Contacts of the helix formed by residues 10 - 41 (chain J) in PDB entry 1VEQ
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 10 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J GLY 4.4 0.6 + - - -
9J LEU* 1.3 72.0 - - - +
11J ASP* 1.3 55.5 + - - +
12J LYS* 2.6 22.6 + - - +
13J LYS* 2.9 51.8 + - - +
14J ALA* 2.9 10.2 + - - +
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Residues in contact with ASP 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J SER 4.7 9.4 - - - +
4J PHE 5.0 1.7 - - - +
5J THR* 3.9 26.1 - - - +
9J LEU 3.4 3.3 + - - +
10J SER* 1.3 69.1 - - - +
12J LYS* 1.3 56.9 + - - +
14J ALA* 4.2 8.3 - - - +
15J SER* 3.6 20.0 + - - -
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Residues in contact with LYS 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J SER* 2.6 11.8 + - - +
11J ASP* 1.3 73.2 - - - +
13J LYS* 1.3 75.4 + - + +
14J ALA 3.1 1.1 - - - -
15J SER* 3.2 6.3 + - - -
16J ASP* 2.6 53.5 + - - +
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Residues in contact with LYS 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J LEU* 4.6 12.6 - - + -
10J SER* 2.9 34.4 + - - +
12J LYS* 1.3 84.5 - - + +
14J ALA* 1.3 64.7 + - - +
16J ASP* 3.1 7.5 + - - +
17J VAL* 3.0 27.4 + - - +
129J ASP 4.1 15.8 + - - +
130J LEU* 4.4 32.9 + - + +
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Residues in contact with ALA 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J THR* 3.6 23.8 - - - +
9J LEU* 4.3 21.7 - - + +
10J SER 2.9 15.0 + - - +
11J ASP* 4.2 7.0 - - - +
13J LYS* 1.3 76.2 - - - +
15J SER* 1.3 62.9 + - - +
17J VAL* 3.2 7.7 + - - +
18J ALA* 3.1 20.7 + - - +
75J LEU* 3.8 18.4 - - + +
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Residues in contact with SER 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ASP 3.6 17.5 + - - -
12J LYS* 3.2 7.4 + - - -
14J ALA* 1.3 78.4 - - - +
16J ASP* 1.3 63.5 + - - +
18J ALA* 3.4 8.2 - - - +
19J ASP* 3.1 31.6 + - - +
77J LYS* 5.8 3.8 - - - +
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Residues in contact with ASP 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J LYS* 2.6 47.1 + - - +
13J LYS* 3.1 10.5 + - - +
15J SER* 1.3 75.6 - - - +
17J VAL* 1.3 64.5 + - - +
19J ASP* 3.6 12.6 + - - +
20J LEU* 3.3 23.0 + - - +
130J LEU* 4.5 16.2 - - + +
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Residues in contact with VAL 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J LEU* 5.3 1.8 - - + -
13J LYS* 3.0 17.1 + - + +
14J ALA* 3.5 8.1 - - - +
16J ASP* 1.3 72.3 - - - +
18J ALA* 1.3 69.9 + - - +
20J LEU* 2.8 19.7 + - - +
21J LEU* 3.0 18.0 + - + +
75J LEU* 3.7 18.2 - - + -
127J LEU* 4.0 16.4 - - + -
130J LEU* 3.7 32.1 - - + -
131J ASP* 4.3 11.9 - - + -
134J SER* 3.9 20.4 - - - +
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Residues in contact with ALA 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14J ALA 3.1 10.1 + - - +
15J SER* 3.4 13.0 - - - +
17J VAL* 1.3 77.6 - - - +
19J ASP* 1.3 65.3 + - - +
20J LEU 2.9 0.9 + - - -
21J LEU* 2.9 7.3 + - - +
22J GLN* 2.9 26.3 + - - +
72J ILE* 4.5 10.7 - - + +
75J LEU* 3.9 15.2 - - + +
77J LYS* 3.8 28.3 - - + -
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Residues in contact with ASP 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J SER* 3.1 21.4 + - - +
16J ASP* 3.7 16.6 - - - +
17J VAL 3.3 0.2 - - - -
18J ALA* 1.3 79.7 - - - +
20J LEU* 1.3 61.7 + - - +
22J GLN* 3.8 8.1 + - - +
23J LYS* 3.5 17.5 + - - +
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Residues in contact with LEU 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ASP 3.3 12.3 + - - +
17J VAL* 2.8 13.8 + - - +
19J ASP* 1.3 76.9 - - - +
21J LEU* 1.3 68.3 + - + +
23J LYS* 3.3 16.1 + - + +
24J GLN* 3.2 16.3 + - - +
123J SER* 3.3 37.8 + - - +
126J LYS* 4.5 25.4 - - + +
127J LEU* 4.1 28.9 - - + -
130J LEU* 4.2 12.3 - - + -
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Residues in contact with LEU 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J VAL* 3.4 29.6 - - + +
18J ALA* 2.9 2.6 + - - +
20J LEU* 1.3 75.0 - - + +
22J GLN* 1.3 61.8 + - - +
23J LYS 2.8 2.0 - - - -
24J GLN* 2.6 27.9 + - + +
25J LEU* 2.7 13.5 + - - +
68J VAL* 3.6 18.1 - - + +
71J ARG* 3.8 30.3 - - + -
72J ILE* 3.7 20.0 - - + -
75J LEU* 4.5 5.6 - - + -
127J LEU* 5.0 9.2 - - + -
134J SER* 4.5 6.3 - - - +
137J LEU* 6.1 0.4 - - + -
138J LEU* 4.0 27.1 - - + -
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Residues in contact with GLN 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J ALA 2.9 15.7 + - - +
19J ASP* 3.9 10.5 - - - +
21J LEU* 1.3 75.3 - - - +
23J LYS* 1.3 60.3 - - - +
25J LEU* 3.7 5.9 + - - +
26J SER* 3.3 18.8 + - - -
72J ILE* 3.5 14.7 - - + +
78J SER 4.4 2.3 - - - +
79J PRO* 3.6 9.4 - - - +
80J LYS* 3.0 52.8 + - + +
89J ASP* 3.3 26.3 + - - +
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Residues in contact with LYS 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J ASP 3.5 9.4 + - - +
20J LEU* 3.3 18.7 + - + +
21J LEU 2.7 1.4 + - - -
22J GLN* 1.3 78.0 - - - +
24J GLN* 1.3 69.2 + - - +
26J SER* 3.1 5.5 + - - -
27J THR* 2.9 28.7 + - - +
89J ASP* 4.6 27.1 - - + +
91J THR* 5.2 14.0 + - - +
119J ASP* 3.4 27.9 + - + +
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Residues in contact with GLN 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J LEU 3.2 5.0 + - - +
21J LEU* 2.6 23.3 + - + +
23J LYS* 1.3 76.1 - - - +
25J LEU* 1.3 58.3 + - - +
27J THR* 2.8 15.3 + - - +
28J TYR* 2.8 65.4 + - + +
68J VAL* 4.8 4.5 - - + -
116J VAL* 5.4 0.8 - - - +
119J ASP* 4.6 6.8 - - - +
120J THR* 2.6 34.6 + - - -
123J SER* 4.3 13.7 + - - -
138J LEU* 3.1 31.7 - - + +
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Residues in contact with LEU 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.5 8.7 - - + -
21J LEU 2.7 17.5 + - - +
22J GLN* 3.7 10.1 - - - +
24J GLN* 1.3 73.1 - - - +
26J SER* 1.3 66.8 + - - +
28J TYR* 3.1 13.1 + - - +
29J ASN* 2.9 56.0 + - - +
65J ALA* 4.3 9.4 - - - +
68J VAL* 4.3 8.2 - - + +
69J ALA* 3.2 43.7 - - + +
72J ILE* 4.4 7.6 - - + -
79J PRO* 4.6 5.8 - - + -
80J LYS 3.4 25.6 - - - +
81J GLY* 4.3 2.0 - - - -
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Residues in contact with SER 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J GLN* 3.3 11.8 + - - -
23J LYS 3.1 8.3 + - - -
25J LEU* 1.3 83.1 - - - +
27J THR* 1.3 63.1 + - - +
29J ASN* 3.4 7.6 + - - +
30J ASP* 3.1 22.9 + - - +
80J LYS 4.5 0.7 + - - -
85J ALA 3.9 0.7 + - - -
86J ILE* 3.7 27.6 + - - +
89J ASP* 3.1 39.3 + - - +
90J ARG* 5.0 4.7 - - - +
92J TRP* 5.3 0.6 - - - -
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Residues in contact with THR 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LYS* 2.9 26.1 + - - +
24J GLN* 2.8 22.6 + - - +
26J SER* 1.3 77.2 - - - +
28J TYR* 1.3 57.8 + - + +
30J ASP* 3.3 4.7 + - - +
31J LEU* 2.9 25.5 + - - +
92J TRP* 3.4 37.0 - - + -
115J GLY 5.5 0.2 - - - +
116J VAL* 4.0 32.2 - - + +
119J ASP* 5.2 8.1 + - + +
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Residues in contact with TYR 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J GLN* 2.8 49.6 + - + +
25J LEU* 3.5 7.4 - - - +
27J THR* 1.3 78.7 - - + +
29J ASN* 1.3 59.1 + - - +
31J LEU* 2.9 12.3 + - + +
32J HIS* 2.7 37.4 + - - +
61J VAL* 3.7 22.4 - - + +
64J TYR* 3.6 29.6 - + + -
65J ALA* 4.2 8.7 - - + -
68J VAL* 3.6 18.4 - - + -
116J VAL* 4.7 10.1 - - + -
120J THR* 4.7 1.1 + - - -
138J LEU* 3.9 2.9 - - - +
141J HIS* 2.7 40.0 + + + +
145J LEU* 4.6 14.0 - - + +
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Residues in contact with ASN 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.8 23.6 - - + +
40A TRP* 4.9 6.0 - - - -
25J LEU* 2.9 49.7 + - - +
26J SER* 3.7 6.9 - - - +
28J TYR* 1.3 75.9 - - - +
30J ASP* 1.3 64.3 + - - +
32J HIS* 3.5 22.5 + - - +
33J LEU* 3.1 27.7 + - - +
65J ALA* 4.2 12.3 - - - +
81J GLY* 4.4 11.3 - - - -
86J ILE* 4.0 16.5 - - + +
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Residues in contact with ASP 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO* 2.8 31.9 - - - +
26J SER 3.1 13.1 + - - +
27J THR 3.6 8.1 - - - +
29J ASN* 1.3 74.5 - - - +
31J LEU* 1.3 56.5 + - - +
33J LEU* 3.0 3.8 + - - +
34J THR* 2.7 45.8 + - - -
86J ILE* 3.5 14.5 - - + +
90J ARG* 3.2 11.5 + - + -
92J TRP* 3.5 32.4 + - + +
94J ASP* 4.4 4.3 - - - +
95J TYR 5.6 0.9 + - - -
112J VAL* 5.0 9.7 - - - +
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Residues in contact with LEU 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J THR 2.9 13.8 + - - +
28J TYR* 2.9 13.2 + - + +
30J ASP* 1.3 77.3 + - - +
32J HIS* 1.3 51.9 + - - +
34J THR* 2.9 8.7 + - - -
35J LEU* 2.7 60.6 + - + +
61J VAL* 3.6 30.5 - - + -
109J LEU* 5.6 1.3 - - + -
112J VAL* 4.6 11.7 - - + -
113J TYR* 3.4 27.8 - - + +
116J VAL* 4.6 24.9 - - + -
145J LEU* 4.0 15.7 - - + -
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Residues in contact with HIS 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 4.3 17.0 - + - -
33A LEU* 4.4 6.4 - - + +
62A ARG* 3.4 23.2 + - - +
28J TYR 2.7 12.0 + - - -
29J ASN* 3.5 40.5 + - - -
31J LEU* 1.3 74.6 - - - +
33J LEU* 1.3 83.2 + - + +
35J LEU* 3.7 10.9 - - - +
36J LYS* 3.3 21.7 + - - +
58J VAL* 4.2 8.3 - - + +
61J VAL* 3.5 23.8 - - + -
62J ARG* 4.2 28.4 - - + +
65J ALA* 5.1 2.2 - - + -
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Residues in contact with LEU 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 3.8 28.9 - - + +
32A HIS* 4.4 7.4 - - - +
33A LEU* 3.5 29.6 - - + -
81A GLY 3.3 28.5 - - - +
82A THR* 5.2 0.7 - - - -
83A PRO* 4.6 22.9 - - + -
86A ILE* 5.3 4.9 - - + -
29J ASN 3.1 18.4 + - - +
30J ASP* 3.0 5.8 + - - +
32J HIS* 1.3 96.1 + - + +
34J THR* 1.3 57.7 + - - +
36J LYS* 3.5 9.7 + - + +
37J HIS 3.1 19.1 + - - -
40J TRP* 5.0 2.8 - - + -
86J ILE* 5.2 1.8 - - + -
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Residues in contact with THR 34 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A THR* 4.6 2.4 - - - +
83A PRO* 4.2 6.8 - - - +
30J ASP* 2.7 36.3 + - - +
31J LEU* 3.3 11.2 - - - -
33J LEU* 1.3 75.8 - - - +
35J LEU* 1.3 58.2 + - - +
37J HIS* 2.8 32.2 + - + +
38J VAL* 3.1 13.7 + - + +
95J TYR* 3.5 47.4 + - + +
109J LEU* 4.7 7.4 - - + -
112J VAL* 5.3 7.9 - - + -
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Residues in contact with LEU 35 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 2.7 66.6 + - + +
32J HIS* 3.7 6.5 - - - +
34J THR* 1.3 72.5 - - - +
36J LYS* 1.3 58.9 + - - +
38J VAL* 3.1 11.9 + - + +
39J HIS* 2.9 25.5 + - - +
54J ILE* 3.5 24.9 - - + +
57J GLN* 4.6 5.8 - - + -
58J VAL* 3.4 22.9 - - + -
61J VAL* 5.1 1.1 - - + -
109J LEU* 4.0 28.3 - - + -
113J TYR* 3.6 15.9 - - + +
148J PHE* 4.2 8.1 - - + -
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Residues in contact with LYS 36 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.5 22.0 - - + +
65A ALA* 6.2 1.1 - - + -
66A ASP* 3.1 26.8 + - - +
32J HIS 3.3 8.0 + - - +
33J LEU* 3.7 12.6 - - + +
34J THR 3.2 0.2 - - - -
35J LEU* 1.3 78.7 - - - +
37J HIS* 1.3 63.6 + - - +
39J HIS* 3.0 46.4 + - + +
40J TRP* 3.1 47.1 - - + -
55J ASP* 3.1 19.2 + - - +
58J VAL* 3.6 28.9 - - + -
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Residues in contact with HIS 37 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO 3.6 2.0 + - - -
80A LYS* 3.5 19.7 - - + -
81A GLY* 2.9 34.3 + - - +
82A THR* 3.7 19.7 - - + +
33J LEU 3.1 11.0 + - - +
34J THR* 2.8 22.0 + - - +
36J LYS* 1.3 77.2 - - - +
38J VAL* 1.3 58.0 + - - -
40J TRP* 3.2 19.1 + - - +
41J ASN* 2.7 44.8 + - - -
95J TYR* 3.5 29.9 + + - -
97J VAL 3.1 17.5 + - - -
98J GLU* 4.8 3.9 + - - -
105J HIS* 5.4 0.2 - + - -
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Residues in contact with VAL 38 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J THR 3.2 17.3 - - - +
35J LEU* 3.7 4.9 - - - +
37J HIS* 1.3 70.1 - - - +
39J HIS* 1.3 65.7 + - - +
40J TRP 2.8 6.5 + - - -
41J ASN 4.2 1.3 - - - +
42J VAL* 2.7 39.1 + - + +
50J VAL* 5.4 1.1 - - + -
54J ILE* 3.1 27.4 - - + -
95J TYR* 3.7 27.1 - - + +
105J HIS* 3.9 26.7 - - + +
106J LEU* 6.4 1.3 - - + -
109J LEU* 4.2 20.9 - - + -
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Residues in contact with HIS 39 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.0 8.2 + - - -
210A FE 2.4 24.6 - - - -
150C TRP* 5.0 0.2 - - - -
35J LEU 2.9 14.2 + - - +
36J LYS* 3.1 41.3 + - + +
38J VAL* 1.3 76.5 - - - +
40J TRP* 1.3 66.7 + + - +
42J VAL* 4.9 1.9 + - - +
47J PHE* 5.0 1.6 - - - -
51J HIS* 2.7 82.6 + + - +
52J GLU* 5.2 0.4 - - - -
54J ILE* 3.9 18.8 - - + +
55J ASP* 3.2 24.6 + - - -
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Residues in contact with TRP 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.4 9.2 - - + -
29A ASN* 4.9 9.2 - - - -
65A ALA* 4.1 10.1 - - + -
66A ASP* 3.2 35.5 + - - +
69A ALA* 3.3 33.2 - - + +
70A GLU* 3.7 22.4 - - + +
73A ALA* 4.4 7.4 - - + +
79A PRO* 4.5 15.9 - - + -
81A GLY* 4.1 22.9 - - - -
150C TRP* 3.7 25.0 - + - -
33J LEU* 5.9 1.8 - - + -
36J LYS* 3.1 48.3 + - + -
37J HIS* 3.5 18.4 - - - +
38J VAL 2.8 1.8 + - - -
39J HIS* 1.3 87.6 - + - +
41J ASN* 1.3 65.1 + - - +
42J VAL 3.4 8.2 + - - +
43J VAL* 5.7 0.7 - - - +
47J PHE* 5.7 0.3 - - - -
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Residues in contact with ASN 41 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 3.0 14.2 + - - -
79A PRO* 2.9 31.8 + - - +
37J HIS* 2.7 57.1 + - - +
38J VAL 3.2 3.2 + - - -
40J TRP* 1.3 75.5 - - - +
42J VAL* 1.3 60.5 + - - +
43J VAL* 4.7 2.7 - - - -
98J GLU* 3.7 6.0 - - - +
99J ARG* 3.2 26.2 - - - +
100J ASP 3.1 23.4 + - - -
105J HIS* 3.1 8.8 + - + +
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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