Contacts of the helix formed by residues 86 - 115 (chain E) in PDB entry 6YOV
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 GLN 86 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E PHE* 1.3 74.0 - - - +
87E SER* 1.3 62.2 + - - +
88E SER* 3.9 17.0 + - - +
89E ALA* 2.8 25.1 + - + +
90E VAL* 3.3 8.0 + - - +
81F THR* 4.2 10.3 - - + +
82F VAL 3.0 18.3 + - - +
83F THR* 3.1 21.4 - - - +
84F ALA* 2.8 27.9 + - - +
51J T 3.7 27.0 + - - +
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Residues in contact with SER 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE 3.6 2.2 + - - -
86E GLN* 1.3 73.2 - - - +
88E SER* 1.3 63.7 + - - +
90E VAL* 3.4 10.8 + - - +
91E MET* 3.4 24.3 + - - +
51J T 3.5 18.6 + - - -
52J T 5.6 2.2 + - - -
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Residues in contact with SER 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E GLN* 3.9 12.5 + - - +
87E SER* 1.3 81.9 + - - +
89E ALA* 1.3 62.1 + - - +
91E MET* 3.8 6.5 - - - -
92E ALA* 2.9 28.4 + - - +
84F ALA* 3.5 17.4 - - - +
101F PHE* 3.7 15.3 - - - -
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Residues in contact with ALA 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E PHE* 4.7 8.5 - - + -
86E GLN* 2.8 20.3 + - + +
88E SER* 1.3 78.4 + - - +
90E VAL* 1.3 60.5 + - - +
92E ALA* 3.3 3.5 + - - +
93E LEU* 3.0 29.8 + - - +
82F VAL 4.0 3.4 - - - +
83F THR 3.8 7.4 - - - +
84F ALA* 3.7 31.9 - - - +
87F VAL* 3.8 12.9 - - + +
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Residues in contact with VAL 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E LYS 5.3 0.2 - - - +
68E PHE* 3.6 23.2 - - + -
69E GLN* 4.1 40.8 - - + +
72E VAL* 5.1 7.6 - - + -
73E ARG* 5.7 1.1 - - - +
85E PHE* 4.0 22.9 - - + +
86E GLN 3.3 13.0 + - - +
87E SER* 3.6 9.6 - - - +
88E SER 3.3 0.2 - - - -
89E ALA* 1.3 79.0 - - - +
91E MET* 1.3 72.0 + - + +
93E LEU* 3.2 8.5 + - - +
94E GLN* 2.9 23.9 + - - +
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Residues in contact with MET 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LEU* 4.0 14.5 - - + +
65E LYS* 3.9 44.0 - - + +
87E SER 3.4 13.5 + - - +
88E SER* 3.9 9.2 - - - +
89E ALA 3.3 0.2 - - - -
90E VAL* 1.3 91.3 - - + +
92E ALA* 1.3 65.2 + - - +
94E GLN* 3.2 22.5 + - - +
95E GLU* 3.0 28.3 + - + +
101F PHE* 4.1 12.6 - - + -
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Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E SER 2.9 19.8 + - - +
89E ALA* 3.5 8.7 - - - +
90E VAL 3.3 0.2 - - - -
91E MET* 1.3 77.8 - - - +
93E LEU* 1.3 61.7 + - - +
95E GLU* 3.4 1.0 + - - +
96E ALA* 3.3 12.6 + - - +
84F ALA* 4.7 5.2 - - + +
87F VAL* 4.3 13.7 - - + -
88F VAL* 5.5 0.7 - - + -
91F LEU* 4.6 0.2 - - - +
98F LEU* 3.3 28.4 - - + +
101F PHE* 3.6 29.6 - - + -
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Residues in contact with LEU 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E PHE* 4.1 1.8 - - + -
72E VAL* 3.7 32.8 - - + -
85E PHE* 6.1 1.3 - - + -
89E ALA 3.0 16.0 + - - +
90E VAL* 3.6 6.3 - - - +
91E MET 3.2 0.2 - - - -
92E ALA* 1.3 78.9 - - - +
94E GLN* 1.3 62.5 + - - +
96E ALA* 3.2 5.6 + - - +
97E CYS* 2.9 34.0 + - - -
62F PHE* 4.9 2.5 - - + -
63F LEU* 3.8 18.2 - - + -
66F VAL* 3.5 36.8 - - + -
67F ILE* 3.8 17.7 - - + -
87F VAL* 4.0 16.5 - - + +
91F LEU* 5.1 2.5 - - + -
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Residues in contact with GLN 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E LEU* 3.7 25.7 - - + +
63E ILE* 2.8 34.1 + - + +
65E LYS* 4.3 4.4 - - - +
68E PHE* 3.5 46.4 - - + +
90E VAL 2.9 11.5 + - - +
91E MET* 3.2 27.3 + - - +
93E LEU* 1.3 76.8 - - - +
95E GLU* 1.3 63.6 + - - +
97E CYS* 3.0 1.9 + - - +
98E GLU* 2.9 45.7 + - + +
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Residues in contact with GLU 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 4.1 4.6 - - + +
103C ILE 3.8 3.8 - - - +
104C ALA* 3.4 5.4 - - - -
105C GLN* 2.7 50.5 + - - +
59E THR 5.2 1.1 - - - +
61E LEU* 3.5 29.3 - - + +
91E MET* 3.0 21.2 + - + +
92E ALA 3.7 5.2 - - - +
94E GLN* 1.3 75.6 - - - +
96E ALA* 1.3 62.8 + - - +
98E GLU* 4.1 3.1 - - - +
99E ALA* 3.1 25.1 + - - +
98F LEU* 4.3 13.7 - - + -
101F PHE* 4.1 17.0 - - + -
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Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 4.6 9.6 - - + +
92E ALA 3.3 4.5 + - - +
93E LEU* 3.2 9.7 + - + +
94E GLN 3.2 0.2 - - - -
95E GLU* 1.3 80.2 - - - +
97E CYS* 1.3 57.0 + - - +
99E ALA* 3.5 5.2 + - - +
100E TYR* 2.9 30.1 + - - +
62F PHE* 3.9 8.1 - - + -
91F LEU* 3.7 42.8 - - + -
96F ARG* 5.9 3.1 + - - -
98F LEU* 4.9 3.3 - - + +
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Residues in contact with CYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ILE* 5.4 2.7 - - + -
68E PHE* 3.8 13.7 - - + -
93E LEU* 2.9 26.0 + - - -
94E GLN* 3.0 9.6 + - - +
96E ALA* 1.3 74.3 - - - +
98E GLU* 1.3 66.3 + - + +
100E TYR* 3.3 2.9 + - - +
101E LEU* 3.0 29.4 + - - +
59F LEU* 4.0 13.5 - - + -
62F PHE* 3.7 25.4 - - - -
63F LEU* 3.4 33.9 - - - -
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Residues in contact with GLU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E GLU 4.4 0.2 - - - +
61E LEU* 3.4 24.3 - - - +
62E LEU 2.8 30.6 + - - -
63E ILE* 2.9 27.3 + - + +
94E GLN* 2.9 25.7 + - + +
95E GLU* 4.1 2.9 - - - +
97E CYS* 1.3 73.3 - - - +
99E ALA* 1.3 66.3 + - - +
101E LEU* 3.0 5.1 + - - +
102E VAL* 2.8 30.0 + - + +
38F LEU* 3.8 24.9 - - + -
41F ARG* 4.1 13.7 + - - +
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Residues in contact with ALA 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C THR* 3.8 28.0 - - + +
95E GLU 3.1 18.4 + - - +
96E ALA 3.8 3.6 - - - +
98E GLU* 1.3 77.4 - - - +
100E TYR* 1.3 62.3 + - - +
102E VAL* 3.5 5.0 + - - +
103E GLY* 3.0 20.4 + - - -
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Residues in contact with TYR 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E ALA 2.9 18.9 + - - +
97E CYS 3.5 5.2 - - - +
99E ALA* 1.3 78.1 - - - +
101E LEU* 1.3 76.6 + - + +
103E GLY* 3.3 1.4 + - - -
104E LEU* 3.0 25.4 + - + +
129E ARG* 4.7 1.0 + - - -
132E ARG* 4.4 7.6 + - - -
134E GLU* 3.1 38.1 + - - -
58F VAL* 3.4 31.4 + - + +
59F LEU* 5.4 0.9 - - + -
62F PHE* 3.6 50.6 + + + +
96F ARG* 3.6 30.1 - - - +
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ILE* 4.7 5.2 - - + -
97E CYS 3.0 20.5 + - - +
98E GLU 3.8 2.7 - - - +
100E TYR* 1.3 93.3 - - + +
102E VAL* 1.3 58.2 + - - +
104E LEU* 3.2 9.6 + - + +
105E PHE* 2.8 41.7 + - + -
30F ILE* 6.1 1.3 - - + -
35F ILE* 6.4 0.7 - - + -
38F LEU* 3.7 29.4 - - + -
55F THR* 4.1 27.6 - - + +
58F VAL* 4.4 6.3 - - + -
59F LEU* 4.0 41.1 - - + +
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C VAL* 4.3 15.9 - - + -
98E GLU* 2.8 21.8 + - + +
99E ALA* 3.9 6.1 - - - +
101E LEU* 1.3 75.5 - - - +
103E GLY* 1.3 64.5 + - - +
105E PHE* 3.0 8.7 + - - +
106E GLU* 2.9 29.1 + - - +
38F LEU* 3.7 33.4 - - + +
41F ARG* 4.1 26.0 - - + +
42F GLY* 3.9 22.8 - - - +
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Residues in contact with GLY 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ALA 3.0 15.0 + - - -
100E TYR 3.8 2.7 - - - -
102E VAL* 1.3 76.1 - - - +
104E LEU* 1.3 61.6 + - - +
106E GLU* 3.3 17.8 + - - +
107E ASP* 3.2 24.9 + - - +
132E ARG* 4.1 9.8 + - - -
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Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E TYR* 3.0 21.2 + - + +
101E LEU* 3.5 14.4 - - + +
103E GLY* 1.3 76.4 - - - +
105E PHE* 1.3 57.5 + - + +
107E ASP* 3.2 2.1 + - - -
108E THR* 2.7 45.3 + - - +
125E ILE* 4.0 19.3 - - + +
128E ALA* 4.1 14.1 - - + -
129E ARG* 3.8 23.8 - - + -
132E ARG* 4.3 23.2 - - - +
134E GLU* 4.9 1.1 - - - +
55F THR* 6.5 0.4 - - + -
58F VAL* 3.7 31.4 - - + -
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Residues in contact with PHE 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 2.8 33.1 + - + -
102E VAL* 3.0 8.5 + - - +
104E LEU* 1.3 79.6 - - + +
106E GLU* 1.3 57.2 + - - +
108E THR* 3.4 12.5 - - + -
109E ASN* 2.7 31.6 + - - +
120E ILE* 5.4 3.1 - - + -
125E ILE* 4.7 9.4 - - + -
35F ILE* 4.1 12.6 - - + -
38F LEU* 4.1 9.4 - - + -
39F ALA* 3.7 48.9 - - + +
42F GLY* 4.5 4.0 - - - -
44F VAL* 4.0 14.8 - - + +
47F ILE* 6.1 0.7 - - + -
51F ILE* 4.2 13.5 - - + -
55F THR* 3.5 38.6 - - + -
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Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 4.9 11.1 - - - +
109C LEU 5.7 0.3 - - - +
111C ASN* 6.0 1.9 - - - +
56E GLN* 5.9 0.5 + - - -
102E VAL* 2.9 27.3 + - - +
103E GLY* 3.5 15.1 - - - +
104E LEU 3.2 0.2 - - - -
105E PHE* 1.3 75.9 - - - +
107E ASP* 1.3 65.1 + - - +
109E ASN* 3.3 4.0 + - - +
110E LEU* 3.1 26.9 + - + +
41F ARG 4.8 2.3 - - - +
42F GLY* 3.4 29.8 - - - +
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Residues in contact with ASP 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 4.8 2.6 + - - +
131A ILE* 3.7 33.7 - - + +
103E GLY 3.2 6.0 + - - +
104E LEU* 3.2 8.1 + - - +
106E GLU* 1.3 78.2 - - - +
108E THR* 1.3 66.5 + - - +
110E LEU* 3.2 20.7 + - - +
111E CYS* 3.1 26.0 + - - -
128E ALA* 3.8 18.4 - - + -
132E ARG* 2.7 31.6 + - - +
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Residues in contact with THR 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E LEU* 2.7 31.6 + - - +
105E PHE* 3.4 12.8 - - + -
107E ASP* 1.3 78.4 - - - +
109E ASN* 1.3 61.8 + - - +
111E CYS* 3.1 12.3 + - - +
112E ALA* 3.1 12.0 + - - +
120E ILE* 3.3 32.8 - - + -
124E ASP* 3.7 19.3 + - + +
125E ILE* 3.6 34.9 - - + +
128E ALA* 4.3 0.8 - - - +
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Residues in contact with ASN 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C GLN* 5.0 5.3 - - - +
116C LEU* 4.2 14.0 - - - +
105E PHE 2.7 17.4 + - - +
106E GLU* 3.5 9.2 - - - +
108E THR* 1.3 76.9 - - - +
110E LEU* 1.3 61.8 + - - +
112E ALA* 3.1 4.5 + - - +
113E ILE* 2.9 48.3 + - - +
118E VAL 4.6 5.2 - - - +
120E ILE* 3.8 20.3 - - - +
42F GLY 4.4 2.8 + - - +
43F GLY* 3.3 30.8 + - - +
44F VAL* 3.8 11.0 - - + -
45F LYS 4.8 0.5 + - - -
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Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.8 20.0 - - + +
130A ARG* 3.7 55.4 - - + +
131A ILE* 4.9 1.8 - - + -
113C GLN* 5.2 12.1 - - + +
106E GLU* 3.1 20.7 + - + +
107E ASP* 3.2 21.0 + - - +
109E ASN* 1.3 77.8 - - + +
111E CYS* 1.3 58.1 + - - +
113E ILE* 3.2 19.6 + - + +
114E HIS* 2.8 29.1 + - - +
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Residues in contact with CYS 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 4.0 4.6 - - - +
127A LEU* 4.5 4.5 - - - -
131A ILE* 3.8 23.1 - - - -
107E ASP 3.1 19.5 + - - -
108E THR 3.3 8.3 - - - +
110E LEU* 1.3 77.8 - - - +
112E ALA* 1.3 62.1 + - - +
114E HIS* 3.1 9.4 + - - +
115E ALA* 3.0 21.7 + - - +
124E ASP* 3.6 34.7 - - + +
127E LEU* 3.8 24.2 - - + -
128E ALA* 4.0 6.5 - - - -
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Residues in contact with ALA 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E THR 3.1 5.6 + - - +
109E ASN* 3.1 4.2 + - - +
111E CYS* 1.3 76.0 - - - +
113E ILE* 1.3 63.8 + - + +
115E ALA* 3.1 9.8 + - - -
117E ARG* 3.1 31.2 + - + +
118E VAL 4.3 5.4 - - - +
119E THR 3.8 15.9 - - - +
120E ILE* 3.5 32.3 - - + -
124E ASP* 3.4 13.8 + - - +
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Residues in contact with ILE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLN* 4.4 15.5 - - + +
115C VAL* 3.7 42.8 - - + -
116C LEU* 5.1 4.0 - - + -
109E ASN* 2.9 43.9 + - - +
110E LEU* 3.2 19.3 + - + +
112E ALA* 1.3 76.3 - - + +
114E HIS* 1.3 57.8 + - - +
116E LYS* 2.8 24.9 + - - +
117E ARG 3.8 12.1 + - - +
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Residues in contact with HIS 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A CYS* 3.9 18.0 + - + +
114A HIS* 5.7 3.1 - + + -
115A ALA* 4.1 14.1 - - + +
117A ARG* 3.7 7.6 + - - -
123A LYS* 3.7 36.3 + - + +
124A ASP* 2.6 34.0 + - - -
127A LEU* 3.5 29.5 - - + +
110E LEU 2.8 13.4 + - - +
111E CYS 3.3 9.9 - - - +
113E ILE* 1.3 77.3 - - - +
115E ALA* 1.3 57.9 + - - +
116E LYS* 3.0 15.8 + - - +
127E LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A HIS* 4.3 22.4 - - + +
115A ALA* 4.9 9.9 - - - +
111E CYS 3.0 12.4 + - - +
112E ALA* 3.4 10.5 - - - +
113E ILE 3.1 0.4 - - - -
114E HIS* 1.3 74.4 - - - +
116E LYS* 1.3 72.0 + - - +
117E ARG* 3.4 25.1 + - - +
----------------------------------------------------------
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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