Contacts of the helix formed by residues 4 - 36 (chain C) in PDB entry 3BKN
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 ASP 4 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GLN 3.9 0.8 + - - -
3C GLY* 1.3 72.4 - - - -
5C PRO* 1.3 75.4 - - - +
6C ASP* 2.7 41.4 + - - +
7C VAL* 3.2 21.0 + - + +
8C LEU* 3.0 20.8 + - - +
65C LEU* 5.2 0.4 - - - +
111C LYS* 3.7 34.4 - - + +
113C ASP* 5.6 4.3 + - + -
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Residues in contact with PRO 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLY 3.5 6.3 - - - +
4C ASP* 1.3 95.6 - - - +
6C ASP* 1.3 63.3 + - - +
8C LEU* 3.6 9.6 + - + +
9C LYS* 3.1 26.2 + - - +
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Residues in contact with ASP 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ASP* 2.7 17.8 + - - +
5C PRO* 1.3 76.6 - - - +
7C VAL* 1.3 59.2 + - - +
9C LYS* 3.4 9.2 + - - +
10C LEU* 3.0 28.8 + - - +
107C LEU* 4.3 24.1 - - + +
111C LYS* 4.0 18.2 + - - -
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Residues in contact with VAL 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ASP* 3.2 31.6 + - + +
6C ASP* 1.3 75.8 - - - +
8C LEU* 1.3 59.3 + - - +
10C LEU* 3.2 7.3 + - - +
11C LEU* 2.8 36.7 + - + +
65C LEU* 4.6 4.5 - - + -
107C LEU* 4.5 9.0 - - + -
108C CYS* 4.0 14.4 - - - -
111C LYS* 4.0 19.5 - - + -
113C ASP* 3.8 28.3 - - + +
116C SER* 3.8 18.2 - - - +
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Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GLN* 4.9 4.7 - - - +
3C GLY* 4.3 11.2 - - - +
4C ASP 3.0 18.1 + - - +
5C PRO* 3.9 8.1 - - + +
7C VAL* 1.3 74.7 - - - +
9C LYS* 1.3 60.3 + - - +
11C LEU* 3.8 6.4 - - + +
12C ASN* 2.9 37.4 + - - +
62C ILE* 4.1 19.3 - - + +
65C LEU* 3.8 41.3 - - + +
66C ASP 4.9 0.7 - - - -
67C GLY* 3.8 29.4 - - - -
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Residues in contact with LYS 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PRO 3.1 18.0 + - - +
6C ASP* 3.7 10.1 - - - +
7C VAL 3.3 0.2 - - - -
8C LEU* 1.3 74.9 - - - +
10C LEU* 1.3 58.2 + - - +
12C ASN* 3.8 6.0 - - + +
13C GLU* 3.0 44.2 + - + +
73C ARG* 5.4 0.2 + - - -
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Residues in contact with LEU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ASP 3.0 17.5 + - - +
7C VAL* 3.4 4.7 - - - +
9C LYS* 1.3 73.6 - - - +
11C LEU* 1.3 60.5 + - + +
13C GLU* 3.2 7.9 + - + +
14C GLN* 2.9 28.2 + - - +
100C ARG* 4.0 27.4 - - + +
101C LEU* 4.8 4.0 - - + -
104C GLY* 3.6 33.4 - - - +
107C LEU* 4.2 10.8 - - + -
108C CYS* 3.8 11.0 - - - -
120C LEU* 3.5 29.8 - - + -
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 2.8 27.4 + - + +
8C LEU* 3.9 6.5 - - + +
10C LEU* 1.3 72.8 - - + +
12C ASN* 1.3 57.4 + - - +
14C GLN* 3.4 3.8 + - - +
15C LEU* 2.8 28.8 + - - +
58C ILE* 3.4 17.7 - - + +
61C ARG* 3.8 28.9 - - + -
62C ILE* 3.8 27.8 - - + +
65C LEU* 4.2 12.8 - - + -
116C SER* 4.2 17.0 - - - +
119C LEU* 5.4 4.3 - - + -
120C LEU* 4.0 32.8 - - + -
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Residues in contact with ASN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 2.9 25.4 + - - +
9C LYS* 3.8 5.6 - - + +
11C LEU* 1.3 74.7 - - - +
13C GLU* 1.3 58.9 + - - +
15C LEU* 3.3 8.2 + - - +
16C THR* 3.0 23.6 + - - -
62C ILE* 3.4 19.3 - - - +
68C LEU 2.9 26.9 + - - +
70C ASN* 2.8 34.7 + - + +
73C ARG* 3.4 17.5 + - - +
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C LYS* 3.0 29.7 + - + +
10C LEU* 3.4 11.7 - - + +
12C ASN* 1.3 72.2 - - - +
14C GLN* 1.3 65.4 + - - +
16C THR* 3.1 7.0 + - - -
17C SER* 3.1 19.1 + - - -
73C ARG* 3.9 18.0 + - - +
75C PHE* 4.3 14.7 - - - -
100C ARG* 3.4 33.1 + - + +
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Residues in contact with GLN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LEU 2.9 15.8 + - - +
11C LEU* 3.7 6.7 - - - +
13C GLU* 1.3 75.9 - - - +
15C LEU* 1.3 60.9 + - - +
17C SER* 3.0 7.9 + - - -
18C GLU* 2.7 49.8 + - - +
58C ILE* 3.5 20.9 - - + -
97C VAL* 3.5 33.7 - - - +
100C ARG* 2.9 35.2 + - - +
101C LEU* 3.7 20.6 - - + +
120C LEU* 4.6 7.0 - - + -
123C ILE* 4.0 4.5 - - + +
127C GLU* 4.4 0.2 + - - -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU 2.8 19.1 + - - +
12C ASN* 3.4 15.3 - - - +
14C GLN* 1.3 68.2 - - - +
16C THR* 1.3 68.1 + - - +
18C GLU* 3.2 5.5 + - - +
19C LEU* 3.0 29.9 + - + +
55C ALA* 3.6 39.5 - - + +
58C ILE* 4.1 11.4 - - + +
59C THR* 3.7 6.5 - - - +
62C ILE* 4.2 5.4 - - + -
69C PRO* 4.2 6.7 - - + -
70C ASN 3.5 37.0 - - - +
71C TYR* 4.0 17.5 - - + -
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Residues in contact with THR 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASN 3.0 8.4 + - - -
13C GLU 3.1 8.2 + - - -
15C LEU* 1.3 74.6 - - - +
17C SER* 1.3 58.3 + - - +
19C LEU* 3.2 6.2 + - - +
20C THR* 2.8 32.6 + - - -
70C ASN* 4.7 5.9 + - - -
73C ARG* 2.8 60.8 + - + +
75C PHE* 3.5 43.5 - - + +
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Residues in contact with SER 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLU 3.1 7.2 + - - -
14C GLN* 3.0 16.9 + - - -
16C THR* 1.3 76.9 - - - +
18C GLU* 1.3 57.3 + - - +
20C THR* 3.3 4.0 + - - -
21C ALA* 2.8 29.1 + - - +
75C PHE* 3.8 12.2 - - - -
93C ILE* 4.9 8.5 + - - +
96C GLU* 5.4 2.4 + - - +
97C VAL* 4.1 12.2 + - - +
100C ARG* 3.0 39.5 + - - -
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLN* 2.7 44.2 + - - +
15C LEU* 3.2 6.0 + - - +
17C SER* 1.3 73.0 - - - +
19C LEU* 1.3 60.8 + - - +
21C ALA* 3.1 4.4 + - - +
22C ILE* 2.8 34.9 + - - +
51C GLU* 2.4 12.3 - - - +
54C HIS* 3.2 20.3 - - + +
55C ALA* 3.9 22.7 - - + +
58C ILE* 4.1 11.0 - - + +
97C VAL* 6.0 0.2 - - - -
123C ILE* 3.5 8.0 - - - +
127C GLU* 4.0 0.2 - - - -
201C ZN 2.1 35.9 - - - -
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.0 28.8 + - + +
16C THR* 3.7 3.8 - - - +
18C GLU* 1.3 76.5 - - - +
20C THR* 1.3 61.1 + - - +
22C ILE* 3.4 12.5 + - + +
23C ASN* 3.4 26.3 + - - +
55C ALA* 4.1 12.1 - - + -
70C ASN 3.7 22.7 - - - +
71C TYR* 3.9 30.3 - - + +
73C ARG 4.4 10.3 - - - +
74C LEU* 3.8 12.7 - - + +
301C HEM 3.4 32.8 - - + +
23D ASN* 4.6 5.6 - - - +
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C THR 2.8 19.9 + - - -
17C SER* 3.5 7.2 - - - -
19C LEU* 1.3 74.8 - - - +
21C ALA* 1.3 59.1 + - - +
23C ASN* 3.3 2.5 + - - +
24C GLN* 3.0 26.7 + - - +
74C LEU* 3.8 11.5 - - + +
75C PHE* 3.0 54.3 + - + +
76C SER 4.3 8.5 - - - +
77C LEU* 3.7 13.2 - - + +
93C ILE* 4.5 15.0 - - + -
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C SER 2.8 18.7 + - - +
18C GLU* 3.1 2.9 + - - +
20C THR* 1.3 71.6 - - - +
22C ILE* 1.3 64.8 - - - +
24C GLN* 4.4 0.4 - - - +
25C TYR* 2.9 41.9 + - + -
51C GLU* 3.5 27.8 - - + +
93C ILE* 3.7 23.0 - - + +
94C GLU* 5.1 1.8 - - - +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C GLU 2.8 24.4 + - - +
19C LEU* 3.5 24.0 - - + +
20C THR 3.3 0.2 - - - -
21C ALA* 1.3 70.9 - - - +
23C ASN* 1.3 64.9 + - - +
26C PHE* 2.9 30.0 + - + +
48C SER* 3.1 11.0 + - - +
51C GLU* 3.7 11.2 - - + +
52C MET* 3.6 57.7 - - + +
55C ALA* 3.9 12.1 - - + -
301C HEM 3.6 37.0 - - + -
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Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU 3.4 10.8 + - - +
20C THR* 3.3 9.1 + - - +
21C ALA 3.3 0.2 - - - -
22C ILE* 1.3 78.3 - - - +
24C GLN* 1.3 63.5 + - - +
26C PHE* 3.9 1.1 - - - +
27C LEU* 2.9 28.8 + - - +
74C LEU* 4.1 19.1 - - + +
77C LEU* 3.9 14.1 - - + -
301C HEM 3.4 23.1 - - - +
19D LEU* 4.5 8.9 - - - +
71D TYR* 2.9 43.4 + - + +
74D LEU* 6.1 1.2 - - - +
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C THR* 3.0 17.2 + - - +
21C ALA 3.2 2.9 + - - +
23C ASN* 1.3 78.2 - - - +
25C TYR* 1.3 57.4 + - + +
27C LEU* 4.0 3.3 - - - +
28C HIS* 2.9 39.5 + - + +
76C SER 4.4 1.7 - - - +
77C LEU* 3.6 15.8 - - + +
78C ARG* 2.7 52.5 + - - +
79C VAL* 5.4 1.1 - - + -
89C ALA 3.3 23.6 + - - -
90C ASP* 2.5 28.0 + - - +
93C ILE* 3.5 21.7 - - + +
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 2.9 41.3 + - + +
24C GLN* 1.3 74.0 - - - +
26C PHE* 1.3 59.9 + - - +
28C HIS* 3.2 5.4 + - - +
29C SER* 2.8 27.9 + - - -
44C THR* 3.6 17.0 - - + +
47C GLU* 3.6 31.4 - - + -
48C SER* 3.9 19.5 - - - +
51C GLU* 3.9 13.9 - - + -
90C ASP* 3.5 34.6 - - + +
93C ILE* 5.3 3.4 - - + -
94C GLU* 2.5 39.6 + - - +
130C HIS* 4.2 4.3 - - - +
134C LEU* 3.7 16.8 - - + +
202C ZN 4.0 1.7 - - - -
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE 2.9 21.6 + - - +
23C ASN* 3.9 3.1 - - - +
25C TYR* 1.3 77.1 - - - +
27C LEU* 1.3 62.7 + - - +
29C SER* 3.2 8.5 + - - -
30C LYS* 3.1 38.3 + - + +
45C ARG* 3.7 33.9 - - + -
48C SER* 3.2 21.7 + - - +
49C PHE* 4.1 17.0 - + - -
52C MET* 4.0 7.6 - - + -
301C HEM 3.5 35.7 - + + -
56D GLU* 3.9 23.3 - - + -
71D TYR* 3.6 24.0 - + + -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASN 2.9 18.3 + - - +
24C GLN* 4.0 3.8 - - - +
26C PHE* 1.3 75.4 - - - +
28C HIS* 1.3 60.7 + - + +
30C LYS* 3.2 5.5 + - - +
31C MET* 2.9 51.5 + - + +
77C LEU* 5.3 2.2 - - + -
79C VAL* 3.8 35.0 - - + -
59D THR* 4.7 4.0 - - + -
63D LEU* 5.1 1.1 - - + -
69D PRO* 3.8 49.6 - - + +
71D TYR* 4.3 24.6 - - + +
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Residues in contact with HIS 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 2.9 23.0 + - + +
25C TYR 3.2 4.7 + - - +
27C LEU* 1.3 76.6 - - + +
29C SER* 1.3 57.9 + - - +
31C MET* 3.3 7.8 + - - +
32C GLN* 2.9 46.9 + - - +
44C THR* 4.0 7.0 - - + -
78C ARG 3.3 18.7 + - - -
79C VAL* 3.7 5.3 - - + -
80C GLY 3.2 24.0 + - - -
86C GLN* 3.5 39.7 - - + +
89C ALA* 3.9 4.9 - - + -
90C ASP* 2.9 38.5 + - - -
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR 2.8 16.3 + - - -
26C PHE* 3.2 8.0 + - - -
28C HIS* 1.3 73.6 - - - +
30C LYS* 1.3 65.5 + - - +
32C GLN* 3.2 3.8 + - - -
33C ASP* 2.9 26.0 + - - +
41C ALA* 3.4 17.7 + - - +
44C THR* 3.6 10.9 - - - +
45C ARG* 3.3 45.9 + - - +
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Residues in contact with LYS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.1 32.7 + - + +
27C LEU* 3.6 6.3 - - - +
29C SER* 1.3 81.0 - - - +
31C MET* 1.3 58.0 + - - +
33C ASP* 3.4 14.3 + - + +
34C ASN* 3.0 28.4 + - - +
45C ARG* 4.1 5.1 - - - +
161C ALA* 5.6 0.2 - - - +
56D GLU* 2.7 38.6 + - - +
59D THR* 3.9 12.3 - - + -
60D ASP* 3.0 45.7 + - - +
63D LEU* 3.6 20.5 - - + +
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Residues in contact with MET 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.9 39.1 + - + +
28C HIS* 3.6 4.7 - - - +
30C LYS* 1.3 74.6 - - - +
32C GLN* 1.3 65.6 + - - +
34C ASN* 3.2 6.9 + - - +
35C TRP* 3.0 48.8 + - + +
79C VAL* 3.8 24.7 - - + -
80C GLY 3.4 22.4 - - - +
81C GLN* 3.9 13.5 - - - +
86C GLN* 3.6 15.3 - - - +
63D LEU* 4.5 14.6 - - + -
69D PRO* 6.2 0.4 - - - -
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Residues in contact with GLN 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C HIS* 2.9 28.6 + - - +
29C SER 3.5 3.6 - - - +
31C MET* 1.3 74.0 - - - +
33C ASP* 1.3 64.1 - - - +
35C TRP* 3.2 13.5 + - + +
37C PHE* 2.9 34.8 + - + +
40C LEU* 3.6 19.8 - - + +
41C ALA* 3.7 12.0 - - + -
44C THR* 2.6 33.8 + - - +
83C LEU* 4.0 16.5 - - + +
86C GLN* 2.7 34.3 + - - +
87C PHE* 5.5 4.9 - - - -
90C ASP* 5.6 0.2 + - - -
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Residues in contact with ASP 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C SER 2.9 13.2 + - - +
30C LYS* 3.5 22.9 + - + +
32C GLN* 1.3 77.0 - - - +
34C ASN* 1.3 61.4 + - - +
36C GLY* 3.1 14.0 + - - -
37C PHE 4.7 1.1 - - - -
38C THR* 3.6 21.3 - - - +
41C ALA* 3.4 19.2 - - + +
160C SER* 3.7 1.8 - - - -
161C ALA* 3.2 47.1 + - + +
60D ASP* 5.3 1.4 - - - +
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Residues in contact with ASN 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASP* 4.2 11.5 + - - +
136A THR* 3.6 17.3 + - - +
139A GLN* 4.8 4.7 - - - +
30C LYS 3.0 16.7 + - - +
31C MET* 3.2 7.4 + - - +
33C ASP* 1.3 75.0 - - - +
35C TRP* 1.3 65.0 + - + +
36C GLY 3.3 0.4 - - - -
161C ALA* 3.5 23.7 - - - +
401C MG 3.3 22.7 - - - -
60D ASP* 4.8 3.4 + - - -
63D LEU* 3.6 38.4 - - + +
64D LEU* 4.2 8.1 - - - +
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Residues in contact with TRP 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 3.6 9.0 - - - +
139A GLN* 5.1 8.2 - - - +
140A LEU* 3.5 22.2 + - - +
143A LYS* 3.6 28.2 + - - +
31C MET* 3.0 38.1 + - + +
32C GLN* 3.7 9.6 - - + +
33C ASP 3.2 0.6 - - - -
34C ASN* 1.3 81.5 - - + +
36C GLY* 1.3 57.9 + - - +
37C PHE* 3.5 26.6 + + + -
81C GLN* 3.6 34.5 - - - -
82C THR* 3.7 13.2 - - - -
83C LEU* 4.1 5.4 - - + -
86C GLN* 3.3 39.0 - - - -
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 3.6 15.5 - - - +
140A LEU* 4.1 6.3 - - - +
32C GLN 3.9 0.2 - - - -
33C ASP 3.1 11.5 + - - -
34C ASN 3.3 1.0 - - - -
35C TRP* 1.3 79.6 - - - +
37C PHE* 1.3 59.5 + - - +
38C THR* 2.8 19.4 + - - +
154C VAL* 3.6 19.2 - - - +
159C GLY 3.7 14.2 + - - +
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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