Contacts of the helix formed by residues 29 - 55 (chain W) 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 W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1W PHE* 3.2 29.5 - - - +
2W ALA 3.7 16.6 - - - +
3W ASN* 2.9 20.3 + - - +
27W LEU* 5.1 0.7 - - - -
28W THR* 1.3 69.0 - - - +
30W GLU* 1.3 64.9 + - - +
32W GLY 3.5 1.8 + - - +
33W LEU* 3.0 45.1 + - - +
295W MET* 4.7 2.3 - - - +
300W LEU* 2.3 87.6 + - + +
301W ALA* 3.6 2.0 - - - +
305W GLU* 2.8 37.0 + - - -
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Residues in contact with GLU 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28W THR* 2.9 9.8 + - - +
29W ARG* 1.3 89.1 - - - +
31W ASP* 1.3 70.8 + - - +
33W LEU* 3.6 5.5 + - - +
34W LYS* 3.5 15.4 + - - +
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Residues in contact with ASP 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W LEU* 3.9 11.2 - - + -
28W THR* 2.7 40.7 + - - +
30W GLU* 1.3 75.0 + - - +
32W GLY* 1.3 54.2 + - - +
33W LEU 3.0 4.7 - - - -
34W LYS* 2.7 40.8 + - - +
35W TYR* 2.8 37.8 + - + -
234W ARG* 4.5 5.4 + - - -
238W ARG* 5.8 0.7 + - - -
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Residues in contact with GLY 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W LEU* 3.5 27.5 - - - +
28W THR 3.0 7.3 + - - -
29W ARG 3.9 1.6 - - - -
31W ASP* 1.3 79.4 - - - +
33W LEU* 1.3 58.3 + - - +
34W LYS 3.3 0.2 - - - -
35W TYR* 3.9 10.1 - - - -
36W TYR* 3.4 15.9 + - - +
291W LEU* 4.2 4.7 - - - +
295W MET* 2.8 24.1 - - - +
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Residues in contact with LEU 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W ARG* 3.0 30.3 + - - +
30W GLU* 3.9 7.2 - - - +
31W ASP 3.0 1.6 - - - -
32W GLY* 1.3 76.7 - - - +
34W LYS* 1.3 64.2 + - - +
36W TYR* 4.2 3.1 - - - +
37W ARG* 3.6 20.8 + - - +
295W MET* 3.5 20.6 - - + -
301W ALA* 3.9 19.1 - - + -
305W GLU* 3.9 21.3 - - - +
306W LEU* 3.9 13.9 - - + -
309W ILE* 4.1 19.4 - - + +
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Residues in contact with LYS 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30W GLU* 3.5 9.5 + - - +
31W ASP* 2.7 20.1 + - - +
33W LEU* 1.3 77.0 - - - +
35W TYR* 1.3 86.5 + - - +
37W ARG* 3.1 12.0 + - + +
38W MET* 3.0 47.0 + - + +
77W ALA* 6.1 1.0 - - - +
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Residues in contact with TYR 35 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27W LEU* 4.0 11.7 - - + -
31W ASP* 2.8 34.0 + - + +
32W GLY* 4.2 10.1 - - - +
34W LYS* 1.3 97.8 + - - +
36W TYR* 1.3 62.3 + - - +
38W MET* 3.3 15.2 + - + +
39W MET* 3.1 27.9 + - + +
73W VAL* 4.0 11.8 - - + +
77W ALA* 3.5 31.6 + - + +
230W ILE* 4.4 20.0 - - + -
231W LEU* 4.9 4.0 - - + -
234W ARG* 3.3 37.8 + - - -
238W ARG* 4.8 3.5 + - - -
291W LEU* 4.0 16.4 - - + -
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Residues in contact with TYR 36 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32W GLY 3.4 17.5 + - - +
33W LEU 4.2 4.0 - - - +
34W LYS 3.2 0.2 - - - -
35W TYR* 1.3 77.7 - - - +
37W ARG* 1.3 60.4 + - - +
38W MET 3.2 0.2 + - - -
39W MET* 3.9 3.2 - - - +
40W GLN* 2.9 47.5 + - + +
288W ILE* 3.5 28.1 - - + +
291W LEU* 3.5 18.5 - - + +
292W LYS* 3.9 34.3 - - + -
295W MET* 4.6 2.2 - - + -
306W LEU* 3.7 42.4 + - + +
309W ILE* 4.3 12.8 - - + -
310W ASP* 2.7 35.8 + - - -
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Residues in contact with ARG 37 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W LEU 3.6 13.5 + - - +
34W LYS* 3.1 13.9 + - - +
36W TYR* 1.3 81.6 - - - +
38W MET* 1.3 60.6 + - + +
40W GLN* 3.8 6.3 - - - +
41W THR* 2.7 41.7 + - - +
309W ILE* 3.3 37.2 - - + +
312W GLU* 3.8 33.3 + - - +
313W VAL* 4.2 10.4 - - + +
316W GLU* 5.5 5.2 + - - +
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Residues in contact with MET 38 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34W LYS* 3.0 54.4 + - + +
35W TYR* 3.7 9.9 - - + +
36W TYR 3.2 0.2 - - - -
37W ARG* 1.3 78.5 - - + +
39W MET* 1.3 60.7 + - - +
41W THR* 3.2 5.1 + - - -
42W VAL* 2.8 33.6 + - - +
73W VAL* 4.0 33.7 - - + +
76W GLU* 5.6 5.4 - - + -
96W PHE* 4.0 19.9 - - + -
97W THR* 4.9 17.5 - - - +
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Residues in contact with MET 39 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W TYR 3.1 13.5 + - - +
36W TYR* 3.9 2.5 - - - +
38W MET* 1.3 75.8 - - - +
40W GLN* 1.3 52.0 + - - +
42W VAL* 3.3 2.5 + - - +
43W ARG* 2.7 36.4 + - - +
69W GLU* 3.6 32.5 - - + +
70W ALA* 4.2 9.2 - - - -
73W VAL* 3.5 23.6 - - + -
230W ILE* 4.2 15.3 - - + -
287W PRO 4.0 14.6 - - - +
288W ILE* 3.5 24.6 - - + +
291W LEU* 3.1 45.3 - - + -
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Residues in contact with GLN 40 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36W TYR* 2.9 33.4 + - + +
37W ARG* 3.8 8.1 - - - +
39W MET* 1.3 74.0 - - - +
41W THR* 1.3 67.5 + - - +
43W ARG* 3.2 6.8 + - - +
44W ARG* 3.1 51.9 + - - +
288W ILE* 3.7 27.2 - - + +
309W ILE* 5.9 0.7 - - + -
310W ASP* 3.5 34.9 + - - +
313W VAL* 4.0 12.8 - - + +
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Residues in contact with THR 41 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W ARG* 2.7 31.2 + - - +
38W MET 3.6 4.0 - - - -
40W GLN* 1.3 78.3 - - - +
42W VAL* 1.3 58.8 + - - +
44W ARG 3.3 0.7 + - - -
45W MET* 2.9 29.2 + - + +
96W PHE* 3.4 39.0 - - + -
102W VAL* 3.7 17.5 - - + -
313W VAL* 3.5 21.5 - - + +
316W GLU* 4.2 16.7 + - + +
317W ILE* 4.1 4.8 - - + +
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Residues in contact with VAL 42 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W MET 2.8 19.0 + - - +
39W MET* 3.7 4.0 - - - +
41W THR* 1.3 75.7 - - - +
43W ARG* 1.3 61.4 + - - +
45W MET* 3.5 10.2 - - - +
46W GLU* 3.0 25.5 + - + +
65W CYS* 4.3 10.5 - - - -
69W GLU* 3.5 23.6 - - + +
72W CYS* 4.5 4.7 - - - -
73W VAL* 5.2 1.1 - - + -
93W GLY* 3.9 34.5 - - - +
96W PHE* 3.8 25.8 - - + -
97W THR* 4.5 7.0 - - + -
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Residues in contact with ARG 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39W MET 2.7 20.7 + - - +
40W GLN* 3.2 9.6 + - - +
42W VAL* 1.3 76.5 - - - +
44W ARG* 1.3 69.6 + - - +
46W GLU* 3.3 2.3 + - - +
47W LEU* 3.0 37.8 + - + +
66W ASP* 3.5 15.7 - - - +
67W GLY* 3.6 10.0 - - - +
69W GLU* 2.5 43.8 + - - +
260W TYR* 4.2 9.9 - - - -
282W ARG* 4.4 6.8 - - - +
286W ASP* 2.9 32.1 + - - -
287W PRO* 3.7 11.7 - - - +
288W ILE* 3.6 20.3 - - + +
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Residues in contact with ARG 44 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40W GLN* 3.1 37.5 + - - +
43W ARG* 1.3 82.2 - - - +
45W MET* 1.3 63.7 + - - +
47W LEU* 3.3 32.7 - - - +
48W LYS* 3.3 21.8 + - - +
310W ASP 6.0 0.2 - - - +
313W VAL* 3.8 10.3 - - + -
314W ARG* 3.1 53.8 - - - +
317W ILE* 3.6 24.9 - - + +
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Residues in contact with MET 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W THR* 2.9 18.7 + - + +
42W VAL* 3.5 11.4 - - - +
44W ARG* 1.3 79.7 - - - +
46W GLU* 1.3 62.6 - - - +
48W LYS* 3.5 4.9 + - - +
49W ALA* 2.9 25.2 + - + +
92W HIS* 4.5 18.6 - - - +
96W PHE* 4.4 8.5 - - + -
102W VAL* 3.4 52.0 - - + +
105W ILE* 3.5 40.4 - - + -
106W LEU* 4.6 11.7 - - + +
317W ILE* 3.8 11.6 - - + +
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Residues in contact with GLU 46 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42W VAL* 3.0 23.2 + - + +
43W ARG 3.7 3.8 - - - +
45W MET* 1.3 77.9 - - + +
47W LEU* 1.3 62.1 + - - +
49W ALA* 3.4 6.5 - - - +
50W ASP 2.9 22.9 + - - -
63W HIS 3.9 0.3 - - - +
64W LEU* 3.1 26.7 - - + +
65W CYS* 2.5 48.4 + - - +
66W ASP* 4.1 22.9 - - + +
90W ARG* 5.5 0.2 - - - +
92W HIS* 3.0 36.2 + - - +
93W GLY 5.1 0.2 - - - -
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Residues in contact with LEU 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43W ARG* 3.0 33.8 + - + +
44W ARG* 3.3 38.8 - - - +
45W MET 3.3 0.2 - - - -
46W GLU* 1.3 77.1 - - - +
48W LYS* 1.3 62.7 + - - +
50W ASP* 3.1 15.3 + - + +
51W GLN* 3.1 13.7 + - - +
66W ASP* 4.0 20.0 - - - +
261W HIS* 5.5 4.5 - - + -
282W ARG* 6.3 0.9 - - - +
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Residues in contact with LYS 48 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W ARG 3.3 17.7 + - - +
45W MET* 3.6 5.4 - - - +
47W LEU* 1.3 74.8 - - - +
49W ALA* 1.3 67.4 + - - +
50W ASP 3.2 0.2 + - - -
51W GLN* 3.2 37.9 + - - +
52W LEU* 3.1 35.2 + - + +
106W LEU* 4.2 6.7 - - + -
317W ILE* 3.7 22.9 - - + -
318W GLU* 3.2 29.5 + - - -
321W ALA* 3.7 29.8 - - + +
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Residues in contact with ALA 49 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45W MET* 2.9 16.2 + - + +
46W GLU* 3.4 17.9 - - - +
48W LYS* 1.3 75.1 - - - +
50W ASP* 1.3 62.8 + - - +
52W LEU* 3.1 10.8 + - - +
53W TYR* 3.0 19.5 + - - +
58W ILE* 3.6 14.3 - - + +
62W CYS* 4.8 1.8 - - - -
64W LEU* 4.1 15.3 - - + -
106W LEU* 4.7 4.7 - - + -
109W LEU* 4.3 19.5 - - + -
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Residues in contact with ASP 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46W GLU 2.9 6.5 + - - +
47W LEU* 3.4 12.3 - - + +
49W ALA* 1.3 76.0 - - - +
51W GLN* 1.3 68.1 + - - +
53W TYR* 3.1 14.9 + - - +
54W LYS* 2.9 48.4 + - - +
62W CYS* 5.6 0.2 - - - -
64W LEU* 3.3 26.9 - - + +
261W HIS* 3.4 27.1 + - + +
----------------------------------------------------------
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Residues in contact with GLN 51 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47W LEU 3.1 9.5 + - - +
48W LYS* 3.2 41.5 + - - +
50W ASP* 1.3 82.9 + - - +
52W LEU* 1.3 65.0 + - - +
54W LYS* 3.2 7.5 + - - +
55W GLN* 3.2 48.0 + - + +
----------------------------------------------------------
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Residues in contact with LEU 52 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W LYS* 3.1 42.0 + - + +
49W ALA* 3.1 8.8 + - - +
51W GLN* 1.3 80.8 - - + +
53W TYR* 1.3 59.1 + - - +
55W GLN* 3.3 13.3 + - - +
56W LYS 3.1 6.4 + - - -
57W ILE* 2.8 51.7 + - + +
58W ILE* 4.0 14.8 - - + -
106W LEU* 4.4 17.3 - - + -
110W THR* 4.8 10.3 - - + -
321W ALA* 4.5 9.0 - - + -
324W ALA* 6.0 0.9 - - + -
325W THR* 4.1 17.9 - - + -
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Residues in contact with TYR 53 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W ALA 3.0 11.6 + - - +
50W ASP* 3.1 17.2 + - - +
52W LEU* 1.3 75.5 - - - +
54W LYS* 1.3 65.3 + - + +
55W GLN 3.0 1.6 - - - -
56W LYS* 2.9 22.7 + - - +
58W ILE* 3.4 31.0 - - + +
59W ARG 4.5 1.1 - - - -
60W GLY 2.7 28.8 + - - -
61W PHE* 4.1 1.0 - - - -
62W CYS* 3.1 46.3 + - + -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W ASP* 2.9 37.3 + - - +
51W GLN* 3.5 11.9 - - - +
53W TYR* 1.3 81.5 - - + +
55W GLN* 1.3 61.0 + - + +
56W LYS* 4.6 4.2 - - - +
261W HIS* 5.3 4.8 + - - -
----------------------------------------------------------
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Residues in contact with GLN 55 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51W GLN* 3.2 37.8 + - + +
52W LEU* 3.8 15.1 - - - +
53W TYR 3.0 0.8 - - - -
54W LYS* 1.3 79.6 - - + +
56W LYS* 1.3 74.4 + - - +
57W ILE* 3.5 28.7 + - + +
----------------------------------------------------------
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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