Contacts of the helix formed by residues 25 - 53 (chain B) in PDB entry 1J38
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 ALA 25 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 1.3 74.8 - - - +
26B LYS* 1.3 58.2 + - - +
27B GLU* 2.9 11.2 - - - -
28B TYR* 3.0 4.8 + - - +
29B LEU* 2.9 31.5 + - - +
83B PHE* 3.8 20.0 - - + -
88B TYR* 3.6 19.4 - - + -
93B LEU* 4.6 5.5 - - + +
97B PHE* 3.5 28.9 - - + -
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 4.0 29.1 + - + +
25B ALA* 1.3 80.1 - - - +
27B GLU* 1.3 68.9 + - + +
29B LEU* 3.2 3.4 + - - +
30B GLU* 2.9 37.9 + - - +
93B LEU* 3.4 42.2 - - + +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A ASN* 5.0 8.1 - - - +
24B GLN* 3.4 38.0 - - + +
25B ALA* 2.9 26.2 - - - -
26B LYS* 1.3 81.5 - - + +
28B TYR* 1.3 64.6 + - - +
30B GLU* 3.5 4.9 + - - +
31B ASN* 3.2 32.6 + - - +
83B PHE* 5.4 3.0 - - - -
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Residues in contact with TYR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A ALA 5.5 0.7 - - - -
598A ILE* 3.7 23.8 - - + -
599A LYS* 3.7 31.6 - - + +
25B ALA 3.0 8.8 + - - +
27B GLU* 1.3 81.1 + - - +
29B LEU* 1.3 61.7 + - + +
31B ASN* 3.4 5.5 + - - +
32B LEU* 2.9 50.4 + - + +
76B VAL* 3.5 28.8 + - - +
79B ASP* 3.9 15.9 + - + +
80B THR* 4.5 4.6 - - + +
83B PHE* 3.5 42.2 - + + -
97B PHE* 3.8 25.4 - + - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ALA 2.9 16.2 + - - +
26B LYS* 3.8 3.4 - - - +
28B TYR* 1.3 79.7 - - + +
30B GLU* 1.3 61.6 + - - +
32B LEU* 3.6 12.3 - - + +
33B ASN* 2.8 38.8 + - - +
93B LEU* 3.5 44.0 - - + +
96B GLN* 3.6 35.4 - - + +
97B PHE* 3.5 40.6 - - + +
100B LEU* 5.4 4.9 - - + -
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LYS* 2.9 31.3 + - - +
27B GLU* 3.7 7.8 - - - +
28B TYR 3.3 0.2 - - - -
29B LEU* 1.3 79.8 - - - +
31B ASN* 1.3 67.1 + - - +
33B ASN* 3.5 4.7 + - - +
34B LYS* 3.2 43.8 + - + +
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Residues in contact with ASN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ILE* 4.4 19.0 - - + +
601A ASN* 2.5 45.2 + - - +
27B GLU* 3.2 18.8 + - - +
28B TYR* 3.8 4.8 - - - +
30B GLU* 1.3 81.5 - - - +
32B LEU* 1.3 64.0 + - - +
34B LYS* 3.3 21.5 + - - +
35B GLU* 3.1 20.6 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ILE* 4.3 15.9 - - + +
28B TYR* 2.9 50.7 + - + +
29B LEU* 3.6 13.5 - - + +
31B ASN* 1.3 74.0 - - - +
33B ASN* 1.3 58.9 + - - +
35B GLU* 2.7 24.5 + - + +
36B LEU* 2.7 31.5 + - + +
72B PHE* 4.5 6.3 - - + -
76B VAL* 3.8 36.1 - - + -
80B THR* 5.9 1.8 - - + -
97B PHE* 6.0 0.2 - - + -
100B LEU* 4.6 19.5 - - + -
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 2.8 28.3 + - - +
30B GLU* 4.0 3.7 - - - +
32B LEU* 1.3 73.8 - - - +
34B LYS* 1.3 53.3 + - + +
36B LEU* 3.1 11.7 + - - +
37B ALA* 2.7 37.3 + - - +
96B GLN* 3.4 21.7 - - - +
100B LEU* 4.6 4.1 - - - +
382B PRO* 3.8 8.9 - - + +
383B PHE* 3.3 29.6 - - + +
384B VAL* 2.9 37.6 - - - +
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Residues in contact with LYS 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 3.2 44.0 + - + +
31B ASN* 3.5 21.7 - - - +
32B LEU 3.1 0.6 - - - -
33B ASN* 1.3 79.9 - - + +
35B GLU* 1.3 56.7 + - - +
37B ALA* 3.9 5.8 - - - +
38B LYS* 3.1 49.3 + - - +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ILE* 3.1 36.5 - - + +
31B ASN 3.1 8.9 + - - +
32B LEU* 2.7 16.2 + - + +
34B LYS* 1.3 70.8 - - - +
36B LEU* 1.3 64.6 + - - +
38B LYS* 3.2 13.7 + - - +
39B ARG* 2.8 59.5 + - - +
72B PHE* 3.7 20.6 - - + -
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 2.7 37.9 + - + +
33B ASN* 3.5 13.9 - - - +
35B GLU* 1.3 71.0 - - - +
37B ALA* 1.3 52.6 + - - +
39B ARG* 3.0 5.8 + - - +
40B THR* 2.6 42.1 + - - +
69B LEU* 5.2 4.4 - - + +
72B PHE* 4.0 21.3 - - + -
73B MET* 3.8 30.1 - - + -
76B VAL* 5.5 1.3 - - + -
100B LEU* 3.5 32.5 - - + -
383B PHE* 3.6 24.5 - - + -
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN 2.7 20.8 + - - +
34B LYS* 3.9 6.5 - - - +
36B LEU* 1.3 73.4 - - - +
38B LYS* 1.3 64.0 + - - +
40B THR 4.0 0.2 - - - -
41B ASN* 3.1 23.4 + - - +
344B TYR* 4.0 23.4 - - + +
383B PHE* 3.8 27.1 - - + -
386B ARG* 4.6 5.6 - - - +
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 3.1 41.8 + - - +
35B GLU* 3.5 20.0 - - - +
37B ALA* 1.3 77.3 - - - +
39B ARG* 1.3 61.5 + - + +
41B ASN* 3.3 17.1 + - - +
42B VAL* 3.7 12.1 + - - +
345B LEU* 5.6 13.0 - - + +
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Residues in contact with ARG 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A GLU* 3.0 37.1 + - - +
35B GLU* 2.8 42.0 + - - +
36B LEU* 3.6 3.4 - - - +
38B LYS* 1.3 74.5 - - + +
40B THR* 1.3 65.9 + - - +
41B ASN 3.0 1.8 - - - -
42B VAL* 3.2 18.5 + - + +
43B GLU* 3.3 10.7 + - - +
65B ILE* 4.8 2.6 - - - +
68B GLU* 3.5 27.0 + - - +
69B LEU* 4.2 20.9 - - + +
72B PHE* 3.0 62.7 - - - +
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 2.6 24.5 + - - +
37B ALA 4.2 1.8 - - - -
39B ARG* 1.3 73.6 - - - +
41B ASN* 1.3 54.2 + - - +
43B GLU* 3.2 20.8 + - - +
44B THR* 2.7 46.4 + - - +
69B LEU* 4.3 11.8 - - + +
344B TYR* 4.1 19.1 - - + -
383B PHE* 3.5 27.7 - - + -
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA 3.1 13.0 + - - +
38B LYS* 3.3 14.5 + - - +
39B ARG 3.0 0.6 - - - -
40B THR* 1.3 78.0 - - - +
42B VAL* 1.3 69.3 + - - +
44B THR* 3.2 5.6 + - - -
45B GLU* 3.0 33.9 + - - +
343B PHE* 2.6 40.4 - - - +
344B TYR* 4.9 0.8 - - + +
345B LEU* 3.7 29.8 - - + +
348B ASP* 4.9 0.9 - - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS 3.8 14.4 - - - +
39B ARG* 3.2 10.0 + - + +
41B ASN* 1.3 84.4 - - - +
43B GLU* 1.3 61.0 + - - +
45B GLU* 3.5 7.5 + - - +
46B ALA* 3.5 17.7 + - - +
65B ILE* 3.9 27.9 - - + +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ARG 3.3 7.8 + - - +
40B THR* 3.2 19.9 + - - +
42B VAL* 1.3 76.3 - - - +
44B THR* 1.3 66.3 + - - +
46B ALA* 3.2 4.3 + - - +
47B ALA* 3.0 24.6 + - + +
62B LYS* 5.1 1.5 - - + +
65B ILE* 3.3 22.4 - - + +
66B SER* 2.8 37.7 + - - +
69B LEU* 3.2 26.2 - - + +
113B TYR* 5.0 1.7 + - - -
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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
----------------------------------------------------------
40B THR* 2.7 34.8 + - - +
41B ASN* 3.6 6.5 - - - -
43B GLU* 1.3 77.6 - - - +
45B GLU* 1.3 57.1 + - - +
47B ALA* 3.3 5.1 + - - -
48B TRP* 2.8 31.7 + - - +
341B TRP* 3.5 25.7 - - + -
342B ASP 3.6 21.1 + - - +
343B PHE* 3.5 24.7 - - + -
344B TYR* 4.0 4.3 - - - -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASN* 3.0 32.1 + - - +
42B VAL* 3.8 8.3 - - + +
43B GLU 3.3 0.4 - - - -
44B THR* 1.3 76.2 - - - +
46B ALA* 1.3 58.1 + - - +
48B TRP* 3.8 5.6 - - - +
49B ALA* 2.9 27.9 + - - +
322B LYS* 5.5 0.3 - - - -
343B PHE* 3.8 11.5 - - + -
348B ASP* 4.6 1.6 - - - +
350B ARG* 2.8 35.9 + - - -
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B VAL 3.5 3.4 + - - +
43B GLU 3.2 8.1 + - - +
45B GLU* 1.3 74.3 - - - +
47B ALA* 1.3 61.4 + - - +
48B TRP 3.1 1.3 - - - -
49B ALA* 3.7 6.0 - - - +
50B TYR* 2.8 32.7 + - - +
58B ASN* 4.8 2.0 - - - +
61B LYS* 4.5 10.5 - - + -
62B LYS* 3.6 30.7 - - - +
65B ILE* 4.0 20.4 - - + -
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Residues in contact with ALA 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 3.0 18.7 + - + +
44B THR* 3.6 2.7 - - - +
46B ALA* 1.3 77.6 - - - +
48B TRP* 1.3 58.4 + - - +
50B TYR* 3.7 0.2 - - - +
51B ARG* 2.8 65.5 + - - +
62B LYS* 4.2 14.7 - - + +
341B TRP* 3.4 15.5 - - + -
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Residues in contact with TRP 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B THR 2.8 17.3 + - - +
45B GLU* 3.8 10.8 - - - +
47B ALA* 1.3 76.4 - - - +
49B ALA* 1.3 71.4 + - + +
51B ARG* 3.4 1.4 + - - +
52B SER* 2.8 41.2 + - - -
322B LYS 3.3 26.0 - - - -
324B ILE* 3.8 22.0 - - + +
341B TRP* 3.4 50.4 - + + -
343B PHE* 3.9 17.5 - + + -
350B ARG* 3.7 34.8 - - + +
351B ILE 3.9 13.5 - - - -
352B LYS* 3.9 19.3 - - + -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU 2.9 20.0 + - - +
46B ALA* 3.1 6.9 + - - +
48B TRP* 1.3 82.6 - - + +
50B TYR* 1.3 62.1 + - - +
52B SER* 3.4 4.3 + - - -
53B ALA* 3.1 23.0 + - - +
58B ASN* 3.8 18.3 + - + +
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Residues in contact with TYR 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ALA 2.8 17.3 + - - +
47B ALA 3.7 2.7 - - - +
49B ALA* 1.3 73.9 - - - +
51B ARG* 1.3 67.0 + - + +
52B SER 3.0 4.8 + - - -
53B ALA 2.8 30.6 - - - +
54B ILE* 3.0 53.4 + - + +
55B THR 3.7 12.6 - - - -
58B ASN* 3.9 10.5 - - + +
59B GLU* 3.8 32.3 + - + -
62B LYS* 3.2 32.1 - - + -
121B SER* 5.0 1.9 + - - -
124B GLU* 3.2 22.9 - - + -
125B SER* 3.4 23.7 + - - -
335B VAL* 5.1 2.0 - - + -
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 2.8 37.8 + - - +
48B TRP 3.4 1.5 + - - +
50B TYR* 1.3 90.7 - - + +
52B SER* 1.3 55.5 + - - +
62B LYS* 4.2 18.5 - - - +
124B GLU* 4.5 15.2 + - - +
334B LEU* 3.6 0.7 - - - +
335B VAL* 2.9 44.5 + - + +
341B TRP* 3.3 30.0 - - + -
352B LYS* 3.1 32.1 + - - +
496B TYR* 5.6 5.4 + - - -
----------------------------------------------------------
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TRP* 2.8 31.2 + - - -
49B ALA* 3.8 6.1 - - - -
50B TYR 3.0 0.6 - - - -
51B ARG* 1.3 78.3 - - - +
53B ALA* 1.3 60.5 + - - +
324B ILE* 3.6 21.9 - - - +
332B ARG* 3.0 28.8 + - - +
334B LEU* 3.3 15.3 - - - +
352B LYS* 3.5 18.9 - - - +
----------------------------------------------------------
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.1 8.9 + - - +
50B TYR* 2.8 12.4 + - - +
52B SER* 1.3 79.2 - - - +
54B ILE* 1.3 60.7 + - - +
55B THR* 3.2 9.9 + - + -
58B ASN* 3.0 29.2 + - - +
332B ARG* 4.2 20.6 - - + +
333B ASP 3.5 4.7 - - - -
----------------------------------------------------------
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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