Contacts of the helix formed by residues 43 - 72 (chain A) in PDB entry 4LL7
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 SER 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ARG* 1.3 66.8 + - - +
45A VAL* 2.8 29.1 - - - +
46A ILE* 3.2 27.3 + - - +
47A GLU* 3.4 22.0 + - - +
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Residues in contact with ARG 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 1.3 78.4 - - - +
45A VAL* 1.3 62.9 + - + +
47A GLU* 5.8 0.7 - - - -
48A SER* 3.0 27.4 + - - -
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER 2.8 31.6 - - - +
44A ARG* 1.3 84.2 - - + +
46A ILE* 1.3 73.1 + - + +
48A SER* 3.5 3.3 - - - -
49A LEU* 3.0 26.4 + - - +
46C ILE* 3.7 30.1 - - + -
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Residues in contact with ILE 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 3.2 21.9 + - - +
45A VAL* 1.3 88.9 - - + +
47A GLU* 1.3 62.8 + - + +
49A LEU* 2.8 14.0 - - - +
50A HIS* 2.8 54.9 + - + +
46C ILE* 5.4 6.5 - - + -
49C LEU* 4.3 12.3 - - + -
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Residues in contact with GLU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 3.4 15.7 + - - +
44A ARG* 5.8 0.4 - - - -
46A ILE* 1.3 75.9 - - + +
48A SER* 1.3 65.4 + - - +
49A LEU 3.1 1.1 - - - -
50A HIS* 3.4 19.0 - - + +
51A ASP* 3.0 30.3 + - - +
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Residues in contact with SER 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ARG 3.0 22.8 + - - -
45A VAL* 3.5 4.5 - - - -
46A ILE 3.2 0.4 - - - -
47A GLU* 1.3 76.2 - - - +
49A LEU* 1.3 64.1 + - - +
51A ASP* 3.3 24.0 + - - +
52A GLN* 3.8 9.0 + - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL 3.0 10.6 + - - +
46A ILE* 2.8 13.0 + - - +
48A SER* 1.3 80.1 - - - +
50A HIS* 1.3 60.2 + - - +
52A GLN* 3.1 24.6 + - - +
53A ILE* 3.5 5.7 + - + +
46C ILE* 3.5 29.4 - - + -
49C LEU* 3.1 52.7 - - + +
50C HIS* 5.1 1.6 - - - +
53C ILE* 4.1 23.1 - - + -
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Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 2.8 48.4 + - + +
47A GLU* 3.4 25.1 - - + +
48A SER 3.3 0.4 - - - -
49A LEU* 1.3 69.2 - - - +
51A ASP* 1.3 55.3 + - - +
52A GLN 2.6 16.6 + - - -
53A ILE* 2.7 29.0 + - + +
54A ASP* 3.0 14.0 + - - +
49C LEU* 4.4 20.6 - - + +
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Residues in contact with ASP 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.0 21.1 + - - +
48A SER* 3.3 15.8 + - - +
50A HIS* 1.3 75.2 - - - +
52A GLN* 1.3 57.7 + - + +
54A ASP* 3.0 30.2 - - - +
55A MET* 3.6 11.3 - - - +
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Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER 3.8 8.3 + - - +
49A LEU* 3.1 18.1 + - - +
50A HIS 2.6 4.9 + - - -
51A ASP* 1.3 77.3 - - + +
53A ILE* 1.3 59.5 + - - +
54A ASP 3.3 0.2 - - - -
55A MET* 3.2 8.5 + - - +
56A LEU* 2.9 33.3 + - + +
53C ILE* 4.0 23.7 - - + +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 4.0 12.3 - - + +
50A HIS* 2.7 24.9 + - + +
52A GLN* 1.3 72.1 - - - +
54A ASP* 1.3 57.7 + - - +
56A LEU* 3.2 3.8 + - - +
57A THR* 2.9 34.7 + - - +
49C LEU* 4.2 9.4 - - + +
52C GLN* 4.3 17.0 - - + +
53C ILE* 3.1 47.8 - - + +
56C LEU* 3.5 16.5 - - + +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A HIS 3.0 7.9 + - - +
51A ASP* 3.0 37.7 - - - +
53A ILE* 1.3 77.7 - - - +
55A MET* 1.3 79.3 + - - +
57A THR* 3.2 9.0 + - - -
58A LYS* 3.0 52.5 + - - +
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Residues in contact with MET 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP 3.6 14.1 - - - +
52A GLN* 3.2 12.2 + - - +
54A ASP* 1.3 88.1 + - - +
56A LEU* 1.3 60.8 + - + +
58A LYS* 3.3 12.3 + - + +
59A THR* 2.9 35.8 + - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLN* 2.9 13.3 + - + +
53A ILE 3.4 2.9 - - - +
55A MET* 1.3 78.3 - - + +
57A THR* 1.3 57.2 + - - +
59A THR* 3.2 9.5 + - + +
60A ASN* 2.7 37.6 + - - +
53C ILE* 3.5 34.3 - - + +
56C LEU* 3.2 42.4 - - + -
57C THR* 3.7 14.6 - - + -
60C ASN* 4.1 18.2 - - - +
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ILE* 2.9 19.0 + - - +
54A ASP* 3.2 11.7 + - - -
56A LEU* 1.3 76.0 - - - +
58A LYS* 1.3 58.5 + - + +
60A ASN* 3.2 9.1 + - + +
61A LEU* 3.0 30.4 + - + +
56C LEU* 3.9 13.1 - - - +
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Residues in contact with LYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 3.0 46.5 + - - +
55A MET* 3.4 13.0 - - + +
56A LEU 3.2 0.2 - - - -
57A THR* 1.3 78.1 - - + +
59A THR* 1.3 61.9 + - - +
61A LEU* 3.3 9.2 + - - +
62A GLN* 3.1 29.1 + - + +
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A MET* 2.9 20.9 + - - +
56A LEU* 3.2 16.1 + - + +
58A LYS* 1.3 77.6 - - - +
60A ASN* 1.3 61.5 + - - +
62A GLN* 3.4 7.1 + - - +
63A LEU* 3.0 50.6 + - + +
60C ASN* 4.6 12.1 - - + +
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Residues in contact with ASN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 2.7 27.6 + - - +
57A THR* 3.5 10.8 - - + +
59A THR* 1.3 74.1 - - - +
61A LEU* 1.3 59.9 + - - +
63A LEU 3.4 0.5 + - - -
64A THR* 2.8 39.5 + - + +
56C LEU* 3.8 16.6 + - - +
59C THR* 3.1 40.2 - - - +
60C ASN* 3.4 16.9 + - - +
63C LEU* 3.3 20.4 - - + +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A THR* 3.0 17.8 + - + +
58A LYS* 3.3 11.2 + - - +
60A ASN* 1.3 76.3 - - - +
62A GLN* 1.3 75.6 + - - +
64A THR* 2.5 22.3 + - - +
65A THR* 2.9 32.0 + - + +
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Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LYS* 3.1 19.5 + - + +
59A THR* 3.6 8.5 - - - +
61A LEU* 1.3 86.2 - - - +
63A LEU* 1.3 70.4 + - + +
65A THR* 2.6 25.9 + - - -
66A GLN* 2.9 11.6 + - - +
210A SO4 2.8 46.7 + - - -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 3.0 37.6 + - + +
60A ASN 3.8 2.7 - - - +
62A GLN* 1.3 85.8 - - + +
64A THR* 1.3 56.4 + - - +
66A GLN* 3.0 18.0 - - - +
67A SER* 3.0 29.9 + - - -
60C ASN* 3.1 38.4 - - + +
63C LEU* 3.7 18.5 - - + +
64C THR* 3.8 21.3 - - - +
67C SER* 5.5 3.8 - - - -
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASN* 2.8 31.5 + - + +
61A LEU* 2.5 27.4 + - - +
63A LEU* 1.3 68.9 - - - +
65A THR* 1.3 59.1 + - - +
66A GLN 3.0 1.6 - - - -
67A SER* 3.1 10.4 + - - +
68A GLN* 2.7 36.6 + - - +
59C THR* 6.5 0.2 - - + -
63C LEU* 3.8 23.1 - - + -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LEU* 2.9 37.4 + - + +
62A GLN* 2.6 25.7 + - - +
64A THR* 1.3 78.3 + - - +
66A GLN* 1.3 56.5 + - - +
68A GLN* 2.9 18.6 - - + +
69A ASN* 2.9 28.2 + - - +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLN* 2.9 12.6 + - - +
63A LEU* 3.0 27.3 - - - +
65A THR* 1.3 74.1 + - - +
67A SER* 1.3 55.5 + - - +
68A GLN 2.8 8.9 + - - -
69A ASN* 2.4 37.8 + - - +
70A LEU* 2.8 22.5 - - + +
67C SER* 3.5 22.7 + - - +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU 3.0 12.9 + - - -
64A THR* 3.1 10.7 + - - -
66A GLN* 1.3 74.0 - - - +
68A GLN* 1.3 59.3 + - - +
70A LEU* 3.7 2.0 - - - +
71A LEU* 3.5 22.4 + - - +
63C LEU* 3.9 18.0 + - - +
66C GLN* 4.0 18.7 + - - +
67C SER* 4.2 3.8 + - - -
70C LEU* 3.6 24.9 - - - +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A THR* 2.7 28.3 - - - +
65A THR* 2.9 26.0 - - - +
66A GLN 2.8 0.4 - - - -
67A SER* 1.3 77.6 - - - +
69A ASN* 1.3 63.6 + - - +
70A LEU 3.1 2.2 + - - -
71A LEU* 3.4 4.1 + - - +
72A SER* 3.3 24.4 + - - -
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Residues in contact with ASN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR 2.9 11.6 + - - +
66A GLN* 2.4 38.9 + - - +
68A GLN* 1.3 78.0 - - - +
70A LEU* 1.3 86.6 + - - +
72A SER* 3.6 7.8 + - - -
73A LYS* 3.4 41.2 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLN* 2.8 44.9 + - + +
67A SER* 3.7 0.7 - - - -
69A ASN* 1.3 97.6 - - - +
71A LEU* 1.3 58.1 + - - +
72A SER 2.8 5.2 - - - -
73A LYS* 2.9 10.7 + - + +
74A LEU* 2.9 33.5 + - - +
67C SER* 4.4 9.2 - - - +
70C LEU* 3.3 45.8 - - + +
71C LEU* 4.6 15.0 - - + +
74C LEU* 5.2 11.9 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER 3.5 18.8 + - - +
68A GLN* 3.4 6.0 + - - +
70A LEU* 1.3 77.7 - - - +
72A SER* 1.3 51.2 + - - +
73A LYS 3.4 0.4 - - - -
74A LEU* 4.5 11.0 - - + -
75A GLU* 2.4 55.2 + - + +
70C LEU* 4.5 20.3 - - + +
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN 3.3 16.2 + - - -
69A ASN* 3.7 9.9 - - - -
70A LEU 2.8 0.8 - - - -
71A LEU* 1.3 79.1 - - - +
73A LYS* 1.3 58.4 + - - +
75A GLU* 3.7 12.6 + - - +
76A LEU* 3.1 26.9 + - - +
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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