Contacts of the helix formed by residues 27 - 57 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO* 4.6 18.2 - - + +
25D PRO* 3.3 4.1 - - - +
26D PRO* 1.3 81.9 - - + +
28D LEU* 1.3 58.5 + - - +
29D VAL* 2.9 24.0 + - - +
30D GLU* 3.0 26.9 + - + +
31D PHE* 2.9 31.1 + - - +
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PRO* 4.2 12.6 - - + -
7C PRO 3.9 13.0 - - - +
8C GLY* 4.0 4.7 - - - +
9C LEU* 3.8 33.7 - - + +
12C LEU* 3.8 11.0 - - + -
16D TYR* 2.8 30.2 + - - +
20D VAL* 3.8 31.6 - - + -
25D PRO* 4.9 9.6 - - + +
26D PRO 4.1 2.3 + - - +
27D ASP* 1.3 71.9 + - - +
29D VAL* 1.3 60.8 + - + +
31D PHE* 3.6 3.0 + - - -
32D ALA* 2.9 18.5 + - - +
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.9 26.7 - - + -
36C PHE* 4.1 7.0 - - + +
39C LEU* 4.4 8.7 - - + +
40C ARG* 3.8 38.6 - - + +
43C ARG* 4.0 24.7 - - + +
27D ASP* 2.9 10.3 + - - +
28D LEU* 1.3 74.1 - - + +
30D GLU* 1.3 68.0 + - - +
32D ALA* 3.1 17.2 + - - +
33D VAL* 3.1 14.7 + - - +
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 3.2 40.2 + - + +
27D ASP* 3.0 31.6 + - + +
29D VAL* 1.3 77.1 - - - +
31D PHE* 1.3 61.2 + - - +
33D VAL* 3.3 5.6 + - - +
34D GLU* 3.2 49.2 + - - +
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Residues in contact with PHE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D TYR* 3.7 16.6 - + - -
19D GLU* 3.9 25.6 - - + -
20D VAL* 3.8 19.5 - - + -
23D GLN* 3.6 41.1 - - + -
25D PRO* 3.5 30.3 - - + -
27D ASP 2.9 18.4 + - - +
28D LEU* 3.8 4.7 - - - +
30D GLU* 1.3 74.0 - - - +
32D ALA* 1.3 59.4 + - - +
34D GLU* 3.4 21.6 + - + +
35D TYR* 2.9 41.5 + + + +
38D ARG* 5.5 4.5 - - - -
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.9 0.2 - - + -
36C PHE* 3.8 35.0 - - + -
16D TYR* 3.7 22.0 - - + +
28D LEU 2.9 16.5 + - - +
29D VAL* 3.2 12.1 - - - +
31D PHE* 1.3 77.2 - - - +
33D VAL* 1.3 62.9 + - - +
35D TYR* 3.4 0.3 + - - -
36D PHE* 3.1 33.0 + - + -
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Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 5.0 4.2 - - + +
36C PHE* 3.5 37.5 - - + +
37C THR* 3.6 21.5 - - - +
40C ARG* 3.9 32.3 - - + +
29D VAL 3.1 13.1 + - - +
30D GLU* 3.3 8.3 + - - +
32D ALA* 1.3 74.8 - - - +
34D GLU* 1.3 61.5 + - + +
36D PHE* 4.6 1.5 - - - +
37D THR* 2.6 41.8 + - - +
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D GLU* 3.2 40.0 + - - +
31D PHE* 3.6 24.1 - - + +
33D VAL* 1.3 79.8 - - + +
35D TYR* 1.3 61.5 + - - +
37D THR* 3.8 3.9 - - - -
38D ARG* 3.1 54.6 + - - +
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Residues in contact with TYR 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU 4.7 2.3 + - - -
15D GLY* 3.7 16.3 + - - -
16D TYR* 4.0 30.7 - + + -
19D GLU* 3.4 36.5 - - + +
23D GLN* 6.2 0.2 - - - -
31D PHE* 2.9 31.5 + + + +
32D ALA 4.0 2.5 - - - +
34D GLU* 1.3 76.3 - - - +
36D PHE* 1.3 79.2 + + - +
38D ARG* 3.4 7.4 + - + +
39D LEU* 2.8 61.6 + - + +
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Residues in contact with PHE 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 5.4 0.4 - - + -
16C TYR* 5.5 0.2 - + - -
29C VAL* 3.7 5.5 - - + +
32C ALA* 3.7 21.1 - - + -
33C VAL* 3.5 20.0 - - + +
36C PHE* 3.6 31.6 - + - -
12D LEU* 3.5 42.0 - - + -
13D LEU* 5.1 4.9 - - + -
16D TYR* 4.1 29.2 - + + -
32D ALA* 3.1 26.3 + - + +
33D VAL* 4.6 0.9 - - - +
35D TYR* 1.3 90.5 - + - +
37D THR* 1.3 56.6 + - - +
39D LEU* 3.5 14.2 - - + +
40D ARG* 2.7 34.1 + - - +
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Residues in contact with THR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 3.7 22.2 - - - +
33D VAL* 2.6 31.3 + - - +
34D GLU* 3.8 4.5 - - - -
36D PHE* 1.3 76.9 - - - +
38D ARG* 1.3 59.5 + - + +
40D ARG* 3.1 23.1 + - - +
41D GLU* 2.9 45.3 + - - +
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Residues in contact with ARG 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLN* 5.4 9.7 + - - +
31D PHE* 5.5 4.2 - - - -
34D GLU* 3.1 46.1 + - - +
35D TYR* 3.7 6.8 - - + +
37D THR* 1.3 77.0 - - + +
39D LEU* 1.3 52.8 + - - +
41D GLU* 3.4 18.3 + - - +
42D ALA* 2.7 33.7 + - - +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 4.2 19.1 - - + -
12D LEU* 5.1 8.5 - - + +
35D TYR* 2.8 53.2 + - + +
36D PHE* 3.6 20.2 - - + +
38D ARG* 1.3 74.7 - - - +
40D ARG* 1.3 63.9 + - - +
42D ALA* 3.9 11.0 - - + -
43D ARG* 3.0 42.1 + - + +
46D GLU* 6.0 1.3 - - - +
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Residues in contact with ARG 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 6.0 1.6 - - - +
29C VAL* 3.7 17.6 - - + +
30C GLU* 2.7 45.4 + - + +
33C VAL* 3.5 34.4 - - + +
36D PHE 2.7 20.8 + - - +
37D THR* 3.1 23.9 + - - +
39D LEU* 1.3 74.1 - - - +
41D GLU* 1.3 65.6 + - + +
43D ARG* 3.5 7.4 - - - +
44D ASN* 3.3 26.4 + - - +
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D THR* 2.9 32.0 + - + +
38D ARG* 3.7 23.6 - - - +
40D ARG* 1.3 79.4 + - + +
42D ALA* 1.3 59.7 + - - +
44D ASN* 3.0 25.3 + - - +
45D LYS* 3.0 14.7 + - - +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ARG 2.7 21.8 + - - +
39D LEU* 3.2 17.7 + - + +
41D GLU* 1.3 71.5 - - - +
43D ARG* 1.3 58.5 + - + +
45D LYS* 3.3 8.7 + - - +
46D GLU* 2.7 49.5 + - - +
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Residues in contact with ARG 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ASP* 4.9 9.1 + - - -
28C LEU* 6.1 1.6 - - - +
29C VAL* 3.0 40.7 - - - +
12D LEU* 5.0 4.2 - - - +
39D LEU* 3.0 34.8 + - + +
40D ARG* 3.5 7.2 - - - +
42D ALA* 1.3 77.2 - - - +
44D ASN* 1.3 65.7 + - - +
46D GLU* 3.7 11.2 - - - +
47D GLN* 2.9 32.9 + - - +
76D PRO* 5.8 1.8 + - - +
77D SER* 4.1 32.3 + - - +
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Residues in contact with ASN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ARG* 3.3 21.0 + - - +
41D GLU* 3.0 16.7 + - - +
43D ARG* 1.3 77.8 - - - +
45D LYS* 1.3 66.5 + - - +
47D GLN* 3.0 11.4 + - - +
48D GLN* 2.9 37.7 + - + +
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Residues in contact with LYS 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLU 3.0 12.2 + - - +
42D ALA* 3.4 11.7 - - - +
44D ASN* 1.3 78.2 - - - +
46D GLU* 1.3 64.8 + - + +
48D GLN* 3.3 24.8 + - - +
49D ASN* 3.0 26.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LEU* 6.0 0.7 - - - +
42D ALA* 2.7 32.8 + - - +
43D ARG* 4.0 10.3 - - - +
44D ASN 3.3 0.2 - - - -
45D LYS* 1.3 74.9 - - + +
47D GLN* 1.3 59.8 + - - +
49D ASN* 4.0 7.8 + - - +
50D ALA* 3.7 16.3 + - - +
79D SER* 4.6 7.8 + - - +
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Residues in contact with GLN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D ARG* 2.9 25.9 + - - +
44D ASN* 3.0 11.2 + - - +
46D GLU* 1.3 73.5 - - - +
48D GLN* 1.3 72.4 + - - +
49D ASN 3.2 0.2 - - - -
50D ALA* 3.1 11.6 + - - +
51D PHE* 3.4 9.9 + - - +
72D LEU* 4.5 9.7 + - + +
76D PRO* 1.7 72.7 - - + +
79D SER* 3.6 22.2 - - - +
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Residues in contact with GLN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ASN* 2.9 30.1 + - + +
45D LYS* 3.8 20.8 - - - +
47D GLN* 1.3 78.0 - - - +
49D ASN* 1.3 64.1 + - - +
51D PHE* 3.0 21.5 + - - +
52D TYR* 3.6 20.9 + - + -
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Residues in contact with ASN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D LYS* 3.0 33.4 + - - +
46D GLU* 4.1 8.9 - - - +
47D GLN 3.2 0.8 - - - -
48D GLN* 1.3 78.9 - - - +
50D ALA* 1.3 63.4 + - - +
52D TYR* 3.6 11.0 + - - +
53D GLU* 3.3 26.4 + - + +
83D LEU* 5.5 0.7 - - - -
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Residues in contact with ALA 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D GLU 3.7 9.4 + - - +
47D GLN 3.1 9.6 + - - +
49D ASN* 1.3 76.9 - - - +
51D PHE* 1.3 65.6 - - - +
53D GLU* 3.0 14.9 + - - +
54D ILE* 3.1 17.0 + - + +
72D LEU* 4.0 13.7 - - + -
79D SER* 4.3 20.9 - - - +
83D LEU* 4.1 28.9 - - + -
----------------------------------------------------------
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Residues in contact with PHE 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLN 3.4 4.1 + - - +
48D GLN* 3.0 13.6 + - - +
50D ALA* 1.3 78.4 - - - +
52D TYR* 1.3 88.5 + + - +
54D ILE* 3.6 5.6 - - - +
55D LEU* 2.9 40.0 + - + +
69D ILE* 3.6 41.8 - - + +
72D LEU* 3.5 21.0 - - + +
73D LYS* 6.5 2.7 - - + -
----------------------------------------------------------
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Residues in contact with TYR 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D GLN* 3.6 24.5 + - + -
49D ASN* 4.0 8.5 - - - +
50D ALA 3.2 0.8 - - - -
51D PHE* 1.3 100.8 - + - +
53D GLU* 1.3 61.3 + - + +
55D LEU* 2.1 54.0 + - + -
56D HIS* 2.9 17.4 + + + -
----------------------------------------------------------
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ASN* 3.3 14.2 + - + +
50D ALA* 3.0 8.9 + - - +
52D TYR* 1.3 83.6 - - + +
54D ILE* 1.3 52.3 + - - +
56D HIS* 2.8 24.7 + - - +
57D LEU* 2.9 22.1 + - + +
83D LEU* 3.8 21.4 - - + +
87D LYS* 3.2 27.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ALA* 3.1 13.6 + - + +
51D PHE 3.6 6.3 - - - +
52D TYR 2.7 2.2 + - - -
53D GLU* 1.3 75.9 - - - +
55D LEU* 1.3 62.3 + - - +
56D HIS 3.2 0.5 + - - -
57D LEU* 3.5 20.3 + - + +
60D LEU* 4.3 10.9 - - + +
65D ARG* 3.7 17.2 + - + +
68D PHE* 4.2 26.2 - - + +
69D ILE* 3.9 20.6 - - + -
72D LEU* 4.2 21.8 - - + -
82D LEU* 4.4 19.7 - - + +
83D LEU* 4.3 18.4 - - + +
86D ALA* 4.1 12.8 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PHE* 2.9 27.6 + - + +
52D TYR* 2.1 51.5 + - + +
54D ILE* 1.3 68.0 - - - +
56D HIS* 1.3 68.3 + - + +
65D ARG* 3.4 31.3 + - - +
69D ILE* 4.2 19.5 - - + -
----------------------------------------------------------
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Residues in contact with HIS 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D TYR* 2.9 24.2 + + + +
53D GLU* 2.8 12.1 + - - +
55D LEU* 1.3 92.4 + - + +
57D LEU* 1.3 61.9 + - - +
58D PRO* 3.2 11.6 - - - +
65D ARG* 5.7 0.2 - - - -
----------------------------------------------------------
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Residues in contact with LEU 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLU* 2.9 16.2 + - + +
54D ILE* 3.5 21.9 + - + +
56D HIS* 1.3 73.8 - - - +
58D PRO* 1.3 73.9 - - + +
59D ASN 3.4 1.6 + - - -
60D LEU* 3.7 21.4 + - + +
65D ARG* 3.5 19.1 + - - -
83D LEU* 5.4 1.6 - - + -
86D ALA* 3.8 33.0 - - + +
87D LYS* 4.3 23.1 - - + -
90D ASN* 3.5 26.7 - - + +
----------------------------------------------------------
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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