Contacts of the helix formed by residues 19 - 45 (chain F) in PDB entry 5MG3
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 PHE 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382C LYS* 4.9 8.3 - - - +
17F TYR* 3.7 17.8 - + + -
18F ASP* 1.3 90.6 - - - +
20F MET* 1.3 91.3 + - + +
21F ARG 3.6 0.9 - - - -
22F TRP* 3.1 15.4 + - + +
23F ASP* 3.0 50.7 + - + -
245F LEU* 4.0 28.5 - - + -
290F TYR* 4.3 17.7 - + + -
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Residues in contact with MET 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR* 4.5 12.8 - - + +
18F ASP 3.7 2.0 + - - -
19F PHE* 1.3 109.8 - - + +
21F ARG* 1.3 64.3 + - + +
23F ASP* 3.5 5.4 - - - +
24F TYR* 3.3 34.0 + - + -
238F ASN 5.6 0.2 - - - +
241F LEU* 4.4 26.0 - - + -
242F THR* 4.0 17.5 - - + -
245F LEU* 3.8 28.0 - - + -
290F TYR* 4.5 6.7 - - + +
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Residues in contact with ARG 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F ASP 5.2 0.2 + - - -
19F PHE 3.6 0.8 - - - -
20F MET* 1.3 80.6 - - + +
22F TRP* 1.4 79.7 + - + +
24F TYR* 3.7 28.9 + - + +
25F TRP* 3.5 26.0 - - + +
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Residues in contact with TRP 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C LYS* 5.6 12.9 - - + +
482C SER* 3.7 28.2 + - - -
484C THR* 4.9 14.2 - - + +
18F ASP* 3.4 28.0 - - + -
19F PHE* 3.1 13.9 + - + +
21F ARG* 1.4 93.6 - - + +
23F ASP* 1.3 52.3 + - - +
25F TRP* 3.6 5.0 + - - +
26F ALA* 2.9 36.5 + - + +
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Residues in contact with ASP 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F PHE* 3.0 40.7 + - + +
20F MET* 3.5 11.0 - - - +
22F TRP* 1.3 78.0 - - - +
24F TYR* 1.3 59.2 + - - +
26F ALA* 3.3 7.0 + - - +
27F PHE* 2.9 27.7 + - - +
286F ALA 4.6 9.9 - - - +
287F SER* 4.7 0.7 - - - +
288F SER* 4.8 2.8 + - - -
290F TYR* 4.0 11.8 - - - +
291F VAL* 3.4 24.4 + - - +
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Residues in contact with TYR 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F MET* 3.3 25.1 + - + -
21F ARG* 3.7 34.1 + - + +
22F TRP 3.5 0.6 - - - -
23F ASP* 1.3 78.8 - - - +
25F TRP* 1.3 82.9 + + - +
27F PHE* 3.5 6.6 - - + +
28F GLY* 3.1 21.5 + - - -
290F TYR 5.7 0.4 - - - -
291F VAL* 4.1 26.9 - - + +
294F ALA* 4.0 26.9 - - + -
295F LEU* 5.9 5.6 - - + -
298F LYS* 5.4 12.4 - - - -
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Residues in contact with TRP 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F ARG* 3.5 19.1 - - + +
22F TRP* 3.6 9.6 - - - +
24F TYR* 1.3 93.8 - + - +
26F ALA* 1.4 56.5 + - - +
28F GLY* 3.1 19.4 + - - -
29F ILE* 3.1 13.9 + - - +
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Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F TRP* 2.9 22.2 + - + +
23F ASP* 3.3 8.5 + - - +
25F TRP* 1.4 69.4 - - - +
27F PHE* 1.4 54.0 + - - +
29F ILE* 3.3 14.0 - - + +
30F SER* 2.9 35.5 + - - -
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Residues in contact with PHE 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F ASP* 2.9 19.3 + - - +
24F TYR 3.5 8.7 - - - +
26F ALA* 1.4 68.4 - - - +
28F GLY* 1.3 54.6 - - - +
30F SER* 3.4 5.6 + - - -
31F GLY* 2.9 26.9 + - - -
175F ILE* 4.5 12.6 - - + -
176F ALA* 4.0 22.2 - - + -
179F HIS* 3.4 53.7 - + + -
287F SER* 3.8 26.2 - - - -
291F VAL* 3.6 29.8 - - + -
295F LEU* 4.7 11.7 - - + -
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Residues in contact with GLY 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR 3.1 10.6 + - - -
25F TRP* 3.1 15.3 + - - -
27F PHE* 1.3 75.1 - - - +
29F ILE* 1.4 60.2 + - - +
30F SER 3.3 0.2 - - - -
31F GLY* 3.4 12.0 + - - -
32F LEU* 4.3 1.6 + - - +
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Residues in contact with ILE 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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526C ILE 4.1 6.0 - - - +
527C GLN* 3.1 39.5 - - + +
528C GLN 3.5 23.6 - - - +
529C GLN* 4.1 7.4 - - - +
25F TRP 3.1 9.5 + - - +
26F ALA* 3.3 19.3 - - + +
28F GLY* 1.4 70.8 - - - +
30F SER* 1.4 60.8 + - - +
31F GLY 3.1 0.2 - - - -
32F LEU* 3.0 34.3 + - + +
33F LEU 4.1 1.6 + - - -
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Residues in contact with SER 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C TYR* 4.2 10.9 + - - -
374C LYS* 5.2 4.5 - - - -
527C GLN* 4.0 23.2 + - - +
26F ALA* 2.9 17.9 + - - +
27F PHE* 3.5 11.6 - - - -
28F GLY 3.3 0.2 - - - -
29F ILE* 1.4 75.8 - - - +
31F GLY* 1.3 62.4 + - - +
32F LEU 3.3 0.2 - - - -
33F LEU* 3.3 5.6 + - - +
34F LEU 3.2 15.2 + - - -
179F HIS* 3.4 18.2 - - - -
183F ILE* 3.3 11.0 - - - +
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Residues in contact with GLY 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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27F PHE 2.9 13.9 + - - -
28F GLY* 3.4 9.1 + - - -
29F ILE 3.1 0.4 - - - -
30F SER* 1.3 78.0 - - - +
32F LEU* 1.3 55.0 + - - -
34F LEU* 3.0 10.8 + - - +
35F ILE* 3.0 29.3 + - - +
179F HIS* 3.5 8.7 - - - -
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Residues in contact with LEU 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C ILE* 3.4 24.8 - - + +
529C GLN* 3.1 36.1 - - - +
530C LEU* 3.7 26.0 - - + +
531C ILE 4.9 1.3 - - - +
28F GLY 4.3 1.8 + - - +
29F ILE* 3.0 21.3 + - + +
31F GLY* 1.3 69.6 - - - -
33F LEU* 1.4 55.2 + - - +
35F ILE* 3.2 22.0 + - + +
36F ALA* 2.9 32.6 + - - +
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Residues in contact with LEU 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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363C PHE* 5.0 6.3 - - + -
367C GLY* 6.5 0.7 - - - -
370C TYR* 3.9 20.0 - - + -
523C VAL* 3.7 32.3 - - + +
526C ILE* 3.6 32.0 + - + +
527C GLN* 3.9 23.3 - - + +
29F ILE 4.1 1.2 + - - -
30F SER* 3.3 11.9 + - - +
32F LEU* 1.4 73.4 - - - +
34F LEU* 1.3 62.1 + - - +
36F ALA* 3.5 4.3 + - + +
37F ALA* 3.1 21.8 + - - +
183F ILE* 3.8 27.9 - - + +
187F ILE* 5.6 8.7 - - + -
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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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30F SER 3.2 4.8 + - - -
31F GLY* 3.0 15.1 + - - +
33F LEU* 1.3 74.0 - - - +
35F ILE* 1.4 72.7 + - + +
37F ALA* 3.3 5.2 + - - +
38F ILE* 3.3 40.9 + - + +
179F HIS* 3.6 49.8 - - + +
182F ILE* 3.9 23.3 - - + -
183F ILE* 3.6 16.0 - - + +
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Residues in contact with ILE 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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31F GLY 3.0 13.7 + - - +
32F LEU* 3.2 25.1 + - + +
34F LEU* 1.4 81.0 - - + +
36F ALA* 1.3 65.9 + - - +
38F ILE* 3.4 8.2 + - + +
39F VAL* 3.0 34.0 + - + +
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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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363C PHE* 5.8 2.2 - - + -
526C ILE* 4.3 22.7 - - + -
32F LEU 2.9 16.1 + - - +
33F LEU* 3.5 12.8 - - + +
35F ILE* 1.3 77.6 - - - +
37F ALA* 1.4 55.8 + - - +
39F VAL* 3.2 7.8 + - - +
40F ILE* 3.0 35.3 + - + +
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Residues in contact with ALA 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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33F LEU 3.1 14.4 + - - +
34F LEU* 3.3 11.2 + - - +
36F ALA* 1.4 73.4 - - - +
38F ILE* 1.3 59.8 + - - +
40F ILE* 3.7 8.1 + - - +
41F MET* 3.1 29.3 + - - +
182F ILE* 3.5 26.0 - - + +
183F ILE* 4.1 9.4 - - - +
186F GLY* 3.7 20.1 - - - -
187F ILE* 6.3 0.9 - - + -
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Residues in contact with ILE 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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34F LEU* 3.3 36.7 + - + +
35F ILE* 3.9 9.0 - - + +
36F ALA 3.3 0.6 - - - -
37F ALA* 1.3 75.2 - - - +
39F VAL* 1.4 63.5 + - + +
41F MET* 3.3 15.7 + - + +
42F GLY* 3.0 23.4 + - - -
182F ILE* 3.8 25.6 - - + -
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Residues in contact with VAL 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F ILE* 3.0 27.4 + - + +
36F ALA* 3.2 6.7 + - - +
38F ILE* 1.4 78.3 - - + +
40F ILE* 1.4 58.1 + - - +
42F GLY* 3.9 0.8 - - - +
43F VAL* 2.8 51.7 + - + +
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Residues in contact with ILE 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C PHE* 4.6 16.6 - - + -
36F ALA* 3.0 22.9 + - + +
37F ALA* 3.9 8.7 - - - +
38F ILE 3.4 0.2 - - - -
39F VAL* 1.4 71.9 - - - +
41F MET* 1.4 68.7 + - - +
43F VAL* 4.5 2.7 - - - +
44F ARG* 2.9 39.3 + - + +
45F GLY 3.5 2.8 + - - -
186F GLY 3.6 29.4 - - - +
187F ILE* 5.0 2.9 - - + -
189F SER* 4.1 3.3 + - - +
190F LEU* 3.8 44.2 - - + +
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Residues in contact with MET 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ALA 3.1 12.9 + - - +
38F ILE* 3.4 22.2 - - + +
40F ILE* 1.4 77.6 - - - +
42F GLY* 1.3 58.3 + - - +
45F GLY* 3.2 21.0 + - - -
46F PHE* 3.9 35.0 + - + +
182F ILE* 4.0 15.0 - - + +
185F LEU* 3.6 22.7 - - + +
186F GLY* 3.6 28.0 - - - +
189F SER* 3.6 19.3 - - - +
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Residues in contact with GLY 42 (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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38F ILE 3.0 15.8 + - - -
39F VAL* 3.9 1.6 - - - -
41F MET* 1.3 73.9 - - - +
43F VAL* 1.3 66.1 + - - +
44F ARG 3.5 0.3 + - - -
45F GLY* 3.9 3.8 + - - -
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Residues in contact with VAL 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F VAL* 2.8 40.7 + - + +
40F ILE* 4.4 2.5 - - - +
42F GLY* 1.3 74.3 - - - +
44F ARG* 1.4 71.9 + - + +
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Residues in contact with ARG 44 (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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356C PHE* 5.2 19.0 - - - -
40F ILE* 2.9 28.4 + - + +
43F VAL* 1.4 88.5 + - + +
45F GLY* 1.4 63.4 + - - +
189F SER 4.7 2.0 - - - +
190F LEU* 3.9 28.3 + - + +
192F HIS* 3.4 43.4 + - + -
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Residues in contact with GLY 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F ILE 3.5 0.4 + - - -
41F MET 3.2 17.6 + - - -
42F GLY 3.9 3.2 + - - -
43F VAL 3.7 1.6 - - - -
44F ARG* 1.4 82.9 - - - +
46F PHE* 1.3 55.6 + - - -
47F ASN 5.6 0.4 - - - -
189F SER* 2.9 27.1 + - - +
192F HIS* 4.4 4.4 + - - -
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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