Contacts of the helix formed by residues 34 - 57 (chain B) in PDB entry 4J00
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 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A HIS 4.5 0.4 - - - -
69A HIS* 4.3 14.7 + - + +
32B GLY 3.5 2.2 + - - -
33B HIS* 1.3 73.5 - - - +
35B HIS* 1.3 64.6 + - - +
36B GLY* 3.0 10.3 + - - +
37B ALA* 3.3 34.3 + - - +
38B PHE* 3.2 17.7 + - - +
40B ASP* 5.3 2.4 + - - -
95B LEU* 3.1 27.3 - - - +
99B GLU* 5.7 2.2 + - - -
102B TYR* 3.1 32.9 + - + +
163B HIS* 6.1 1.2 - - - -
176B MET* 5.0 17.6 - - - +
182B LEU* 5.4 6.5 - - + -
185B HIS* 3.6 23.8 - - + +
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Residues in contact with HIS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 3.5 20.3 - - + +
50A ILE* 4.0 11.3 - - + +
68A HIS* 3.1 26.5 + - + +
69A HIS 4.9 1.2 + - - +
70A LEU* 3.5 19.3 - - + +
28B MET* 3.4 37.0 - - - -
33B HIS 3.4 2.0 + - - -
34B ARG* 1.3 71.3 - - - +
36B GLY* 1.3 63.8 + - - +
38B PHE* 3.6 2.8 - - - +
39B LEU* 3.0 59.2 + - + +
15C A 4.1 16.7 - - - -
16C C 4.9 4.9 + - - -
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A HIS 4.9 0.4 + - - -
69A HIS* 5.2 4.6 + - - -
34B ARG* 3.0 8.7 - - - +
35B HIS* 1.3 82.3 + - - +
37B ALA* 1.3 54.7 + - - +
39B LEU* 3.1 7.5 + - - +
40B ASP* 2.7 39.2 + - - +
15C A 5.3 0.2 - - - -
16C C 3.8 28.5 + - - -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 3.3 26.7 + - - +
36B GLY* 1.3 71.3 - - - +
38B PHE* 1.3 59.2 + - - +
40B ASP* 3.6 15.5 - - + +
41B ALA* 2.8 26.9 + - - +
93B LYS 5.2 5.0 - - - +
94B MET* 5.6 0.6 - - - -
95B LEU* 3.2 46.2 + - + +
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Residues in contact with PHE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 5.1 13.9 - - + +
42A ALA* 4.1 19.1 - - + -
45A ALA* 5.0 1.1 - - + -
46A ALA* 3.9 18.2 - - + -
20B MET* 5.6 2.5 - - - -
23B LEU* 5.3 4.7 - - + -
24B ALA* 3.8 35.0 - - + -
27B ALA* 5.0 14.4 - - + -
28B MET* 3.8 25.4 - - + -
33B HIS* 5.4 3.6 - - + +
34B ARG 3.2 12.2 + - - +
35B HIS* 3.6 11.2 - - - +
36B GLY 3.1 0.6 - - - -
37B ALA* 1.3 74.7 - - - +
39B LEU* 1.3 89.8 + - + +
41B ALA* 3.1 17.2 + - + +
42B ALA* 3.2 10.6 + - + +
95B LEU* 4.7 4.4 - - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 4.8 2.0 - - + +
43A ALA* 4.4 22.2 - - + +
46A ALA* 4.2 5.8 - - + -
35B HIS* 3.0 47.1 + - + +
36B GLY* 3.3 9.4 - - - +
38B PHE* 1.3 96.6 - - + +
40B ASP* 1.3 64.5 + - - +
42B ALA* 3.2 17.8 + - + +
43B ALA* 3.3 10.6 + - - +
15C A 3.5 21.1 - - - +
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ARG* 5.3 2.6 + - - -
36B GLY* 2.7 30.9 + - - +
37B ALA* 3.6 15.2 - - + +
39B LEU* 1.3 80.9 - - - +
41B ALA* 1.3 59.9 + - - +
43B ALA* 3.0 21.8 + - - +
44B THR* 3.2 14.4 - - - +
93B LYS* 3.7 43.4 + - + +
16C C 4.6 7.1 + - - -
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASP* 4.6 14.8 - - - +
20A MET* 4.7 11.7 - - + +
37B ALA 2.8 15.2 + - - +
38B PHE* 3.1 15.9 + - + +
40B ASP* 1.3 77.0 - - - +
42B ALA* 1.3 61.4 + - - +
44B THR* 3.3 12.3 - - - +
45B ALA* 3.1 25.0 + - - +
93B LYS 4.9 0.6 + - - -
94B MET* 4.7 10.9 - - + +
95B LEU* 5.7 3.4 - - + -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 3.7 23.7 - - + +
38A PHE* 3.3 25.6 - - + -
39A LEU* 4.4 6.5 - - + +
42A ALA* 3.6 31.0 - - + -
38B PHE* 3.2 8.2 + - + +
39B LEU* 3.2 13.3 + - - +
41B ALA* 1.3 77.6 - - - +
43B ALA* 1.3 63.0 + - - +
45B ALA* 3.8 2.0 - - - +
46B ALA* 3.6 5.2 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.1 13.7 - - + -
39B LEU 3.3 6.4 + - - +
40B ASP* 3.0 16.2 + - - +
42B ALA* 1.3 75.8 - - - +
44B THR* 1.3 59.0 + - - +
45B ALA 3.1 4.3 - - - -
46B ALA* 3.1 20.9 + - - +
47B LYS* 3.1 29.2 + - + +
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.7 0.2 - - - +
40B ASP 3.2 17.3 - - - +
41B ALA* 3.3 16.4 - - - +
43B ALA* 1.3 72.7 - - - +
45B ALA* 1.3 60.5 + - - +
47B LYS* 3.6 18.8 - - - +
48B CYS* 3.1 32.7 + - - -
92B LEU* 4.0 27.2 - - + +
93B LYS* 4.3 11.0 - - + +
94B MET* 4.3 22.2 - - - +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A MET* 4.1 23.8 - - + -
21A LEU* 3.5 25.5 - - + +
24A ALA* 3.3 30.4 - - + +
25A PHE* 4.5 1.2 - - - -
38A PHE* 4.6 0.9 - - + -
41B ALA 3.1 17.4 + - - +
42B ALA 3.8 7.0 - - - +
43B ALA 3.1 0.4 - - - -
44B THR* 1.3 80.3 - - - +
46B ALA* 1.3 60.0 + - - +
48B CYS* 3.7 5.9 + - - +
49B ALA* 3.9 3.3 + - - +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 4.5 3.6 - - - -
28A MET* 3.7 28.4 - - + +
35A HIS* 5.6 2.0 - - + -
38A PHE* 3.8 20.2 - - + -
39A LEU* 4.4 8.5 - - + -
42B ALA 3.6 3.0 + - - +
43B ALA 3.1 9.0 + - - +
45B ALA* 1.3 78.5 - - - +
47B LYS* 1.3 60.2 + - + +
48B CYS 3.2 0.9 - - - -
49B ALA* 3.1 20.6 + - - +
50B ILE* 3.2 18.7 + - + +
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Residues in contact with LYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA* 3.1 18.8 + - + +
44B THR* 3.6 30.0 + - - +
45B ALA 3.4 0.4 - - - -
46B ALA* 1.3 76.4 - - + +
48B CYS* 1.3 60.4 + - - +
49B ALA 3.3 0.2 - - - -
50B ILE* 3.4 12.6 + - + +
51B TYR* 3.1 25.6 + - - +
74B ARG* 5.2 8.5 - - - +
78B ILE* 3.6 39.4 - - + +
81B GLU* 3.5 31.3 + - - -
82B VAL* 4.6 4.4 - - + +
92B LEU* 5.3 4.1 - - - +
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Residues in contact with CYS 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 5.3 6.1 - - + -
11A LEU* 4.6 21.5 - - - -
21A LEU* 3.7 29.8 - - + -
25A PHE* 4.2 8.3 - - + -
44B THR* 3.1 26.2 + - - -
45B ALA 3.8 0.7 - - - +
46B ALA 3.2 0.4 - - - -
47B LYS* 1.3 76.8 - - - +
49B ALA* 1.3 59.7 + - - +
51B TYR* 3.4 6.7 + - - +
52B MET* 2.9 33.9 + - - +
82B VAL* 5.5 7.2 - - - -
92B LEU* 6.2 2.9 - - - -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA 4.6 6.7 - - - +
25A PHE* 4.1 15.0 - - + -
28A MET* 4.5 14.4 - - - -
29A ARG* 3.7 24.0 - - + -
45B ALA 3.9 3.0 + - - +
46B ALA* 3.1 14.1 + - - +
48B CYS* 1.3 77.6 - - - +
50B ILE* 1.3 56.5 - - - +
52B MET* 3.3 8.0 + - - +
53B THR* 2.7 38.6 + - - -
68B HIS* 4.6 0.9 - - + -
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Residues in contact with ILE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A MET* 4.1 7.9 - - - -
35A HIS* 5.2 4.9 - - + +
46B ALA* 3.2 18.6 + - + +
47B LYS* 3.5 16.6 - - + +
49B ALA* 1.3 77.2 - - - +
51B TYR* 1.3 51.2 + - - +
53B THR* 3.3 6.7 + - - -
54B TYR* 2.8 32.5 + - + +
64B THR* 3.6 15.2 - - + +
68B HIS* 3.5 37.5 - - + +
70B LEU* 4.4 22.0 - - + -
75B VAL* 4.2 14.4 - - + -
78B ILE* 4.2 17.0 - - + -
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Residues in contact with TYR 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 6.2 4.7 - - + -
47B LYS 3.1 13.6 + - - +
48B CYS* 3.8 6.1 - - - +
50B ILE* 1.3 79.0 - - - +
52B MET* 1.3 65.8 + - + +
54B TYR* 3.4 10.3 - + - +
55B LEU* 3.1 62.2 + - + +
78B ILE* 4.6 3.3 - - + +
79B VAL* 3.9 33.2 - - + -
82B VAL* 3.5 49.7 - - + -
83B ARG* 5.0 7.1 + - + +
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Residues in contact with MET 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASN* 5.5 5.2 - - + +
4A ASP* 3.3 29.2 - - - +
7A LEU* 4.5 15.3 - - + -
25A PHE* 3.5 43.5 - - + -
29A ARG* 3.5 34.8 + - - +
48B CYS 2.9 17.2 + - - +
49B ALA* 3.6 5.8 - - - +
51B TYR* 1.3 76.6 - - + +
53B THR* 1.3 65.2 + - - +
55B LEU* 3.6 6.3 + - - +
56B GLU* 3.1 23.6 + - - +
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 3.3 21.3 + - - +
192A TYR* 6.1 0.4 - - + +
49B ALA 2.7 16.5 + - - -
50B ILE 3.5 4.7 - - - -
52B MET* 1.3 74.1 - - - +
54B TYR* 1.3 58.1 + - - +
56B GLU* 4.4 1.1 - - - -
57B GLN* 2.6 45.7 + - + +
64B THR* 3.9 12.6 - - + -
67B LEU* 3.8 24.5 - - + -
68B HIS* 2.5 41.1 + - + +
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE 2.8 17.9 + - - +
51B TYR* 3.3 13.4 + + - +
53B THR* 1.3 77.1 - - - +
55B LEU* 1.3 67.9 + - + +
57B GLN 4.0 0.9 - - - -
58B GLY 3.5 2.3 + - - -
59B GLN* 2.8 79.1 + - + +
60B ASN 4.2 0.8 + - - -
61B LEU* 3.6 30.0 - - + +
64B THR* 3.8 20.6 - - + +
75B VAL* 4.2 8.7 - - + -
79B VAL* 3.6 43.4 - - + +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.1 49.8 + - + +
52B MET* 4.0 6.3 - - - +
54B TYR* 1.3 85.4 - - + +
56B GLU* 1.3 66.9 + - - +
57B GLN 3.3 0.2 - - - -
58B GLY* 3.2 11.1 + - - -
59B GLN* 3.4 28.6 - - - +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 4.2 19.1 + - - +
192A TYR* 3.8 16.7 + - - +
52B MET 3.1 19.0 + - - +
53B THR 3.8 2.2 - - - +
55B LEU* 1.3 73.4 - - - +
57B GLN* 1.3 85.4 + - - +
58B GLY* 3.0 8.1 + - - -
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Residues in contact with GLN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A TYR* 3.9 12.3 - - - -
53B THR* 2.6 24.3 + - + +
54B TYR 4.0 0.7 - - - +
56B GLU* 1.3 94.5 + - - +
58B GLY* 1.3 61.2 + - - +
59B GLN 3.6 1.1 - - - -
60B ASN* 3.2 22.4 + - + -
63B MET* 3.5 51.5 - - + +
64B THR* 4.2 13.0 - - - +
67B LEU* 3.6 24.7 - - + +
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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