Contacts of the helix formed by residues 13 - 42 (chain E) in PDB entry 5JKL
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 HIS 13 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ARG* 3.7 2.3 + - - -
11E ASN 3.9 2.8 + - - -
12E TYR* 1.3 77.1 - - - +
14E GLN* 1.3 78.0 + - + +
15E ASP* 3.0 47.5 + - - +
16E SER* 3.0 29.4 + - - +
17E GLU* 3.1 9.2 + - - +
124E LYS* 3.7 42.6 + - + +
126E ASP* 4.8 1.6 + - - +
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Residues in contact with GLN 14 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ARG* 3.7 14.0 - - - +
12E TYR 3.6 2.6 + - - -
13E HIS* 1.3 87.2 + - + +
15E ASP* 1.3 72.0 + - - +
17E GLU* 3.5 7.8 - - - +
18E LYS* 3.0 28.4 + - - +
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Residues in contact with ASP 15 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E HIS* 3.0 26.7 + - + +
14E GLN* 1.3 90.7 + - - +
16E SER* 1.4 56.5 + - - +
18E LYS* 3.4 8.9 + - - +
19E ALA* 3.0 28.6 + - - +
120E LEU* 3.6 24.0 - - + +
124E LYS* 3.9 11.1 + - - -
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Residues in contact with SER 16 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E TYR* 4.2 10.5 - - - -
13E HIS* 3.0 25.9 + - - +
15E ASP* 1.4 73.5 - - - +
17E GLU* 1.3 61.0 + - - +
19E ALA* 3.2 2.7 + - - +
20E ILE* 2.8 35.4 + - - +
117E LEU* 4.5 1.1 - - - +
120E LEU* 3.9 20.1 - - - +
121E ALA* 4.7 2.9 - - - -
124E LYS* 4.3 8.3 - - - +
126E ASP* 4.6 3.1 + - - -
129E LEU* 3.7 26.1 - - - +
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Residues in contact with GLU 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ARG* 2.8 28.4 + - - -
12E TYR* 3.7 20.5 - - + -
13E HIS 3.1 8.4 + - - +
14E GLN* 3.5 13.7 - - - +
16E SER* 1.3 78.0 - - - +
18E LYS* 1.3 62.0 + - - +
20E ILE 3.3 0.5 + - - -
21E ASN* 3.2 11.7 + - - +
73E GLN* 3.0 37.8 + - - +
78E GLY* 3.5 9.9 - - - -
79E ARG* 2.9 33.4 + - - +
81E PHE* 5.3 2.9 - - - -
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Residues in contact with LYS 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E GLN 3.0 17.0 + - - +
15E ASP* 3.8 8.1 - - - +
16E SER 3.3 0.2 - - - -
17E GLU* 1.3 77.5 - - - +
19E ALA* 1.3 61.4 + - - +
21E ASN* 3.2 8.9 + - - +
22E ARG* 3.1 68.1 + - - +
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Residues in contact with ALA 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ASP 3.0 18.2 + - - +
16E SER 3.6 1.6 - - - +
18E LYS* 1.3 76.0 - - - +
20E ILE* 1.3 59.1 + - - +
22E ARG* 3.2 9.6 + - - +
23E GLN* 2.9 27.4 + - - +
117E LEU* 3.5 27.1 - - + +
120E LEU* 3.8 12.1 - - + -
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Residues in contact with ILE 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E TYR* 3.6 15.3 - - - +
16E SER 2.8 21.5 + - - +
17E GLU 3.8 4.3 - - - +
18E LYS 3.3 0.2 - - - -
19E ALA* 1.3 72.3 - - - +
21E ASN* 1.3 60.3 + - - +
23E GLN* 3.1 4.0 + - - +
24E ILE* 2.9 33.1 + - + +
69E LEU* 3.8 45.3 - - + +
72E LEU* 4.2 8.7 - - + -
73E GLN* 3.7 17.7 - - + +
117E LEU* 3.9 22.0 - - + -
129E LEU* 3.9 24.7 - - + -
132E PHE* 5.2 0.9 - - + -
133E ILE* 5.6 0.4 - - + -
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Residues in contact with ASN 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E GLU* 3.2 15.2 + - - +
18E LYS* 3.2 11.0 + - - +
20E ILE* 1.3 77.3 - - - +
22E ARG* 1.3 76.1 + - - +
24E ILE* 3.4 16.0 + - - +
25E ARG* 3.2 19.6 + - - +
73E GLN* 3.0 19.9 + - - +
79E ARG 3.0 21.0 + - - -
80E ILE* 3.4 15.6 - - - +
81E PHE* 3.5 37.2 + - - +
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Residues in contact with ARG 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E LYS* 3.1 70.3 + - - +
19E ALA* 3.2 11.2 + - - +
21E ASN* 1.3 94.5 - - - +
23E GLN* 1.3 62.0 + - - +
25E ARG* 3.2 12.2 + - - +
26E LEU* 3.1 20.1 + - - +
81E PHE* 5.3 5.9 + - - +
83E GLN* 3.8 28.0 - - - +
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Residues in contact with GLN 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ALA 2.9 14.6 + - - +
20E ILE* 3.1 8.5 + - - +
22E ARG* 1.3 77.0 - - - +
24E ILE* 1.3 62.7 + - - +
26E LEU* 3.1 12.6 + - - +
27E GLU* 2.9 47.4 + - - +
69E LEU* 3.6 22.0 - - + -
110E VAL* 3.8 11.3 + - - +
113E SER* 2.7 34.5 + - - +
114E LEU* 3.6 30.7 - - + +
117E LEU* 4.2 14.9 - - + +
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Residues in contact with ILE 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E ILE* 2.9 31.4 + - + +
21E ASN* 3.6 24.5 - - - +
22E ARG 3.3 0.2 - - - -
23E GLN* 1.3 75.4 - - - +
25E ARG* 1.3 64.8 + - - +
27E GLU* 3.3 5.0 + - - +
28E LEU* 3.0 38.7 + - + +
66E ALA* 4.1 5.3 - - + +
69E LEU* 3.5 24.0 - - + +
70E MET* 3.7 43.3 - - + +
73E GLN* 4.7 4.0 - - + -
80E ILE* 4.7 5.8 - - + -
82E LEU* 4.3 13.2 - - + -
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Residues in contact with ARG 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ASN 3.2 10.3 + - - +
22E ARG* 3.2 13.2 + - - +
24E ILE* 1.3 83.2 - - - +
26E LEU* 1.3 55.5 + - - +
28E LEU* 3.3 9.5 + - - +
29E TYR* 2.9 29.6 + - + +
82E LEU* 6.4 0.2 - - - -
83E GLN* 3.5 44.5 + - + +
84E ASP* 2.7 35.4 + - - +
85E ILE* 4.9 6.4 - - + +
86E GLN* 3.6 27.9 - - - +
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Residues in contact with LEU 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ARG 3.1 12.8 + - - +
23E GLN* 3.1 16.3 + - - +
25E ARG* 1.3 71.2 - - - +
27E GLU* 1.3 60.2 + - - +
29E TYR* 3.4 23.1 + - + +
30E ALA* 2.9 28.4 + - - +
106E LEU* 5.4 2.5 - - + -
109E LYS* 4.5 6.7 - - + +
110E VAL* 4.0 28.7 - - + +
113E SER* 3.4 35.4 - - - +
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Residues in contact with GLU 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E GLN* 2.9 42.4 + - - +
24E ILE 3.7 5.2 - - - +
26E LEU* 1.3 76.2 - - - +
28E LEU* 1.3 58.1 + - - +
30E ALA* 3.3 3.5 + - - +
31E SER* 3.0 23.9 + - - -
62E GLU* 2.8 23.3 - - - +
65E HIS* 3.3 13.0 - - + +
66E ALA* 3.7 18.4 - - + +
69E LEU* 3.7 16.8 - - + -
110E VAL* 3.5 11.3 - - - +
114E LEU* 4.5 0.3 - - - +
137E TYR* 4.2 13.0 - - - -
201E FE 2.0 32.2 - - - -
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Residues in contact with LEU 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ILE* 3.0 34.5 + - + +
25E ARG* 3.7 7.6 - - + +
27E GLU* 1.3 75.0 - - - +
29E TYR* 1.3 62.8 + - - +
31E SER* 3.3 8.2 + - - -
32E TYR* 3.0 21.5 + - - +
63E ARG* 3.9 30.5 - - - +
66E ALA* 3.6 20.4 - - + -
70E MET* 5.5 6.1 - - - -
82E LEU* 4.7 13.0 - - + -
85E ILE* 3.9 35.8 - - + +
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Residues in contact with TYR 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E ARG* 2.9 19.2 + - + +
26E LEU* 3.5 23.6 - - + +
27E GLU 3.3 0.2 - - - -
28E LEU* 1.3 73.3 - - - +
30E ALA* 1.3 61.9 + - - +
32E TYR* 3.0 4.9 + - + +
33E VAL* 2.9 53.5 + - + +
85E ILE* 3.7 10.9 - - + +
86E GLN* 3.3 37.7 - - + +
87E LYS 3.8 10.9 + - - -
88E PRO* 4.1 1.6 - - + -
89E ASP* 3.9 26.7 + - - +
106E LEU* 4.2 15.3 - - + -
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Residues in contact with ALA 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E LEU 2.9 17.7 + - - +
27E GLU* 3.3 6.0 + - - +
29E TYR* 1.3 78.2 - - - +
31E SER* 1.3 62.2 + - - +
33E VAL* 3.3 2.6 + - - +
34E TYR* 3.0 29.6 + - + -
62E GLU* 3.9 23.6 - - + +
106E LEU* 4.0 29.4 - - + -
107E GLU* 5.9 0.4 - - - +
110E VAL* 4.5 9.4 - - + -
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Residues in contact with SER 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLU 3.0 13.5 + - - -
28E LEU* 3.4 15.3 - - - -
29E TYR 3.3 0.2 - - - -
30E ALA* 1.3 74.4 - - - +
32E TYR* 1.3 56.8 + - - +
35E LEU* 3.0 14.9 + - - +
59E SER* 2.7 52.7 + - - +
60E HIS* 5.8 0.3 - - - -
62E GLU* 3.5 12.9 - - - +
63E ARG* 3.9 16.4 + - - +
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Residues in contact with TYR 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E LEU 3.0 12.2 + - - +
29E TYR* 3.0 9.9 + - + +
31E SER* 1.3 75.4 - - - +
33E VAL* 1.3 65.4 + - - +
35E LEU* 3.3 23.8 + - + +
36E SER* 3.0 23.5 + - - -
85E ILE* 3.9 24.2 - - + -
86E GLN 3.4 24.7 - - - +
87E LYS* 3.9 16.1 - - + +
88E PRO* 3.7 14.0 - - + +
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Residues in contact with VAL 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E TYR* 2.9 55.3 + - + +
30E ALA 3.3 6.7 + - - +
32E TYR* 1.3 75.7 - - - +
34E TYR* 1.3 57.1 + - - +
36E SER* 3.3 4.7 + - - -
37E MET* 3.0 49.6 + - + +
88E PRO* 3.7 16.1 - - + +
93E TRP* 4.0 13.7 - - + -
106E LEU* 3.8 22.9 - - + -
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Residues in contact with TYR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ALA* 3.0 23.5 + - + +
33E VAL* 1.3 72.2 - - - +
35E LEU* 1.3 61.4 + - - +
37E MET* 3.4 8.2 + - - -
38E SER* 2.9 30.3 + - - -
55E PHE* 3.5 48.6 - + - +
58E GLN* 3.8 26.9 + - + +
59E SER* 3.6 9.2 - - - +
62E GLU* 3.8 23.8 - - + -
103E ALA* 3.8 24.9 + - + +
106E LEU* 4.2 14.6 - - + -
107E GLU* 2.4 43.8 + - - +
148E LEU* 4.0 5.2 - - + +
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Residues in contact with LEU 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E SER 3.0 15.8 + - - +
32E TYR* 3.3 30.7 + - + +
34E TYR* 1.3 77.5 - - - +
36E SER* 1.3 61.7 + - - +
38E SER* 3.4 3.3 + - - -
39E TYR* 3.3 51.7 + - + +
56E LEU* 4.0 14.1 - - + -
59E SER* 3.7 11.3 - - - +
60E HIS* 6.0 0.2 - - - +
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Residues in contact with SER 36 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E TYR* 3.0 14.3 + - - -
33E VAL 3.3 9.6 + - - -
35E LEU* 1.3 74.6 - - - +
37E MET* 1.3 65.1 + - - +
39E TYR* 3.4 4.4 + - - +
40E TYR* 3.0 21.5 + - - +
88E PRO* 3.9 16.3 - - - +
90E LYS 3.9 6.9 + - - -
91E ASP* 4.6 5.9 + - - +
93E TRP* 2.9 21.1 + - - -
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Residues in contact with MET 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E VAL* 3.0 28.5 + - + +
34E TYR* 3.7 17.9 - - - +
36E SER* 1.3 75.3 - - - +
38E SER* 1.3 64.8 + - - +
40E TYR* 3.2 8.3 + - - +
41E PHE* 3.0 24.2 + - + -
55E PHE* 3.9 38.8 - - + -
93E TRP* 3.7 49.8 - - + +
99E ALA* 3.4 24.9 - - + +
102E LYS* 3.8 11.2 - - + -
103E ALA* 3.9 8.7 - - - +
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Residues in contact with SER 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E TYR 2.9 17.9 + - - -
35E LEU* 3.6 7.2 - - - -
36E SER 3.3 0.2 - - - -
37E MET* 1.3 79.3 - - - +
39E TYR* 1.3 67.6 + - - +
41E PHE 3.2 11.8 + - - -
42E ASP 3.3 7.6 + - - -
52E ALA* 2.7 41.3 + - - +
55E PHE* 3.7 7.5 - - - +
56E LEU* 3.5 26.4 - - - +
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Residues in contact with TYR 39 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35E LEU* 3.3 42.4 + - + +
36E SER* 3.4 2.7 + - - +
38E SER* 1.3 81.1 - - - +
40E TYR* 1.3 66.4 + - - +
42E ASP* 3.4 35.3 + - + +
43E ARG* 3.5 13.7 + - - +
56E LEU* 4.1 24.6 - - + +
----------------------------------------------------------
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Residues in contact with TYR 40 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E SER 3.0 13.2 + - - +
37E MET 3.2 8.7 + - - +
39E TYR* 1.3 77.0 - - - +
41E PHE* 1.3 88.5 + + - +
42E ASP 3.2 0.2 - - - -
43E ARG* 3.1 48.7 + - - +
46E VAL* 3.5 33.7 - - + +
91E ASP 4.4 4.3 - - - +
92E ASP* 3.5 30.0 + - - -
93E TRP* 3.6 28.9 - + + -
94E GLU* 3.2 39.1 + - - -
95E SER* 4.1 3.4 - - - -
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Residues in contact with PHE 41 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E MET* 3.0 25.3 + - + -
38E SER 3.2 8.5 + - - +
40E TYR* 1.3 93.7 - + - +
42E ASP* 1.3 56.1 + - - +
43E ARG 3.4 0.4 - - - -
46E VAL* 3.6 16.6 - - + -
47E ALA* 3.3 8.8 + - - -
48E LEU* 3.0 53.9 + - + +
49E LYS* 5.0 0.7 - - - +
51E PHE* 3.6 16.2 - + + -
52E ALA* 3.7 8.7 - - - +
55E PHE* 3.5 31.2 - + - -
95E SER* 3.6 20.2 - - - -
96E GLY* 3.6 27.1 - - - -
99E ALA* 3.7 12.3 - - + -
----------------------------------------------------------
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Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E SER 3.3 5.9 + - - +
39E TYR* 3.6 43.8 - - + +
40E TYR 3.2 0.6 - - - -
41E PHE* 1.3 75.0 - - - +
43E ARG* 1.3 62.7 + - - +
44E ASP* 3.7 1.0 + - - -
47E ALA* 5.2 1.5 - - - +
49E LYS* 6.1 1.9 - - - +
52E ALA* 4.1 9.7 - - + +
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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