Contacts of the helix formed by residues 27 - 56 (chain B) in PDB entry 5XBY
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 ASP 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PRO* 4.2 3.9 - - - +
26B PRO* 1.3 81.8 - - + +
28B LEU* 1.3 61.9 + - - +
29B VAL* 2.9 24.0 + - - +
30B GLU* 3.3 23.5 + - + +
31B PHE* 3.1 23.7 + - - +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 4.6 10.3 - - + -
7A PRO 3.6 14.6 - - - +
8A GLY* 3.8 5.8 - - - +
9A LEU* 3.6 37.5 - - + +
12A LEU* 3.7 15.9 - - + +
16B TYR* 2.8 25.4 + - - +
20B VAL* 3.9 30.7 - - + -
25B PRO* 4.5 13.9 - - + +
26B PRO 4.1 1.3 - - - +
27B ASP* 1.3 73.4 + - - +
29B VAL* 1.3 59.4 + - + +
31B PHE* 3.6 3.0 + - - +
32B ALA* 3.0 18.2 + - - +
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Residues in contact with VAL 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.7 27.1 - - + -
36A PHE* 3.8 15.0 - - + +
39A LEU* 4.3 14.1 - - + +
40A ARG* 3.8 35.4 - - + +
27B ASP* 2.9 11.4 + - - +
28B LEU* 1.3 73.6 - - + +
30B GLU* 1.3 67.5 + - - +
32B ALA* 3.1 7.7 + - - +
33B VAL* 3.0 22.3 + - - +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.0 46.2 + - + +
27B ASP* 3.3 26.7 + - + +
29B VAL* 1.3 79.8 - - - +
31B PHE* 1.3 62.2 + - - +
33B VAL* 3.3 6.1 + - - +
34B GLU* 3.0 50.8 + - - +
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Residues in contact with PHE 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.7 18.6 - + - -
19B GLU* 4.1 24.0 - - + -
20B VAL* 4.4 3.8 - - + -
23B GLN* 3.7 45.8 - - + -
25B PRO* 3.6 32.5 - - + -
27B ASP 3.1 18.1 + - - +
28B LEU 3.9 3.4 - - - +
30B GLU* 1.3 73.9 - - - +
32B ALA* 1.3 56.7 + - - +
34B GLU* 3.2 18.0 + - + +
35B TYR* 2.6 48.3 + + + +
38B ARG* 4.6 14.1 - - - -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 5.1 0.4 - - + -
32A ALA 6.0 0.2 - - - -
36A PHE* 3.7 35.7 - - + -
16B TYR* 3.7 22.8 - - + +
28B LEU 3.0 15.6 + - - +
29B VAL 3.1 8.7 + - - +
31B PHE* 1.3 73.0 - - - +
33B VAL* 1.3 67.7 + - - +
35B TYR 3.1 0.6 + - - +
36B PHE* 2.9 34.3 + - + +
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Residues in contact with VAL 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 5.2 6.6 - - + +
36A PHE* 3.7 32.5 - - - +
37A THR* 3.7 18.4 - - - +
40A ARG* 3.4 41.5 - - - +
29B VAL 3.0 13.9 + - - +
30B GLU* 3.6 7.6 - - - +
32B ALA* 1.3 76.4 - - - +
34B GLU* 1.3 61.3 + - + +
36B PHE* 4.6 1.0 - - - +
37B THR* 2.6 38.3 + - - +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B GLU* 3.0 43.8 + - - +
31B PHE* 3.3 23.3 - - + +
33B VAL* 1.3 78.6 - - + +
35B TYR* 1.3 63.3 + - - +
37B THR* 3.7 3.7 - - - -
38B ARG* 3.1 60.0 + - - +
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.5 3.7 + - - -
15B GLY* 3.5 8.3 - - - -
16B TYR* 3.5 51.5 + + + -
19B GLU* 3.6 33.6 - - + +
31B PHE* 2.6 32.8 + + + +
32B ALA 3.9 2.0 - - - +
34B GLU* 1.3 73.0 - - - +
36B PHE* 1.3 75.9 + + - +
38B ARG* 3.3 10.0 + - - +
39B LEU* 2.7 58.5 + - + +
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Residues in contact with PHE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LEU* 5.9 0.4 - - + -
16A TYR* 5.6 1.1 - + - -
29A VAL* 3.9 10.6 - - + +
32A ALA* 3.5 24.2 - - + -
33A VAL* 3.5 20.9 - - + +
36A PHE* 3.6 29.6 - + - -
12B LEU* 3.6 35.9 - - + -
13B LEU* 5.4 5.2 - - + -
16B TYR* 4.1 22.9 - + + -
32B ALA* 2.9 24.6 + - + +
33B VAL 4.6 0.2 - - - +
35B TYR* 1.3 101.0 - + - +
37B THR* 1.3 57.9 + - - +
39B LEU* 3.9 11.3 - - + +
40B ARG* 2.7 34.1 + - - +
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Residues in contact with THR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.7 22.6 - - - +
33B VAL* 2.6 31.3 + - - +
34B GLU* 3.7 5.2 - - - -
36B PHE* 1.3 75.2 - - - +
38B ARG* 1.3 58.9 + - + +
40B ARG* 3.0 16.9 + - - +
41B GLU* 2.8 51.8 + - + +
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 5.4 4.2 + - - +
31B PHE* 4.6 14.3 - - - -
34B GLU* 3.1 49.5 + - - +
35B TYR* 3.7 6.4 - - - +
37B THR* 1.3 76.7 - - + +
39B LEU* 1.3 61.6 + - - +
41B GLU* 3.9 18.1 - - - +
42B ALA* 2.9 29.8 + - - +
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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
----------------------------------------------------------
29A VAL* 4.3 14.6 - - + -
12B LEU* 4.9 5.8 - - + -
35B TYR* 2.7 52.8 + - + +
36B PHE* 3.9 16.6 - - + +
38B ARG* 1.3 73.8 - - - +
40B ARG* 1.3 66.8 + - - +
42B ALA* 3.6 7.8 + - + +
43B ARG* 3.4 40.7 + - + +
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.9 17.1 - - + +
30A GLU* 2.7 62.1 + - + +
33A VAL* 3.9 31.6 - - + +
36B PHE 2.7 22.3 + - - +
37B THR* 3.0 16.3 + - - +
39B LEU* 1.3 71.9 - - - +
41B GLU* 1.3 58.8 + - - +
43B ARG* 2.7 28.2 + - + +
44B ASN* 3.0 28.9 + - - +
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B THR* 2.8 42.0 + - + +
38B ARG* 3.9 17.8 - - - +
40B ARG* 1.3 74.7 - - + +
42B ALA* 1.3 58.7 + - - +
44B ASN* 3.1 8.5 + - - +
45B LYS* 2.8 40.9 + - + +
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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
----------------------------------------------------------
38B ARG 2.9 18.8 + - - +
39B LEU* 3.7 13.5 - - + +
41B GLU* 1.3 75.7 - - - +
43B ARG* 1.3 58.9 + - + +
45B LYS* 3.6 7.5 - - - +
46B GLU* 2.8 44.5 + - - +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ASP* 5.6 7.6 + - - -
29A VAL* 3.2 36.6 - - - +
12B LEU* 4.9 3.4 - - - +
39B LEU* 3.4 31.7 + - + +
40B ARG* 2.7 10.0 + - + +
42B ALA* 1.3 80.1 - - + +
44B ASN* 1.3 68.0 + - - +
46B GLU* 3.7 11.2 - - - +
47B GLN* 2.9 35.0 + - - +
77B SER* 5.4 14.5 - - - +
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Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 3.0 35.1 + - - +
41B GLU* 3.1 8.5 + - - +
43B ARG* 1.3 76.6 - - - +
45B LYS* 1.3 64.9 + - - +
47B GLN* 3.0 13.1 + - - +
48B GLN* 2.9 38.7 + - + +
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 2.8 24.3 + - + +
42B ALA* 3.6 7.4 - - - +
44B ASN* 1.3 77.5 - - - +
46B GLU* 1.3 62.9 + - + +
47B GLN 3.1 0.3 + - - -
48B GLN* 3.4 20.7 + - - +
49B ASN* 3.0 29.2 + - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 2.8 35.5 + - - +
43B ARG* 3.9 10.9 - - - +
45B LYS* 1.3 74.7 - - + +
47B GLN* 1.3 60.7 + - - +
49B ASN* 4.0 6.3 + - - +
50B ALA* 3.7 16.3 + - - +
79B SER* 4.7 8.0 + - - +
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ARG* 2.9 27.1 + - - +
44B ASN* 3.6 11.7 - - - +
46B GLU* 1.3 73.5 - - - +
48B GLN* 1.3 72.2 + - + +
50B ALA* 3.1 11.4 + - - +
51B PHE* 3.4 9.4 + - - +
72B LEU* 4.4 9.6 + - + +
76B PRO* 1.7 74.5 - - + +
79B SER* 3.6 21.5 - - - +
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASN* 2.9 34.0 + - + +
45B LYS* 3.8 13.1 - - - +
47B GLN* 1.3 79.3 - - - +
49B ASN* 1.3 64.1 + - - +
51B PHE* 3.0 22.6 + - - +
52B TYR* 3.6 20.0 + - + -
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Residues in contact with ASN 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LYS* 3.0 34.5 + - - +
46B GLU* 4.1 7.0 - - - +
47B GLN 3.1 0.8 - - - -
48B GLN* 1.3 81.7 - - - +
50B ALA* 1.3 64.1 + - - +
52B TYR* 3.6 12.5 + - - +
53B GLU* 3.3 32.1 + - + +
83B LEU* 5.5 0.2 - - - -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU 3.7 10.0 + - - +
47B GLN 3.1 9.9 + - - +
49B ASN* 1.3 75.4 - - - +
51B PHE* 1.3 65.8 + - - +
53B GLU* 3.0 14.9 + - - +
54B ILE* 3.1 18.0 + - + +
72B LEU* 4.0 13.7 - - + -
79B SER* 4.4 19.5 - - - +
83B LEU* 4.1 28.9 - - + +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN 3.4 4.3 + - - +
48B GLN* 3.0 13.2 + - - +
50B ALA* 1.3 77.1 - - - +
52B TYR* 1.3 88.2 + + - +
54B ILE* 3.6 6.3 - - - +
55B LEU* 2.9 39.7 + - + +
69B ILE* 3.6 41.5 - - + +
72B LEU* 3.4 21.6 - - + +
73B LYS* 6.0 7.2 - - + -
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Residues in contact with TYR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLN* 3.6 22.9 + - + -
49B ASN* 4.0 11.4 - - - +
50B ALA 3.2 0.4 - - - -
51B PHE* 1.3 100.8 - + - +
53B GLU* 1.3 60.1 + - + +
55B LEU* 2.1 54.5 + - + +
56B HIS* 3.3 12.3 + - + +
----------------------------------------------------------
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ASN* 3.3 20.7 + - + +
50B ALA 3.0 7.8 + - - +
52B TYR* 1.3 83.0 - - + +
54B ILE* 1.3 59.3 + - - +
56B HIS* 3.2 29.0 + - + +
57B LEU* 3.2 22.1 + - + +
83B LEU* 3.8 26.4 - - + +
87B LYS* 3.2 27.5 + - - -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 3.1 14.1 + - + +
51B PHE 3.6 6.5 - - - +
52B TYR 2.7 1.8 + - - -
53B GLU* 1.3 77.4 - - - +
55B LEU* 1.3 62.9 + - - +
56B HIS 3.3 0.5 + - - -
57B LEU* 3.5 20.2 + - - +
60B LEU* 4.3 10.7 - - + +
65B ARG* 3.6 17.7 + - + +
68B PHE* 4.2 31.0 - - + +
69B ILE* 3.8 20.2 - - + -
72B LEU* 4.2 22.2 - - + -
82B LEU* 4.6 10.1 - - + +
83B LEU* 4.3 16.8 - - + +
86B ALA* 4.1 17.3 - - + -
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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 PHE* 2.9 28.3 + - + +
52B TYR* 2.1 53.1 + - + +
54B ILE* 1.3 68.8 - - - +
56B HIS* 1.3 57.4 + - + +
65B ARG* 3.1 29.7 + - - +
69B ILE* 4.2 19.5 - - + -
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Residues in contact with HIS 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 4.0 16.9 - - + +
53B GLU* 3.2 21.5 + - + +
55B LEU* 1.3 79.3 - - + +
57B LEU* 1.3 69.7 + - + +
58B PRO* 3.0 13.6 - - - +
65B ARG* 5.0 1.8 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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