Contacts of the helix formed by residues 3 - 34 (chain Y) in PDB entry 2X17
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 SER 3 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Y MET 3.9 1.2 + - - -
2Y LEU* 1.3 74.6 - - - +
4Y GLU* 1.3 59.7 + - - +
5Y ARG* 4.3 3.1 - - - -
6Y MET* 2.9 13.6 + - - +
7Y LEU* 2.9 28.2 + - - +
111Y GLU* 2.7 37.6 + - - -
113Y ASP* 5.5 1.2 + - - -
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Residues in contact with GLU 4 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Y LEU 3.9 1.4 + - - -
3Y SER* 1.3 72.1 - - - +
5Y ARG* 1.3 62.0 + - - +
7Y LEU* 3.6 12.2 + - + +
8Y LYS* 3.2 24.5 + - + +
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Residues in contact with ARG 5 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Y SER* 3.2 2.1 + - - +
4Y GLU* 1.3 78.9 - - - +
6Y MET* 1.3 61.8 + - - +
8Y LYS* 3.7 6.8 + - + +
9Y ALA* 3.2 22.0 + - - +
107Y LEU* 4.3 21.1 - - + +
111Y GLU* 3.7 20.9 - - - +
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Residues in contact with MET 6 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Y LEU* 4.0 13.0 - - + -
3Y SER* 2.9 26.4 + - - +
5Y ARG* 1.3 77.2 - - - +
7Y LEU* 1.3 60.3 + - - +
9Y ALA* 3.1 4.3 + - - +
10Y LEU* 2.8 47.2 + - + +
104Y LEU* 3.9 18.8 - - - +
107Y LEU* 3.9 15.3 - - + -
108Y ALA* 3.6 37.9 - - + +
111Y GLU* 3.4 17.0 + - - +
113Y ASP* 4.0 10.8 - - + +
116Y THR* 3.8 17.9 - - - +
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Residues in contact with LEU 7 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Y LEU* 4.0 20.8 - - + +
3Y SER 2.9 14.8 + - - +
4Y GLU* 3.9 11.0 - - + +
6Y MET* 1.3 74.4 - - - +
8Y LYS* 1.3 57.0 + - - +
10Y LEU* 3.5 6.9 + - - +
11Y ASN* 2.8 49.0 + - - +
61Y ILE* 3.8 14.8 - - + -
66Y GLY* 4.2 3.4 - - - -
67Y ARG* 3.6 41.7 - - + +
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Residues in contact with LYS 8 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y GLU* 3.2 15.6 + - + +
5Y ARG* 3.8 7.9 - - + +
6Y MET 3.2 0.2 - - - -
7Y LEU* 1.3 77.8 - - - +
9Y ALA* 1.3 58.1 + - - +
11Y ASN* 3.5 7.5 + - + +
12Y ASP* 2.9 55.1 + - - +
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Residues in contact with ALA 9 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Y ARG 3.2 12.1 + - - +
6Y MET 3.1 8.6 + - - +
8Y LYS* 1.3 79.7 - - - +
10Y LEU* 1.3 56.8 + - - +
12Y ASP* 3.6 8.5 - - - +
13Y GLN* 3.1 27.2 + - - +
16Y ARG* 4.4 2.0 + - - +
104Y LEU* 3.7 26.4 - - + +
107Y LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 10 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y LEU* 3.9 31.9 - - + -
6Y MET* 2.8 35.8 + - + +
7Y LEU* 3.9 4.5 - - - +
9Y ALA* 1.3 74.6 - - - +
11Y ASN* 1.3 59.9 + - - +
13Y GLN* 3.5 2.8 + - - +
14Y LEU* 3.1 27.7 + - - +
57Y PHE* 3.7 33.1 - - + -
60Y TYR* 4.1 11.7 - - + -
61Y ILE* 4.0 19.3 - - + +
104Y LEU* 4.1 9.6 - - + -
116Y THR* 3.9 19.3 - - + -
119Y PHE* 4.3 7.9 - - + -
120Y LEU* 5.2 0.7 - - + -
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Residues in contact with ASN 11 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y LEU* 2.8 40.0 + - - +
8Y LYS* 3.8 7.4 - - - +
9Y ALA 3.4 0.2 - - - -
10Y LEU* 1.3 75.0 - - - +
12Y ASP* 1.3 65.6 + - - +
14Y LEU* 3.5 9.0 - - - +
15Y ASN* 3.2 21.5 + - - +
61Y ILE* 4.2 7.1 - - - +
67Y ARG 3.3 18.8 + - - -
68Y VAL* 3.4 11.8 - - - +
69Y GLU* 2.8 46.0 + - + +
71Y ASP* 4.7 4.2 - - - +
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Residues in contact with ASP 12 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y LYS* 2.9 46.4 + - - +
9Y ALA* 3.6 9.1 - - - +
10Y LEU 3.2 0.2 - - - -
11Y ASN* 1.3 76.5 - - - +
13Y GLN* 1.3 59.2 + - - +
15Y ASN* 3.1 8.5 + - - +
16Y ARG* 2.8 51.9 + - - +
71Y ASP* 3.9 15.6 - - - +
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Residues in contact with GLN 13 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y ALA 3.1 9.5 + - - +
10Y LEU 3.9 3.6 - - - +
11Y ASN 3.5 0.2 - - - -
12Y ASP* 1.3 72.5 - - - +
14Y LEU* 1.3 56.3 + - - +
16Y ARG* 3.0 21.2 + - - +
17Y GLU* 2.8 61.0 + - - +
57Y PHE* 3.4 31.9 - - + -
97Y ILE* 3.9 8.9 - - - +
100Y SER* 2.9 42.1 + - - +
101Y ILE* 3.7 12.5 - - + +
104Y LEU* 3.6 19.8 - - + +
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Residues in contact with LEU 14 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G PHE* 4.5 7.2 - - + -
10Y LEU 3.1 15.8 + - - +
11Y ASN* 3.5 10.5 - - - +
13Y GLN* 1.3 74.7 - - - +
15Y ASN* 1.3 57.7 + - - +
17Y GLU* 3.5 6.8 + - - +
18Y LEU* 3.1 46.2 + - + +
54Y ALA* 3.6 16.8 - - + +
57Y PHE* 3.9 12.7 - - + -
58Y TYR* 3.6 33.2 - - + +
61Y ILE* 4.0 13.9 - - + -
68Y VAL* 4.1 15.3 - - + -
69Y GLU 5.9 0.9 - - - +
70Y LEU* 3.8 18.8 - - + -
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Residues in contact with ASN 15 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 3.4 11.9 + - - -
11Y ASN 3.2 11.2 + - - +
12Y ASP* 3.1 12.0 + - - +
14Y LEU* 1.3 79.3 - - - +
16Y ARG* 1.3 58.1 + - - +
17Y GLU 3.4 0.2 - - - -
18Y LEU* 3.9 5.4 - - - +
19Y TYR* 3.2 25.5 + - - +
70Y LEU* 5.2 0.4 - - - +
71Y ASP* 2.9 48.9 + - + +
72Y GLU 3.3 17.4 + - - +
73Y ILE* 4.3 5.4 - - - +
74Y PRO* 5.0 4.7 - - - +
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Residues in contact with ARG 16 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y ALA* 4.4 3.4 + - - +
12Y ASP* 2.8 34.8 + - - +
13Y GLN* 3.0 49.0 + - - +
15Y ASN* 1.3 75.5 - - - +
17Y GLU* 1.3 59.3 + - - +
19Y TYR* 3.3 9.5 + - - +
20Y SER* 3.0 30.6 + - - -
96Y PHE* 4.3 26.4 - - + -
97Y ILE* 4.0 9.3 - - + +
100Y SER* 3.9 28.7 + - - -
103Y GLU* 5.9 0.8 + - - -
104Y LEU* 5.0 3.0 - - - +
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Residues in contact with GLU 17 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Y GLN* 2.8 44.0 + - - +
14Y LEU 3.7 4.5 - - - +
16Y ARG* 1.3 71.4 - - - +
18Y LEU* 1.3 63.9 + - - +
20Y SER* 3.3 7.1 + - - -
21Y ALA* 3.2 17.5 + - - +
50Y GLU* 3.0 40.4 - - - +
53Y HIS* 3.4 24.5 + - + +
54Y ALA* 3.9 16.4 - - + +
57Y PHE* 4.4 12.2 - - + -
97Y ILE* 3.9 14.6 - - - +
101Y ILE* 4.5 1.6 - - - +
123Y PHE* 4.3 14.2 - - - -
127Y GLN* 4.4 5.1 + - - -
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Residues in contact with LEU 18 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G TYR* 3.6 39.7 - - + +
25G PHE* 4.2 11.9 - - + -
14Y LEU* 3.1 39.0 + - + +
15Y ASN* 3.9 7.6 - - - +
16Y ARG 3.3 0.2 - - - -
17Y GLU* 1.3 75.3 - - - +
19Y TYR* 1.3 62.6 + - - +
21Y ALA* 3.5 8.2 - - + +
22Y TYR* 3.2 19.9 + - - +
50Y GLU 5.4 0.2 - - - -
51Y ILE* 5.1 18.2 - - + -
54Y ALA* 3.9 16.4 - - + -
70Y LEU* 4.1 2.9 - - + -
73Y ILE* 4.3 17.5 - - + +
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Residues in contact with TYR 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Y ASN* 3.2 15.2 + - - +
16Y ARG* 3.6 9.9 - - - +
17Y GLU 3.3 0.2 - - - -
18Y LEU* 1.3 74.6 - - - +
20Y SER* 1.3 53.6 + - - +
22Y TYR* 2.9 4.4 + - + -
23Y LEU* 2.6 50.5 + - + +
73Y ILE* 4.1 13.8 - - + +
74Y PRO* 3.6 50.5 - - + -
75Y LYS 4.7 1.5 + - - -
76Y PRO* 3.9 14.2 - - + +
77Y PRO* 3.6 24.4 - - - +
93Y HIS* 3.8 29.2 - + - -
96Y PHE* 6.0 2.9 - + - -
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Residues in contact with SER 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Y ARG 3.0 14.8 + - - -
17Y GLU* 3.4 11.8 + - - -
19Y TYR* 1.3 76.9 - - - +
21Y ALA* 1.3 55.4 + - - +
23Y LEU* 3.3 3.0 + - - +
24Y TYR* 3.0 40.0 + - - -
50Y GLU* 3.6 23.4 + - - -
93Y HIS* 2.8 33.9 + - - -
94Y GLU* 5.7 0.2 - - - -
97Y ILE* 3.4 13.2 - - - +
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Residues in contact with ALA 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Y GLU 3.2 5.3 + - - +
18Y LEU* 3.5 12.1 - - + +
20Y SER* 1.3 79.9 - - - +
22Y TYR* 1.3 57.3 + - - +
25Y PHE* 3.0 28.8 + - - +
47Y ALA* 3.3 34.5 - - + +
50Y GLU* 3.6 13.6 - - + +
51Y ILE* 3.8 19.7 - - + +
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Residues in contact with TYR 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ASN* 3.6 11.3 + - - -
18G LEU* 3.7 27.3 - - + +
70G LEU* 3.3 32.7 - - + +
71G ASP 2.6 30.7 + - - -
73G ILE* 3.7 21.3 - - + +
18Y LEU 3.2 10.4 + - - +
19Y TYR* 2.9 9.0 + - + +
21Y ALA* 1.3 76.4 - - - +
23Y LEU* 1.3 59.4 + - - +
25Y PHE* 3.5 10.6 + + - +
26Y ALA* 3.0 25.6 + - - +
73Y ILE* 3.7 25.1 - - + -
74Y PRO 4.0 4.7 - - - -
76Y PRO* 3.6 29.3 - - + +
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Residues in contact with LEU 23 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Y TYR* 2.6 32.8 + - + +
20Y SER 3.3 4.7 + - - +
22Y TYR* 1.3 73.6 - - - +
24Y TYR* 1.3 62.3 + - + +
26Y ALA* 3.1 5.4 + - - +
27Y MET* 3.0 40.1 + - + +
76Y PRO* 4.2 7.6 - - + +
77Y PRO* 3.8 30.3 - - + -
80Y TRP* 4.2 17.5 - - + -
89Y ALA 5.4 0.7 - - - +
93Y HIS* 3.5 47.3 - - + +
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Residues in contact with TYR 24 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Y SER* 3.0 29.1 + - - +
21Y ALA 4.1 3.6 - - - +
23Y LEU* 1.3 77.0 - - + +
25Y PHE* 1.3 60.4 + - - +
27Y MET* 3.8 13.9 - - + +
28Y ALA* 3.0 21.1 + - - +
42Y TRP* 5.8 0.7 - + - -
43Y MET* 3.3 51.9 - - + +
46Y GLN* 3.8 21.5 - - + -
47Y ALA* 4.2 3.4 - - + -
50Y GLU* 3.7 22.7 - - + -
90Y ALA* 3.7 30.4 + - + +
93Y HIS* 4.2 9.7 - + - -
94Y GLU* 2.5 43.1 + - - +
134Y VAL* 4.7 5.1 - - + +
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Residues in contact with PHE 25 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LEU* 4.5 4.9 - - + -
18G LEU* 4.2 18.8 - - + -
54G ALA* 5.2 4.0 - - + -
55G LEU* 3.8 30.5 - - + -
58G TYR* 3.7 36.7 - + + -
70G LEU* 3.6 38.1 - - + +
21Y ALA 3.0 18.4 + - - +
22Y TYR* 3.6 17.0 - + + +
24Y TYR* 1.3 76.2 - - - +
26Y ALA* 1.3 58.6 + - - +
28Y ALA* 3.5 8.4 - - + +
29Y ALA* 3.2 23.2 + - - +
43Y MET 5.4 0.2 - - - -
44Y LYS* 4.8 9.0 - - + -
47Y ALA* 4.2 8.7 - - + +
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Residues in contact with ALA 26 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67G ARG* 5.0 0.2 + - - -
70G LEU* 3.7 12.3 - - + -
22Y TYR 3.0 13.8 + - - +
23Y LEU 3.1 10.0 + - - +
25Y PHE* 1.3 75.4 - - - +
27Y MET* 1.3 62.8 + - - +
29Y ALA* 3.3 7.0 + - - +
30Y TYR* 3.2 19.8 + - - +
76Y PRO* 3.8 19.5 - - + -
77Y PRO 3.7 20.9 - - - +
78Y LYS* 4.5 4.1 - - - +
80Y TRP* 4.1 5.5 - - + -
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Residues in contact with MET 27 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Y LEU* 3.0 34.5 + - + +
24Y TYR* 3.8 18.4 - - + +
26Y ALA* 1.3 72.8 - - - +
28Y ALA* 1.3 59.7 + - - +
30Y TYR* 3.1 3.4 + - - +
31Y PHE* 2.9 41.4 + - + -
43Y MET* 3.8 31.9 - - + -
80Y TRP* 3.5 41.5 - - + -
86Y ALA* 3.5 27.4 - - + +
89Y ALA* 4.3 4.7 - - + -
90Y ALA* 3.9 20.4 - - + +
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Residues in contact with ALA 28 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G TYR* 2.9 16.0 + - - +
24Y TYR 3.0 18.5 + - - +
25Y PHE* 3.5 12.1 - - + +
27Y MET* 1.3 76.7 - - - +
29Y ALA* 1.3 56.1 + - - +
31Y PHE 3.5 0.3 + - - -
32Y GLU* 3.0 22.9 + - - +
40Y ALA* 3.6 29.1 - - - +
43Y MET* 3.7 11.1 - - + +
44Y LYS* 4.0 15.5 - - + +
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Residues in contact with ALA 29 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G TYR* 3.4 20.8 + - + -
62G TYR* 2.5 30.1 + - - +
67G ARG* 3.7 10.9 + - - +
68G VAL* 3.9 13.7 - - + +
70G LEU* 5.4 2.7 - - + -
25Y PHE 3.2 10.8 + - - +
26Y ALA* 3.5 12.1 - - - +
27Y MET 3.2 0.4 - - - -
28Y ALA* 1.3 77.8 - - - +
30Y TYR* 1.3 62.3 + - - +
32Y GLU 3.5 0.2 + - - -
33Y ASP* 3.2 14.4 + - - +
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Residues in contact with TYR 30 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ARG* 3.9 19.0 - - - +
26Y ALA 3.2 11.8 + - - +
27Y MET 3.1 9.5 + - - +
29Y ALA* 1.3 76.2 - - - +
31Y PHE* 1.3 76.3 + + - +
33Y ASP* 3.3 20.3 + - - +
34Y LEU* 3.4 36.8 + - + +
78Y LYS 4.0 10.8 - - - +
79Y GLU* 4.3 8.1 - - + -
80Y TRP* 3.0 54.1 + + + -
81Y GLU 3.8 2.3 + - - -
82Y SER* 3.3 22.1 - - - -
83Y PRO* 3.6 1.9 - - - +
86Y ALA* 4.1 22.7 - - + -
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Residues in contact with PHE 31 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27Y MET* 2.9 31.5 + - + +
28Y ALA 4.0 2.0 - - - +
30Y TYR* 1.3 83.7 - + - +
32Y GLU* 1.3 63.0 + - - +
34Y LEU* 3.2 9.4 + - + +
36Y LEU* 3.0 44.6 + - + +
39Y PHE* 3.5 36.8 - + + -
40Y ALA 3.9 5.8 - - - +
43Y MET* 4.1 21.8 - - + -
83Y PRO* 3.7 29.6 - - + -
86Y ALA* 3.7 24.7 - - + -
87Y PHE* 3.7 31.2 - + - -
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Residues in contact with GLU 32 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G TYR* 3.2 25.4 + - - +
59G ASN* 5.8 0.7 - - - -
62G TYR* 3.7 35.2 - - + +
28Y ALA 3.0 6.8 + - - +
29Y ALA 3.6 5.6 - - - +
31Y PHE* 1.3 77.2 - - - +
33Y ASP* 1.3 62.2 + - - +
35Y GLY* 3.2 13.4 + - - +
36Y LEU 4.7 2.2 - - - +
37Y GLU* 3.4 30.5 - - - +
40Y ALA* 3.4 15.4 - - + +
41Y ASN* 5.2 0.3 - - - +
44Y LYS* 3.1 27.9 + - - -
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Residues in contact with ASP 33 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G TYR* 3.7 8.4 - - + -
66G GLY 4.4 8.8 - - - +
67G ARG* 3.6 34.3 + - - +
29Y ALA 3.2 13.3 + - - +
30Y TYR* 3.3 14.8 - - - +
31Y PHE 3.2 0.2 - - - -
32Y GLU* 1.3 78.1 - - - +
34Y LEU* 1.3 64.6 + - - +
35Y GLY* 3.1 1.1 + - - -
79Y GLU* 5.1 3.6 - - - +
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Residues in contact with LEU 34 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J ASP* 5.9 2.1 - - - +
143J PHE* 5.3 9.4 - - - -
30Y TYR* 3.4 48.2 + - + +
31Y PHE* 3.2 10.1 + - + +
33Y ASP* 1.3 81.6 - - - +
35Y GLY* 1.3 60.4 + - - +
36Y LEU* 3.3 18.3 + - + +
83Y PRO* 4.1 20.4 - - + -
----------------------------------------------------------
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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