Contacts of the helix formed by residues 16 - 46 (chain J) in PDB entry 3L73
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 ARG 16 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 5.3 5.8 - - + -
11J SER 5.1 7.4 + - - -
12J ALA* 5.1 5.7 + - - +
13J LEU 3.9 0.2 - - - +
15J ARG* 1.3 92.6 - - + +
17J THR* 1.3 60.8 + - - +
18J SER* 4.1 13.1 + - - +
19J THR* 2.6 59.2 + - - +
20J PHE* 3.0 7.7 + - - +
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Residues in contact with THR 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 4.1 14.1 + - - -
442A TYR* 4.4 6.0 - - + -
443A TRP* 4.3 41.2 - - + +
2005E PEE 4.2 44.3 + - + +
15J ARG 3.3 4.6 + - - -
16J ARG* 1.3 70.5 - - - +
18J SER* 1.3 61.5 + - - +
20J PHE* 3.7 8.8 - - + +
21J ALA* 3.3 20.4 + - - +
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Residues in contact with SER 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A TRP* 5.7 9.5 - - - -
16J ARG* 2.9 12.7 + - - +
17J THR* 1.3 78.9 - - - +
19J THR* 1.3 68.8 + - - +
21J ALA* 3.5 6.3 + - - +
22J LEU* 3.2 25.3 + - - +
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Residues in contact with THR 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12J ALA 3.6 19.5 + - - +
13J LEU* 3.2 15.1 + - - +
16J ARG* 2.6 57.0 + - - +
18J SER* 1.3 83.4 + - - +
20J PHE* 1.3 59.4 - - - +
21J ALA 3.3 0.2 - - - -
22J LEU* 3.5 14.3 - - + +
23J THR* 2.9 32.4 + - - -
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Residues in contact with PHE 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E TYR* 3.7 13.7 - - + -
40E THR* 4.1 13.2 - - + -
41E ALA* 3.3 39.0 - - + -
44E CYS* 4.2 9.6 - - - -
2005E PEE 4.2 40.4 - - + -
13J LEU 3.2 10.9 + - - +
14J PHE* 3.8 33.7 - + + +
16J ARG 3.0 9.6 + - - +
17J THR* 3.7 14.6 - - + +
18J SER 3.2 0.2 - - - -
19J THR* 1.3 77.6 - - - +
21J ALA* 1.3 65.3 + - - +
23J THR* 3.0 7.3 + - - -
24J VAL* 3.0 38.6 + - + +
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005E PEE 3.9 36.3 - - + -
17J THR 3.3 10.0 + - - +
18J SER* 3.7 8.7 - - - +
19J THR 3.3 0.4 - - - -
20J PHE* 1.3 75.7 - - - +
22J LEU* 1.3 67.8 + - - +
24J VAL* 3.0 2.9 + - - +
25J VAL* 2.9 29.5 + - + +
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Residues in contact with LEU 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J SER 3.2 12.2 + - - +
19J THR* 3.5 18.2 - - + +
21J ALA* 1.3 81.1 - - - +
23J THR* 1.3 57.0 + - - +
25J VAL* 3.4 7.8 + - + +
26J LEU* 2.9 37.0 + - + +
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Residues in contact with THR 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ALA* 5.2 5.8 - - + -
45E VAL* 4.6 0.7 - - - +
13J LEU* 3.5 38.2 - - + +
14J PHE* 4.3 20.6 - - + -
19J THR 2.9 19.9 + - - -
20J PHE* 3.0 11.2 + - - -
22J LEU* 1.3 74.8 - - - +
24J VAL* 1.3 57.1 + - - +
26J LEU* 4.4 2.6 - - - +
27J GLY* 2.7 33.8 + - - +
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Residues in contact with VAL 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E ALA* 3.9 11.4 - - + +
44E CYS* 3.5 33.2 - - + +
45E VAL* 3.6 17.7 - - - +
48E ALA* 4.8 3.4 - - + -
2005E PEE 3.7 28.5 - - + -
20J PHE* 3.0 43.9 + - + +
21J ALA 3.5 6.5 - - - +
23J THR* 1.3 77.4 - - - +
25J VAL* 1.3 52.9 + - - +
27J GLY 3.6 0.3 - - - -
28J ALA* 2.7 36.9 + - - +
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Residues in contact with VAL 25 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005E PEE 3.5 44.7 - - + +
21J ALA* 2.9 21.2 + - + +
22J LEU* 3.7 9.2 - - + +
24J VAL* 1.3 73.4 - - - +
26J LEU* 1.3 68.5 + - + +
28J ALA* 3.2 7.6 + - - +
29J VAL* 3.1 27.8 + - + +
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Residues in contact with LEU 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J LEU* 2.9 25.8 + - + +
23J THR* 4.4 2.5 - - - +
25J VAL* 1.3 79.3 - - + +
27J GLY* 1.3 60.5 + - - +
29J VAL* 3.7 12.5 + - + +
30J LEU* 3.3 42.3 + - + +
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Residues in contact with GLY 27 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E VAL* 3.6 12.5 - - - +
23J THR* 2.7 22.7 + - - -
24J VAL 3.6 1.1 - - - -
26J LEU* 1.3 75.5 - - - +
28J ALA* 1.3 58.3 + - - +
30J LEU* 3.6 7.1 + - - +
31J PHE* 2.9 29.5 + - - +
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Residues in contact with ALA 28 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E VAL* 3.4 19.0 - - + +
48E ALA* 4.2 17.3 - - + -
49E TYR* 5.2 3.0 - - - +
2005E PEE 4.1 23.1 - - + -
24J VAL 2.7 21.5 + - - +
25J VAL* 3.5 6.5 - - - +
27J GLY* 1.3 70.2 - - - +
29J VAL* 1.3 68.1 + - - +
31J PHE* 2.9 3.8 + - - +
32J GLU* 2.8 24.4 + - - +
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Residues in contact with VAL 29 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2005E PEE 4.1 25.6 - - + -
25J VAL* 3.1 21.4 + - + +
26J LEU* 3.9 13.9 - - + +
27J GLY 3.4 0.2 - - - -
28J ALA* 1.3 79.4 - - - +
30J LEU* 1.3 66.0 + - + +
32J GLU* 3.3 3.7 + - - +
33J ARG* 3.3 45.2 + - - +
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Residues in contact with LEU 30 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26J LEU* 3.3 35.6 + - + +
27J GLY* 3.9 5.4 - - - +
28J ALA 3.2 0.8 - - - -
29J VAL* 1.3 77.7 - - + +
31J PHE* 1.3 62.9 - - - +
33J ARG* 3.5 32.6 + - - +
34J ALA* 3.1 25.3 + - - +
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Residues in contact with PHE 31 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D ILE* 3.5 33.9 - - + -
214D LEU* 4.1 19.7 - - + -
45E VAL* 3.7 19.7 - - + -
46E ALA* 4.8 4.5 - - - -
49E TYR* 3.9 26.2 - + + -
27J GLY 2.9 17.6 + - - +
28J ALA 2.9 5.2 + - - +
30J LEU* 1.3 75.5 - - - +
32J GLU* 1.3 55.4 + - - +
34J ALA* 3.9 3.9 - - + +
35J PHE* 2.7 66.4 + + + +
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Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E TYR* 3.5 26.5 - - + -
52E LYS* 2.8 41.2 + - - +
53E ASN* 4.1 9.7 + - - +
2005E PEE 3.4 15.4 - - + +
28J ALA 2.8 11.5 + - - +
29J VAL* 3.6 8.3 - - - +
30J LEU 3.3 0.2 - - - -
31J PHE* 1.3 74.5 - - - +
33J ARG* 1.3 67.5 + - - +
34J ALA 3.1 0.2 + - - -
36J ASP* 2.8 46.5 + - - +
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Residues in contact with ARG 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J VAL* 3.3 33.2 + - - +
30J LEU* 3.7 30.7 - - - +
32J GLU* 1.3 80.7 + - - +
34J ALA* 1.3 66.3 + - - +
36J ASP* 4.0 3.9 - - - +
37J GLN* 3.3 42.5 + - - +
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Residues in contact with ALA 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J LEU 3.1 15.1 + - - +
31J PHE* 3.9 4.7 - - + +
33J ARG* 1.3 77.4 - - - +
35J PHE* 1.3 67.0 + - - +
36J ASP 3.2 0.3 + - - -
37J GLN* 3.2 8.8 + - - +
38J GLY* 3.0 21.3 + - - -
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Residues in contact with PHE 35 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LYS* 3.7 41.1 - - + -
210D LEU* 3.7 31.4 - - + -
211D ILE* 3.7 18.2 - - + -
214D LEU* 6.4 0.4 - - + -
49E TYR* 3.3 35.4 - + - -
31J PHE* 2.7 51.9 + + + +
32J GLU* 3.8 2.5 - - - +
34J ALA* 1.3 73.7 - - - +
36J ASP* 1.3 62.6 + - - +
38J GLY* 3.9 0.8 - - - +
39J ALA* 3.0 24.7 + - + +
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Residues in contact with ASP 36 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LYS* 3.1 19.5 + - - +
2009D BOG 5.8 0.5 - - - -
49E TYR* 2.8 26.0 + - - -
53E ASN* 5.6 1.0 - - - +
32J GLU* 2.8 46.2 + - - +
33J ARG* 4.0 4.3 - - - +
35J PHE* 1.3 73.3 - - - +
37J GLN* 1.3 64.1 + - + +
39J ALA* 3.0 2.6 + - - +
40J ASP* 2.8 38.3 + - - +
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Residues in contact with GLN 37 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ARG* 3.3 34.5 + - - +
34J ALA* 3.2 9.3 + - - +
36J ASP* 1.3 78.0 - - + +
38J GLY* 1.3 63.2 + - - +
40J ASP* 3.6 5.4 + - - +
41J ALA* 2.9 25.2 + - - +
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Residues in contact with GLY 38 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J ALA 3.0 14.5 + - - -
35J PHE* 3.9 1.6 - - - -
37J GLN* 1.3 78.0 - - - +
39J ALA* 1.3 54.3 + - - +
41J ALA* 3.1 8.6 + - - +
42J ILE* 2.8 39.1 + - - +
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Residues in contact with ALA 39 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ARG* 5.9 1.3 - - + -
206D LEU* 3.7 13.1 - - + +
207D LYS* 3.8 32.1 - - + -
210D LEU* 5.1 4.0 - - + -
35J PHE* 3.0 27.0 + - + +
36J ASP 3.6 2.9 - - - +
38J GLY* 1.3 73.9 - - - +
40J ASP* 1.3 66.8 + - - +
42J ILE* 3.0 14.4 + - - +
43J PHE* 2.9 23.3 + - - +
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Residues in contact with ASP 40 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ARG* 2.7 41.9 + - - +
207D LYS* 4.0 14.3 + - - +
2009D BOG 4.2 2.8 + - - -
2091D BOG 4.8 1.0 + - - -
36J ASP* 2.8 35.5 + - - +
37J GLN* 3.9 5.6 - - - +
39J ALA* 1.3 73.0 - - - +
41J ALA* 1.3 63.8 + - - +
43J PHE* 3.2 3.1 + - - +
44J GLU* 2.9 36.7 + - - +
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Residues in contact with ALA 41 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J GLN 2.9 16.3 + - - +
38J GLY* 3.2 11.9 - - - +
40J ASP* 1.3 76.3 - - - +
42J ILE* 1.3 62.9 + - + +
44J GLU* 3.9 4.9 - - - +
45J HIS* 3.0 26.4 + - - +
----------------------------------------------------------
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Residues in contact with ILE 42 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D LEU* 4.2 14.8 - - + -
210D LEU* 4.7 16.8 - - + -
38J GLY 2.8 25.9 + - - +
39J ALA* 3.5 9.2 - - - +
41J ALA* 1.3 76.0 - - + +
43J PHE* 1.3 63.8 + - - +
45J HIS* 4.0 4.6 + - - +
46J LEU* 3.0 49.5 + - + +
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Residues in contact with PHE 43 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 3.2 30.5 - - + -
20D ALA* 4.0 18.6 - - + -
199D ASP* 3.8 19.1 - - + -
202D LYS* 4.1 8.5 - - + -
203D ARG* 3.0 68.0 - - + -
206D LEU* 4.2 13.4 - - + +
39J ALA 2.9 12.7 + - - +
40J ASP 3.6 7.9 - - - +
42J ILE* 1.3 78.6 - - - +
44J GLU* 1.3 64.3 + - - +
46J LEU* 3.4 5.7 + - + +
47J ASN* 3.1 42.2 + - - -
51J LEU* 4.7 9.9 - - + -
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Residues in contact with GLU 44 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ARG* 3.6 22.4 + - - +
40J ASP* 2.9 27.5 + - - +
41J ALA* 4.1 4.3 - - - +
43J PHE* 1.3 72.2 - - - +
45J HIS* 1.3 68.6 + - - +
47J ASN 2.9 20.2 + - - +
48J GLU* 3.2 7.9 + - - +
51J LEU* 4.2 16.8 - - + -
53J LYS* 3.2 46.0 + - - +
54J HIS* 4.0 15.1 + - - +
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Residues in contact with HIS 45 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J ALA 3.0 18.0 + - - +
42J ILE* 4.0 4.7 + - - +
44J GLU* 1.3 77.4 - - - +
46J LEU* 1.3 72.0 + - + +
47J ASN 2.8 5.5 + - - -
48J GLU* 3.3 31.7 + - + +
----------------------------------------------------------
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Residues in contact with LEU 46 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 4.3 32.3 - - + +
19D SER* 5.6 2.0 - - - -
206D LEU* 5.4 1.3 - - + -
42J ILE* 3.0 41.2 + - + +
43J PHE* 3.6 8.7 - - + +
45J HIS* 1.3 87.7 - - + +
47J ASN* 1.3 68.3 + - - +
48J GLU 3.8 0.4 + - - -
50J LYS* 5.3 1.4 + - - +
----------------------------------------------------------
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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