Contacts of the helix formed by residues 3 - 35 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET 3.9 1.0 + - - -
2H LEU* 1.3 77.0 - - - +
4H GLU* 1.3 59.2 + - - +
5H ARG* 4.3 2.9 - - - -
6H MET* 3.2 11.1 + - - +
7H LEU* 2.9 28.9 + - - +
111H GLU* 2.8 35.5 + - - -
113H ASP* 5.6 0.8 + - - -
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Residues in contact with GLU 4 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU 4.1 0.4 + - - -
3H SER* 1.3 72.4 - - - +
5H ARG* 1.3 62.6 + - - +
7H LEU* 3.6 10.7 + - + +
8H LYS* 3.3 27.8 + - + +
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Residues in contact with ARG 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H SER* 3.2 2.5 + - - +
4H GLU* 1.3 77.6 - - - +
6H MET* 1.3 63.0 + - - +
8H LYS* 3.7 7.5 + - + +
9H ALA* 3.4 20.6 + - - +
107H LEU* 4.2 20.9 - - + +
111H GLU* 3.7 19.5 - - - +
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Residues in contact with MET 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU* 3.9 22.0 - - + -
3H SER* 3.2 24.7 + - - +
5H ARG* 1.3 77.8 - - - +
7H LEU* 1.3 59.0 + - - +
9H ALA* 3.1 4.8 + - - +
10H LEU* 2.9 32.8 + - + +
104H LEU* 4.2 17.9 - - - +
107H LEU* 3.8 17.3 - - + -
108H ALA* 3.6 36.8 - - + +
111H GLU* 3.5 17.0 + - - +
113H ASP* 3.9 12.3 - - + +
116H THR* 3.8 19.7 - - - +
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Residues in contact with LEU 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU* 3.9 22.4 - - + +
3H SER 2.9 17.3 + - - +
4H GLU* 3.9 10.8 - - + +
6H MET* 1.3 77.2 - - - +
8H LYS* 1.3 57.4 + - - +
10H LEU* 3.5 7.4 + - - +
11H ASN* 3.1 41.8 + - - +
61H ILE* 3.9 16.2 - - + -
66H GLY* 4.0 4.0 - - - -
67H ARG* 3.7 41.1 - - + +
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Residues in contact with LYS 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H GLU* 3.3 19.4 + - + +
5H ARG* 3.9 7.4 - - - +
6H MET 3.2 0.4 - - - -
7H LEU* 1.3 78.4 - - - +
9H ALA* 1.3 58.0 + - - +
11H ASN* 3.5 6.1 + - + +
12H ASP* 2.9 54.5 + - - +
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Residues in contact with ALA 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H ARG 3.4 11.9 + - - +
6H MET 3.1 8.8 + - - +
8H LYS* 1.3 77.3 - - - +
10H LEU* 1.3 57.9 + - - +
12H ASP* 3.7 9.0 - - - +
13H GLN* 3.2 25.8 + - - +
16H ARG* 4.3 2.1 + - - +
104H LEU* 3.7 26.2 - - + +
107H LEU* 3.9 15.9 - - + -
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Residues in contact with LEU 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU* 3.8 39.3 - - + -
6H MET* 2.9 25.6 + - + +
7H LEU* 3.9 4.3 - - - +
8H LYS 3.3 0.2 - - - -
9H ALA* 1.3 75.2 - - - +
11H ASN* 1.3 59.5 + - - +
13H GLN* 3.4 3.6 + - - +
14H LEU* 3.0 26.7 + - - +
57H PHE* 3.9 32.5 - - + -
60H TYR* 4.0 13.0 - - + -
61H ILE* 4.0 21.3 - - + +
104H LEU* 4.1 10.1 - - + -
116H THR* 3.9 20.9 - - + -
119H PHE* 4.3 7.4 - - + -
120H LEU* 5.2 0.7 - - + -
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Residues in contact with ASN 11 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LEU* 3.1 36.4 + - - +
8H LYS* 3.8 6.7 - - - +
10H LEU* 1.3 76.3 - - - +
12H ASP* 1.3 62.4 + - - +
14H LEU* 3.5 8.8 - - - +
15H ASN* 3.2 20.4 + - - +
61H ILE* 4.1 7.9 - - - +
67H ARG 3.2 22.4 + - - -
68H VAL* 3.3 13.0 - - - +
69H GLU* 2.8 46.9 + - + +
71H ASP* 4.6 5.0 - - - +
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Residues in contact with ASP 12 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H LYS* 2.9 47.6 + - - +
9H ALA* 3.7 7.6 - - - +
10H LEU 3.2 0.2 - - - -
11H ASN* 1.3 75.1 - - - +
13H GLN* 1.3 59.9 + - - +
15H ASN* 3.3 9.0 + - - +
16H ARG* 3.0 51.3 + - - +
71H ASP* 3.6 17.0 - - - +
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Residues in contact with GLN 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ALA 3.2 8.3 + - - +
10H LEU 3.4 4.9 + - - +
12H ASP* 1.3 73.2 - - - +
14H LEU* 1.3 59.7 + - - +
15H ASN 3.1 0.2 - - - -
16H ARG* 3.0 30.4 + - - +
17H GLU* 2.8 49.0 + - - +
57H PHE* 3.4 30.7 - - + -
97H ILE* 3.9 12.3 - - - +
100H SER* 3.0 34.2 + - - +
101H ILE* 3.8 16.9 - - + +
104H LEU* 3.6 21.7 - - + +
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Residues in contact with LEU 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU 3.0 11.9 + - - +
11H ASN* 3.5 13.5 - - - +
13H GLN* 1.3 75.3 - - - +
15H ASN* 1.3 60.7 + - - +
17H GLU* 3.7 4.2 + - - +
18H LEU* 3.3 40.3 + - + +
54H ALA* 3.5 21.4 - - + +
57H PHE* 3.8 13.3 - - + -
58H TYR* 3.5 32.8 - - + +
61H ILE* 3.9 14.8 - - + -
68H VAL* 4.1 14.1 - - + -
69H GLU 6.1 0.2 - - - +
70H LEU* 3.9 18.2 - - + -
25Z PHE* 4.4 8.1 - - + -
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Residues in contact with ASN 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H ASN 3.2 13.5 + - - +
12H ASP* 3.4 12.5 - - - +
13H GLN 3.1 0.4 - - - -
14H LEU* 1.3 76.9 - - - +
16H ARG* 1.3 60.9 + - - +
18H LEU* 3.4 7.8 + - - +
19H TYR* 3.0 26.3 + - - +
71H ASP* 3.3 35.0 + - + +
72H GLU 3.1 27.9 + - - +
73H ILE* 4.4 6.7 - - - +
74H PRO* 4.6 7.6 - - - +
22Z TYR* 4.0 6.4 + - - -
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Residues in contact with ARG 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ALA* 4.3 3.4 + - - +
12H ASP* 3.0 32.1 + - - +
13H GLN* 3.0 61.3 + - - +
15H ASN* 1.3 77.2 - - + +
17H GLU* 1.3 59.9 + - - +
19H TYR* 3.3 8.2 + - - +
20H SER* 2.9 32.1 + - - -
93H HIS* 4.7 0.7 + - - -
96H PHE* 4.4 26.4 - - + -
97H ILE* 4.0 8.8 - - + +
100H SER* 3.8 21.9 + - - -
104H LEU* 5.2 2.0 - - - +
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Residues in contact with GLU 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H GLN* 2.8 37.2 + - - +
14H LEU 4.0 0.2 - - - +
15H ASN 3.4 0.2 - - - -
16H ARG* 1.3 76.4 - - - +
18H LEU* 1.3 57.5 + - - +
20H SER* 3.5 5.1 + - - -
21H ALA* 3.2 20.4 + - - +
50H GLU* 2.9 52.3 - - - +
53H HIS* 3.7 15.8 + - + +
54H ALA* 3.8 13.2 - - + +
57H PHE* 3.9 15.9 - - + -
97H ILE* 4.4 12.0 - - - +
101H ILE* 4.6 1.6 - - - +
123H PHE* 3.8 23.7 - - - -
127H GLN* 4.8 3.3 + - - -
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Residues in contact with LEU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 3.3 37.3 + - + +
15H ASN* 3.8 7.0 - - - +
16H ARG 3.3 0.2 - - - -
17H GLU* 1.3 77.9 - - - +
19H TYR* 1.3 58.8 + - - +
21H ALA* 3.5 6.0 - - + +
22H TYR* 3.1 24.9 + - - +
51H ILE* 4.8 21.3 - - + -
54H ALA* 3.8 16.6 - - + -
70H LEU* 4.1 2.2 - - + -
73H ILE* 4.3 18.9 - - + +
22Z TYR* 3.7 37.5 - - + +
25Z PHE* 4.2 11.0 - - + -
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Residues in contact with TYR 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ASN* 3.0 18.1 + - - +
16H ARG* 3.3 6.9 + - - +
18H LEU* 1.3 73.4 - - - +
20H SER* 1.3 56.7 + - - +
21H ALA 3.2 0.2 - - - -
22H TYR* 3.0 6.1 + - + -
23H LEU* 2.6 50.3 + - + +
73H ILE* 4.2 9.6 - - + +
74H PRO* 3.7 50.0 - - + -
75H LYS 4.4 2.2 + - - -
76H PRO* 3.8 14.6 - - + +
77H PRO* 3.6 25.1 - - - +
93H HIS* 3.7 30.1 - + - -
96H PHE* 6.1 1.3 - + - -
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Residues in contact with SER 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H ARG 2.9 19.3 + - - -
17H GLU* 3.5 11.5 - - - -
19H TYR* 1.3 76.6 - - - +
21H ALA* 1.3 59.5 + - - +
23H LEU* 3.5 2.8 + - - +
24H TYR* 3.1 36.0 + - - -
50H GLU* 3.5 23.3 + - - -
93H HIS* 3.0 29.3 + - - -
94H GLU* 5.6 0.9 - - - -
97H ILE* 3.4 14.9 - - - +
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Residues in contact with ALA 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLU 3.2 6.2 + - - +
18H LEU* 3.5 10.8 - - + +
19H TYR 3.2 0.4 - - - -
20H SER* 1.3 80.0 - - - +
22H TYR* 1.3 55.9 + - - +
24H TYR 3.5 0.2 + - - -
25H PHE* 3.0 26.7 + - - +
47H ALA* 3.3 37.2 - - + +
50H GLU* 3.6 12.0 - - + +
51H ILE* 3.7 20.9 - - + +
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Residues in contact with TYR 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU 3.1 15.0 + - - +
19H TYR* 3.0 6.3 + - + +
21H ALA* 1.3 75.3 - - - +
23H LEU* 1.3 60.2 + - - +
25H PHE* 3.9 10.3 - + + +
26H ALA* 3.2 25.3 + - - +
73H ILE* 3.7 24.5 - - + -
74H PRO 3.9 5.6 - - - -
76H PRO* 3.6 34.6 - - + +
15Z ASN* 3.5 12.0 + - - -
18Z LEU* 3.6 27.8 - - + +
70Z LEU* 3.5 28.4 - - + +
71Z ASP 2.6 29.2 + - - -
72Z GLU* 4.7 1.1 - - - -
73Z ILE* 3.7 20.0 - - + -
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Residues in contact with LEU 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H TYR* 2.6 33.6 + - + +
20H SER 3.8 3.6 - - - +
22H TYR* 1.3 73.4 - - - +
24H TYR* 1.3 63.0 + - + +
26H ALA* 3.1 5.4 + - - +
27H MET* 2.9 45.9 + - + +
76H PRO* 4.1 6.7 - - + +
77H PRO* 3.8 29.2 - - + -
80H TRP* 4.1 17.9 - - + -
89H ALA 5.2 0.7 - - - +
93H HIS* 3.5 46.4 - - + +
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Residues in contact with TYR 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H SER* 3.1 26.7 + - - +
21H ALA 4.0 3.1 - - - +
22H TYR 3.4 0.2 - - - -
23H LEU* 1.3 78.6 - - + +
25H PHE* 1.3 61.1 + - - +
27H MET* 3.3 14.0 + - + +
28H ALA* 2.9 23.7 + - - +
42H TRP* 5.9 0.7 - + - -
43H MET* 3.4 50.4 - - + +
46H GLN* 3.7 22.4 - - + -
47H ALA* 4.2 2.5 - - + -
50H GLU* 3.8 22.7 - - + -
90H ALA* 3.6 30.8 + - + +
93H HIS* 4.5 8.2 - + - -
94H GLU* 2.5 40.9 + - - +
130H GLU* 5.2 0.2 - - - -
134H VAL* 4.7 4.6 - - + +
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Residues in contact with PHE 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ALA 3.0 17.9 + - - +
22H TYR* 3.9 16.4 - + + +
23H LEU 3.3 0.2 - - - -
24H TYR* 1.3 75.0 - - - +
26H ALA* 1.3 58.4 + - - +
28H ALA* 3.7 4.1 + - + +
29H ALA* 3.3 23.9 + - - +
43H MET 5.4 0.4 - - - -
44H LYS* 4.7 16.8 - - + -
47H ALA* 4.3 8.4 - - + +
14Z LEU* 4.4 5.8 - - + -
18Z LEU* 4.3 18.2 - - + -
54Z ALA* 5.2 2.5 - - + -
55Z LEU* 3.7 31.4 - - + -
58Z TYR* 3.8 36.7 - + + -
70Z LEU* 3.6 38.6 - - + +
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H TYR 3.2 13.4 + - - +
23H LEU 3.1 10.6 + - - +
25H PHE* 1.3 75.4 - - - +
27H MET* 1.3 63.4 + - - +
29H ALA* 3.4 6.6 + - - +
30H TYR* 3.2 20.3 + - - +
76H PRO* 3.8 18.2 - - + -
77H PRO 3.7 20.6 - - - +
78H LYS* 4.4 4.6 - - - +
80H TRP* 3.9 5.8 - - + -
67Z ARG* 5.2 0.2 + - - -
70Z LEU* 3.6 13.0 - - + +
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Residues in contact with MET 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H LEU* 2.9 34.0 + - + +
24H TYR* 3.3 18.6 + - + +
26H ALA* 1.3 74.4 - - - +
28H ALA* 1.3 58.9 + - - +
30H TYR* 3.0 4.2 + - - +
31H PHE* 2.9 39.5 + - + -
43H MET* 3.8 31.6 - - + -
80H TRP* 3.5 38.4 - - + -
86H ALA* 3.4 28.9 - - + +
89H ALA* 4.3 4.5 - - + -
90H ALA* 3.8 22.2 - - + +
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TYR 2.9 17.5 + - - +
25H PHE* 3.7 10.3 - - + +
26H ALA 3.4 0.2 - - - -
27H MET* 1.3 74.9 - - - +
29H ALA* 1.3 56.7 + - - +
31H PHE 3.4 0.3 + - - -
32H GLU* 3.0 24.9 + - - +
40H ALA* 3.4 32.1 - - - +
43H MET* 3.7 11.4 - - + +
44H LYS* 3.9 16.2 - - + +
58Z TYR* 3.1 12.8 + - - +
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Residues in contact with ALA 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PHE 3.3 12.0 + - - +
26H ALA* 3.5 11.7 - - - +
27H MET 3.2 0.2 - - - -
28H ALA* 1.3 78.1 - - - +
30H TYR* 1.3 62.0 + - - +
33H ASP* 3.3 12.8 + - - +
58Z TYR* 3.5 19.4 + - + -
62Z TYR* 2.6 31.3 + - - +
67Z ARG* 3.6 12.5 + - - +
68Z VAL* 4.1 13.7 - - + +
70Z LEU* 5.2 2.9 - - + -
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Residues in contact with TYR 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H ALA 3.2 12.0 + - - +
27H MET* 3.0 10.6 + - - +
29H ALA* 1.3 76.5 - - - +
31H PHE* 1.3 72.3 + + - +
33H ASP* 3.4 14.3 + - + +
34H LEU* 3.5 42.8 + - + +
78H LYS 4.1 4.5 - - - +
79H GLU* 4.4 5.4 - - + -
80H TRP* 2.9 60.6 + + + -
81H GLU 3.7 2.4 + - - -
82H SER* 3.4 24.4 - - - -
83H PRO* 3.8 1.5 - - - +
86H ALA* 4.0 23.6 - - + -
67Z ARG* 4.0 19.5 - - - +
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Residues in contact with PHE 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H MET* 2.9 32.7 + - + +
28H ALA 3.9 1.8 - - - +
30H TYR* 1.3 82.3 - + - +
32H GLU* 1.3 63.7 + - - +
34H LEU* 3.2 8.4 + - + +
35H GLY 3.1 4.3 + - - -
36H LEU* 3.1 51.3 + - + +
39H PHE* 3.5 28.3 - + + -
40H ALA 3.8 8.5 - - - +
43H MET* 4.1 31.4 - - + -
83H PRO* 3.7 28.9 - - + -
86H ALA* 3.9 15.5 - - + -
87H PHE* 3.7 27.1 - + - -
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Residues in contact with GLU 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ALA 3.0 8.3 + - - +
29H ALA 3.8 4.9 - - - +
31H PHE* 1.3 76.2 - - - +
33H ASP* 1.3 61.2 + - - +
35H GLY* 3.2 12.9 + - - +
36H LEU 4.8 2.2 - - - +
37H GLU* 3.4 32.1 - - - +
40H ALA* 3.4 14.9 - - - +
41H ASN* 5.3 0.2 - - - +
44H LYS* 3.1 21.3 + - - -
58Z TYR* 3.1 31.0 + - - +
59Z ASN* 6.0 0.2 - - - -
62Z TYR* 3.7 34.0 - - + +
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Residues in contact with ASP 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ALA 3.3 12.1 + - - +
30H TYR* 3.5 13.2 - - + +
31H PHE 3.2 0.2 - - - -
32H GLU* 1.3 80.3 - - - +
34H LEU* 1.3 63.4 + - - +
35H GLY* 3.2 0.9 + - - -
79H GLU* 5.4 2.4 - - - +
62Z TYR* 3.8 7.6 - - + -
66Z GLY 4.4 8.7 - - - +
67Z ARG* 3.6 35.4 + - - +
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1390 ASP* 6.1 1.4 - - - +
1430 PHE* 5.9 2.8 - - - -
30H TYR* 3.5 49.8 + - + +
31H PHE* 3.2 11.5 + - + +
33H ASP* 1.3 81.3 - - - +
35H GLY* 1.3 57.7 + - - +
36H LEU* 3.3 21.5 + - + +
83H PRO* 4.1 20.0 - - + -
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Residues in contact with GLY 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360 LYS* 5.9 1.7 - - - +
1390 ASP* 6.3 2.9 - - - -
1400 LYS* 4.8 13.5 - - - +
31H PHE 3.1 2.4 + - - -
32H GLU 3.2 11.3 + - - -
33H ASP 3.2 4.6 - - - -
34H LEU* 1.3 79.2 - - - +
36H LEU* 1.3 60.6 + - - +
37H GLU* 3.0 19.7 + - - +
155H ASP* 4.7 1.9 - - - +
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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