Contacts of the helix formed by residues 52 - 77 (chain A) in PDB entry 3EUP
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 ASN 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TYR* 3.3 14.5 - - - -
50A PHE* 3.4 0.9 - - - +
51A GLU* 1.3 97.5 - - + +
53A LYS* 1.3 64.9 + - - +
54A GLU* 3.1 17.0 + - - +
55A ALA* 2.9 41.1 + - - +
56A VAL* 3.2 14.4 + - - +
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Residues in contact with LYS 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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22A PHE* 4.0 15.3 - - + -
27A LEU* 2.9 35.2 + - + +
28A ALA* 4.5 4.9 + - - +
30A THR 2.6 32.1 + - - +
31A SER* 4.7 6.0 - - - +
32A LEU* 5.4 0.4 - - - +
35A LEU* 4.5 8.5 - - + -
47A TYR* 3.3 25.6 + - - +
52A ASN* 1.3 75.7 - - - +
54A GLU* 1.3 56.5 + - - +
56A VAL* 3.1 7.7 + - - +
57A ALA* 2.9 25.5 + - - +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.2 14.8 - - + +
52A ASN* 3.1 13.9 + - - +
53A LYS* 1.3 77.1 - - - +
55A ALA* 1.3 61.4 + - - +
57A ALA* 3.2 2.4 + - + +
58A ILE* 3.0 44.3 + - + +
119A HIS* 3.2 38.0 + - + -
121A ALA* 4.3 6.1 - - - +
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PHE* 3.9 11.8 - - + -
51A GLU* 4.1 16.4 - - + +
52A ASN* 2.9 28.1 + - - +
54A GLU* 1.3 76.9 - - - +
56A VAL* 1.3 61.2 + - - +
58A ILE* 3.5 9.2 + - - +
59A ALA* 3.2 23.9 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.4 14.1 - - + -
15A ILE* 5.5 2.1 - - - +
18A THR* 3.6 16.6 - - + +
22A PHE* 3.4 23.1 - - + -
35A LEU* 4.9 6.1 - - + -
46A ILE* 4.6 6.7 - - + -
47A TYR* 4.1 13.0 - - + -
50A PHE* 3.6 34.3 - - + -
52A ASN 3.4 14.4 - - - +
53A LYS* 3.1 8.6 + - - +
55A ALA* 1.3 77.0 - - - +
57A ALA* 1.3 55.9 + - - +
59A ALA* 3.4 2.6 + - - +
60A ALA* 2.8 27.5 + - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.9 22.6 - - + +
27A LEU* 3.8 24.2 - - + -
53A LYS 2.9 12.9 + - - +
54A GLU 3.2 8.3 + - - +
56A VAL* 1.3 74.9 - - - +
58A ILE* 1.3 58.2 + - - +
60A ALA* 3.3 5.0 + - - +
61A PHE* 2.9 28.1 + - - +
122A LEU* 4.5 16.3 - - + +
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 3.0 43.1 + - + +
55A ALA* 3.9 8.3 - - - +
57A ALA* 1.3 74.1 - - - +
59A ALA* 1.3 65.0 + - - +
61A PHE* 3.2 4.7 + - - +
62A ASP* 3.0 24.7 + - - +
119A HIS* 4.9 0.4 - - - +
121A ALA* 4.5 14.1 - - + -
122A LEU* 4.0 26.0 - - + -
125A LYS* 3.6 31.4 - - + +
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Residues in contact with ALA 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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11A ARG* 4.2 9.6 - - - +
15A ILE* 3.8 33.3 - - + +
50A PHE* 3.8 11.4 - - + -
55A ALA 3.2 15.2 + - - +
56A VAL 3.7 3.6 - - - +
58A ILE* 1.3 75.5 - - - +
60A ALA* 1.3 60.7 + - - +
62A ASP* 3.2 10.2 + - - +
63A TYR* 2.9 29.1 + - - +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 4.3 8.1 - - - +
18A THR* 4.9 1.6 - - - +
19A ALA* 3.9 23.8 - - - +
22A PHE* 3.7 29.6 - - + -
56A VAL 2.8 15.5 + - - +
57A ALA 3.5 8.3 - - - +
58A ILE 3.3 0.2 - - - -
59A ALA* 1.3 76.5 - - - +
61A PHE* 1.3 57.1 + - - +
63A TYR* 3.2 1.9 + - - +
64A ASN* 2.9 36.8 + - - +
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 2.9 13.3 + - - +
58A ILE 3.2 7.4 + - - +
60A ALA* 1.3 74.6 - - - +
62A ASP* 1.3 79.6 + - - +
64A ASN* 4.5 4.7 - - - -
65A TRP* 2.9 44.8 + + + +
107A PRO* 3.7 32.1 - - + -
108A LEU* 4.3 5.4 - - - -
111A THR* 3.3 29.6 - - + +
122A LEU* 4.2 13.9 - - + -
125A LYS* 3.9 31.9 - - + -
126A ALA* 4.3 7.4 - - + -
129A ALA* 4.1 18.4 - - + -
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.0 17.4 + - - +
59A ALA* 3.2 10.5 + - - +
61A PHE* 1.3 83.0 - - - +
63A TYR* 1.3 56.8 + - - +
65A TRP* 5.1 0.7 - - - -
66A GLY* 2.8 28.2 + - - +
125A LYS* 2.7 42.6 + - - -
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Residues in contact with TYR 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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12A GLN* 3.7 19.3 - - - -
15A ILE* 3.4 26.7 - - + -
16A GLU* 3.6 36.8 + - + +
19A ALA* 3.8 14.8 - - + -
20A PRO* 6.0 0.4 - - + -
59A ALA 2.9 7.9 + - - +
60A ALA 3.7 2.2 - - - +
61A PHE 3.2 0.2 - - - -
62A ASP* 1.3 75.5 - - - +
64A ASN* 1.3 77.0 + - - +
66A GLY* 3.7 1.0 - - - -
67A HIS* 2.8 42.2 + + + +
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 3.0 41.2 + - - +
20A PRO* 4.8 1.8 - - - +
22A PHE* 5.4 0.2 - - - +
23A ASN* 3.6 12.6 + - - +
60A ALA* 2.9 25.4 + - - +
61A PHE* 3.8 2.1 - - - +
63A TYR* 1.3 82.5 - - - +
65A TRP* 1.3 62.3 + - - +
67A HIS* 3.3 7.4 + - - +
68A VAL* 3.2 23.6 + - - +
102A PRO* 3.6 27.2 - - + +
107A PRO* 3.7 23.6 - - + +
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Residues in contact with TRP 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 PHE* 2.9 35.4 + + + +
62A ASP* 4.6 1.3 - - - +
64A ASN* 1.3 73.7 - - - +
66A GLY* 1.3 66.9 + - - +
68A VAL* 3.0 29.4 + - + -
69A LYS* 2.9 66.0 + - + +
72A LEU* 6.4 1.8 - - + -
106A CYS* 4.1 11.7 - - - -
107A PRO* 3.6 16.3 - - + +
108A LEU* 3.6 37.7 - - + -
129A ALA* 3.5 34.7 + - + +
132A SER* 6.1 0.8 - - - -
133A TRP* 3.8 29.4 - + + -
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Residues in contact with GLY 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 ASP 2.8 22.0 + - - -
63A TYR* 3.7 1.8 - - - -
65A TRP* 1.3 76.6 - - - +
67A HIS* 1.3 55.5 + - - +
69A LYS* 3.4 15.5 + - - +
70A SER* 2.9 34.9 + - - -
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Residues in contact with HIS 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 TYR* 2.8 30.2 + + + +
64A ASN* 3.4 11.7 - - - +
65A TRP 3.1 0.2 - - - -
66A GLY* 1.3 73.9 - - - +
68A VAL* 1.3 65.9 + - - +
70A SER* 3.3 7.2 + - - -
71A VAL* 3.1 37.6 + - + +
99A SER 5.2 2.0 - - - -
100A LEU* 3.0 32.4 + - - -
101A PHE 4.8 3.4 - - - -
102A PRO* 4.4 14.8 - - + +
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Residues in contact with VAL 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 ASN 3.2 13.2 + - - +
65A TRP* 3.0 33.2 + - + +
67A HIS* 1.3 78.2 - - - +
69A LYS* 1.3 62.9 + - - +
71A VAL* 3.3 6.9 + - - +
72A LEU* 3.0 27.0 + - + +
92A MET* 4.0 17.3 - - - +
100A LEU 5.7 0.7 - - - -
101A PHE* 4.0 21.1 - - + -
102A PRO* 3.7 23.1 - - + -
107A PRO* 4.0 15.0 - - + -
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 2.9 57.4 + - + +
66A GLY* 3.5 11.1 - - - +
67A HIS 3.3 0.2 - - - -
68A VAL* 1.3 77.0 - - - +
70A SER* 1.3 52.1 + - - +
72A LEU* 3.3 10.6 + - + +
73A THR* 2.8 40.3 + - - +
132A SER* 5.9 7.1 - - - -
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Residues in contact with SER 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLY 2.9 17.8 + - - -
67A HIS* 3.8 9.0 - - - -
69A LYS* 1.3 73.1 - - - +
71A VAL* 1.3 60.3 + - - +
73A THR* 3.5 7.5 + - - +
74A ALA* 3.0 29.3 + - - +
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.1 26.7 + - + +
68A VAL* 3.7 7.6 - - - +
70A SER* 1.3 72.5 - - - +
72A LEU* 1.3 65.6 + - - +
74A ALA* 3.1 6.8 + - - +
75A LYS* 2.9 40.6 + - + +
92A MET* 3.4 30.3 - - + -
100A LEU* 3.8 33.2 - - + +
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Residues in contact with LEU 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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65A TRP* 6.4 2.0 - - + -
68A VAL* 3.0 20.9 + - + +
69A LYS* 3.6 9.0 - - + +
71A VAL* 1.3 77.5 - - - +
73A THR* 1.3 55.8 + - - +
75A LYS* 3.4 2.6 + - - +
76A VAL* 2.8 61.6 + - + +
88A VAL* 4.5 1.6 - - + -
89A TYR* 3.4 38.4 - - + +
92A MET* 3.6 25.1 - - + -
133A TRP* 3.9 17.3 - - + +
136A ASN* 6.5 1.3 - - + -
137A LEU* 6.2 0.4 - - + -
140A ILE* 5.7 3.8 - - + -
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Residues in contact with THR 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 LYS* 2.8 22.0 + - - +
70A SER* 3.7 8.7 - - - -
72A LEU* 1.3 79.8 - - - +
74A ALA* 1.3 63.7 + - - +
76A VAL* 3.8 3.9 - - - +
77A GLN* 3.0 61.7 + - + +
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Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER 3.0 17.4 + - - +
71A VAL* 3.1 6.7 + - - +
73A THR* 1.3 78.0 - - - +
75A LYS* 1.3 62.4 + - + +
77A GLN* 3.5 9.4 + - - +
78A ALA* 3.4 20.3 + - - +
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Residues in contact with LYS 75 (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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71A VAL* 2.9 23.6 + - + +
72A LEU* 3.9 3.4 - - - +
74A ALA* 1.3 76.1 - - + +
76A VAL* 1.3 64.1 + - - +
78A ALA* 3.2 15.8 + - - +
79A CYS* 3.3 15.1 + - - -
88A VAL* 4.0 20.9 - - + +
91A SER* 3.3 27.0 + - - +
92A MET* 4.1 21.1 - - + +
95A ASP* 4.3 8.3 + - - -
100A LEU* 3.9 26.7 - - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 2.8 46.2 + - + +
73A THR* 3.8 5.2 - - - +
75A LYS* 1.3 73.0 - - - +
77A GLN* 1.3 61.4 + - + +
79A CYS* 3.0 32.0 + - - +
85A MET* 3.7 51.1 - - + +
88A VAL* 4.2 5.6 - - + -
140A ILE* 4.4 12.8 - - + -
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Residues in contact with GLN 77 (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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73A THR* 3.0 46.5 + - + +
74A ALA* 4.0 8.1 - - - +
75A LYS 3.4 0.2 - - - -
76A VAL* 1.3 79.0 - - + +
78A ALA* 1.3 57.3 + - - +
79A CYS 3.4 3.2 - - - +
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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