Contacts of the helix formed by residues 17 - 41 (chain F) in PDB entry 2AXT
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 THR 17 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7E GLU* 3.4 31.2 + - + +
8E ARG* 5.6 4.0 - - + -
14F PRO* 5.3 11.9 - - - +
15F ILE 5.1 4.0 - - - +
16F PHE* 1.3 76.0 - - - +
18F VAL* 1.3 82.1 + - - +
19F ARG* 3.1 13.2 + - + +
20F TRP* 2.9 34.8 + - + +
21F VAL* 3.2 11.3 + - - +
51F HEM 4.3 8.5 - - - +
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Residues in contact with VAL 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TRP* 5.4 4.5 - - + -
26D ARG* 3.7 52.9 - - + +
27D PHE 5.5 0.4 - - - +
28D VAL* 5.3 5.8 - - + +
30D VAL* 4.8 10.3 - - + -
7E GLU* 5.2 1.1 - - - +
17F THR* 1.3 83.2 + - - +
19F ARG* 1.3 77.6 + - + +
21F VAL* 2.9 29.9 + - + +
22F ALA* 3.2 6.8 + - - +
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Residues in contact with ARG 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484C UNK 5.3 0.2 - - + -
27D PHE* 3.4 50.7 - - + -
28D VAL* 4.9 7.4 - - + +
6E GLY 5.5 0.2 + - - -
7E GLU* 3.6 26.0 + - - +
8E ARG* 2.7 34.9 + - - +
9E PRO* 4.9 0.8 - - - +
10E PHE* 2.9 36.6 - - - +
17F THR* 3.1 4.7 - - - +
18F VAL* 1.3 86.5 - - + +
20F TRP* 1.3 51.2 + - - +
22F ALA* 3.2 7.2 + - + +
23F VAL* 2.7 48.3 + - + +
51F HEM 2.7 39.2 + - - -
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Residues in contact with TRP 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ILE 4.2 8.1 - - - +
16F PHE* 3.8 39.0 - + + -
17F THR* 2.9 28.9 + - + +
19F ARG* 1.3 78.6 - - - +
21F VAL* 1.3 77.3 + - + +
23F VAL* 4.5 2.5 - - - -
24F HIS* 3.1 66.7 + + + +
51F HEM 3.0 76.0 + + + +
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Residues in contact with VAL 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F THR 3.5 10.3 - - - +
18F VAL* 2.9 23.2 + - + +
20F TRP* 1.3 92.1 - - + +
22F ALA* 1.3 55.5 + - - +
24F HIS* 3.6 2.7 + - - +
25F THR* 2.8 43.6 + - + +
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Residues in contact with ALA 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C UNK 3.8 20.2 - - + -
485C UNK 5.2 3.8 - - + -
28D VAL* 5.5 6.5 - - + -
18F VAL 3.2 6.9 + - - +
19F ARG* 3.2 12.2 + - + +
21F VAL* 1.3 74.6 - - - +
23F VAL* 1.3 54.4 + - - +
24F HIS 2.5 17.7 + - - -
25F THR* 2.8 25.7 + - - -
26F LEU* 3.6 6.5 + - - +
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Residues in contact with VAL 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484C UNK 3.9 27.1 - - + -
10E PHE* 3.9 20.4 - - + -
19F ARG* 2.7 44.1 + - + +
20F TRP* 4.1 6.7 - - - +
22F ALA* 1.3 70.3 - - - +
24F HIS* 1.3 61.0 + - - +
26F LEU* 4.4 3.3 - - - +
27F ALA* 2.9 27.4 + - + +
51F HEM 4.3 31.6 - - + +
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Residues in contact with HIS 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F TRP* 3.1 52.1 + + + +
21F VAL* 4.0 4.0 - - - +
22F ALA 2.5 7.1 + - - -
23F VAL* 1.3 79.8 + - - +
25F THR* 1.3 60.6 + - + +
26F LEU 3.0 2.2 - - - -
27F ALA* 4.0 2.5 - - - -
28F VAL* 2.8 46.3 + - + +
51F HEM 2.4 89.7 + + + -
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Residues in contact with THR 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 2.7 50.3 + - + +
21F VAL* 2.8 32.9 + - + +
22F ALA* 2.8 19.3 + - - -
24F HIS* 1.3 77.3 - - + +
26F LEU* 1.3 61.8 + - - +
28F VAL* 5.3 0.4 - - - -
29F PRO* 2.8 17.4 - - - +
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Residues in contact with LEU 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A PQ9 5.8 6.7 - - + -
484C UNK 5.1 7.9 - - + -
485C UNK 5.0 16.4 - - + -
42D TYR* 3.4 34.8 - - + -
45D LEU* 5.0 6.1 - - + -
357D BCR 4.5 8.5 - - + +
358D MGE 3.9 34.0 - - + +
22F ALA 3.6 5.9 + - - +
23F VAL* 4.9 2.7 - - - +
24F HIS 3.0 0.2 - - - -
25F THR* 1.3 83.1 + - - +
27F ALA* 1.3 60.2 + - - +
28F VAL 3.6 0.4 - - - -
29F PRO* 3.7 1.6 - - - +
30F THR* 2.6 35.0 + - - -
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Residues in contact with ALA 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D MGE 5.8 0.4 - - - -
23F VAL* 2.9 23.4 + - + +
24F HIS* 3.2 5.6 + - - +
26F LEU* 1.3 78.0 - - - +
28F VAL* 1.3 64.7 + - - +
30F THR* 3.6 3.5 + - - -
31F ILE* 3.3 30.5 + - - +
51F HEM 3.4 42.8 - - + -
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Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LEU* 3.4 31.0 - - + +
24F HIS* 2.8 40.3 + - + +
25F THR* 5.3 0.2 - - - -
27F ALA* 1.3 71.6 - - - +
29F PRO* 1.4 74.7 - - + +
32F PHE* 3.1 20.2 + - + +
51F HEM 4.1 28.0 - - + -
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Residues in contact with PRO 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D TYR* 3.8 10.3 - - - +
357D BCR 3.4 33.2 - - + -
25F THR* 2.8 32.5 - - - +
26F LEU 3.7 1.8 - - - -
28F VAL* 1.4 92.8 - - + +
30F THR* 1.3 70.8 + - - +
32F PHE* 3.0 10.8 + - + +
33F PHE* 2.9 26.8 + - + -
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Residues in contact with THR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D BCR 3.6 34.0 - - + +
358D MGE 3.5 19.4 - - + +
26F LEU 2.6 23.1 + - - -
27F ALA* 3.7 5.6 - - - -
28F VAL 3.3 0.2 - - - -
29F PRO* 1.3 78.2 - - - +
31F ILE* 1.3 61.6 + - + +
33F PHE* 2.6 26.5 + - - +
34F LEU* 2.7 37.0 + - + -
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Residues in contact with ILE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E ILE* 3.5 39.3 - - + +
30E LEU* 3.8 4.7 - - + -
31E PHE* 3.7 21.2 - - + +
27F ALA 3.3 17.6 + - - +
28F VAL 4.1 2.5 - - - +
30F THR* 1.3 82.6 - - + +
32F PHE* 1.3 63.6 + - - +
34F LEU* 4.2 19.3 - - + -
35F GLY* 2.9 21.1 + - - -
51F HEM 3.4 30.1 - - + -
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Residues in contact with PHE 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 4.8 3.8 - + - -
30E LEU* 4.0 21.7 - - + +
33E ALA* 3.9 11.9 - - + -
34E GLY* 3.2 39.8 - - - -
37E PHE* 3.7 39.7 - + + -
28F VAL* 3.1 15.7 + - + +
29F PRO* 3.0 12.9 + - + +
30F THR 3.0 0.2 + - - -
31F ILE* 1.3 77.1 - - - +
33F PHE* 1.3 80.6 + + - +
35F GLY* 3.5 0.5 + - - -
36F ALA* 3.1 21.7 + - + +
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Residues in contact with PHE 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU 3.4 23.6 - - - -
50D THR* 4.0 13.7 - - + -
53D THR* 4.0 24.2 - - + -
54D PHE* 3.9 17.9 - + - -
357D BCR 3.5 59.9 - - + -
29F PRO* 2.9 20.2 + - + -
30F THR 2.6 14.3 + - - +
32F PHE* 1.3 87.2 - + - +
34F LEU* 1.3 52.9 + - - +
35F GLY 2.9 4.5 - - - -
36F ALA* 2.7 10.5 + - - -
37F ILE* 2.6 39.7 + - + +
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Residues in contact with LEU 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D BCR 4.1 32.1 - - + -
31E PHE* 3.5 8.0 - - + -
30F THR* 2.7 41.9 + - + +
31F ILE* 3.8 19.7 - - + +
33F PHE* 1.3 72.4 - - - +
35F GLY* 1.3 56.0 + - - +
37F ILE* 4.3 4.2 - - - +
38F ALA* 3.0 28.8 + - - +
24J ILE* 3.2 34.3 - - + +
28J PHE* 3.8 20.1 - - + -
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Residues in contact with GLY 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 3.3 36.7 - - - -
35E TRP* 3.6 16.4 - - - -
31F ILE 2.9 11.2 + - - -
32F PHE 3.8 1.1 - - - -
33F PHE 2.9 0.8 - - - -
34F LEU* 1.3 78.0 - - - +
36F ALA* 1.3 63.5 + - - +
38F ALA 3.5 0.3 + - - -
39F ALA* 3.2 21.8 + - - +
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Residues in contact with ALA 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PHE* 3.9 23.3 - - + -
34E GLY* 3.7 17.7 - - - +
37E PHE* 5.1 1.8 - - + -
38E VAL* 3.3 27.4 - - + +
32F PHE* 3.1 14.7 + - + +
33F PHE* 2.7 13.9 + - - +
35F GLY* 1.3 71.1 - - - +
37F ILE* 1.3 60.7 + - + +
39F ALA* 3.0 22.8 + - - +
40F MET* 3.2 8.3 + - + +
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Residues in contact with ILE 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D THR* 3.9 15.3 - - + +
67D TYR* 3.5 31.6 - - + -
357D BCR 3.7 31.0 - - + -
358D MGE 3.9 19.3 - - - +
33F PHE* 2.6 23.0 + - + +
34F LEU* 4.3 1.1 - - - +
36F ALA* 1.3 72.6 - - + +
38F ALA* 1.3 60.8 + - - +
39F ALA 3.0 2.0 + - - -
40F MET* 3.3 23.4 + - + +
41F GLN* 3.1 16.6 - - - +
28J PHE* 3.1 31.2 - - + -
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PHE* 3.7 22.2 - - + -
35E TRP* 3.7 4.9 - - + -
34F LEU 3.0 22.4 + - - +
35F GLY 3.8 1.1 - - - +
36F ALA 3.2 0.4 - - - -
37F ILE* 1.3 77.5 - - - +
39F ALA* 1.3 60.2 + - - +
41F GLN* 3.4 8.3 - - - +
42F PHE* 3.4 22.5 - - - -
24J ILE* 4.7 4.5 - - + -
27J LEU* 3.5 21.4 - - + +
28J PHE* 3.8 12.3 - - + -
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Residues in contact with ALA 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E TRP* 3.6 46.5 - - + +
38E VAL* 4.0 10.9 - - + +
39E SER* 4.9 1.3 - - - +
35F GLY 3.2 13.1 + - - +
36F ALA 3.0 13.8 + - - +
38F ALA* 1.3 77.5 - - - +
40F MET* 1.3 62.5 + - - +
41F GLN 3.2 0.7 - - - -
42F PHE* 3.4 17.2 + - - +
43F ILE* 4.0 5.5 - - - +
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Residues in contact with MET 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D THR* 3.6 13.0 - - - +
54D PHE* 3.7 21.8 - - + -
67D TYR* 3.9 11.9 - - + -
68D LEU* 3.4 48.2 - - + -
358D MGE 3.7 20.5 + - - +
38E VAL* 3.8 11.2 - - + -
36F ALA 3.2 8.7 + - - +
37F ILE* 3.3 22.4 + - + +
39F ALA* 1.3 73.7 - - - +
41F GLN* 1.3 54.0 + - - +
42F PHE 2.5 19.2 + - - -
43F ILE* 2.6 46.0 + - + +
36J LEU* 5.5 1.6 + - - +
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Residues in contact with GLN 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358D MGE 2.7 45.6 + - - +
37F ILE* 3.1 12.3 - - - +
38F ALA* 3.4 20.9 - - - +
39F ALA 3.2 0.4 - - - -
40F MET* 1.3 72.5 - - - +
42F PHE* 1.3 71.9 + - + +
43F ILE 3.7 2.0 - - - -
27J LEU* 3.8 28.3 - - + +
28J PHE* 3.1 25.8 - - + -
30J TYR* 4.3 13.5 - - + -
31J GLY* 3.3 15.2 - - - -
34J ALA* 5.4 0.9 - - - +
35J GLY* 4.5 13.6 + - - -
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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
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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