Contacts of the helix formed by residues 45 - 69 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D TYR* 4.4 5.4 - - - -
43D PHE* 3.5 3.5 - - - +
44D LYS* 1.3 99.4 - - + +
46D LYS* 1.3 56.5 + - - +
47D GLU* 3.8 8.4 + - - +
48D ASN* 3.0 29.5 + - - +
49D LEU* 2.8 37.0 + - - +
26F G 3.6 28.9 - - - +
27F T 5.9 0.4 - - - +
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Residues in contact with LYS 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 4.1 12.7 - - + -
20D TYR* 3.1 51.7 + - + +
21D ASN* 3.9 8.1 + - - +
23D THR 2.5 30.2 + - - +
24D THR 5.6 0.2 - - - -
25D THR* 4.2 15.0 - - + -
28D ILE* 5.9 1.6 - - + -
39D LEU* 6.5 0.4 - - - -
40D TYR* 4.2 2.4 + - - -
45D THR* 1.3 71.2 - - - +
47D GLU* 1.3 62.4 + - - +
49D LEU* 3.3 12.9 + - + +
50D PHE* 3.0 22.0 + - - +
25F G 3.1 37.7 + - - -
26F G 2.7 20.1 + - - +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D TYR* 3.4 14.5 + - - +
45D THR* 3.8 9.5 + - - +
46D LYS* 1.3 80.1 - - - +
48D ASN* 1.3 72.5 + - - +
50D PHE* 3.1 7.4 + - - +
51D LEU* 3.0 24.3 + - + +
102D PHE* 3.8 20.6 - - + -
106D TYR* 3.5 25.1 - - + +
111D SER* 5.7 0.2 - - - -
112D ILE* 3.1 28.6 - - + +
26F G 4.6 2.2 + - - +
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Residues in contact with ASN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE* 5.4 0.4 - - + -
44D LYS* 3.9 26.5 - - + +
45D THR* 3.0 25.2 + - - +
47D GLU* 1.3 90.1 - - - +
49D LEU* 1.3 66.5 + - - +
51D LEU* 3.8 12.2 - - - +
52D GLU* 2.9 28.3 + - - +
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ILE* 5.1 1.1 - - + -
8D LEU* 3.8 10.5 - - + -
11D ALA* 4.1 11.7 - - + -
15D PHE* 4.4 12.3 - - + -
25D THR* 6.0 1.1 - - + -
28D ILE* 3.9 28.3 - - + -
39D LEU* 4.6 15.7 - - + -
43D PHE* 3.4 50.8 - - + +
45D THR 2.8 20.8 + - - +
46D LYS* 3.4 12.1 - - + +
48D ASN* 1.3 73.1 - - - +
50D PHE* 1.3 60.9 + - - +
52D GLU* 3.6 2.5 + - - +
53D ILE* 3.0 36.5 + - + +
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D PHE* 3.6 38.4 - + + -
20D TYR* 3.7 14.8 - + + -
46D LYS 3.0 12.4 + - - +
47D GLU 3.1 8.5 + - - +
49D LEU* 1.3 78.4 - - - +
51D LEU* 1.3 64.7 + - + +
53D ILE* 3.0 9.0 + - + +
54D LEU* 3.0 49.7 + - + +
95D LEU* 4.6 6.1 - - + -
98D ALA* 3.7 38.1 - - + -
99D ILE* 4.1 4.0 - - + -
102D PHE* 3.5 50.7 - + + -
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLU* 3.0 18.3 + - - +
48D ASN* 3.3 15.2 + - - +
50D PHE* 1.3 75.8 - - - +
52D GLU* 1.3 67.0 + - - +
54D LEU* 2.9 31.1 + - + +
55D ASN* 2.8 25.9 + - - +
102D PHE* 3.8 24.2 - - + -
112D ILE* 4.0 26.9 - - + -
115D LYS* 4.1 34.3 - - + +
116D MET* 4.8 3.4 - - + -
119D LEU* 5.5 0.2 - - + -
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Residues in contact with GLU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D LYS* 3.0 31.4 + - - -
8D LEU* 4.6 5.1 - - + +
43D PHE* 3.5 26.6 - - - -
48D ASN 2.9 17.0 + - - +
49D LEU 3.8 4.7 - - - +
51D LEU* 1.3 76.7 - - - +
53D ILE* 1.3 63.3 + - + +
55D ASN* 3.4 8.1 + - - +
56D ILE* 3.0 45.2 + - + +
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Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.0 21.1 - - + +
11D ALA* 3.8 28.7 - - + -
12D LYS* 3.9 25.8 - - + +
15D PHE* 4.0 16.2 - - + -
49D LEU* 3.0 21.1 - - + +
50D PHE* 3.0 9.6 + - + +
52D GLU* 1.3 76.6 - - - +
54D LEU* 1.3 64.5 + - + +
56D ILE* 3.8 7.4 - - - +
57D GLU* 3.0 34.6 + - - +
95D LEU* 4.2 18.6 - - + -
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D PHE* 3.0 29.7 + - + +
51D LEU* 2.9 26.9 + - + +
53D ILE* 1.3 79.9 - - + +
55D ASN* 1.3 53.2 + - - +
57D GLU* 3.6 3.4 - - - +
58D GLU* 2.8 36.8 + - - +
92D TYR* 3.9 12.7 - - + +
95D LEU* 4.1 15.0 - - + -
99D ILE* 3.4 30.5 - - + -
116D MET* 4.1 24.7 - - + -
119D LEU* 3.7 26.5 - - + -
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Residues in contact with ASN 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D LEU* 2.8 29.9 + - - +
52D GLU* 3.9 6.3 - - - +
54D LEU* 1.3 71.5 - - - +
56D ILE* 1.3 68.0 + - + +
58D GLU* 3.5 3.3 + - - +
59D SER* 3.0 22.5 + - - -
115D LYS* 3.5 30.4 + - - +
119D LEU* 4.2 22.7 - - - +
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Residues in contact with ILE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 3.8 28.5 - - + -
52D GLU* 3.0 34.2 + - + +
53D ILE* 3.8 6.1 - - - +
55D ASN* 1.3 76.1 - - + +
57D GLU* 1.3 66.8 + - - +
59D SER* 2.7 31.4 + - - -
60D LYS* 3.0 32.9 + - + +
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Residues in contact with GLU 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 2.7 41.7 + - - +
53D ILE* 3.0 26.6 + - - +
54D LEU 3.6 2.7 - - - +
56D ILE* 1.3 86.5 - - - +
58D GLU* 1.3 67.6 + - - +
60D LYS* 3.2 10.3 + - - +
61D TRP* 3.0 22.2 + - - +
91D TYR* 3.4 27.2 - - - +
92D TYR* 3.3 28.7 - - + +
95D LEU* 4.2 10.1 - - + -
899D SO4 5.2 0.3 + - - -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LEU 2.8 15.1 + - - +
55D ASN* 3.8 4.5 - - - +
57D GLU* 1.3 70.9 - - - +
59D SER* 1.3 66.1 + - - +
61D TRP* 3.0 5.6 + - - +
62D GLN* 2.8 43.0 + - - +
92D TYR* 3.6 18.7 - - + -
119D LEU* 3.4 44.0 - - + +
122D LYS* 3.0 41.3 + - - +
123D TYR* 3.8 11.7 - - - -
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Residues in contact with SER 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ASN 3.0 14.6 + - - -
56D ILE* 2.7 18.6 + - - -
58D GLU* 1.3 81.2 - - - +
60D LYS* 1.3 64.0 + - - +
62D GLN* 2.9 19.6 + - - +
63D GLU* 3.0 11.4 + - - +
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Residues in contact with LYS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ILE* 3.0 38.4 + - + +
57D GLU* 3.2 18.6 + - - +
59D SER* 1.3 76.4 + - - +
61D TRP* 1.3 56.7 + - - +
63D GLU* 3.4 16.8 - - - +
64D GLN* 2.9 28.1 + - - +
67D LYS* 4.9 0.2 + - - -
91D TYR* 3.8 26.1 - - + -
899D SO4 2.9 41.7 + - - -
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Residues in contact with TRP 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D GLU 3.0 12.4 + - - +
58D GLU* 3.0 10.3 + - - +
60D LYS* 1.3 72.7 - - - +
62D GLN* 1.3 71.4 + - - +
64D GLN* 2.8 35.3 + - + +
65D TRP* 2.7 43.1 + - + +
82D TYR* 3.3 46.1 + + - -
85D LEU* 3.3 38.1 - - + -
86D SER* 4.4 4.9 - - - -
89D THR* 3.3 31.2 - - + -
91D TYR* 4.0 15.2 - - + +
93D TYR* 5.6 1.3 - + - -
123D TYR* 3.0 36.5 - + - +
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Residues in contact with GLN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLU* 2.8 31.6 + - - +
59D SER* 2.9 11.8 + - - +
61D TRP* 1.3 86.2 - - - +
63D GLU* 1.3 58.6 + - - +
65D TRP* 3.4 16.0 + - - +
66D LYS* 2.9 29.9 + - - +
82D TYR* 5.7 1.2 + - - -
122D LYS* 4.3 28.9 + - + +
123D TYR* 6.2 0.2 - - - -
126D ALA* 6.0 2.4 - - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D SER 3.0 10.2 + - - +
60D LYS* 3.4 20.9 - - - +
61D TRP 3.0 0.4 - - - -
62D GLN* 1.3 76.2 - - - +
64D GLN* 1.3 64.4 + - - +
66D LYS* 3.0 22.4 + - + +
67D LYS* 3.1 41.6 + - + +
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LYS 2.9 14.7 + - - +
61D TRP* 2.8 39.1 + - + +
63D GLU* 1.3 72.5 - - - +
65D TRP* 1.3 63.0 + - - +
67D LYS* 3.3 14.3 - - - +
68D GLU* 3.0 46.0 + - + +
85D LEU* 3.2 24.9 - - - +
88D THR* 5.4 0.2 + - - -
89D THR* 3.3 16.2 + - - +
90D GLU* 4.6 1.2 + - - +
91D TYR* 3.3 28.4 - - + -
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Residues in contact with TRP 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D TRP* 2.7 31.3 + - + +
62D GLN* 3.7 19.5 - - - +
64D GLN* 1.3 72.4 - - - +
66D LYS* 1.3 64.5 + - - +
68D GLU* 4.5 0.4 - - - -
69D GLN* 2.9 72.0 + - + +
78D LYS* 3.8 28.5 - - + -
81D LEU* 3.8 25.8 - - + -
82D TYR* 3.5 40.8 - + + -
85D LEU* 4.0 13.2 - - + -
126D ALA* 4.3 14.5 - - + +
130D ILE* 4.0 19.8 - - + +
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Residues in contact with LYS 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLN* 2.9 15.0 + - - +
63D GLU* 3.0 14.8 + - + +
65D TRP* 1.3 77.3 - - - +
67D LYS* 1.3 69.3 + - + +
69D GLN* 3.3 21.7 + - - +
70D ILE* 4.1 7.1 - - - +
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Residues in contact with LYS 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D LYS 4.9 0.4 + - - -
63D GLU* 3.1 45.6 + - + +
64D GLN* 3.3 23.6 - - + +
66D LYS* 1.3 79.2 - - + +
68D GLU* 1.3 55.8 + - + +
69D GLN 2.7 15.4 + - - -
70D ILE* 2.7 36.7 + - + +
91D TYR* 6.3 0.2 - - - -
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Residues in contact with GLU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLN* 3.0 44.1 + - + +
65D TRP* 4.1 2.0 - - + +
67D LYS* 1.3 77.3 - - + +
69D GLN* 1.3 61.0 + - - +
70D ILE 3.1 1.0 + - - -
71D LYS* 3.5 24.1 + - - +
81D LEU* 3.3 21.2 - - + +
85D LEU* 3.9 34.1 - - + +
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Residues in contact with GLN 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D TRP* 2.9 68.8 + - + +
66D LYS* 3.3 25.9 + - - +
67D LYS 2.7 5.7 + - - -
68D GLU* 1.3 70.4 - - - +
70D ILE* 1.3 60.0 + - + +
71D LYS 3.1 2.7 - - - -
72D ALA* 2.8 26.8 + - - +
78D LYS* 3.0 34.5 + - + +
81D LEU* 4.1 4.7 - - - -
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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
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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