Contacts of the helix formed by residues 45 - 69 (chain C) in PDB entry 1JT0
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 THR 45 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TYR* 4.2 4.0 - - - -
43C PHE* 4.6 3.0 - - - +
44C LYS* 1.3 98.3 + - + +
46C LYS* 1.3 67.4 + - - +
47C GLU* 3.7 9.4 - - - +
48C ASN* 2.9 27.8 + - - +
49C LEU* 2.8 22.1 + - - +
26E G 3.5 28.7 - - - +
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 4.1 13.1 - - + -
20C TYR* 3.2 50.4 + - + +
21C ASN* 4.1 8.5 + - - +
23C THR 2.7 28.3 + - - +
24C THR 5.6 0.2 - - - -
25C THR* 4.4 14.4 - - + +
28C ILE* 5.8 2.2 - - + -
39C LEU* 6.4 1.3 - - - -
40C TYR* 4.3 2.6 + - - -
45C THR* 1.3 70.7 - - - +
47C GLU* 1.3 63.3 + - - +
49C LEU* 3.0 14.9 + - + +
50C PHE* 2.9 22.3 + - - +
25E G 2.9 38.5 + - - +
26E G 2.8 17.7 + - - +
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Residues in contact with GLU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.3 13.9 + - - +
45C THR* 3.7 10.9 - - - +
46C LYS* 1.3 79.9 - - - +
48C ASN* 1.3 68.4 + - - +
50C PHE* 3.0 7.4 + - - +
51C LEU* 3.0 33.2 + - + +
102C PHE* 3.5 25.1 - - + -
106C TYR* 4.4 16.0 - - + -
112C ILE* 3.7 23.4 - - - +
115C LYS* 4.9 5.2 + - - -
26E G 4.8 1.3 + - - +
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PHE* 5.2 1.6 - - - -
44C LYS* 3.9 31.4 + - + +
45C THR* 2.9 24.6 + - - +
47C GLU* 1.3 89.7 + - - +
49C LEU* 1.3 64.7 + - - +
51C LEU* 4.0 16.9 - - - +
52C GLU* 3.1 26.7 + - - +
115C LYS* 5.3 4.8 - - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ILE* 4.9 2.2 - - + -
8C LEU* 3.8 6.1 - - + -
11C ALA* 4.0 12.3 - - + -
15C PHE* 4.7 5.4 - - + -
25C THR* 6.4 0.7 - - + -
28C ILE* 3.9 27.1 - - + -
39C LEU* 4.3 19.7 - - + -
43C PHE* 3.6 39.9 - - + -
45C THR 2.8 11.5 + - - +
46C LYS* 3.0 18.1 + - + +
48C ASN* 1.3 74.5 - - - +
50C PHE* 1.3 71.3 + - - +
52C GLU* 3.6 1.6 - - - +
53C ILE* 3.2 36.0 + - + +
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Residues in contact with PHE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 3.8 37.0 - + + -
20C TYR* 3.8 15.5 - + + -
46C LYS 2.9 12.0 + - - +
47C GLU 3.2 9.0 - - - +
49C LEU* 1.3 76.5 - - - +
51C LEU* 1.3 56.1 + - - +
53C ILE* 2.8 29.6 + - + +
54C LEU* 3.0 47.9 + - + +
95C LEU* 4.7 5.4 - - + -
98C ALA* 3.6 33.4 - - + -
99C ILE* 4.0 11.2 - - + -
102C PHE* 3.5 42.4 - + + -
116C MET* 5.2 0.2 - - + -
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C GLU* 3.0 22.7 + - + +
48C ASN* 4.3 19.7 - - - +
50C PHE* 1.3 75.1 - - + +
52C GLU* 1.3 68.9 + - - +
54C LEU* 3.4 24.5 + - + +
55C ASN* 3.1 32.9 + - - +
102C PHE* 4.8 9.6 - - + -
112C ILE* 4.5 10.8 - - + -
115C LYS* 3.7 39.5 - - + +
116C MET* 4.5 14.1 - - - -
119C LEU* 5.2 3.4 - - + -
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Residues in contact with GLU 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LYS* 3.3 33.3 + - - -
8C LEU* 4.3 3.8 - - + +
42C HIS 5.0 0.5 - - - +
43C PHE* 3.5 24.3 - - - -
48C ASN 3.1 19.3 + - - +
49C LEU* 3.6 4.9 - - - +
50C PHE 3.0 0.2 + - - -
51C LEU* 1.3 78.8 - - - +
53C ILE* 1.3 54.8 - - - +
55C ASN* 3.0 4.2 + - - +
56C ILE* 2.8 60.3 + - + +
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Residues in contact with ILE 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.3 40.6 - - + +
11C ALA* 4.0 11.2 - - + -
12C LYS* 4.1 21.5 - - + +
15C PHE* 4.4 9.9 - - + -
49C LEU* 3.3 28.0 - - + +
50C PHE* 2.8 10.1 + - + +
52C GLU* 1.3 73.1 - - - +
54C LEU* 1.3 68.3 + - + +
56C ILE* 3.7 7.8 - - + +
57C GLU* 2.7 33.6 + - - +
95C LEU* 4.1 22.2 - - + -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C PHE* 3.0 60.1 + - + +
51C LEU* 3.8 24.0 - - + +
52C GLU 3.3 0.2 + - - -
53C ILE* 1.3 76.8 - - + +
55C ASN* 1.3 53.8 + - - +
57C GLU* 3.2 5.5 - - - +
58C GLU* 2.7 37.7 + - - +
92C TYR* 4.0 7.3 - - + +
95C LEU* 4.2 14.8 - - + -
99C ILE* 4.3 21.1 - - + -
116C MET* 4.1 13.9 - - - -
119C LEU* 3.5 26.5 - - + -
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Residues in contact with ASN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.1 21.7 + - - +
52C GLU* 3.0 9.7 + - - +
54C LEU* 1.3 74.5 - - - +
56C ILE* 1.3 66.6 + - + +
57C GLU 3.0 2.5 + - - -
58C GLU* 3.4 1.4 + - - +
59C SER* 3.1 24.3 + - - -
118C LYS* 3.5 35.6 + - - +
119C LEU* 3.7 22.4 - - - +
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Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.8 27.4 - - + -
52C GLU* 2.8 51.0 + - + +
53C ILE* 3.5 9.9 - - - +
55C ASN* 1.3 72.9 - - + +
57C GLU* 1.3 61.5 + - - +
59C SER* 2.7 20.9 + - - +
60C LYS* 2.8 48.4 + - - +
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 2.3 46.1 + - - +
53C ILE* 2.7 25.3 + - + +
54C LEU* 3.2 5.6 - - - +
56C ILE* 1.3 80.8 - - - +
58C GLU* 1.3 68.5 + - - +
59C SER 2.9 3.0 + - - -
60C LYS* 2.9 26.6 + - - +
61C TRP* 3.0 10.4 + - - +
91C TYR* 3.0 23.5 - - - +
92C TYR* 3.5 29.4 - - - +
95C LEU* 4.2 8.1 - - + -
699C SO4 4.4 4.7 + - - -
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU 2.7 19.0 + - - +
55C ASN* 3.9 3.4 - - - +
57C GLU* 1.3 72.3 - - - +
59C SER* 1.3 65.0 + - - +
61C TRP* 3.3 7.7 - - - +
62C GLN* 3.1 22.3 + - - +
92C TYR* 3.9 14.7 - - + -
119C LEU* 3.7 25.3 - - + +
122C LYS* 2.9 52.6 + - + +
123C TYR* 3.6 29.5 - - + -
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASN 3.1 11.3 + - - -
56C ILE* 2.7 28.1 + - - +
57C GLU 2.9 1.8 + - - -
58C GLU* 1.3 79.1 + - - +
60C LYS* 1.3 62.2 + - - +
61C TRP 2.9 4.3 - - - -
62C GLN* 2.8 24.6 + - - +
63C GLU* 2.9 16.6 + - - +
122C LYS* 5.5 0.7 - - - +
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C ILE* 2.8 44.4 + - - +
57C GLU* 2.9 13.6 + - - +
59C SER* 1.3 83.0 + - - +
61C TRP* 1.3 60.7 + - - +
63C GLU* 3.6 12.8 + - - +
64C GLN* 3.2 16.1 + - - +
91C TYR* 3.5 40.6 - - + +
699C SO4 3.1 35.9 + - - +
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Residues in contact with TRP 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU 3.0 9.8 + - - +
58C GLU* 3.3 16.8 - - - +
59C SER 2.9 0.4 - - - -
60C LYS* 1.3 77.5 - - - +
62C GLN* 1.3 73.9 + - + +
64C GLN* 2.8 44.5 + - + +
65C TRP* 2.9 20.4 + - + +
82C TYR* 3.1 41.0 + + - -
85C LEU* 3.1 44.0 - - + -
86C SER* 3.8 13.5 - - - -
89C THR* 3.5 24.2 - - + -
91C TYR* 3.9 16.3 - - + +
93C TYR* 4.6 2.9 - + - -
123C TYR* 3.3 44.4 - + - +
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLU* 3.1 11.2 + - - +
59C SER* 2.8 11.3 + - - +
61C TRP* 1.3 88.7 - - + +
63C GLU* 1.3 60.6 + - - +
65C TRP* 3.8 9.9 - - + +
66C LYS* 3.0 40.4 + - + +
122C LYS* 2.8 37.9 + - - +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C SER* 2.9 14.8 + - - +
60C LYS* 3.7 14.6 - - - +
62C GLN* 1.3 76.7 - - - +
64C GLN* 1.3 63.1 + - - +
66C LYS* 3.2 28.9 + - - +
67C LYS* 3.2 22.2 + - - +
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Residues in contact with GLN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LYS 3.2 7.4 + - - +
61C TRP* 2.8 28.7 + - - +
63C GLU* 1.3 78.6 - - - +
65C TRP* 1.3 54.8 + - - +
67C LYS* 3.1 8.1 + - - +
68C GLU* 2.8 43.6 + - - +
85C LEU* 3.2 14.9 - - + +
89C THR* 2.8 30.1 + - - -
90C GLU* 3.1 22.9 - - - +
91C TYR* 3.5 14.6 - - + -
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Residues in contact with TRP 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TRP* 2.9 24.0 + - + +
62C GLN* 3.8 15.3 - - + +
64C GLN* 1.3 75.1 - - - +
66C LYS* 1.3 66.0 + - - +
68C GLU* 3.8 6.3 - - + -
69C GLN* 2.9 82.0 + - + +
78C LYS* 3.9 13.5 - - + -
81C LEU* 3.7 24.0 - - + -
82C TYR* 3.6 57.2 - + + -
85C LEU* 4.8 8.4 - - + +
126C ALA* 4.7 10.8 - - + +
130C ILE* 4.3 20.4 - - + +
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Residues in contact with LYS 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C GLN* 3.0 34.8 + - + +
63C GLU* 3.2 33.3 + - - +
65C TRP* 1.3 77.9 - - - +
67C LYS* 1.3 61.7 + - - +
69C GLN* 3.6 21.5 + - - +
70C ILE* 3.6 17.7 - - - +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLU 3.2 8.2 + - - +
64C GLN* 3.1 9.9 + - - +
66C LYS* 1.3 80.0 - - - +
68C GLU* 1.3 69.4 + - + +
70C ILE* 3.6 18.2 - - - +
71C LYS* 4.3 4.0 + - - +
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Residues in contact with GLU 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C GLN* 2.8 38.7 + - - +
65C TRP* 3.8 15.9 - - + -
67C LYS* 1.3 83.1 - - + +
69C GLN* 1.3 61.0 + - - +
70C ILE 3.0 6.6 + - - -
71C LYS* 3.3 15.3 + - - +
81C LEU* 3.1 27.5 - - + +
85C LEU* 3.9 30.7 - - + +
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Residues in contact with GLN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C TRP* 2.9 67.5 + - + +
66C LYS* 3.6 25.5 + - - +
68C GLU* 1.3 74.8 - - - +
70C ILE* 1.3 69.0 + - + +
71C LYS 3.4 0.2 - - - -
72C ALA* 3.4 19.6 - - - +
78C LYS* 3.4 30.1 + - + -
81C LEU* 4.3 3.1 - - - -
130C ILE* 5.0 2.4 - - - +
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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
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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) + - + + + + + -
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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