Contacts of the helix formed by residues 10 - 36 (chain A) in PDB entry 4U7I
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLU* 1.3 98.7 + - + +
11A ALA* 1.3 64.4 + - - +
12A GLU* 4.4 2.2 - - + +
13A ILE* 3.3 44.0 + - + +
14A LYS* 3.5 11.5 + - - +
71A TRP* 3.9 23.6 - - + +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU 3.6 3.0 + - - -
10A PRO* 1.3 70.5 - - - +
12A GLU* 1.3 64.9 + - + +
14A LYS* 3.0 35.3 - - + +
15A ILE* 3.3 18.7 + - + +
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.2 1.4 - - + +
11A ALA* 1.3 79.8 - - + +
13A ILE* 1.3 61.9 + - - +
15A ILE* 3.5 13.7 + - + +
16A ILE* 3.2 26.0 + - - +
59A ILE* 3.7 19.9 - - + +
60A SER 5.4 1.3 - - - +
66A HIS* 5.9 2.0 - - - +
71A TRP* 3.5 27.6 - - + -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU 5.4 3.1 - - - +
10A PRO* 3.3 37.2 + - + +
11A ALA 3.2 0.6 - - - -
12A GLU* 1.3 76.0 - - - +
14A LYS* 1.3 60.8 + - - +
16A ILE* 3.1 9.0 + - - +
17A ARG* 2.8 39.4 + - + +
70A GLY* 3.7 38.4 - - - +
71A TRP* 3.7 36.3 - - + +
74A ALA* 4.2 8.7 - - + -
77A MET* 6.5 0.7 - - - -
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Residues in contact with LYS 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLU 5.7 1.6 - - - +
10A PRO 3.5 5.6 + - - +
11A ALA* 3.0 36.1 - - + +
13A ILE* 1.3 79.2 - - - +
15A ILE* 1.3 54.4 + - + +
17A ARG* 4.2 9.2 - - - +
18A GLU* 2.7 52.8 + - + +
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Residues in contact with ILE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA* 3.3 18.9 + - + +
12A GLU* 3.6 15.3 - - + +
14A LYS* 1.3 79.7 - - + +
16A ILE* 1.3 62.7 + - - +
18A GLU* 3.4 6.2 + - - +
19A ALA* 3.0 23.4 + - - +
55A ARG* 4.4 25.0 + - + +
59A ILE* 3.8 30.7 - - + -
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Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 3.2 15.1 + - - +
13A ILE* 3.1 7.0 + - - +
15A ILE* 1.3 76.2 - - - +
17A ARG* 1.3 64.6 - - - +
19A ALA* 3.2 2.9 + - - +
20A TYR* 2.9 22.0 + - - +
56A GLY* 3.7 21.8 - - - +
59A ILE* 3.7 20.0 - - + +
71A TRP* 4.2 11.4 - - + -
74A ALA* 3.8 38.8 - - + +
77A MET* 4.0 10.3 - - + -
78A GLN* 3.5 24.2 - - + +
81A MET* 3.9 18.0 - - + +
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Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 2.8 28.8 + - + +
14A LYS* 3.7 7.5 - - - +
16A ILE* 1.3 77.8 - - - +
18A GLU* 1.3 71.7 + - - +
20A TYR* 3.3 2.6 + - - +
21A LYS* 3.1 50.7 + - + +
77A MET* 3.9 31.4 - - + +
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A LYS* 2.7 42.0 + - + +
15A ILE* 3.9 6.1 - - - +
17A ARG* 1.3 84.4 - - - +
19A ALA* 1.3 58.5 + - - +
21A LYS* 3.4 15.1 + - - +
22A LYS* 3.0 41.5 + - + +
55A ARG* 5.0 3.1 - - - +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE 3.0 17.9 + - - +
16A ILE 3.6 1.3 - - - +
18A GLU* 1.3 75.9 - - - +
20A TYR* 1.3 55.3 + - - +
23A ALA* 2.8 37.6 + - - +
52A HIS* 3.4 24.7 - - - +
55A ARG* 4.0 20.3 - - - +
56A GLY* 3.5 22.4 - - - +
81A MET* 4.1 3.4 - - - -
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE 2.9 16.9 + - - +
17A ARG 3.4 5.8 - - - +
18A GLU 3.3 0.2 - - - -
19A ALA* 1.3 77.3 - - - +
21A LYS* 1.3 69.5 + - + +
24A PHE* 3.0 20.1 + - - +
77A MET* 3.6 65.3 - - + -
80A LYS* 4.1 13.4 - - + +
81A MET* 3.7 16.3 - - + -
319B ILE* 3.7 32.0 + - + +
321B PHE* 3.4 44.9 + + - -
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.1 39.7 + - + +
18A GLU* 3.8 17.0 - - - +
19A ALA 3.3 0.2 - - - -
20A TYR* 1.3 83.3 - - + +
22A LYS* 1.3 59.0 + - + +
24A PHE* 3.4 3.5 + - - +
25A LEU* 3.0 27.4 + - - +
77A MET* 6.1 0.7 - - - -
319B ILE* 3.9 24.8 - - + +
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Residues in contact with LYS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 3.0 23.7 + - + +
19A ALA 4.1 0.7 - - - +
21A LYS* 1.3 74.9 - - + +
23A ALA* 1.3 66.3 + - - +
25A LEU* 3.2 10.8 + - + +
26A PHE* 3.0 38.4 + - + -
52A HIS* 3.6 38.1 - - + +
55A ARG* 4.4 6.3 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA 2.8 24.5 + - - +
20A TYR* 3.9 3.8 - - - +
22A LYS* 1.3 72.6 - - - +
24A PHE* 1.3 58.4 + - - +
26A PHE* 3.3 0.5 + - - +
27A VAL* 2.9 35.9 + - - +
49A GLY* 4.1 5.8 - - - +
52A HIS* 3.8 13.8 - - + +
53A LEU* 3.5 39.9 - - + +
321B PHE* 4.4 3.1 - - + -
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Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR 3.0 17.8 + - - +
21A LYS 3.7 4.0 - - - +
23A ALA* 1.3 77.6 - - - +
25A LEU* 1.3 67.4 - - - +
27A VAL 4.6 0.2 - - - +
28A ASN* 2.9 45.6 + - + +
318B ASP 5.4 1.6 - - - -
319B ILE* 3.7 36.1 - - + -
320B ASP* 3.6 33.9 - - + -
321B PHE* 3.7 16.7 - + + -
323B ASP* 6.2 1.3 - - + -
324B LEU* 3.6 37.2 - - + -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS 3.0 14.1 + - - +
22A LYS* 3.4 15.3 - - + +
24A PHE* 1.3 82.0 - - - +
26A PHE* 1.3 81.2 + - + +
28A ASN* 3.7 4.3 + - - +
29A LYS* 3.1 52.9 + - + +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LYS* 3.0 35.0 + - + +
25A LEU* 1.3 93.5 - - + +
27A VAL* 1.3 60.8 + - - +
29A LYS* 3.3 7.7 + - + -
30A GLY* 2.8 24.4 + - - -
45A TYR* 3.4 37.9 - + - +
48A GLN* 3.2 44.2 - - + -
49A GLY* 3.8 10.8 - - - +
52A HIS* 3.6 28.3 - + - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA 2.9 23.5 + - - +
24A PHE 4.2 1.3 - - - +
26A PHE* 1.3 76.8 - - - +
28A ASN* 1.3 59.3 + - - +
30A GLY* 3.2 1.4 + - - -
31A LEU* 2.8 30.6 + - + +
45A TYR 5.2 0.2 - - - -
46A TYR* 4.0 7.0 - - + -
49A GLY* 4.1 16.8 - - - -
53A LEU* 4.3 5.6 - - + -
84A THR* 4.2 9.9 - - + -
88A VAL* 3.8 35.7 - - + -
324B LEU* 4.0 20.0 - - + -
328B PHE* 3.8 20.2 - - + -
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Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 2.9 41.8 + - + +
25A LEU* 3.7 4.3 + - - +
27A VAL* 1.3 75.7 - - - +
29A LYS* 1.3 62.0 + - - +
31A LEU* 3.3 1.7 + - - +
32A ASN* 2.8 45.5 + - - +
324B LEU* 4.4 10.2 - - + +
327B ARG* 2.9 28.4 + - - +
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Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU* 3.1 39.8 + - + +
26A PHE* 3.6 15.0 - - + +
28A ASN* 1.3 80.3 - - - +
30A GLY* 1.3 64.7 + - - +
32A ASN* 3.3 8.3 + - - +
33A THR* 3.0 29.7 + - + +
45A TYR* 3.5 46.3 + - + -
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE 2.8 11.3 + - - -
27A VAL 3.2 3.3 + - - -
29A LYS* 1.3 76.9 - - - +
31A LEU* 1.3 56.4 + - - +
33A THR* 3.0 8.1 + - - -
34A ASP* 2.8 30.5 + - - +
42A ALA* 3.6 4.9 - - - +
45A TYR* 3.6 17.2 - - - +
46A TYR* 3.4 20.1 + - - -
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Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 2.8 20.5 + - + +
28A ASN 3.8 1.3 - - - +
30A GLY* 1.3 70.5 - - - +
32A ASN* 1.3 65.6 + - - +
34A ASP* 3.6 0.3 - - - +
35A GLU* 2.9 30.6 + - - +
46A TYR* 3.6 14.8 - - - +
324B LEU* 3.6 38.8 - - + +
327B ARG* 3.3 39.0 - - + +
328B PHE* 3.6 39.5 - - + -
331B LEU* 3.7 18.6 - - + -
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Residues in contact with ASN 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASN* 2.8 38.8 + - - +
29A LYS* 3.3 8.9 + - - +
31A LEU* 1.3 73.9 - - - +
33A THR* 1.3 65.2 + - + +
35A GLU* 3.4 7.9 + - - +
36A LEU* 3.2 23.5 + - - +
327B ARG* 2.8 22.9 + - - +
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LYS* 3.0 16.2 + - - +
30A GLY* 3.0 15.1 + - - -
32A ASN* 1.3 77.1 - - + +
34A ASP* 1.3 63.0 + - - +
36A LEU* 3.2 2.9 + - - -
37A GLY 3.1 4.2 + - - -
38A GLN* 2.8 62.9 + - - +
41A GLU* 3.8 11.7 - - - +
42A ALA* 3.2 16.8 + - - -
45A TYR* 3.7 20.3 - - + -
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Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 2.8 18.2 + - - +
31A LEU* 3.6 4.0 - - - +
33A THR* 1.3 77.7 + - - +
35A GLU* 1.3 60.8 + - - +
37A GLY* 3.0 14.8 + - - +
38A GLN 4.7 2.2 - - - +
39A LYS* 4.6 6.6 - - - +
42A ALA* 3.9 11.4 - - + +
46A TYR* 2.7 27.5 + - - +
91A ARG* 2.7 45.9 + - - -
95A LEU* 3.8 8.4 - - - +
331B LEU* 3.6 11.9 - - + +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 2.9 15.7 + - - +
32A ASN* 3.8 8.7 - - - +
34A ASP* 1.3 76.3 - - - +
36A LEU* 1.3 60.0 + - - +
37A GLY 3.2 0.7 + - - -
327B ARG* 2.9 56.9 + - - +
331B LEU* 4.1 22.7 - - + -
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ASN 3.2 16.4 + - - +
33A THR* 3.2 6.1 + - + +
34A ASP 3.1 1.0 - - - -
35A GLU* 1.3 76.1 - - - +
37A GLY* 1.3 60.6 + - - +
38A GLN* 3.3 33.6 + - - +
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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) + - + + + + + -
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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