Contacts of the helix formed by residues 22 - 49 (chain F) in PDB entry 6M04
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 PRO 22 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU 4.0 4.7 - - - +
21F LYS* 1.3 88.7 + - + +
23F TRP* 1.3 65.4 + - - +
24F TRP* 3.4 50.7 - - + +
25F ASP* 3.7 20.4 - - + -
26F VAL* 3.3 26.9 + - - +
183F TRP* 5.7 4.7 - - + -
422F MET* 4.5 15.9 - - + +
425F GLN* 5.7 5.4 - - + -
426F TYR* 5.8 3.1 - - + +
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Residues in contact with TRP 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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186E TYR* 5.5 11.0 - + - -
188E LYS* 5.7 16.6 - - + +
22F PRO* 1.3 73.0 - - - +
24F TRP* 1.3 99.1 + + + +
26F VAL* 3.2 9.6 + - - +
27F PHE* 3.2 56.5 + + - +
379F ILE* 4.4 20.2 - - + -
382F TYR* 6.0 1.1 - + - -
383F THR* 3.2 35.0 - - + -
425F GLN* 5.9 4.1 + - - +
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Residues in contact with TRP 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F PRO* 3.4 31.9 - - + +
23F TRP* 1.3 115.5 - + + +
25F ASP* 1.3 74.9 + - + +
27F PHE* 3.2 7.9 + - - +
28F MET* 2.9 54.0 + - + +
308F TYR* 4.6 14.9 - + - -
379F ILE* 5.4 0.4 - - + -
380F CYS* 5.5 0.2 - - - -
383F THR* 3.6 18.6 - - + -
384F LEU* 3.5 32.3 - - + +
387F LEU* 3.6 30.7 - - + -
422F MET* 5.1 8.7 - - + -
425F GLN* 5.1 17.7 - - + -
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Residues in contact with ASP 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F GLN* 3.1 33.0 + - - +
21F LYS* 4.7 0.7 - - - +
22F PRO* 3.7 29.1 + - + +
23F TRP 3.3 0.6 - - - -
24F TRP* 1.3 86.1 - - + +
26F VAL* 1.3 57.9 + - - +
28F MET* 3.3 6.7 + - - +
29F ASP* 3.0 30.5 + - - +
180F SER* 4.3 22.5 - - - +
311F GLN* 5.7 0.9 - - - +
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Residues in contact with VAL 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186E TYR* 5.2 10.1 - - + -
187E PRO* 4.1 25.4 - - + -
188E LYS 6.2 0.2 - - - +
14F GLN* 4.8 4.7 - - - +
21F LYS* 4.1 30.3 - - + +
22F PRO 3.3 16.2 - - - +
23F TRP* 3.2 9.0 + - - +
25F ASP* 1.3 76.2 - - - +
27F PHE* 1.3 68.5 + - + +
29F ASP* 4.1 3.8 - - - +
30F TYR* 3.0 31.7 + - + +
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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
----------------------------------------------------------
182E PHE* 5.7 10.8 - + - -
186E TYR* 6.0 8.5 - + - -
23F TRP* 3.2 60.3 + + - +
24F TRP* 3.5 9.9 - - - +
26F VAL* 1.3 81.1 - - + +
28F MET* 1.3 62.2 + - + +
30F TYR* 3.3 22.6 - + - +
31F LEU* 2.9 33.1 + - + +
379F ILE* 5.2 8.5 - - + -
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Residues in contact with MET 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TRP* 2.9 43.0 + - + +
25F ASP* 4.0 7.0 - - - +
26F VAL 3.2 0.2 - - - -
27F PHE* 1.3 79.8 - - + +
29F ASP* 1.3 62.0 + - - +
31F LEU* 3.8 6.0 - - + +
32F ALA* 2.9 29.3 + - - +
176F LEU* 5.4 0.3 - - - +
180F SER* 6.3 3.4 - - - -
376F TYR* 3.6 33.1 - - + +
379F ILE* 3.8 18.2 - - + -
380F CYS* 3.6 50.3 - - + +
384F LEU* 4.9 0.2 - - + -
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Residues in contact with ASP 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ASP* 2.9 57.6 - - - +
13F ILE* 3.9 6.8 + - - +
14F GLN* 4.2 9.3 - - - +
25F ASP* 3.0 20.1 + - - +
26F VAL* 4.1 4.3 - - - +
28F MET* 1.3 75.7 - - - +
30F TYR* 1.3 64.5 + - - +
32F ALA* 3.3 3.6 + - - +
33F VAL* 3.0 27.6 + - - +
180F SER* 5.5 8.9 - - - +
181F ASN* 5.4 0.3 - - - +
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Residues in contact with TYR 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175E ILE* 6.1 1.4 - - - +
178E VAL* 4.1 19.2 - - + +
182E PHE* 3.9 36.5 - + + -
26F VAL* 3.0 23.9 + - + +
27F PHE* 3.3 24.2 - + - +
29F ASP* 1.3 76.1 - - - +
31F LEU* 1.3 65.7 + - + +
33F VAL* 3.3 5.9 + - - +
34F VAL* 3.1 33.7 + - + +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F PHE* 2.9 21.6 + - + +
28F MET* 3.8 6.7 - - + +
29F ASP 3.2 0.2 - - - -
30F TYR* 1.3 78.7 - - + +
32F ALA* 1.3 63.9 + - - +
34F VAL* 3.2 11.5 + - + +
35F MET* 2.9 23.8 + - + +
176F LEU* 6.1 0.9 - - + -
372F ILE* 3.7 27.4 - - + +
373F ILE* 4.6 7.0 - - + -
375F VAL* 5.0 9.6 - - + -
376F TYR* 3.6 50.9 - - + +
379F ILE* 6.5 0.7 - - + -
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Residues in contact with ALA 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12F ASP* 4.6 11.2 - - - +
28F MET 2.9 19.1 + - - +
29F ASP* 3.3 6.5 + - - +
31F LEU* 1.3 74.9 - - - +
33F VAL* 1.3 61.3 + - - +
35F MET* 3.3 9.8 + - + +
36F LEU* 3.0 28.1 + - - +
173F THR* 4.1 8.7 - - + +
176F LEU* 4.0 31.2 - - + -
177F MET* 5.7 0.9 - - - +
180F SER* 6.6 0.4 - - - -
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Residues in contact with VAL 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8F ALA 5.1 1.1 - - - +
9F SER* 3.3 42.0 - - - +
12F ASP* 4.9 7.9 - - + +
29F ASP* 3.0 27.9 + - - +
30F TYR* 3.7 6.7 - - - +
32F ALA* 1.3 75.6 - - - +
34F VAL* 1.3 65.6 + - + +
36F LEU* 3.4 10.1 + - + +
37F MET* 3.0 23.2 + - + +
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Residues in contact with VAL 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F TYR* 3.1 29.7 + - + +
31F LEU* 3.4 12.3 - - + +
33F VAL* 1.3 76.9 - - + +
35F MET* 1.3 57.1 + - - +
37F MET* 3.2 24.1 + - + +
38F VAL* 3.0 28.1 + - + +
372F ILE* 3.9 28.5 - - + -
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Residues in contact with MET 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F LEU* 2.9 16.4 + - + +
32F ALA* 3.7 5.4 - - - +
33F VAL 3.3 0.2 - - - -
34F VAL* 1.3 74.5 - - - +
36F LEU* 1.3 60.5 + - - +
38F VAL* 3.3 8.8 + - - +
39F ALA* 3.0 25.3 + - - +
169F ALA 4.3 2.0 - - - +
172F HIS* 3.5 27.4 - - + +
173F THR* 3.0 41.3 - - + +
176F LEU* 4.3 16.4 - - + -
369F TYR* 3.5 36.9 - - + -
372F ILE* 4.9 6.5 - - + -
373F ILE* 3.8 20.4 - - + -
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Residues in contact with LEU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F THR* 5.8 4.3 - - + -
5F ALA* 4.9 17.0 - - + +
8F ALA* 3.7 32.8 - - + -
9F SER* 6.0 0.9 - - - +
32F ALA 3.0 17.1 + - - +
33F VAL* 3.7 10.8 - - + +
34F VAL 3.4 0.2 - - - -
35F MET* 1.3 74.2 - - - +
37F MET* 1.3 62.7 + - - +
39F ALA* 3.8 2.6 - - + +
40F ILE* 2.9 53.3 + - + +
173F THR* 3.7 30.3 - - + -
174F ILE* 5.5 9.4 - - + -
177F MET* 6.3 2.7 - - - -
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Residues in contact with MET 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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3E THR* 4.5 24.5 - - - +
170E LEU* 6.4 1.3 - - - -
171E ILE* 4.4 23.3 - - + -
174E ILE* 5.7 13.9 - - + -
5F ALA* 6.2 2.0 - - - -
33F VAL* 3.0 15.8 + - + +
34F VAL* 3.3 31.0 - - + +
36F LEU* 1.3 79.3 - - - +
38F VAL* 1.3 68.3 + - + +
40F ILE* 4.1 2.4 - - - +
41F PHE* 3.0 30.2 + - + +
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Residues in contact with VAL 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F VAL* 3.0 17.3 + - + +
35F MET* 3.6 9.2 - - - +
36F LEU 3.3 0.2 - - - -
37F MET* 1.3 81.9 - - + +
39F ALA* 1.3 59.1 + - - +
41F PHE* 3.9 4.7 - - - +
42F ALA* 2.9 29.2 + - + +
365F LEU* 4.1 30.9 - - + +
368F SER* 5.4 4.7 - - - +
369F TYR* 4.3 28.5 - - + +
372F ILE* 4.5 20.2 - - + -
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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
----------------------------------------------------------
35F MET* 3.0 17.8 + - - +
36F LEU* 3.8 6.7 - - - +
37F MET 3.3 0.2 - - - -
38F VAL* 1.3 79.0 - - - +
40F ILE* 1.3 64.4 + - + +
42F ALA* 3.2 8.5 + - - +
43F GLY* 3.0 22.2 + - - -
166F PRO* 3.8 11.8 - - - +
169F ALA* 3.8 37.0 - - + +
170F LEU* 4.5 3.4 - - - +
173F THR* 4.8 2.2 - - - +
369F TYR* 5.5 2.0 - - + -
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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
----------------------------------------------------------
3F THR* 4.8 31.2 - - + +
5F ALA* 6.4 1.6 - - + -
36F LEU* 2.9 36.7 + - + +
37F MET* 4.4 2.2 - - - +
39F ALA* 1.3 78.2 - - + +
41F PHE* 1.3 65.1 + - - +
43F GLY* 3.2 2.8 + - - +
44F THR* 3.0 30.9 + - - +
166F PRO 5.8 0.7 - - - +
170F LEU* 4.0 28.7 - - + -
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Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE* 4.2 32.5 - - + +
3E THR* 5.4 7.2 - - - +
167E TYR* 3.5 43.7 - + + -
37F MET* 3.0 21.0 + - + +
38F VAL* 3.9 4.3 - - - +
40F ILE* 1.3 77.7 - - - +
42F ALA* 1.3 58.2 + - - +
44F THR* 4.7 4.5 - - - -
45F MET* 3.0 61.8 + - + +
361F MET* 5.6 2.9 - - - -
365F LEU* 4.0 21.3 - - + -
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Residues in contact with ALA 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL* 2.9 20.2 + - + +
39F ALA* 3.2 9.2 + - - +
41F PHE* 1.3 77.2 - - - +
43F GLY* 1.3 56.9 + - - +
45F MET* 4.6 5.3 - - - +
46F GLN* 2.9 34.1 + - - +
165F PHE* 6.4 1.3 - - + -
166F PRO* 3.9 14.8 - - + -
362F LEU* 6.3 4.5 - - + -
365F LEU* 3.7 22.2 - - + -
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Residues in contact with GLY 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F ALA 3.0 12.2 + - - -
40F ILE* 3.2 4.2 + - - -
42F ALA* 1.3 76.2 - - - +
44F THR* 1.3 56.6 + - - +
46F GLN* 3.8 4.5 - - - +
47F LEU* 3.0 29.5 + - - +
166F PRO* 3.7 20.5 - - - +
167F TYR* 5.7 5.8 - - - -
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Residues in contact with THR 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E PHE* 4.7 25.6 + - + +
2F PHE* 5.7 6.9 - - + -
40F ILE* 3.0 24.1 + - - +
41F PHE* 4.0 6.5 - - + -
43F GLY* 1.3 75.6 - - - +
45F MET* 1.3 59.0 + - + +
47F LEU* 3.0 9.9 + - + +
48F THR* 3.0 37.1 + - - +
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Residues in contact with MET 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LEU* 6.2 4.3 - - + -
167E TYR* 4.3 14.4 - - + +
41F PHE* 3.0 55.5 + - + +
42F ALA* 4.6 3.6 - - - +
44F THR* 1.3 77.5 - - + +
46F GLN* 1.3 59.5 + - - +
48F THR* 3.7 13.2 + - - -
49F LYS* 3.8 29.1 + - + +
358F MET* 3.7 21.3 - - + +
361F MET* 3.6 30.1 - - + +
362F LEU* 6.1 0.7 - - - -
365F LEU* 4.2 14.8 - - + -
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Residues in contact with GLN 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F ALA 2.9 21.1 + - - +
43F GLY* 3.9 6.0 - - - +
45F MET* 1.3 77.6 - - - +
47F LEU* 1.3 65.7 + - - +
48F THR 3.3 0.4 - - - -
49F LYS 3.3 12.5 - - - +
50F ASP* 2.4 37.8 + - - +
154F TYR* 4.6 0.8 + - - -
162F SER 5.0 1.2 + - - -
163F LYS* 3.7 36.7 + - - +
166F PRO* 5.1 8.3 - - + +
167F TYR* 5.8 0.7 + - - -
356F HIS* 5.2 2.0 - - - -
358F MET* 4.0 19.7 - - + +
362F LEU* 4.1 25.1 - - + -
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.8 20.9 - - + -
44A THR* 6.2 5.8 - - + -
45A MET* 5.6 11.0 - - + -
48A THR* 4.6 24.4 - - + +
49A LYS* 5.9 8.7 - - - +
43F GLY 3.0 18.0 + - - +
44F THR* 3.0 7.8 + - - +
46F GLN* 1.3 82.5 + - - +
48F THR* 1.3 67.3 + - - +
50F ASP* 4.5 7.4 - - - +
167F TYR* 5.3 5.6 - - - +
----------------------------------------------------------
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Residues in contact with THR 48 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LEU* 4.5 32.9 - - + +
44F THR* 3.0 23.3 + - - +
45F MET* 4.1 9.8 - - - -
46F GLN 3.3 0.6 - - - -
47F LEU* 1.3 85.6 - - - +
49F LYS* 1.3 65.0 + - + +
50F ASP 4.0 1.4 + - - -
51F GLN* 5.0 1.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 49 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLN* 4.6 12.5 - - - +
50E ASP* 4.9 3.6 + - - +
154E TYR* 3.9 23.7 + - + -
155E HIS* 6.0 0.6 + - - -
167E TYR* 5.2 5.1 + - - -
45F MET* 3.8 23.3 + - + +
46F GLN 3.3 7.5 - - - +
48F THR* 1.3 80.7 - - + +
50F ASP* 1.3 59.8 + - - +
51F GLN* 4.1 7.6 - - - +
357F ASN* 4.3 24.1 - - - +
358F MET* 3.3 35.9 - - - +
361F MET* 5.0 14.7 - - - +
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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