Contacts of the helix formed by residues 29 - 55 (chain E) 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 ARG 29 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E PHE* 2.7 33.2 - - - +
2E ALA 3.7 19.3 + - - +
3E ASN* 2.8 14.8 + - - +
27E LEU* 5.0 2.0 - - - -
28E THR* 1.3 70.2 - - - +
30E GLU* 1.3 70.6 + - - +
32E GLY* 4.0 0.4 - - - +
33E LEU* 3.3 35.2 + - + +
295E MET* 5.3 0.8 - - - +
300E LEU* 2.4 80.2 + - + +
301E ALA* 3.5 4.8 - - - +
305E GLU* 2.9 36.1 + - - -
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Residues in contact with GLU 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E ASN 4.5 0.8 + - - -
28E THR* 3.1 11.2 + - - +
29E ARG* 1.3 88.6 - - - +
31E ASP* 1.3 76.7 + - - +
33E LEU* 3.5 16.3 - - - +
34E LYS* 3.7 5.0 + - - +
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Residues in contact with ASP 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 4.4 4.0 - - + -
28E THR* 3.2 36.3 + - + +
30E GLU* 1.3 82.8 + - - +
32E GLY* 1.3 57.4 + - - +
33E LEU 3.1 2.0 - - - -
34E LYS* 2.7 54.6 + - - +
35E TYR* 3.2 30.2 + - + -
234E ARG* 4.0 6.8 + - - -
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Residues in contact with GLY 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 3.6 32.1 - - - +
28E THR 2.8 14.5 + - - -
29E ARG 4.0 1.3 - - - -
31E ASP* 1.3 72.5 - - - +
33E LEU* 1.3 57.4 + - - +
35E TYR* 3.4 8.8 + - - +
36E TYR* 3.1 20.1 + - - +
291E LEU* 3.8 3.6 - - - +
295E MET* 3.1 20.0 - - - +
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Residues in contact with LEU 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ARG* 3.3 33.2 + - - +
30E GLU* 3.5 13.2 - - - +
32E GLY* 1.3 77.3 - - - +
34E LYS* 1.3 61.8 + - - +
35E TYR 3.3 0.2 - - - -
36E TYR* 4.0 3.2 - - - +
37E ARG* 3.3 21.8 + - - +
295E MET* 3.6 20.2 - - + -
300E LEU 4.9 0.2 - - - +
301E ALA* 3.8 20.6 - - + -
305E GLU* 4.2 9.6 - - - +
306E LEU* 4.3 5.8 - - + -
309E ILE* 4.2 19.6 - - + +
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Residues in contact with LYS 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E GLU 3.7 4.4 + - - +
31E ASP* 2.7 34.3 + - - +
33E LEU* 1.3 73.7 - - - +
35E TYR* 1.3 86.9 + - - +
37E ARG* 3.5 6.2 + - - +
38E MET* 3.0 47.2 + - + +
77E ALA* 5.5 5.1 - - - +
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Residues in contact with TYR 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LEU* 4.0 19.5 - - + -
31E ASP* 3.2 24.0 + - - -
32E GLY* 3.7 6.3 - - - +
34E LYS* 1.3 111.7 + - - +
36E TYR* 1.3 66.6 + - - +
38E MET* 3.0 8.7 + - + +
39E MET* 2.9 29.0 + - - +
73E VAL* 4.2 10.9 - - + +
77E ALA* 3.4 22.6 + - + +
230E ILE* 4.2 26.5 - - + -
231E LEU* 4.7 3.6 - - + -
234E ARG* 2.9 45.7 + - - -
238E ARG* 4.8 1.7 + - - -
291E LEU* 4.2 11.4 - - + -
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Residues in contact with TYR 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E GLY 3.1 14.7 + - - +
33E LEU 4.1 3.6 - - - +
35E TYR* 1.3 81.3 - - - +
37E ARG* 1.3 65.4 + - - +
38E MET 3.0 0.7 + - - -
39E MET* 3.2 3.9 + - - +
40E GLN* 3.1 35.4 + - + +
288E ILE* 3.5 35.0 - - + +
291E LEU* 3.5 21.9 - - + +
292E LYS* 4.5 11.9 - - + +
295E MET* 3.9 7.9 - - + -
306E LEU* 3.7 54.8 + - + +
309E ILE* 4.3 14.6 - - + -
310E ASP* 3.2 27.1 + - - -
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Residues in contact with ARG 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E LEU 3.3 16.8 + - - +
34E LYS* 3.5 6.3 + - - +
36E TYR* 1.3 79.3 - - - +
38E MET* 1.3 57.7 + - + +
40E GLN* 4.1 2.4 - - - +
41E THR* 2.6 42.1 + - - +
309E ILE* 3.5 45.2 - - + +
312E GLU* 2.7 45.8 + - - +
313E VAL* 4.1 11.5 - - + +
316E GLU* 5.5 5.7 + - - +
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Residues in contact with MET 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LYS* 3.0 61.0 + - + +
35E TYR* 3.5 13.5 - - + +
36E TYR 3.0 0.6 - - - -
37E ARG* 1.3 77.1 - - + +
39E MET* 1.3 67.8 + - - +
41E THR* 3.8 4.2 - - - -
42E VAL* 3.1 25.1 + - - +
73E VAL* 3.9 24.9 - - + -
76E GLU* 5.1 11.9 - - + -
96E PHE* 4.1 19.1 - - + -
97E THR* 4.8 19.1 - - - +
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Residues in contact with MET 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E TYR 2.9 14.5 + - - +
36E TYR* 3.9 4.3 - - + +
38E MET* 1.3 75.9 - - - +
40E GLN* 1.3 49.5 + - - +
42E VAL* 3.0 6.1 + - - +
43E ARG* 2.7 34.1 + - - +
69E GLU* 3.9 30.6 - - + +
70E ALA* 4.2 9.2 - - - -
73E VAL* 3.7 16.4 - - + -
230E ILE* 4.1 21.3 - - + -
287E PRO* 4.2 11.2 - - - +
288E ILE* 3.6 27.5 - - + +
291E LEU* 3.4 43.7 - - + -
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Residues in contact with GLN 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E TYR* 3.1 32.2 + - + +
37E ARG* 4.1 4.3 - - - +
39E MET* 1.3 75.1 - - - +
41E THR* 1.3 53.6 + - - +
43E ARG* 3.6 10.8 - - - +
44E ARG* 2.8 62.2 + - - +
288E ILE* 3.3 34.9 - - + +
309E ILE* 5.7 0.4 - - + -
310E ASP* 3.0 34.6 - - - +
313E VAL* 3.8 14.4 - - + -
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Residues in contact with THR 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ARG* 2.6 27.1 + - - +
38E MET 3.8 3.6 - - - -
40E GLN* 1.3 74.4 - - - +
42E VAL* 1.3 67.5 + - - +
44E ARG* 3.4 0.7 + - - +
45E MET* 2.9 27.9 + - + +
96E PHE* 3.5 31.6 - - + -
102E VAL* 3.7 22.9 - - + -
313E VAL* 3.7 21.0 - - + +
316E GLU* 5.7 5.4 - - + -
317E ILE* 4.2 6.8 - - + +
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Residues in contact with VAL 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E MET 3.1 12.9 + - - +
39E MET 3.0 8.2 + - - +
41E THR* 1.3 79.5 - - - +
43E ARG* 1.3 65.6 + - - +
45E MET* 3.7 9.3 - - - +
46E GLU* 2.9 25.9 + - + +
65E CYS* 3.9 24.9 - - - -
69E GLU* 3.4 25.6 - - + -
72E CYS* 4.7 4.3 - - - -
73E VAL* 4.9 2.0 - - + -
93E GLY* 4.1 19.7 - - - +
96E PHE* 3.8 22.7 - - + -
97E THR* 4.4 8.5 - - + -
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Residues in contact with ARG 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E MET 2.7 20.0 + - - +
40E GLN* 3.6 13.3 - - - +
41E THR 3.2 0.2 - - - -
42E VAL* 1.3 76.1 - - - +
44E ARG* 1.3 67.8 + - - +
46E GLU* 3.3 3.4 + - - +
47E LEU* 3.2 35.4 + - + +
66E ASP* 3.8 13.7 - - - +
67E GLY* 3.5 10.3 - - - +
69E GLU* 2.5 44.3 + - - +
260E TYR* 3.6 13.9 - - - -
282E ARG* 4.5 8.6 - - - +
286E ASP* 2.7 37.2 + - - -
287E PRO* 4.0 2.2 - - - +
288E ILE* 3.6 19.7 - - + +
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Residues in contact with ARG 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLN* 2.8 43.1 + - - +
41E THR 4.1 0.2 - - - +
43E ARG* 1.3 77.9 - - - +
45E MET* 1.3 59.0 + - - +
47E LEU* 3.1 36.8 + - - +
48E LYS* 2.9 28.8 + - - +
310E ASP 5.4 0.7 - - - +
313E VAL* 3.6 17.3 - - + -
314E ARG* 3.2 54.6 - - + +
317E ILE* 3.6 22.3 - - + +
286L ASN 5.4 0.2 + - - -
289L ASP* 4.8 7.5 + - - -
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Residues in contact with MET 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E THR 2.9 18.6 + - - +
42E VAL* 3.7 8.1 - - - +
44E ARG* 1.3 77.7 - - - +
46E GLU* 1.3 66.8 + - - +
48E LYS* 3.3 4.6 + - - +
49E ALA* 2.9 22.2 + - + +
92E HIS* 4.6 16.4 - - - +
93E GLY* 6.0 0.2 - - - -
96E PHE* 4.5 9.0 - - + -
102E VAL* 3.5 44.2 - - + +
105E ILE* 3.3 49.4 - - + -
106E LEU* 4.1 13.5 - - + +
317E ILE* 3.8 16.5 - - + +
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Residues in contact with GLU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E VAL* 2.9 23.2 + - + +
43E ARG 3.3 5.6 + - - +
45E MET* 1.3 77.8 - - - +
47E LEU* 1.3 60.6 + - - +
49E ALA* 3.1 5.5 + - - +
50E ASP* 2.8 28.2 + - - +
63E HIS 4.0 0.9 - - - +
64E LEU* 3.2 22.9 - - + +
65E CYS* 2.7 52.9 + - - +
66E ASP* 4.0 20.6 - - + +
92E HIS* 3.2 34.9 + - - +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E ARG* 3.2 25.9 + - + +
44E ARG* 3.1 45.7 + - - +
46E GLU* 1.3 77.5 - - - +
48E LYS* 1.3 64.0 + - - +
50E ASP* 3.1 9.5 + - - +
51E GLN* 2.9 23.8 + - - +
66E ASP* 3.8 22.2 - - - +
261E HIS* 4.5 11.0 - - + +
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Residues in contact with LYS 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ARG 2.9 10.3 + - - +
45E MET* 3.8 3.8 - - - +
47E LEU* 1.3 75.4 - - - +
49E ALA* 1.3 59.8 + - - +
51E GLN* 2.8 34.2 + - - +
52E LEU* 2.8 46.8 + - + +
106E LEU* 3.8 8.5 - - + -
317E ILE* 3.6 22.0 - - + -
318E GLU* 3.0 42.0 + - - -
321E ALA* 3.7 24.9 - - + -
286L ASN* 3.5 8.7 + - - +
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Residues in contact with ALA 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E MET* 2.9 14.1 + - + +
46E GLU* 3.4 13.0 - - - +
48E LYS* 1.3 77.1 - - - +
50E ASP* 1.3 57.1 + - - +
52E LEU* 2.9 7.2 + - - +
53E TYR* 2.8 32.2 + - - +
58E ILE* 3.7 10.4 - - + +
62E CYS* 4.6 2.2 - - - -
64E LEU* 4.1 14.1 - - + -
92E HIS* 5.1 0.4 - - - +
106E LEU* 4.4 5.8 - - + +
109E LEU* 4.1 25.4 - - + -
----------------------------------------------------------
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Residues in contact with ASP 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46E GLU 2.8 15.2 + - - +
47E LEU* 3.5 12.0 - - - +
49E ALA* 1.3 69.3 - - - +
51E GLN* 1.3 65.7 + - - +
53E TYR* 3.9 11.4 - - - +
54E LYS* 3.0 45.1 + - - +
62E CYS* 5.4 0.4 - - - -
64E LEU* 3.5 33.1 - - + +
261E HIS* 3.5 19.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E LEU 2.9 12.6 + - - +
48E LYS* 2.8 40.9 + - - +
50E ASP* 1.3 79.5 - - - +
52E LEU* 1.3 63.9 + - - +
54E LYS* 3.1 19.6 + - + +
55E GLN* 3.3 46.3 + - - +
289J ASP 5.8 1.1 - - - +
286L ASN* 2.9 24.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48E LYS* 2.8 43.3 + - + +
49E ALA* 2.9 9.6 + - - +
51E GLN* 1.3 77.0 - - - +
53E TYR* 1.3 63.2 + - - +
55E GLN* 3.3 22.7 + - - +
57E ILE* 3.3 39.2 + - + +
58E ILE* 3.8 20.2 - - + -
106E LEU* 4.5 11.0 - - + -
110E THR* 5.1 7.4 - - + -
321E ALA* 4.3 11.2 - - + -
324E ALA* 5.8 0.9 - - + -
325E THR* 3.7 28.0 - - + -
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Residues in contact with TYR 53 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ALA 2.8 16.0 + - - +
50E ASP* 3.9 12.1 - - - +
52E LEU* 1.3 76.6 - - - +
54E LYS* 1.3 67.5 + - + +
55E GLN 3.2 0.2 - - - -
56E LYS* 3.2 17.0 + - - +
58E ILE* 3.2 36.5 - - + +
59E ARG* 4.5 0.9 - - - -
60E GLY 3.1 25.8 + - - -
61E PHE* 4.3 1.4 - - - -
62E CYS* 3.3 42.5 + - + -
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Residues in contact with LYS 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ASP* 3.0 49.2 + - - +
51E GLN* 3.1 12.8 + - + +
53E TYR* 1.3 80.4 - - + +
55E GLN* 1.3 62.5 + - + +
56E LYS* 3.2 10.5 + - - +
258J HIS* 5.7 1.6 + - - -
289J ASP* 3.3 44.6 - - + +
----------------------------------------------------------
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Residues in contact with GLN 55 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLN* 3.3 46.9 + - + +
52E LEU* 3.3 24.6 + - - +
53E TYR 3.2 0.6 - - - -
54E LYS* 1.3 75.4 - - + +
56E LYS* 1.3 71.5 + - - +
57E ILE* 3.3 22.3 - - + +
258J HIS* 5.4 7.6 + - - +
289J ASP* 3.1 28.5 - - - +
290J ALA* 4.0 14.7 - - + +
291J PRO* 4.9 3.6 - - - +
327J LEU 4.3 13.2 - - - +
328J ASN* 5.0 10.5 - - + +
----------------------------------------------------------
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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