Contacts of the helix formed by residues 52 - 75 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.4 1.1 - - - +
51A GLU* 1.3 86.7 + - - +
53A LEU* 1.3 83.4 + - - +
54A ASN* 3.0 21.6 + - - +
55A GLU* 3.7 24.8 + - + +
56A TRP* 3.1 24.3 + - - +
140A PHE* 4.7 5.9 - - - -
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 3.7 20.3 - - + +
51A GLU 3.6 2.8 + - - -
52A ASP* 1.3 75.8 + - - +
54A ASN* 1.3 77.4 + - - +
56A TRP* 3.2 3.2 + - - +
57A ILE* 2.9 39.6 + - + +
145A MET* 3.7 26.5 - - + -
193A PHE* 4.0 27.4 - - + -
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.0 11.1 + - - +
53A LEU* 1.3 94.1 - - - +
55A GLU* 1.3 57.3 + - - +
57A ILE* 4.5 1.1 - - - +
58A ALA* 2.9 29.6 + - - +
140A PHE* 3.5 37.5 + - + +
141A PRO 4.7 3.4 + - - -
144A PHE* 3.0 36.5 + - + +
145A MET* 4.2 8.0 - - - +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A HIS* 4.0 16.6 + - - -
25A GLN* 3.1 31.0 - - - +
28A LEU* 3.9 10.8 - - + +
51A GLU* 2.7 31.2 - - - +
52A ASP* 3.7 20.0 + - + +
53A LEU 3.2 0.6 - - - -
54A ASN* 1.3 79.0 - - - +
56A TRP* 1.3 63.2 + - - +
58A ALA* 3.1 2.4 + - - +
59A VAL* 2.9 29.9 + - - +
136A ILE* 4.7 14.0 - - - +
140A PHE* 3.7 18.2 - - + -
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Residues in contact with TRP 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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28A LEU* 3.6 47.5 - - + +
31A HIS* 4.3 5.4 - - + -
32A ALA* 3.8 24.5 - - + -
35A THR* 5.6 0.2 - - - -
44A ALA 4.1 12.6 - - - -
45A VAL* 3.0 24.2 + - - -
46A MET 3.7 15.6 + - - -
47A LEU* 3.5 13.5 - - + -
48A PRO* 3.9 19.7 - - + -
51A GLU* 5.0 0.9 - - + -
52A ASP 3.1 19.7 + - - +
53A LEU 3.5 2.7 - - - +
55A GLU* 1.3 76.1 - - - +
57A ILE* 1.3 62.8 + - - +
59A VAL* 3.2 3.8 + - + +
60A ASN* 2.7 49.4 + - - -
189A PHE* 3.2 16.9 - + - -
193A PHE* 3.4 26.0 - + - -
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 2.9 35.3 + - + +
54A ASN* 3.9 5.4 - - - +
56A TRP* 1.3 74.4 - - + +
58A ALA* 1.3 55.1 + - - +
60A ASN* 4.4 0.2 - - - +
61A THR* 2.4 46.3 + - - +
144A PHE* 4.6 3.8 - - + -
145A MET* 4.9 7.2 - - - -
148A ALA* 3.8 20.0 - - + -
189A PHE* 3.4 26.8 - - + -
193A PHE* 3.5 34.8 - - + -
195A LEU* 3.6 26.0 - - + -
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Residues in contact with ALA 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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25A GLN* 5.3 5.4 - - - +
54A ASN 2.9 19.3 + - - +
55A GLU 3.1 5.3 + - - +
57A ILE* 1.3 76.8 - - - +
59A VAL* 1.3 64.4 + - + +
61A THR* 3.3 3.4 + - - -
62A VAL* 3.0 29.9 + - + +
132A PHE* 3.6 30.9 - - + -
140A PHE* 3.7 19.5 - - + -
144A PHE* 4.1 2.0 - - + -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 5.9 2.9 - - + -
25A GLN* 4.0 37.5 - - + +
28A LEU* 4.0 18.4 - - + +
29A LEU* 3.6 44.2 - - + +
32A ALA* 5.7 0.7 - - + -
55A GLU 2.9 22.8 + - - +
56A TRP* 3.2 3.8 + - - +
58A ALA* 1.3 76.4 - - - +
60A ASN* 1.3 68.0 + - - +
62A VAL* 3.1 9.6 + - - +
63A ASP* 3.1 19.9 + - - +
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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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32A ALA* 3.3 26.0 - - - +
45A VAL* 5.9 0.2 - - - -
56A TRP* 2.7 55.5 + - - +
59A VAL* 1.3 75.4 - - - +
61A THR* 1.3 60.5 + - - +
63A ASP* 3.9 6.8 - - - +
64A PHE* 2.8 45.6 + - + -
185A HIS* 4.2 14.2 + - + -
189A PHE* 3.6 33.2 - - + -
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Residues in contact with THR 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 ILE* 2.4 38.8 + - - +
58A ALA* 3.5 7.6 - - - -
59A VAL 3.2 0.2 - - - -
60A ASN* 1.3 78.1 - - - +
62A VAL* 1.3 56.6 + - - +
64A PHE* 3.4 9.2 + - - +
65A PHE* 2.9 27.3 + - + +
126A LEU* 4.4 9.0 - - + -
132A PHE* 4.7 4.9 - - + -
148A ALA* 4.5 4.8 - - - +
151A ILE* 3.7 40.8 - - + -
152A LEU* 3.9 18.7 - - + +
155A LEU* 4.5 1.4 - - - +
189A PHE* 5.2 0.7 - - - -
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Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 5.7 8.5 - - + -
29A LEU* 6.6 0.2 - - + -
58A ALA 3.0 16.5 + - - +
59A VAL* 3.1 9.4 + - - +
61A THR* 1.3 75.8 - - - +
63A ASP* 1.3 57.4 + - - +
65A PHE* 3.0 9.2 + - + +
66A ASN* 2.9 43.9 + - - +
126A LEU* 3.8 33.2 - - + -
132A PHE* 5.2 5.6 - - + -
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.6 33.1 - - + +
32A ALA* 6.0 1.4 - - - +
33A GLU* 4.0 17.0 - - - +
59A VAL 3.1 11.3 + - - +
60A ASN* 3.3 7.2 + - - +
62A VAL* 1.3 77.1 - - - +
64A PHE* 1.3 60.6 + - + +
66A ASN* 3.9 12.2 + - - +
67A GLN* 2.9 53.5 + - - +
185A HIS* 5.1 11.3 + - + -
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Residues in contact with PHE 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 31.3 + - + +
61A THR* 3.6 5.2 - - - +
63A ASP* 1.3 77.3 - - + +
65A PHE* 1.3 65.5 + - - +
67A GLN* 3.8 4.2 - - + +
68A ILE* 2.9 33.0 + - + +
152A LEU* 4.3 11.9 - - + -
155A LEU* 4.2 9.0 - - + -
159A TYR* 4.5 5.2 - - - -
182A SER* 4.4 6.5 - - - -
185A HIS* 3.4 48.5 - + + -
186A PHE* 3.6 50.9 - + + -
189A PHE* 3.5 30.5 - + + -
190A VAL* 5.2 0.4 - - + -
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Residues in contact with PHE 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 THR 2.9 14.4 + - - +
62A VAL* 3.0 7.4 + - + +
64A PHE* 1.3 76.2 - - - +
66A ASN* 1.3 75.3 + - - +
69A ASN* 2.9 51.7 + - - +
119A MET* 3.5 52.6 - - + +
122A VAL* 3.4 24.7 - - + -
123A GLN* 3.4 31.4 - - + -
126A LEU* 3.6 25.1 - - + -
155A LEU* 3.9 14.9 - - + +
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Residues in contact with ASN 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 VAL* 2.9 36.4 + - - +
63A ASP* 3.9 12.0 + - - +
65A PHE* 1.3 92.2 - - - +
67A GLN* 1.3 64.4 + - + +
69A ASN* 3.4 5.8 + - - +
70A MET* 3.0 31.4 + - + +
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Residues in contact with GLN 67 (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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63A ASP* 2.9 42.7 + - - +
64A PHE* 3.8 8.1 - - + +
66A ASN* 1.3 77.6 - - + +
68A ILE* 1.3 58.4 + - + +
70A MET* 3.4 4.6 + - - +
71A LEU* 2.9 34.5 + - - +
178A HIS* 2.9 32.2 + - - -
182A SER* 3.8 24.8 - - - +
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Residues in contact with ILE 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 PHE* 2.9 26.1 + - + +
65A PHE 3.9 2.5 - - - +
67A GLN* 1.3 75.1 - - + +
69A ASN* 1.3 68.3 + - - +
71A LEU* 3.7 6.7 - - + +
72A TYR* 2.9 25.5 + - - +
119A MET* 4.1 12.1 - - + -
155A LEU* 4.2 15.0 - - + +
158A VAL* 3.5 36.1 - - + -
159A TYR* 3.1 54.1 - - + +
162A ILE* 5.8 1.8 - - + -
182A SER* 4.1 6.1 - - - +
186A PHE* 5.5 0.2 - - + -
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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
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65A PHE* 2.9 42.0 + - + +
66A ASN* 3.7 8.0 + - - +
68A ILE* 1.3 77.0 - - - +
70A MET* 1.3 66.7 + - + +
72A TYR* 3.9 5.5 - - - +
73A GLY* 2.9 25.3 + - - -
119A MET* 3.8 24.7 - - + +
123A GLN* 5.3 1.4 + - - -
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Residues in contact with MET 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 ASN* 3.0 20.3 + - + +
67A GLN* 3.8 5.8 - - - +
69A ASN* 1.3 86.4 - - + +
71A LEU* 1.3 63.3 + - - +
73A GLY* 2.9 13.9 + - - -
74A THR* 3.2 16.1 + - - +
175A GLU* 5.5 1.1 - - - +
178A HIS* 5.5 7.2 - - + -
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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 GLN 2.9 21.9 + - - +
68A ILE* 3.7 11.0 - - + +
70A MET* 1.3 76.2 - - - +
72A TYR* 1.3 61.0 + - - +
74A THR* 2.2 34.8 + - - +
75A ILE* 3.9 2.6 + - - +
159A TYR* 5.1 2.2 - - + -
162A ILE* 4.5 8.4 - - + +
170A VAL* 6.2 1.1 - - + -
175A GLU* 3.2 33.9 - - + +
178A HIS* 3.7 20.9 - - + +
179A LEU* 3.5 48.9 - - + +
182A SER* 4.1 15.9 - - - +
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Residues in contact with TYR 72 (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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68A ILE 2.9 19.6 + - - +
69A ASN* 4.1 4.7 - - - +
71A LEU* 1.3 73.9 - - - +
73A GLY* 1.3 64.4 + - - +
75A ILE* 3.0 20.2 + - + +
76A THR* 3.3 25.0 + - + -
79A CYS* 3.1 43.1 + - + +
112A PRO* 3.8 18.9 - - + +
115A ILE* 3.8 32.9 - - + +
119A MET* 6.4 0.7 - - - -
158A VAL* 4.2 17.3 - - + -
161A HIS* 4.2 9.0 - + - -
162A ILE* 3.6 31.0 - - + +
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Residues in contact with GLY 73 (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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69A ASN* 2.9 18.0 + - - -
70A MET* 2.9 8.8 + - - -
72A TYR* 1.3 77.8 - - - +
74A THR* 1.3 60.6 + - - +
76A THR* 3.2 28.2 + - - +
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Residues in contact with THR 74 (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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70A MET 3.2 11.0 + - - +
71A LEU* 2.2 28.1 + - - +
73A GLY* 1.3 77.9 - - - +
75A ILE* 1.3 67.8 + - - +
76A THR* 3.6 1.7 + - - -
77A GLU* 4.8 2.9 + - - +
78A PHE* 6.0 0.5 - - - -
170A VAL* 5.4 0.7 - - - +
173A LEU* 4.0 16.8 - - - +
175A GLU* 3.4 39.6 - - + +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 4.7 0.4 - - - +
72A TYR* 3.3 25.6 - - + +
74A THR* 1.3 84.2 + - - +
76A THR* 1.3 64.7 + - - +
77A GLU 3.1 3.6 - - - -
78A PHE* 2.8 26.4 + - + +
79A CYS* 3.1 9.9 + - + +
162A ILE* 3.6 43.3 - - + -
166A HIS* 4.2 21.3 - - + -
169A SER* 4.5 7.4 - - - +
170A VAL* 3.7 25.4 - - + -
173A LEU* 3.8 15.3 - - + -
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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