Contacts of the helix formed by residues 52 - 75 (chain B) in PDB entry 5TWF
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 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 3.9 0.2 - - - +
51B GLU* 1.3 87.3 + - - +
53B LEU* 1.3 81.7 + - - +
54B ASN* 3.1 21.2 + - - +
55B GLU* 3.4 24.7 + - + +
56B TRP* 3.1 18.2 + - - +
140B PHE* 4.9 6.1 - - - -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.7 25.4 - - + -
51B GLU 3.4 3.8 + - - -
52B ASP* 1.3 74.7 + - - +
54B ASN* 1.3 65.4 + - - +
56B TRP* 3.0 3.5 + - + +
57B ILE* 2.9 38.5 + - + +
145B MET* 4.8 12.8 - - + -
193B PHE* 3.3 42.4 - - + -
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Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 3.1 11.3 + - - +
53B LEU* 1.3 78.2 - - - +
55B GLU* 1.3 56.8 + - - +
57B ILE* 3.4 3.4 + - - -
58B ALA* 2.9 29.3 + - - +
140B PHE* 3.6 36.8 + - + +
141B PRO 5.0 1.4 + - - -
144B PHE* 3.3 35.2 - - + +
145B MET* 3.3 22.9 + - - +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B HIS* 3.7 20.5 + - - +
25B GLN* 2.6 30.9 - - - +
28B LEU* 4.3 7.6 - - + -
51B GLU* 2.6 31.1 - - - +
52B ASP* 3.4 22.1 + - + +
53B LEU 3.1 0.8 - - - -
54B ASN* 1.3 76.1 - - - +
56B TRP* 1.3 65.3 + - - +
58B ALA* 3.1 2.7 + - - +
59B VAL* 2.9 30.7 + - - +
140B PHE* 3.8 20.0 - - + -
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Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.7 46.3 - - + +
31B HIS* 5.0 3.6 - - + -
32B ALA* 3.5 25.8 - - + -
35B THR* 5.6 0.7 - - - -
44B ALA 4.1 13.0 - - - -
45B VAL* 2.9 23.9 + - - -
46B MET 3.9 10.9 + - - -
47B LEU* 3.7 21.8 - - + -
48B PRO* 3.9 21.1 - - + -
51B GLU* 5.1 0.9 - - + -
52B ASP 3.1 2.6 + - - +
53B LEU* 3.0 9.7 + - + +
55B GLU* 1.3 78.8 - - - +
57B ILE* 1.3 63.0 + - - +
59B VAL* 4.0 2.1 - - + -
60B ASN* 3.0 51.8 + - - +
189B PHE* 3.2 23.8 - + - -
193B PHE* 3.5 21.3 - + - -
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Residues in contact with ILE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 2.9 21.4 + - + +
54B ASN* 3.8 6.1 - - - +
56B TRP* 1.3 75.7 - - + +
58B ALA* 1.3 54.1 + - - +
60B ASN* 4.3 0.2 - - - +
61B THR* 2.3 49.9 + - - +
144B PHE* 4.6 3.6 - - + -
145B MET* 4.2 19.1 - - + -
148B ALA* 3.7 24.0 - - + -
152B LEU* 4.7 0.2 - - + -
189B PHE* 3.4 26.6 - - + -
193B PHE* 3.8 29.2 - - + -
195B LEU* 3.7 21.5 - - + -
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLN* 4.9 7.4 - - - +
54B ASN 2.9 17.6 + - - +
55B GLU* 3.1 5.1 + - - +
57B ILE* 1.3 76.8 - - - +
59B VAL* 1.3 63.7 + - - +
61B THR* 3.5 2.3 - - - -
62B VAL* 3.0 29.3 + - - +
132B PHE* 3.8 25.9 - - + -
140B PHE* 3.7 23.8 - - + -
144B PHE* 3.9 5.1 - - + -
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Residues in contact with VAL 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLN* 3.7 41.5 - - + +
28B LEU* 4.2 15.9 - - + +
29B LEU* 3.5 46.1 - - + +
55B GLU 2.9 20.3 + - - +
56B TRP* 4.0 4.3 - - + +
58B ALA* 1.3 75.4 - - - +
60B ASN* 1.3 67.4 + - - +
62B VAL* 3.1 9.4 + - - +
63B ASP* 3.1 21.1 + - - +
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Residues in contact with ASN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 6.2 0.2 - - - -
32B ALA* 3.7 23.0 - - - +
45B VAL* 6.0 0.2 - - - +
56B TRP* 3.0 46.5 + - - +
59B VAL* 1.3 78.3 - - - +
61B THR* 1.3 57.5 + - - +
63B ASP* 3.8 5.5 - - - +
64B PHE* 2.9 40.0 + - + -
185B HIS* 3.8 24.7 + - - -
189B PHE* 3.5 38.1 - - + -
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ILE* 2.3 43.0 + - - +
58B ALA* 3.5 6.7 - - - -
60B ASN* 1.3 77.8 - - - +
62B VAL* 1.3 57.8 + - - +
64B PHE* 3.3 10.1 + - - +
65B PHE* 2.9 28.0 + - + +
122B VAL* 5.8 0.2 - - + -
126B LEU* 5.2 2.9 - - + -
132B PHE* 4.6 17.3 - - + -
148B ALA* 4.5 5.4 - - + +
151B ILE* 4.1 28.5 - - + -
152B LEU* 4.0 20.9 - - + +
155B LEU* 4.6 0.9 - - - +
189B PHE* 5.1 0.9 - - - -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 6.5 0.7 - - + -
58B ALA 3.0 17.2 + - - +
59B VAL* 3.1 8.7 + - - +
61B THR* 1.3 74.4 - - - +
63B ASP* 1.3 58.8 + - - +
65B PHE* 3.1 8.9 + - - +
66B ASN* 2.9 42.3 + - - +
126B LEU* 3.9 35.2 - - + -
132B PHE* 4.6 7.6 - - + -
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.6 33.5 - - + +
33B GLU* 3.8 19.7 - - - +
59B VAL 3.1 11.2 + - - +
60B ASN* 4.0 7.0 - - - +
62B VAL* 1.3 73.6 - - - +
64B PHE* 1.3 63.7 + - + +
66B ASN* 4.2 15.7 + - - +
67B GLN* 2.8 47.5 + - - +
185B HIS* 5.9 4.3 - - + -
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Residues in contact with PHE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ASN* 2.9 29.2 + - + +
61B THR* 3.6 5.2 - - - +
63B ASP* 1.3 78.8 - - + +
65B PHE* 1.3 56.4 + - - +
67B GLN* 3.2 3.9 + - + -
68B ILE* 2.8 39.6 + - + +
152B LEU* 4.0 13.0 - - + -
155B LEU* 4.0 7.6 - - + -
159B TYR* 5.0 3.1 - - - -
182B SER* 4.5 6.7 - - - -
185B HIS* 3.6 38.6 - + + -
186B PHE* 3.5 57.9 - + + -
189B PHE* 3.6 34.1 - + + -
190B VAL* 5.2 0.2 - - + -
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B THR 2.9 13.7 + - - +
62B VAL* 3.3 10.3 - - - +
64B PHE* 1.3 76.1 - - - +
66B ASN* 1.3 74.7 + - - +
68B ILE* 4.0 0.9 - - - +
69B ASN* 3.0 45.1 + - - +
119B MET* 3.4 53.6 - - + -
122B VAL* 3.4 26.2 - - + -
123B GLN* 4.1 26.7 - - + -
126B LEU* 3.7 24.2 - - + -
155B LEU* 3.6 18.3 - - + +
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Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B VAL* 2.9 34.4 + - - +
63B ASP* 3.7 18.0 + - - +
64B PHE 3.3 0.2 - - - -
65B PHE* 1.3 87.1 - - - +
67B GLN* 1.3 58.7 + - - +
69B ASN* 3.6 5.2 - - - +
70B MET* 3.0 35.0 + - + +
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASP* 2.8 32.4 + - - +
64B PHE* 3.8 6.1 - - + +
66B ASN* 1.3 75.2 - - - +
68B ILE* 1.3 61.9 + - + +
70B MET* 4.2 4.0 - - - +
71B LEU* 2.9 34.6 + - - +
178B HIS* 2.8 35.1 + - - +
182B SER* 3.3 28.0 - - - +
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Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 2.8 27.1 + - + +
65B PHE 4.0 2.5 - - - +
67B GLN* 1.3 75.7 - - + +
69B ASN* 1.3 65.9 + - - +
71B LEU* 3.3 4.7 + - + +
72B TYR* 2.8 24.9 + - - +
119B MET* 4.5 5.2 - - + -
155B LEU* 4.1 22.7 - - + +
158B VAL* 3.5 40.4 - - + -
159B TYR* 3.1 55.6 - - + +
162B ILE* 6.0 1.6 - - + -
182B SER* 4.7 1.1 - - - +
186B PHE* 5.2 1.6 - - + -
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Residues in contact with ASN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 3.0 35.8 + - + +
66B ASN* 3.6 6.7 - - - +
67B GLN 3.3 0.2 - - - -
68B ILE* 1.3 78.2 - - - +
70B MET* 1.3 66.4 + - + +
72B TYR* 3.8 5.0 - - - +
73B GLY* 2.9 26.9 + - - -
119B MET* 3.4 31.4 - - + +
123B GLN* 5.7 1.0 + - - -
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Residues in contact with MET 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B ASN* 3.0 21.0 + - + +
67B GLN* 4.2 4.3 - - - +
69B ASN* 1.3 84.0 - - + +
71B LEU* 1.3 64.8 + - - +
73B GLY* 3.4 9.8 + - - +
74B THR* 3.5 16.5 + - - +
178B HIS* 5.4 7.0 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLN 2.9 20.8 + - - +
68B ILE* 3.6 5.4 - - - +
70B MET* 1.3 77.8 - - - +
72B TYR* 1.3 58.9 + - - +
74B THR* 2.3 36.6 + - + +
75B ILE* 4.0 2.6 + - - +
159B TYR* 4.5 10.1 - - + -
162B ILE* 4.6 5.8 - - + +
170B VAL* 5.9 3.3 - - + +
175B GLU* 5.3 7.6 - - + +
178B HIS* 3.4 40.8 - - + +
179B LEU* 3.5 52.5 - - + +
182B SER* 3.9 16.4 - - - +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ILE 2.8 20.4 + - - +
69B ASN* 3.8 5.8 - - - +
71B LEU* 1.3 73.3 - - - +
73B GLY* 1.3 64.9 + - - +
74B THR 3.0 1.2 + - - -
75B ILE* 3.0 21.0 + - + +
76B THR* 3.1 27.8 + - + -
79B CYS* 2.8 42.1 - - + +
112B PRO* 3.8 16.7 - - + +
115B ILE* 3.8 32.6 - - + +
119B MET* 6.1 1.6 - - + -
158B VAL* 3.9 25.4 - - + -
161B HIS* 4.5 9.9 - + - -
162B ILE* 4.0 20.3 - - + +
166B HIS* 5.7 0.2 - + - -
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ASN* 2.9 16.1 + - - -
70B MET* 3.4 5.8 + - - -
71B LEU 3.2 1.0 - - - -
72B TYR* 1.3 78.3 - - - +
74B THR* 1.3 57.7 + - - +
76B THR* 2.4 38.2 + - - +
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B MET 3.5 14.8 - - - +
71B LEU* 2.3 31.5 + - + +
73B GLY* 1.3 79.6 - - - +
75B ILE* 1.3 65.8 + - - +
76B THR* 3.3 1.7 + - - -
77B GLU* 4.7 3.6 + - - +
78B PHE* 5.0 2.3 - - - -
170B VAL* 5.3 2.4 - - - +
173B LEU* 3.7 18.3 - - - +
175B GLU* 3.0 34.0 + - - +
178B HIS* 6.3 0.9 - - - +
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Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 4.5 0.7 - - - +
72B TYR* 3.3 22.4 - - + +
74B THR* 1.3 81.5 + - - +
76B THR* 1.3 65.7 + - - +
77B GLU 3.1 3.6 - - - -
78B PHE* 2.9 29.6 + - + +
79B CYS* 3.1 10.3 + - - +
161B HIS* 6.2 0.2 - - + -
162B ILE* 3.6 44.2 - - + -
166B HIS* 4.1 24.9 - - + +
169B SER* 4.5 2.2 - - - -
170B VAL* 3.5 28.9 - - + +
173B LEU* 4.2 13.7 - - + -
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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) + - + + + + + -
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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