Contacts of the helix formed by residues 17 - 50 (chain L) in PDB entry 5GJQ
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 LEU 17 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L LYS 3.3 5.7 - - - +
16L LEU* 1.3 76.5 - - - +
18L GLU* 1.3 60.0 + - - +
19L HIS 3.4 0.4 + - - -
20L LYS* 3.7 10.5 + - - +
21L GLU* 3.4 18.6 + - - +
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Residues in contact with GLU 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L LYS 3.9 10.4 + - - +
16L LEU 3.1 2.0 - - - -
17L LEU* 1.3 76.7 - - - +
19L HIS* 1.3 55.5 + - - +
21L GLU* 3.0 9.1 + - - +
22L ILE* 2.4 39.2 + - - +
46M ARG* 4.9 12.6 - - + +
50M SER* 4.0 22.2 - - - -
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Residues in contact with HIS 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L LEU 3.6 10.5 + - - +
17L LEU 3.4 0.8 - - - -
18L GLU* 1.3 76.7 - - - +
20L LYS* 1.3 50.6 + - - +
22L ILE* 3.2 8.2 + - - +
23L ASP* 2.3 42.3 + - + +
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Residues in contact with LYS 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L LEU 4.7 0.8 + - - +
17L LEU* 3.7 11.3 + - - +
19L HIS* 1.3 75.8 - - - +
21L GLU* 1.3 53.0 + - - +
22L ILE 2.7 2.3 + - - -
23L ASP* 2.6 10.8 + - - -
24L GLY* 2.1 41.7 + - - +
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Residues in contact with GLU 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L LEU 3.4 10.9 + - - +
18L GLU* 3.0 14.6 + - + +
20L LYS* 1.3 74.5 - - - +
22L ILE* 1.3 59.9 + - - +
24L GLY* 4.2 2.9 - - - +
25L ARG* 3.7 17.6 + - - +
50M SER* 5.5 8.0 - - - +
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Residues in contact with ILE 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L GLU 2.4 29.4 + - - +
19L HIS* 3.3 9.0 - - - +
20L LYS 2.7 4.1 + - - -
21L GLU* 1.3 67.5 - - - +
23L ASP* 1.3 58.3 + - - +
25L ARG* 3.7 3.0 - - - +
26L LEU* 2.8 28.4 + - - +
50M SER* 5.1 12.9 - - - -
53M LYS* 5.3 13.4 - - + +
57M SER* 5.4 1.4 - - - -
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Residues in contact with ASP 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L HIS* 2.3 33.9 + - + +
20L LYS* 2.6 3.9 + - - +
22L ILE* 1.3 66.3 - - - +
24L GLY* 1.3 57.6 + - - +
26L LEU* 3.5 9.2 - - + -
27L LYS* 2.4 41.7 + - + +
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Residues in contact with GLY 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LYS* 2.1 30.9 + - - +
21L GLU* 4.8 1.6 - - - -
23L ASP* 1.3 66.7 - - - +
25L ARG* 1.3 64.2 + - - +
27L LYS* 4.3 2.7 - - - +
28L GLU* 3.4 20.1 + - - +
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Residues in contact with ARG 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L GLU* 3.7 15.1 + - - +
22L ILE* 3.6 7.7 + - - +
23L ASP 3.4 0.4 - - - -
24L GLY* 1.3 73.4 - - - +
26L LEU* 1.3 55.5 + - - +
28L GLU* 3.9 1.8 - - - +
29L LEU* 2.7 40.0 + - + +
54M ILE* 5.5 3.6 - - + -
57M SER* 3.9 21.5 - - - -
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Residues in contact with LEU 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L ILE 2.8 23.0 + - - +
23L ASP* 3.4 11.4 - - + +
25L ARG* 1.3 70.9 - - - +
27L LYS* 1.3 56.9 - - - +
29L LEU* 4.1 4.7 - - - -
30L ARG* 2.5 42.1 + - + +
57M SER* 4.7 6.2 - - - +
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Residues in contact with LYS 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ASP* 2.4 33.8 + - + +
24L GLY* 4.3 3.4 - - - +
26L LEU* 1.3 67.0 - - - +
28L GLU* 1.3 53.6 + - - +
30L ARG* 3.7 3.3 - - - +
31L GLU* 2.8 38.6 + - - +
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Residues in contact with GLU 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLY 3.4 13.5 + - - +
25L ARG* 3.4 3.0 + - - +
27L LYS* 1.3 75.3 - - - +
29L LEU* 1.3 54.1 + - - +
31L GLU* 2.8 9.6 + - - +
32L GLN* 2.6 40.6 + - + +
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Residues in contact with LEU 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L ARG* 2.7 28.6 + - + +
26L LEU* 3.5 4.5 - - - +
28L GLU* 1.3 70.8 - - - +
30L ARG* 1.3 63.3 + - - +
32L GLN* 4.0 3.2 - - - +
33L LEU* 3.2 23.9 + - - +
57M SER* 3.9 25.6 - - - +
60M LEU* 4.0 10.5 - - + +
61M ARG* 4.4 17.4 + - + +
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Residues in contact with ARG 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L LEU* 2.5 31.6 + - + +
27L LYS* 4.1 3.1 - - - +
29L LEU* 1.3 73.9 - - - +
31L GLU* 1.3 58.2 + - - +
33L LEU* 3.5 14.9 - - - +
34L LYS* 4.2 5.2 + - - +
60M LEU* 4.5 5.8 - - + +
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Residues in contact with GLU 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L LYS 2.8 20.6 + - - +
28L GLU* 2.8 7.0 + - - +
30L ARG* 1.3 74.6 - - - +
32L GLN* 1.3 54.8 + - - +
33L LEU 2.6 15.8 + - - -
34L LYS* 3.0 16.1 + - - +
35L GLU* 3.3 11.0 + - - +
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Residues in contact with GLN 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L GLU* 2.6 21.8 + - + +
29L LEU* 4.2 4.7 - - - +
31L GLU* 1.3 70.8 - - - +
33L LEU* 1.3 60.9 + - - +
35L GLU* 3.8 12.6 - - - +
36L LEU* 3.4 22.5 + - - +
61M ARG* 5.7 8.1 - - + -
64M HIS* 4.7 2.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L LEU 3.2 17.7 + - - +
30L ARG* 3.5 14.4 - - - +
31L GLU 2.6 5.1 + - - -
32L GLN* 1.3 76.3 - - - +
34L LYS* 1.3 57.1 + - - +
36L LEU* 3.9 2.1 - - - +
37L THR* 3.0 27.4 + - - -
60M LEU* 4.6 15.0 - - + +
61M ARG* 5.9 0.2 - - - +
64M HIS* 4.2 17.3 - - + +
----------------------------------------------------------
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Residues in contact with LYS 34 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L ARG 4.2 4.5 + - - +
31L GLU 3.0 7.1 + - - +
33L LEU* 1.3 73.8 - - - +
35L GLU* 1.3 68.7 + - - +
36L LEU 3.1 2.0 - - - -
37L THR* 3.8 8.7 - - - -
38L LYS* 2.8 28.7 + - + +
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Residues in contact with GLU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L GLU 3.3 11.0 + - - +
32L GLN* 3.8 15.5 - - - +
34L LYS* 1.3 80.5 - - - +
36L LEU* 1.3 59.5 + - + +
38L LYS* 3.7 9.0 + - - +
39L GLN* 3.8 10.4 + - - +
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Residues in contact with LEU 36 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32L GLN 3.4 14.3 + - - +
33L LEU 4.2 1.8 - - - +
34L LYS 3.1 0.2 - - - -
35L GLU* 1.3 77.2 - - - +
37L THR* 1.3 64.4 + - - +
39L GLN* 3.8 16.6 + - - +
40L TYR* 4.0 5.4 + - - +
64M HIS* 4.9 12.1 - - + +
67M GLN 4.9 6.3 - - - +
68M ALA* 4.9 19.7 - - + -
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Residues in contact with THR 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L LEU 3.0 19.9 + - - -
34L LYS* 3.0 9.8 + - - -
36L LEU* 1.3 76.3 - - - +
38L LYS* 1.3 63.8 + - - +
40L TYR* 3.3 19.9 + - - +
41L GLU* 3.6 5.0 + - - +
64M HIS* 6.2 0.2 - - - -
67M GLN* 5.4 14.1 - - - -
----------------------------------------------------------
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Residues in contact with LYS 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L LYS* 2.8 17.3 + - + +
35L GLU* 3.9 5.6 - - - +
37L THR* 1.3 73.3 - - - +
39L GLN* 1.3 66.0 + - - +
40L TYR 3.0 2.0 - - - -
41L GLU* 2.8 21.5 + - - +
42L LYS* 3.1 13.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN 39 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L GLU 3.8 8.9 + - - +
36L LEU* 3.8 13.4 + - - +
37L THR 3.4 0.2 - - - -
38L LYS* 1.3 76.9 - - - +
40L TYR* 1.3 50.6 + - - +
42L LYS* 4.1 5.3 - - - +
43L SER* 2.6 39.0 + - - -
72M LYS* 5.8 7.0 - - - -
75M GLU* 2.9 7.5 - - - +
----------------------------------------------------------
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Residues in contact with TYR 40 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L LEU 4.0 3.2 + - - +
37L THR* 3.3 14.8 + - - +
38L LYS 3.0 0.6 - - - -
39L GLN* 1.3 78.0 - - - +
41L GLU* 1.3 52.3 + - - +
43L SER* 3.2 0.3 + - - -
44L GLU* 2.6 42.7 + - + +
67M GLN 4.6 8.5 - - - +
71M ASP* 3.2 27.8 - - + +
75M GLU* 3.1 10.7 + - - -
----------------------------------------------------------
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Residues in contact with GLU 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L THR 3.6 3.7 + - - +
38L LYS* 2.8 16.6 + - - +
40L TYR* 1.3 80.2 - - - +
42L LYS* 1.3 57.5 + - - +
44L GLU* 3.4 4.9 - - - +
45L ASN* 2.9 30.0 + - - +
48L LYS* 5.1 2.9 + - - +
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Residues in contact with LYS 42 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L LYS 3.1 11.0 + - - +
39L GLN* 4.1 5.4 - - - +
41L GLU* 1.3 75.9 - - - +
43L SER* 1.3 64.5 + - - +
45L ASN* 3.1 18.1 + - - +
46L ASP* 3.1 11.8 + - - +
----------------------------------------------------------
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Residues in contact with SER 43 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLN 2.6 10.9 + - - -
40L TYR 3.2 1.7 + - - -
42L LYS* 1.3 78.6 - - - +
44L GLU* 1.3 55.1 + - - +
46L ASP* 2.9 5.1 + - - -
47L LEU* 2.6 32.3 + - - +
75M GLU* 2.0 55.3 + - - +
79M LYS* 2.7 20.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 44 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L TYR* 2.6 28.0 + - + +
41L GLU* 3.4 5.6 - - - +
43L SER* 1.3 73.9 + - - +
45L ASN* 1.3 53.7 + - - +
47L LEU* 2.9 11.3 + - + +
48L LYS* 2.5 60.5 + - - +
71M ASP* 5.8 2.0 - - + -
75M GLU* 5.1 2.7 - - + -
----------------------------------------------------------
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Residues in contact with ASN 45 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L GLU 2.9 12.6 + - - +
42L LYS* 3.1 12.6 - - - +
44L GLU* 1.3 74.0 - - - +
46L ASP* 1.3 54.2 + - - +
48L LYS* 3.7 12.3 - - - +
49L ALA* 2.7 39.4 + - - +
----------------------------------------------------------
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Residues in contact with ASP 46 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L LYS 3.1 7.0 + - - +
43L SER* 2.9 3.9 + - - +
45L ASN* 1.3 81.6 - - - +
47L LEU* 1.4 57.0 + - - +
49L ALA* 3.5 6.9 + - - +
50L LEU* 3.5 20.8 + - - +
79M LYS* 3.1 32.5 - - - +
138M GLY 6.5 0.9 - - - -
139M LEU* 4.6 16.7 - - + +
----------------------------------------------------------
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Residues in contact with LEU 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L SER 2.6 15.6 + - - +
44L GLU* 2.9 16.4 + - - +
46L ASP* 1.4 64.4 - - - +
48L LYS* 1.3 67.4 + - + +
50L LEU* 3.0 29.9 - - - +
51L GLN* 5.4 0.5 - - - +
74M LYS* 4.6 18.2 - - + +
75M GLU* 4.7 8.7 - - - +
78M GLU* 3.8 19.5 - - + +
79M LYS* 3.6 7.4 - - - +
----------------------------------------------------------
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Residues in contact with LYS 48 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L GLU* 5.1 2.8 + - - +
44L GLU* 2.5 47.3 + - + +
45L ASN* 3.7 8.9 - - - +
47L LEU* 1.3 69.0 - - + +
49L ALA* 1.3 55.4 + - - +
50L LEU 2.6 16.6 + - - -
51L GLN* 3.3 27.7 + - - +
52L SER* 4.1 0.9 + - - -
78M GLU* 5.5 0.2 - - - -
----------------------------------------------------------
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Residues in contact with ALA 49 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L ASN 2.7 23.4 + - - +
46L ASP* 3.7 7.6 - - - +
48L LYS* 1.3 72.4 - - - +
50L LEU* 1.3 53.3 + - - +
52L SER* 1.7 49.7 + - - +
136M VAL* 3.9 18.8 - - + -
138M GLY* 5.3 5.4 - - - -
159M LEU* 3.4 7.7 - - + +
----------------------------------------------------------
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Residues in contact with LEU 50 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ASP 3.5 11.0 + - - +
47L LEU* 3.0 17.8 + - - +
48L LYS 2.6 5.7 + - - -
49L ALA* 1.3 69.0 - - - +
51L GLN* 1.3 61.9 - - + +
52L SER 3.0 12.0 + - - +
78M GLU* 3.2 37.9 - - + +
79M LYS* 3.6 12.6 - - + +
82M VAL* 3.1 59.3 - - + +
83M ASN* 5.1 0.9 - - - +
139M LEU* 5.1 7.0 - - + -
157M SER* 4.3 7.1 + - - -
159M LEU* 4.0 20.9 - - + +
161M LEU* 5.0 2.7 - - + -
----------------------------------------------------------
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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