Contacts of the helix formed by residues 21 - 51 (chain A) in PDB entry 2B6U
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 ILE 21 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 3.0 31.4 + - + +
20A ARG* 1.4 77.6 - - - +
22A VAL* 1.3 67.4 + - + +
23A GLN 3.3 0.2 - - - -
24A LEU* 3.0 11.4 + - + +
25A VAL* 2.8 44.5 + - + +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 3.2 26.5 - - - +
18A ASP* 5.5 4.5 - - - +
19A THR* 3.6 15.0 + - + +
21A ILE* 1.3 88.6 - - + +
23A GLN* 1.4 58.0 + - - +
24A LEU 3.1 4.5 - - - -
25A VAL* 3.1 20.0 + - + -
26A PHE* 3.2 36.1 + - + +
276A ILE* 5.8 5.8 - - + -
279A GLU* 3.3 19.7 - - - +
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A CYS 4.2 11.8 + - - +
17A ARG* 3.2 37.9 - - - +
19A THR 4.3 1.1 + - - +
20A ARG* 4.1 27.9 - - + +
22A VAL* 1.4 79.0 - - - +
24A LEU* 1.4 51.4 + - - +
27A PRO* 2.7 18.8 - - - +
83A SER* 2.7 51.1 + - - +
84A HIS* 4.5 3.0 - - - +
86A ALA* 3.9 25.5 - - + +
169A SER* 3.5 24.2 + - - -
171A LYS* 4.6 2.3 - - - +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ARG 3.8 13.8 + - - +
21A ILE* 3.0 18.8 + - + +
23A GLN* 1.4 77.5 - - - +
25A VAL* 1.4 64.0 + - + +
26A PHE 3.3 0.2 - - - -
27A PRO* 3.4 8.2 - - + +
28A ALA* 3.2 23.1 + - + +
84A HIS* 4.7 25.8 - - + +
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Residues in contact with VAL 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ILE* 2.8 30.1 + - + +
22A VAL* 3.1 10.9 + - + +
24A LEU* 1.4 78.9 - - + +
26A PHE* 1.3 86.2 + - + +
28A ALA* 3.1 8.1 + - + +
29A LEU* 2.8 27.8 + - + +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 5.6 0.2 - - - -
22A VAL* 3.2 37.9 + - + +
25A VAL* 1.3 95.0 - - + +
27A PRO* 1.4 65.3 - - + +
28A ALA 3.3 0.2 - - - -
29A LEU* 3.8 31.4 - - + -
30A TYR* 2.8 34.5 + + + +
83A SER* 4.0 8.1 - - - +
171A LYS* 4.2 3.8 - - - +
279A GLU* 3.6 21.5 - - - -
280A THR* 6.1 3.1 - - + -
283A PHE* 3.2 48.2 - + + -
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Residues in contact with PRO 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN 2.7 30.1 - - - +
24A LEU* 3.4 13.2 - - + +
26A PHE* 1.4 84.3 - - - +
28A ALA* 1.4 59.7 + - - +
30A TYR* 4.7 0.4 - - + -
31A THR* 2.8 36.0 + - - -
80A LEU* 3.2 22.1 - - + +
83A SER* 3.4 32.1 - - - +
84A HIS* 3.6 17.9 - - + +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.2 16.8 + - + +
25A VAL* 3.1 13.3 + - + +
27A PRO* 1.4 80.2 - - - +
29A LEU* 1.3 62.7 - - - +
31A THR* 3.5 5.1 + - - -
32A VAL* 3.1 30.3 + - + +
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 2.8 17.7 + - + +
26A PHE* 3.8 33.0 - - + +
28A ALA* 1.3 77.2 - - - +
30A TYR* 1.4 79.3 + - + +
32A VAL* 3.2 12.1 + - + +
33A VAL* 2.9 39.9 + - + +
283A PHE* 4.8 9.2 - - + +
287A THR* 5.8 2.9 - - - +
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Residues in contact with TYR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 2.8 24.2 + - + +
27A PRO* 4.3 2.9 - - + +
29A LEU* 1.4 91.7 - - + +
31A THR* 1.3 60.1 + - - +
33A VAL* 3.2 29.3 + - + +
34A PHE* 2.8 39.2 + - + -
75A LEU* 5.6 0.2 - - + -
76A PRO* 4.1 13.7 - - + -
79A ILE* 3.6 32.3 - - + -
80A LEU* 4.8 4.7 - - - -
171A LYS* 3.2 22.9 - - - +
283A PHE* 2.8 31.1 + + - -
286A ALA* 2.8 39.0 - - + +
287A THR* 5.1 0.2 + - - -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PRO 2.8 25.3 + - - -
28A ALA* 3.8 5.6 - - - -
30A TYR* 1.3 74.8 - - - +
32A VAL* 1.4 63.7 + - + +
34A PHE* 3.1 26.0 + - + +
35A LEU* 3.2 24.5 + - + +
80A LEU* 3.4 23.4 - - + +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ALA* 3.1 17.7 + - + +
29A LEU* 3.2 14.8 + - + +
31A THR* 1.4 78.6 - - + +
33A VAL* 1.3 58.7 + - + +
35A LEU* 3.0 30.1 + - + +
36A THR* 3.0 26.0 + - + +
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Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 2.9 30.4 + - + +
30A TYR* 3.2 38.3 + - + +
32A VAL* 1.3 73.0 - - + +
34A PHE* 1.4 61.6 + - - +
36A THR* 3.8 7.9 - - - +
37A GLY* 2.9 27.1 + - - -
72A THR* 4.2 1.6 + - - -
76A PRO* 5.2 1.8 - - + -
286A ALA 4.2 1.8 - - - +
287A THR* 5.3 11.4 - - + +
289A ILE* 3.4 37.2 - - + -
290A CYS* 5.6 1.1 - - + -
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Residues in contact with PHE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 2.8 35.5 + - + -
31A THR* 3.1 13.2 + - + +
33A VAL* 1.4 76.3 - - - +
35A LEU* 1.4 62.6 - - + +
38A ILE* 2.9 39.4 + - + +
72A THR* 3.8 15.7 + - + +
76A PRO* 3.1 51.6 - - + -
77A PHE* 3.6 28.3 - + + -
80A LEU* 3.3 35.9 - - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR* 3.4 22.4 - - + +
32A VAL* 3.0 18.0 + - + +
34A PHE* 1.4 84.8 - - + +
36A THR* 1.4 64.3 + - + +
38A ILE* 3.7 7.0 - - + +
39A LEU* 3.3 26.2 + - - +
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Residues in contact with THR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.0 28.3 + - + +
33A VAL* 3.6 9.7 + - - +
35A LEU* 1.4 76.9 - - + +
37A GLY* 1.4 74.6 + - - +
38A ILE 3.3 0.3 + - - -
39A LEU* 3.3 0.9 + - - -
40A LEU* 2.9 42.4 + - + +
290A CYS* 3.5 25.0 - - - +
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Residues in contact with GLY 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL 2.9 14.4 + - - -
36A THR* 1.4 81.9 + - - +
38A ILE* 1.4 61.5 + - - -
40A LEU* 4.0 0.9 - - - +
41A ASN* 3.0 32.4 + - - +
72A THR* 3.9 9.0 - - - -
289A ILE* 4.0 23.1 - - - -
290A CYS* 4.6 5.1 - - - +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 2.9 31.7 + - + +
35A LEU* 3.7 10.3 - - + +
37A GLY* 1.4 71.9 - - - +
39A LEU* 1.4 71.0 + - + +
41A ASN* 4.8 1.8 - - - -
42A THR* 2.8 47.3 + - - +
69A LEU* 4.2 11.7 - - + +
72A THR* 3.4 29.8 + - + -
73A LEU* 6.3 3.1 - - + -
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU 3.3 14.8 + - - +
36A THR 3.3 2.7 + - - +
38A ILE* 1.4 84.6 - - + +
40A LEU* 1.4 78.3 + - + +
42A THR* 4.2 3.8 - - - -
43A LEU* 3.0 48.6 + - + +
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A THR* 2.9 35.3 + - + +
37A GLY* 4.0 2.5 - - - +
39A LEU* 1.4 90.0 - - + +
41A ASN* 1.3 66.7 + - - +
43A LEU* 3.7 4.9 - - - +
44A ALA* 3.2 20.6 + - - +
290A CYS* 5.1 9.0 - - - +
293A PRO* 4.2 23.9 - - + +
294A LEU* 3.7 29.6 - - + -
297A ILE* 4.2 17.0 - - + -
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 3.0 19.8 + - - +
38A ILE 4.0 1.1 - - - +
40A LEU* 1.3 75.2 - - - +
42A THR* 1.3 59.0 + - - +
43A LEU 3.0 1.1 - - - -
44A ALA 2.7 24.4 + - - -
45A LEU 2.9 10.4 + - - -
64A THR 4.6 0.2 - - - +
65A LEU* 2.9 49.1 - - + +
68A ASP* 3.1 18.1 + - - +
69A LEU* 4.6 7.4 - - + +
289A ILE 2.7 29.7 + - - -
290A CYS* 5.0 0.2 - - - +
293A PRO* 3.4 19.8 - - - +
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 2.8 37.9 + - - +
39A LEU* 4.2 5.2 - - - -
41A ASN* 1.3 72.3 - - - +
43A LEU* 1.4 55.0 + - - +
45A LEU* 3.8 7.7 - - + +
46A TRP* 3.0 31.6 + - + +
65A LEU* 3.9 4.9 - - - +
69A LEU* 3.6 22.6 - - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.0 39.7 + - + +
40A LEU* 3.7 6.5 - - + +
41A ASN 2.8 3.6 + - - -
42A THR* 1.4 73.9 - - - +
44A ALA* 1.4 61.3 + - + +
46A TRP* 3.1 8.7 + - + +
47A VAL* 2.8 51.7 + - + +
297A ILE* 5.6 7.2 - - + -
303A PHE* 5.6 2.5 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU 3.2 8.6 + - - +
41A ASN 2.7 7.3 + - - -
43A LEU* 1.4 74.9 - - + +
45A LEU* 1.4 60.1 + - - -
47A VAL* 4.0 1.8 - - - -
48A PHE* 3.3 18.4 + - - +
61A LEU* 4.1 9.2 - - + +
62A LYS* 5.5 1.0 - - - -
65A LEU* 3.3 24.4 - - + +
293A PRO* 4.3 11.0 - - + -
297A ILE* 5.1 3.4 - - + -
303A PHE* 3.5 34.8 - - + -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN 2.9 5.7 + - - -
42A THR* 3.8 11.9 - - + +
44A ALA* 1.4 73.4 - - - +
46A TRP* 1.3 75.6 + - + +
48A PHE* 3.0 5.4 + - + -
49A VAL* 3.0 43.4 + - + -
62A LYS* 4.7 22.0 - - + +
65A LEU* 3.3 24.5 - - + +
66A VAL* 4.2 22.7 - - + -
69A LEU* 5.7 4.0 - - + -
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Residues in contact with TRP 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A THR* 3.0 21.8 + - + +
43A LEU* 3.1 8.3 + - + +
45A LEU* 1.3 85.5 - - + +
47A VAL* 1.4 76.2 + - + +
49A VAL* 3.9 2.0 - - - +
50A HIS* 2.9 85.7 + + + +
51A ILE* 5.1 4.7 - - + -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 2.8 41.2 + - + +
44A ALA* 4.5 0.2 - - - -
46A TRP* 1.4 90.8 - - + +
48A PHE* 1.4 65.8 + - - +
51A ILE* 2.8 48.2 + - + +
58A ILE* 5.9 0.2 - - + -
303A PHE* 3.5 42.6 - - + +
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Residues in contact with PHE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 3.3 12.8 + - - +
45A LEU* 3.0 7.4 + - + +
47A VAL* 1.4 82.6 - - - +
49A VAL* 1.3 73.4 + - + +
51A ILE 4.0 2.7 - - - -
52A PRO* 2.9 35.9 - - + +
53A SER* 3.7 15.0 - - - -
58A ILE* 3.5 50.5 - - + +
59A ILE* 4.0 18.2 - - + -
61A LEU* 6.0 0.2 - - + -
62A LYS* 3.3 46.9 - - + -
303A PHE* 4.7 1.8 - - + -
----------------------------------------------------------
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.0 46.5 + - + +
46A TRP* 4.0 2.9 - - + +
48A PHE* 1.3 89.1 - - + +
50A HIS* 1.3 66.2 + - + +
51A ILE 3.4 0.2 + - - -
52A PRO* 3.7 12.7 - - - +
62A LYS* 5.9 0.7 - - + -
----------------------------------------------------------
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Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 2.9 67.0 + + + +
47A VAL 4.3 0.2 - - - +
49A VAL* 1.3 80.5 - - + +
51A ILE* 1.4 63.8 + - + +
52A PRO* 3.9 4.0 - - - +
----------------------------------------------------------
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Residues in contact with ILE 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 5.1 3.8 - - + -
47A VAL* 2.8 55.5 + - + +
48A PHE* 3.6 1.7 - - - +
50A HIS* 1.4 87.7 - - + +
52A PRO* 1.4 75.1 - - + +
58A ILE* 4.9 4.0 - - - +
302A LYS* 6.3 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