Contacts of the helix formed by residues 28 - 55 (chain O) in PDB entry 3EXG
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 28 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O ASN 3.6 16.2 - - - +
4O ASP* 3.7 3.1 - - + -
26O VAL* 4.7 13.9 - - + +
27O LEU* 1.3 75.3 - - - +
29O ARG* 1.3 63.4 + - - +
30O GLU* 3.5 9.6 + - - +
31O ASP* 2.8 41.5 + - - +
32O GLY 2.9 11.8 + - - -
234O ARG* 5.6 1.3 - - - +
300O LEU* 4.6 0.4 - - - -
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Residues in contact with ARG 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1O PHE* 4.3 18.9 - - + +
2O ALA 3.7 19.3 - - - +
3O ASN* 3.5 9.6 + - - +
28O THR* 1.3 68.9 - - - +
30O GLU* 1.3 76.2 + - - +
32O GLY* 3.7 1.7 + - - +
33O LEU* 3.0 56.1 + - + +
295O MET* 4.6 1.5 - - - +
300O LEU* 3.0 56.9 + - + +
305O GLU* 4.7 10.3 + - - -
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Residues in contact with GLU 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3O ASN 5.0 0.4 + - - -
28O THR* 3.0 8.8 - - - +
29O ARG* 1.3 102.0 - - - +
31O ASP* 1.3 65.5 + - - +
33O LEU* 3.9 6.2 + - - +
34O LYS* 3.8 13.0 + - - +
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Residues in contact with ASP 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LEU* 4.0 10.1 - - + -
28O THR* 2.8 35.4 + - - +
30O GLU* 1.3 74.6 - - - +
32O GLY* 1.3 54.7 + - - +
33O LEU 2.9 4.0 - - - -
34O LYS* 2.7 40.5 + - - +
35O TYR* 3.0 39.3 + - + -
234O ARG* 5.5 4.9 + - - +
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Residues in contact with GLY 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LEU* 3.3 19.6 - - - +
28O THR 2.9 13.8 + - - -
29O ARG 3.8 0.4 - - - -
31O ASP* 1.3 71.9 - - - +
33O LEU* 1.3 58.3 + - - +
34O LYS 3.4 0.2 - - - -
35O TYR* 3.9 13.4 - - - +
36O TYR* 3.4 16.1 + - - +
291O LEU* 4.2 2.9 - - - +
295O MET* 3.0 32.8 - - - +
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Residues in contact with LEU 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O ARG* 3.0 42.3 + - - +
30O GLU* 4.0 7.9 - - - +
31O ASP 2.8 2.0 + - - -
32O GLY* 1.3 75.9 - - - +
34O LYS* 1.3 64.5 + - - +
35O TYR 3.3 0.2 - - - -
36O TYR* 3.8 2.6 + - - +
37O ARG* 3.5 21.5 + - - +
295O MET* 3.6 20.2 - - + -
300O LEU 4.8 2.9 - - - +
301O ALA* 4.1 15.0 - - + -
305O GLU* 4.8 11.0 - - + +
309O ILE* 4.6 22.2 - - + +
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Residues in contact with LYS 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30O GLU 3.8 7.5 + - - +
31O ASP* 2.7 29.8 + - - +
33O LEU* 1.3 74.0 - - - +
35O TYR* 1.3 71.1 + - - +
37O ARG* 3.6 10.5 + - - +
38O MET* 3.2 46.3 + - + +
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Residues in contact with TYR 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O LEU* 4.1 6.1 - - + -
31O ASP* 3.0 45.3 + - + +
32O GLY* 3.9 12.6 - - - -
33O LEU 3.3 0.2 - - - -
34O LYS* 1.3 87.1 - - + +
36O TYR* 1.3 68.0 + - - +
38O MET* 3.2 13.0 + - + +
39O MET* 3.1 26.5 + - + +
73O VAL* 4.3 15.9 - - + -
77O ALA* 3.3 34.1 + - + +
230O ILE* 4.4 20.4 - - + -
231O LEU* 5.3 0.9 - - + -
234O ARG* 3.7 34.7 + - - -
238O ARG* 4.9 1.2 + - - -
291O LEU* 3.8 16.6 - - + -
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Residues in contact with TYR 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32O GLY 3.4 15.5 + - - +
33O LEU 3.8 3.8 + - - +
34O LYS 3.4 0.2 - - - -
35O TYR* 1.3 80.3 - - - +
37O ARG* 1.3 66.8 + - - +
38O MET 3.0 0.7 + - - -
39O MET* 3.2 8.0 + - + +
40O GLN* 3.0 40.0 + - + +
288O ILE* 3.5 35.6 - - + +
291O LEU* 4.0 12.2 - - + +
292O LYS* 3.9 28.2 - - + -
295O MET* 4.8 3.6 - - + -
306O LEU* 3.6 39.1 - - + +
309O ILE* 3.7 19.5 - - + -
310O ASP* 2.6 35.7 + - - -
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Residues in contact with ARG 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33O LEU 3.5 16.8 + - - +
34O LYS* 3.8 10.8 - - - +
35O TYR 3.4 0.4 - - - -
36O TYR* 1.3 83.5 - - - +
38O MET* 1.3 63.6 + - + +
40O GLN* 3.6 4.0 - - - +
41O THR* 2.9 39.3 + - - +
96O PHE* 6.2 1.6 - - + -
309O ILE* 2.9 37.6 - - + +
312O GLU* 3.4 28.3 + - - +
313O VAL* 3.9 22.9 - - - +
316O GLU* 5.3 8.1 + - - +
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Residues in contact with MET 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O LYS* 3.2 53.9 + - + +
35O TYR* 3.2 16.7 + - + +
36O TYR 3.1 0.8 - - - -
37O ARG* 1.3 81.6 - - + +
39O MET* 1.3 61.0 + - - +
41O THR* 3.2 7.4 + - - -
42O VAL* 2.8 32.6 + - - +
73O VAL* 4.1 19.5 - - + +
76O GLU* 5.6 7.9 - - + -
96O PHE* 3.7 21.9 - - + -
97O THR* 4.5 22.4 - - + +
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Residues in contact with MET 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O TYR 3.1 15.0 + - - +
36O TYR* 4.0 5.6 - - + +
38O MET* 1.3 73.3 - - - +
40O GLN* 1.3 59.0 + - - +
42O VAL* 3.4 1.0 + - - +
43O ARG* 2.8 31.0 + - - +
69O GLU* 3.6 15.1 - - + +
70O ALA* 4.4 16.2 - - - -
73O VAL* 3.5 26.2 - - + -
230O ILE* 4.1 23.1 - - - -
287O PRO 3.7 10.8 - - - +
288O ILE* 3.5 41.7 - - + +
291O LEU* 4.0 26.2 - - + -
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Residues in contact with GLN 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36O TYR* 3.0 45.0 + - + +
37O ARG* 3.6 4.7 - - - +
39O MET* 1.3 75.0 - - - +
41O THR* 1.3 66.2 + - - +
43O ARG* 3.3 6.2 + - - +
44O ARG* 2.9 57.9 + - - +
288O ILE* 3.5 31.8 - - + +
310O ASP* 3.1 28.8 - - - +
313O VAL* 4.1 10.4 - - + +
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Residues in contact with THR 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37O ARG* 2.9 29.6 + - - +
38O MET 3.2 8.7 + - - -
40O GLN* 1.3 77.0 - - - +
42O VAL* 1.3 63.4 + - + +
44O ARG* 3.3 2.1 + - - +
45O MET* 3.1 21.0 + - + +
96O PHE* 3.5 36.5 - - + -
102O VAL* 3.7 24.5 - - + -
313O VAL* 3.7 22.0 - - - +
316O GLU* 5.6 6.0 - - + +
317O ILE* 4.1 4.5 - - + +
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Residues in contact with VAL 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38O MET 2.8 17.2 + - - +
39O MET* 3.9 3.4 - - - +
41O THR* 1.3 74.6 - - + +
43O ARG* 1.3 63.7 + - - +
45O MET* 3.4 9.8 + - - +
46O GLU* 3.0 26.4 + - + +
65O CYS* 4.3 13.9 - - - -
69O GLU* 3.8 18.2 - - + -
72O CYS* 4.5 7.6 - - - -
73O VAL* 5.3 0.4 - - + -
93O GLY* 3.8 36.8 - - - +
96O PHE* 3.8 30.1 - - + -
97O THR* 4.6 6.7 - - + -
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Residues in contact with ARG 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O MET 2.8 21.4 + - - +
40O GLN* 3.5 8.1 - - - +
42O VAL* 1.3 74.4 - - - +
44O ARG* 1.3 69.3 + - - +
46O GLU* 3.3 3.0 + - - +
47O LEU* 2.9 45.3 + - + +
66O ASP* 3.9 15.9 - - - +
67O GLY* 4.0 5.8 - - - +
69O GLU* 2.4 46.5 + - - +
282O ARG* 4.9 14.1 - - - +
286O ASP* 3.1 37.0 + - - -
287O PRO* 3.9 7.5 - - - +
288O ILE* 3.8 19.8 - - + +
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Residues in contact with ARG 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40O GLN* 2.9 37.5 + - - +
41O THR 3.9 0.2 - - - +
43O ARG* 1.3 80.8 - - - +
45O MET* 1.3 56.3 - - - +
47O LEU* 3.1 37.0 - - - +
48O LYS* 3.0 26.3 + - - +
310O ASP 5.9 0.2 - - - +
313O VAL* 3.3 17.7 - - + -
314O ARG* 3.1 48.3 - - - +
317O ILE* 3.6 25.4 - - + +
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Residues in contact with MET 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41O THR 3.1 16.0 + - - +
42O VAL* 3.7 10.8 - - - +
44O ARG* 1.3 73.7 - - - +
46O GLU* 1.3 72.5 - - - +
47O LEU 3.3 0.2 - - - -
48O LYS* 3.4 5.5 + - - +
49O ALA* 2.8 27.9 + - + +
92O HIS* 4.7 10.8 - - - +
96O PHE* 4.8 7.0 - - + -
102O VAL* 3.3 50.7 - - + +
105O ILE* 3.5 40.4 - - + -
106O LEU* 4.5 14.3 - - + +
109O LEU* 6.2 1.1 - - + -
317O ILE* 3.8 15.1 - - + +
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Residues in contact with GLU 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O VAL* 3.0 26.0 + - + +
43O ARG 3.8 3.6 - - - +
45O MET* 1.3 81.0 - - - +
47O LEU* 1.3 61.5 + - - +
49O ALA* 4.3 2.6 - - - +
50O ASP* 3.0 28.4 + - - +
63O HIS 3.9 0.5 - - - +
64O LEU* 3.4 22.2 - - + +
65O CYS* 3.0 43.8 + - - +
66O ASP* 4.4 15.3 - - + +
92O HIS* 3.1 44.6 + - - +
93O GLY 4.9 0.7 - - - -
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Residues in contact with LEU 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43O ARG* 2.9 33.5 + - - +
44O ARG* 3.1 39.7 - - - +
46O GLU* 1.3 78.7 - - - +
48O LYS* 1.3 63.0 + - - +
50O ASP* 3.3 12.5 + - + +
51O GLN* 3.2 23.8 + - - +
66O ASP* 4.2 21.5 - - - +
282O ARG* 6.2 2.7 - - - +
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Residues in contact with LYS 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O ARG 3.0 18.3 + - - +
45O MET* 3.5 6.7 - - - +
46O GLU 3.3 0.2 - - - -
47O LEU* 1.3 72.9 - - - +
49O ALA* 1.3 67.4 + - - +
51O GLN* 3.2 35.7 + - - +
52O LEU* 3.0 37.3 + - + +
106O LEU* 4.2 9.6 - - + -
317O ILE* 3.7 24.7 - - + -
318O GLU* 3.6 26.2 + - - -
321O ALA* 3.5 31.3 - - + +
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Residues in contact with ALA 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45O MET* 2.8 20.9 + - + +
46O GLU* 3.8 9.2 - - - +
48O LYS* 1.3 72.2 - - - +
50O ASP* 1.3 65.6 + - - +
52O LEU* 2.9 15.3 + - - +
53O TYR* 3.0 16.7 + - - +
58O ILE* 3.6 12.2 - - + +
62O CYS* 4.2 2.5 - - - -
64O LEU* 4.0 14.1 - - + -
106O LEU* 4.6 5.4 - - + -
109O LEU* 4.0 25.8 - - + -
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Residues in contact with ASP 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46O GLU 3.0 13.0 + - - +
47O LEU* 3.4 15.1 - - + +
48O LYS 3.2 0.2 - - - -
49O ALA* 1.3 77.5 - - - +
51O GLN* 1.3 59.3 + - - +
53O TYR* 3.3 10.3 + - - +
54O LYS* 2.9 60.0 + - - +
62O CYS* 5.4 0.2 - - - -
64O LEU* 3.4 33.6 - - + +
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Residues in contact with GLN 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47O LEU 3.2 9.2 + - - +
48O LYS* 3.2 38.9 + - - +
50O ASP* 1.3 79.8 + - - +
52O LEU* 1.3 64.7 + - + +
53O TYR 3.0 5.8 + - - -
54O LYS* 3.4 8.2 + - - +
55O GLN* 3.1 43.0 + - + +
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Residues in contact with LEU 52 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48O LYS* 3.0 35.5 + - + +
49O ALA 2.9 8.6 + - - +
51O GLN* 1.3 80.3 - - + +
53O TYR* 1.3 53.5 + - - +
55O GLN* 3.6 12.2 - - - +
56O LYS 3.2 3.3 + - - -
57O ILE* 2.8 49.7 + - + +
58O ILE* 3.4 17.5 + - + -
106O LEU* 4.5 17.9 - - + -
110O THR* 4.1 24.5 - - + -
321O ALA* 4.8 8.5 - - + -
324O ALA* 5.5 1.1 - - + -
325O THR* 4.3 15.9 - - + -
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Residues in contact with TYR 53 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O ALA 3.0 13.4 + - - +
50O ASP* 3.6 9.4 - - - +
51O GLN 3.0 0.2 - - - -
52O LEU* 1.3 78.4 - - - +
54O LYS* 1.3 61.9 + - + +
55O GLN 2.8 3.8 - - - -
56O LYS* 2.7 26.0 + - - +
58O ILE* 3.5 36.9 - - + +
59O ARG 4.6 0.7 - - - -
60O GLY 3.1 27.9 + - - -
61O PHE* 3.8 2.8 - - - -
62O CYS* 3.1 41.6 + - + -
64O LEU* 6.4 0.9 - - + -
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Residues in contact with LYS 54 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O ASP* 2.9 51.4 + - - +
51O GLN* 3.7 8.3 - - - +
53O TYR* 1.3 79.4 - - + +
55O GLN* 1.3 61.8 + - + +
56O LYS* 4.3 12.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN 55 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51O GLN* 3.1 33.1 + - + +
52O LEU* 3.8 19.9 - - - +
53O TYR 2.8 0.8 - - - -
54O LYS* 1.3 80.7 - - + +
56O LYS* 1.3 72.8 + - - +
57O ILE* 3.3 17.7 + - + +
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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