Contacts of the helix formed by residues 59 - 86 (chain A) in PDB entry 1DPS
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 PHE 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS 4.4 1.8 - - - -
52A TRP 5.5 0.2 - - - -
54A MET* 3.2 41.3 - - + +
56A GLY 3.2 10.0 + - - +
57A ALA 3.2 0.2 - - - -
58A ASN* 1.3 79.0 - - - +
60A ILE* 1.3 79.3 + - + +
62A VAL* 3.8 0.7 - - - +
63A HIS* 2.8 64.3 + + + +
114A VAL* 4.0 8.7 - - + -
160H TRP* 4.2 9.9 - + - -
161H PHE* 3.6 36.6 - + - -
164H CYS* 3.2 42.4 - - + +
165H ASN* 3.5 18.2 + - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 1.3 84.8 - - + +
61A ALA* 1.3 61.2 + - - +
63A HIS* 3.5 2.7 - - + +
64A GLU* 3.0 59.8 + - + +
58H ASN* 4.6 3.6 - - - +
61H ALA* 3.7 33.2 - - + +
62H VAL 4.5 1.6 - - - +
65H MET* 3.9 17.9 - - + -
161H PHE* 3.5 44.4 - - + -
165H ASN* 3.3 27.2 + - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASN* 3.6 18.9 + - - +
59A PHE 3.4 0.4 - - - -
60A ILE* 1.3 81.6 - - - +
62A VAL* 1.3 58.9 + - - +
64A GLU* 3.6 7.8 + - - +
65A MET* 2.9 28.2 + - - +
61H ALA* 4.1 19.3 - - + -
60K ILE* 3.8 19.2 - - + +
61K ALA* 4.1 10.8 - - + -
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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
----------------------------------------------------------
54A MET* 3.8 26.9 - - + -
58A ASN* 3.2 42.3 + - + +
59A PHE 4.0 1.3 - - - +
61A ALA* 1.3 74.5 - - - +
63A HIS* 1.3 66.1 + - - +
65A MET* 3.2 10.0 + - + +
66A LEU* 3.0 31.3 + - + +
114A VAL* 4.4 10.5 - - + -
118A LEU* 4.0 20.2 - - + -
165A ASN* 4.2 20.6 - - + +
60K ILE* 4.8 1.3 - - + -
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Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 2.7 83.0 + + - -
52A TRP* 4.6 3.4 - + - -
54A MET* 4.1 9.3 - - - -
59A PHE* 2.8 40.4 + + + +
60A ILE* 3.5 4.7 - - + +
62A VAL* 1.3 74.4 - - - +
64A GLU* 1.3 70.3 - - + +
66A LEU* 3.6 1.4 + - - +
67A ASP 3.3 5.9 + - - -
82C GLU* 4.9 6.5 + - - -
160H TRP* 4.0 20.2 - + - -
161H PHE* 3.9 30.7 - + - -
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ILE* 3.0 46.3 + - + +
61A ALA* 4.0 5.6 - - - +
63A HIS* 1.3 80.9 - - + +
65A MET* 1.3 64.4 + - - +
67A ASP* 3.2 17.7 + - - +
68A GLY* 3.3 9.5 + - - -
161H PHE* 5.2 3.6 - - + -
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Residues in contact with MET 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ALA 2.9 20.1 + - - +
62A VAL* 3.2 16.6 + - + +
64A GLU* 1.3 75.1 - - - +
66A LEU* 1.3 76.5 + - + +
68A GLY* 3.1 12.5 + - - -
69A PHE* 3.1 55.4 + - + -
118A LEU* 4.7 2.0 - - + -
161A PHE* 4.0 15.7 - - + +
162A ILE* 4.4 9.2 - - + -
165A ASN* 3.6 28.7 - - - +
60K ILE* 3.9 25.8 - - + -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR* 3.3 24.8 - - + +
48A LYS* 5.8 0.2 - - - -
51A HIS* 4.0 25.1 - - + +
54A MET* 3.7 25.6 - - + -
62A VAL* 3.0 26.2 + - + +
63A HIS 3.9 4.0 - - - +
64A GLU 3.3 0.2 - - - -
65A MET* 1.3 81.6 - - + +
67A ASP* 1.3 64.5 - - - +
69A PHE* 3.1 27.3 + - + +
70A ARG* 3.1 17.8 + - - +
118A LEU* 5.7 0.2 - - + -
121A LEU* 3.6 33.4 - - + -
125A TYR* 4.9 1.1 - - - +
162A ILE* 4.6 7.0 - - + -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 2.7 36.8 + - - +
51A HIS* 3.9 19.9 + - + -
63A HIS 3.3 4.4 + - - +
64A GLU* 3.2 13.5 + - - +
66A LEU* 1.3 77.7 - - - +
68A GLY* 1.3 64.9 + - - +
70A ARG* 3.2 17.7 + - - +
71A THR* 3.3 17.8 + - - -
78C ASP* 4.4 0.5 - - - +
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.3 5.5 + - - -
65A MET* 3.1 8.9 + - - -
67A ASP* 1.3 80.6 + - - +
69A PHE* 1.3 63.9 + - - +
71A THR* 3.4 9.6 + - - -
72A ALA* 3.2 20.6 + - - +
158A PHE* 5.2 0.4 - - - -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 3.1 42.9 + - + -
66A LEU* 3.1 22.0 + - + +
68A GLY* 1.3 78.2 - - - +
70A ARG* 1.3 62.6 + - - +
72A ALA* 3.3 2.9 + - - +
73A LEU* 3.0 27.9 + - - +
125A TYR* 3.6 26.2 - + - +
158A PHE* 3.4 62.0 - + + -
161A PHE* 3.8 29.2 - + + -
162A ILE* 3.9 14.8 - - + -
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Residues in contact with ARG 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 3.8 28.2 - - - +
47A THR* 4.3 6.2 - - + +
48A LYS* 3.4 37.0 - - + +
66A LEU 3.1 11.6 + - - +
67A ASP* 3.2 14.5 + - - +
69A PHE* 1.3 76.9 - - - +
71A THR* 1.3 65.6 + - - +
73A LEU* 3.2 10.3 + - - +
74A ILE* 3.0 46.2 + - - +
74C ILE* 4.3 33.6 - - - +
75C ASP* 5.4 2.4 + - - -
77C LEU* 5.8 1.6 - - - +
78C ASP* 3.2 30.1 + - - -
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 3.3 15.6 + - - -
68A GLY* 3.5 11.6 - - - -
69A PHE 3.3 0.2 - - - -
70A ARG* 1.3 82.1 + - - +
72A ALA* 1.3 63.1 + - - +
74A ILE* 3.2 19.1 - - + +
75A ASP* 3.2 34.2 + - - +
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 3.2 8.4 + - - +
69A PHE 3.3 4.0 + - - +
71A THR* 1.3 80.3 - - - +
73A LEU* 1.3 63.5 + - - +
75A ASP* 3.2 9.5 + - - +
76A HIS* 3.0 30.5 + - + +
154A ASP* 4.0 11.9 - - - +
158A PHE* 3.6 32.5 - - + -
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 4.1 18.1 - - + +
43A LEU* 4.1 17.0 - - + -
44A SER* 3.9 35.2 - - - +
47A THR* 4.0 3.4 - - - +
69A PHE 3.0 21.4 + - - +
70A ARG* 3.2 4.9 + - - +
72A ALA* 1.3 76.6 - - - +
74A ILE* 1.3 61.3 + - - +
76A HIS* 3.3 6.3 + - + +
77A LEU* 3.0 28.4 + - - +
125A TYR* 3.6 22.7 - - + +
155A LEU* 3.6 32.3 - - + -
158A PHE* 4.5 10.8 - - + -
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 4.2 16.4 - - - +
70A ARG* 3.0 46.1 + - - +
71A THR* 3.2 23.1 - - + +
73A LEU* 1.3 76.0 - - - +
75A ASP* 1.3 64.3 + - - +
77A LEU* 3.7 11.3 - - + +
78A ASP* 3.0 35.5 + - - +
70C ARG* 4.3 26.2 - - - +
74C ILE* 4.2 20.2 - - + -
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A THR* 3.2 28.4 + - - +
72A ALA* 3.6 10.1 - - - +
73A LEU 3.2 0.2 - - - -
74A ILE* 1.3 81.4 - - - +
76A HIS* 1.3 64.1 + - + +
78A ASP* 3.5 8.7 + - - +
79A THR* 2.9 28.3 + - - -
70C ARG* 5.4 1.6 + - - -
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Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 4.1 8.1 - + + -
72A ALA* 3.0 28.1 + - - +
73A LEU* 3.8 8.5 - - + +
75A ASP* 1.3 77.7 - - + +
77A LEU* 1.3 61.6 + - - +
79A THR* 3.2 9.9 + - - -
80A MET* 3.0 40.1 + - + +
147A ILE* 4.9 3.1 + - - +
150A ALA* 3.6 29.4 - - + +
151A ALA* 3.6 22.9 + - + +
154A ASP* 2.7 37.6 + - + +
155A LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.9 12.8 - - + +
40A PHE* 3.7 23.3 - - + +
41A ILE* 3.6 48.2 - - + +
44A SER* 4.6 0.4 - - - +
73A LEU 3.0 21.9 + - - +
74A ILE* 3.7 23.3 - - + +
76A HIS* 1.3 76.3 - - - +
78A ASP* 1.3 71.0 + - - +
80A MET* 3.2 12.0 + - - +
81A ALA* 2.9 28.6 + - - +
52C TRP* 4.0 17.0 - - + -
70C ARG* 5.8 2.0 - - - +
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Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE 3.0 23.2 + - - +
75A ASP* 3.8 8.8 - - - +
76A HIS 3.3 0.2 - - - -
77A LEU* 1.3 80.5 - - - +
79A THR* 1.3 58.7 + - - +
81A ALA* 3.3 2.7 + - - +
82A GLU* 2.9 43.1 + - - +
48C LYS* 3.0 23.6 + - - +
52C TRP* 3.3 28.0 + - - +
67C ASP* 4.7 0.2 - - - +
70C ARG* 2.9 29.0 + - - -
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP 2.9 13.5 + - - -
76A HIS* 3.4 12.2 - - - -
78A ASP* 1.3 77.6 - - - +
80A MET* 1.3 62.2 + - - +
82A GLU* 3.4 10.7 + - - +
83A ARG* 3.1 21.7 + - - +
147A ILE* 3.7 22.1 - - + +
153E ARG* 3.5 28.6 + - - +
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 3.7 26.1 - - + +
36A GLN* 3.6 32.3 - - - -
37A VAL* 3.9 10.8 - - + -
40A PHE* 3.8 25.8 - - + -
76A HIS* 3.0 21.2 + - + +
77A LEU* 3.5 12.3 - - - +
79A THR* 1.3 73.6 - - - +
81A ALA* 1.3 63.7 + - - +
83A ARG* 3.3 4.7 + - - +
84A ALA* 3.1 20.1 + - - +
147A ILE* 3.8 19.3 - - + -
148A LEU* 4.4 11.2 - - + -
151A ALA* 3.7 30.7 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.9 10.7 - - + +
77A LEU 2.9 15.0 + - - +
78A ASP 3.6 0.7 - - - +
80A MET* 1.3 75.1 - - - +
82A GLU* 1.3 62.9 + - - +
84A ALA* 3.3 6.7 + - - +
85A VAL* 3.1 27.0 + - - +
91A ALA* 3.8 13.1 - - + +
52C TRP* 3.3 46.4 - - + +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 2.9 29.5 + - - +
79A THR* 3.8 8.6 - - - +
80A MET 3.3 0.2 - - - -
81A ALA* 1.3 74.6 - - - +
83A ARG* 1.3 64.1 + - - +
85A VAL* 3.2 9.6 - - - +
86A GLN* 3.0 41.2 + - - +
48C LYS* 5.5 0.7 + - - -
51C HIS* 4.6 12.3 + - - -
52C TRP* 4.3 11.6 - - + -
63C HIS* 4.8 5.6 + - + -
157E LYS* 4.0 24.4 + - - +
160E TRP* 3.8 21.2 - - + -
161E PHE* 6.0 0.4 - - - -
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 4.7 0.2 - - - +
33A LEU* 3.7 10.1 - - + -
79A THR 3.1 13.9 + - - +
80A MET* 3.6 9.2 - - - +
81A ALA 3.3 0.2 - - - -
82A GLU* 1.3 74.5 - - - +
84A ALA* 1.3 63.5 + - - +
86A GLN* 3.2 18.2 + - - +
87A LEU* 3.2 45.6 + - + +
141A ASP* 3.0 36.2 + - - -
143A ASP* 3.2 28.1 + - - +
144A THR* 3.5 17.5 + - - +
147A ILE* 3.8 23.3 - - + -
133E ARG* 4.1 5.5 - - - +
152E SER 5.0 0.2 + - - -
153E ARG* 5.1 3.7 - - - +
156E ASP* 2.8 40.2 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.5 26.5 - - + +
33A LEU* 3.6 22.4 - - + +
34A ASN* 4.9 4.0 - - - +
37A VAL* 6.3 0.2 - - + -
80A MET 3.1 12.7 + - - +
81A ALA* 3.5 11.7 - - - +
83A ARG* 1.3 76.3 - - - +
85A VAL* 1.3 60.2 + - - +
87A LEU* 3.3 7.4 + - - -
89A GLY* 3.0 23.1 + - - -
90A VAL 5.3 0.2 - - - -
91A ALA* 4.9 13.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 5.9 1.1 - - + -
81A ALA 3.1 13.8 + - - +
82A GLU* 3.2 19.7 - - - +
84A ALA* 1.3 73.7 - - - +
86A GLN* 1.3 65.4 + - - +
88A GLY* 3.0 14.4 + - - -
89A GLY 3.6 14.9 - - - +
91A ALA* 3.8 13.9 - - + +
52C TRP* 3.7 15.5 - - + +
53C ASN* 3.5 24.9 - - - +
55C ARG* 4.3 15.0 + - - +
160E TRP* 3.3 38.0 - - + +
----------------------------------------------------------
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.9 18.5 + - - +
19A ASN* 4.1 10.5 + - - +
82A GLU* 3.0 39.5 + - - +
83A ARG* 3.5 38.6 + - - +
85A VAL* 1.3 77.6 - - - +
87A LEU* 1.3 59.1 + - - +
88A GLY 3.3 3.3 + - - -
153E ARG 4.7 2.3 + - - +
156E ASP* 3.9 10.0 - - + +
157E LYS* 3.6 24.9 + - - +
160E TRP* 3.5 49.7 - - + +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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