4 - - - +
12I LEU 3.1 14.6 + - - +
13I LEU* 3.1 13.1 + - - +
15I ARG* 1.3 81.4 - - - +
17I LEU* 1.3 64.2 + - - +
19I PHE* 3.5 5.3 + - - +
20I HIS* 3.1 44.0 + - + +
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Residues in contact with LEU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS* 3.6 34.8 - - + +
44B LEU* 4.5 8.5 - - + -
45B MET* 4.3 11.4 - - + -
303B PSC 3.9 59.9 - - + -
13I LEU 3.0 12.3 + - - +
14I ALA* 3.4 12.8 - - + +
16I ARG* 1.3 74.1 - - - +
18I ARG* 1.3 67.9 + - - +
20I HIS* 3.2 2.6 + - - +
21I ILE* 2.9 48.5 + - + +
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Residues in contact with ARG 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PSC 6.1 2.9 - - - -
14I ALA 2.9 16.8 + - - +
15I ARG* 3.6 7.2 - - - +
17I LEU* 1.3 78.7 - - - +
19I PHE* 1.3 64.6 + - - +
21I ILE* 3.4 4.5 + - - +
22I VAL* 3.2 33.0 + - + +
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Residues in contact with PHE 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ARG* 3.2 14.3 + - - +
16I ARG* 3.6 10.3 - - - +
17I LEU 3.2 0.4 - - - -
18I ARG* 1.3 80.4 - - - +
20I HIS* 1.3 91.7 + + - +
22I VAL* 3.5 6.5 + - - +
23I GLY* 3.2 17.5 + - - -
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Residues in contact with HIS 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TYR* 3.4 25.6 + - - +
44B LEU* 3.7 28.7 - - + +
201D TGL 4.1 27.1 - - + +
16I ARG* 3.1 42.0 + - + +
19I PHE* 1.3 100.6 - + - +
21I ILE* 1.3 62.1 + - - +
22I VAL 3.2 0.4 - - - -
23I GLY* 3.8 2.4 - - - +
24I ALA* 3.0 29.1 + - - +
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Residues in contact with ILE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 6.5 0.2 - - + -
40B TYR* 5.9 0.7 - - + -
41B ILE* 4.3 28.7 - - + -
44B LEU* 4.7 7.6 - - + -
303B PSC 4.4 39.5 - - + -
17I LEU* 2.9 42.8 + - + +
18I ARG* 4.0 4.5 - - - +
20I HIS* 1.3 77.0 - - - +
22I VAL* 1.3 66.0 + - + +
24I ALA* 3.4 10.1 + - + +
25I PHE* 3.1 22.6 + - + +
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Residues in contact with VAL 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG* 3.2 27.1 + - + +
19I PHE* 3.7 5.6 - - - +
20I HIS 3.2 0.4 - - - -
21I ILE* 1.3 79.1 - - + +
23I GLY* 1.3 66.1 + - - +
25I PHE* 3.2 11.5 + - + +
26I MET* 3.1 41.3 + - + +
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Residues in contact with GLY 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I PHE* 3.2 12.0 + - - -
20I HIS* 3.3 4.4 + - - -
22I VAL* 1.3 78.9 - - - +
24I ALA* 1.3 56.5 + - - +
26I MET* 3.0 13.1 + - - +
27I VAL* 2.9 34.6 + - - +
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Residues in contact with ALA 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.5 16.1 - - + +
40B TYR* 3.9 28.6 + - + -
41B ILE* 6.0 0.2 - - + -
20I HIS 3.0 17.7 + - - +
21I ILE* 3.5 13.0 - - + +
23I GLY* 1.3 74.5 - - - +
25I PHE* 1.3 57.5 + - - +
27I VAL* 3.5 8.5 + - - +
28I SER* 2.9 31.5 + - - -
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Residues in contact with PHE 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 6.1 0.4 - - - -
21I ILE* 3.1 14.5 + - + +
22I VAL* 3.3 14.6 - - + +
23I GLY 3.2 0.2 - - - -
24I ALA* 1.3 74.7 - - - +
26I MET* 1.3 81.1 + - + +
28I SER* 3.1 10.4 + - - -
29I LEU* 3.0 60.8 + - + +
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Residues in contact with MET 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I VAL* 3.1 31.1 + - + +
23I GLY* 3.0 12.2 + - - +
25I PHE* 1.3 93.7 - - + +
27I VAL* 1.3 59.5 + - + +
29I LEU* 3.2 12.1 + - - +
30I GLY* 2.9 24.4 + - - -
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Residues in contact with VAL 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLY 2.9 22.3 + - - +
24I ALA* 3.8 8.3 - - - +
26I MET* 1.3 74.1 - - + +
28I SER* 1.3 56.4 + - - +
30I GLY* 3.2 2.3 + - - +
31I PHE* 2.8 36.7 + - + +
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Residues in contact with SER 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.9 30.7 - - - +
37B LEU* 4.0 16.3 - - - +
24I ALA 2.9 18.2 + - - -
25I PHE* 3.1 14.6 + - - -
27I VAL* 1.3 75.3 - - - +
29I LEU* 1.3 63.0 + - - +
31I PHE* 3.3 3.4 + - - +
32I ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I PHE* 3.0 60.6 + - + +
26I MET* 3.5 14.1 - - - +
28I SER* 1.3 79.5 - - - +
30I GLY* 1.3 64.0 + - - +
32I ALA* 3.3 8.1 + - + +
33I THR* 3.0 28.4 + - - +
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Residues in contact with GLY 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I MET 2.9 14.4 + - - -
27I VAL* 3.2 3.8 + - - -
29I LEU* 1.3 75.8 - - - +
31I PHE* 1.3 57.1 + - - +
33I THR* 3.4 8.6 - - - +
34I PHE* 3.0 28.7 + - - +
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Residues in contact with PHE 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 4.0 18.6 - - + -
32B PHE* 4.1 21.5 - + + -
33B LEU* 3.5 38.8 - - + -
27I VAL* 2.8 22.1 + - + +
28I SER* 3.6 3.8 - - - +
30I GLY* 1.3 74.5 - - - +
32I ALA* 1.3 60.8 + - - +
34I PHE* 3.7 19.7 - + - +
35I TYR* 2.8 53.9 + + + +
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Residues in contact with ALA 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 4.3 21.8 - - + -
33B LEU* 5.0 2.7 - - + -
28I SER 2.9 16.9 + - - +
29I LEU* 3.3 10.5 + - + +
31I PHE* 1.3 78.4 - - - +
33I THR* 1.3 64.4 + - - +
35I TYR* 3.6 1.6 - - - +
36I LYS* 2.9 49.0 + - - +
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Residues in contact with THR 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I LEU* 3.0 14.8 + - - +
30I GLY* 3.4 13.0 - - - +
32I ALA* 1.3 77.1 - - - +
34I PHE* 1.3 64.8 + - + +
36I LYS* 3.6 15.5 + - - +
37I PHE* 3.6 15.7 - - + +
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Residues in contact with PHE 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I GLY 3.0 17.5 + - - +
31I PHE* 3.7 24.7 - + - +
33I THR* 1.3 75.9 - - + +
35I TYR* 1.3 68.0 + + + +
37I PHE* 3.2 18.6 + + - +
38I ALA* 2.8 49.8 + - + +
39I VAL* 6.0 2.7 - - + -
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Residues in contact with TYR 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 3.0 39.9 + - + -
26B HIS* 5.3 0.2 - - - -
28B LEU* 3.8 17.8 - - + +
29B MET* 3.5 35.0 - - + -
32B PHE* 4.5 15.5 - + - -
31I PHE* 2.8 42.2 + + + +
32I ALA 3.6 3.4 - - - +
34I PHE* 1.3 75.2 - + - +
36I LYS* 1.3 58.2 + - + +
37I PHE 2.7 16.6 + - - -
38I ALA 4.6 0.4 - - - +
39I VAL* 2.9 62.8 + - + +
40I ALA* 3.1 12.1 + - + -
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Residues in contact with LYS 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 4.4 18.4 - - + -
32I ALA* 2.9 44.0 + - - +
33I THR* 3.7 10.0 + - - +
35I TYR* 1.3 74.0 - - + +
37I PHE* 1.3 58.9 + - - +
40I ALA* 3.7 18.6 - - + -
41I GLU* 3.5 23.5 - - - +
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Residues in contact with PHE 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I THR* 3.6 10.1 - - + +
34I PHE* 3.4 24.7 - + - +
35I TYR 2.7 7.3 + - - -
36I LYS* 1.3 76.2 - - - +
38I ALA* 1.3 88.0 + - + +
39I VAL 3.2 1.5 - - - +
41I GLU* 4.0 11.4 - - + +
42I LYS* 3.4 21.6 + - - +
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Residues in contact with ALA 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I PHE* 2.8 41.4 + - + +
37I PHE* 1.3 91.6 - - + +
39I VAL* 1.3 67.9 + - + +
42I LYS* 3.8 22.0 - - - +
----------------------------------------------------------
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Residues in contact with VAL 39 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ASP* 3.8 16.6 - - - +
302B TGL 5.5 9.4 - - + +
34I PHE* 6.0 2.2 - - + -
35I TYR* 2.9 54.7 + - + +
37I PHE 3.2 0.8 - - - -
38I ALA* 1.3 89.4 - - + +
40I ALA* 1.3 66.0 + - - +
41I GLU 3.6 0.4 - - - -
42I LYS* 3.8 3.4 - - - +
43I ARG* 3.0 39.0 + - - +
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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