Contacts of the helix formed by residues 106 - 130 (chain E) in PDB entry 6AHU
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 THR 106 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A U 4.9 1.1 - - - +
26A G 4.3 17.6 - - - +
271A U 3.6 7.8 + - - -
272A U 2.4 34.1 + - - -
274A A 4.3 16.2 - - - -
275A A 4.3 15.0 - - - +
8E TYR* 4.8 0.2 - - - -
103E VAL* 3.8 8.3 - - + -
104E GLY 3.4 15.0 + - - +
105E GLY* 1.3 75.8 - - - +
107E ILE* 1.3 63.7 + - - +
108E ARG 3.1 2.7 + - - -
109E THR* 3.3 23.2 + - + +
110E CYS* 3.2 15.2 + - - +
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Residues in contact with ILE 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A U 5.1 3.3 + - - -
273A C 3.3 53.2 - - + +
274A A 5.3 1.5 - - - +
119B LEU* 4.6 14.1 - - + -
8E TYR* 3.6 45.8 - - + -
56E ARG* 6.4 0.7 - - + -
66E LEU* 4.3 15.0 - - + -
105E GLY 3.4 0.4 + - - -
106E THR* 1.3 70.7 - - - +
108E ARG* 1.3 58.0 + - + +
110E CYS* 3.2 9.0 + - + +
111E GLN* 2.9 41.8 + - + +
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Residues in contact with ARG 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A U 3.3 81.0 - - - +
273A C 4.0 11.2 + - - +
119B LEU* 6.2 2.2 - - + -
120B LYS* 3.8 19.8 + - + +
123B THR* 3.4 41.7 + - + +
124B GLN* 3.4 36.4 - - - +
127B SER* 5.7 2.0 - - - +
106E THR 3.1 1.0 + - - -
107E ILE* 1.3 76.3 - - + +
109E THR* 1.3 58.1 + - - +
111E GLN* 3.1 9.4 + - - +
112E LYS* 3.0 41.0 + - - +
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Residues in contact with THR 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A G 3.4 31.0 + - - +
27A G 3.9 17.2 + - - -
272A U 5.2 0.4 - - - -
103E VAL* 4.3 5.6 - - + +
106E THR* 3.3 32.1 + - + +
108E ARG* 1.3 75.2 - - - +
110E CYS* 1.3 60.9 + - - +
111E GLN 3.3 0.2 - - - -
112E LYS* 3.6 24.4 - - - +
113E PHE* 3.2 24.9 + - - +
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Residues in contact with CYS 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E TYR* 4.7 4.3 - - - -
10E LEU* 3.9 34.0 - - - +
66E LEU* 4.1 17.5 - - - -
103E VAL* 3.8 33.2 - - + -
105E GLY 4.6 1.3 - - - +
106E THR 3.2 12.7 + - - +
107E ILE* 3.2 17.2 + - + +
109E THR* 1.3 79.3 - - - +
111E GLN* 1.3 66.4 + - - +
113E PHE* 3.8 1.8 + - - +
114E LEU* 3.6 17.5 + - - +
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Residues in contact with GLN 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 6.3 0.4 - - - +
116B SER* 2.9 46.9 + - - +
119B LEU* 4.2 30.6 - - + +
120B LYS* 5.4 4.3 - - + -
10E LEU* 5.6 1.2 - - - +
57E TYR* 4.6 25.0 - - - -
66E LEU* 4.9 7.4 - - - +
107E ILE* 2.9 23.5 + - + +
108E ARG* 3.6 8.1 - - - +
110E CYS* 1.3 84.7 - - - +
112E LYS* 1.3 64.6 + - - +
114E LEU* 3.4 17.2 + - - +
115E ILE* 3.2 27.6 + - - +
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Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A G 4.4 13.4 + - - +
120B LYS* 3.7 31.0 - - - +
124B GLN* 5.4 7.4 - - - +
108E ARG* 3.0 29.8 + - - +
109E THR* 3.7 24.2 - - - +
110E CYS 3.3 0.4 - - - -
111E GLN* 1.3 77.0 - - - +
113E PHE* 1.3 59.1 + - - +
115E ILE* 3.2 14.9 + - + +
116E GLN* 2.4 37.2 + - - +
61G ARG* 3.2 42.6 - - + +
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Residues in contact with PHE 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E LEU* 4.3 10.3 - - + -
100E THR* 3.7 30.1 - - + -
101E LEU* 3.7 49.1 - - + -
103E VAL* 5.5 4.0 - - + -
109E THR 3.2 14.7 + - - +
110E CYS* 4.2 6.5 - - - +
111E GLN 3.4 0.2 - - - -
112E LYS* 1.3 77.0 - - - +
114E LEU* 1.3 57.9 + - - +
115E ILE 3.3 0.2 - - - -
116E GLN* 3.6 10.0 + - + +
117E TYR* 3.0 42.1 + + + +
120E ARG* 6.3 0.7 - - - -
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Residues in contact with LEU 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 3.9 21.5 - - + +
116B SER* 3.4 22.7 - - - +
10E LEU* 4.9 11.7 - - + -
57E TYR* 3.9 21.8 - - + +
62E THR* 6.5 0.2 - - + -
64E ILE* 3.8 37.9 - - + -
110E CYS 3.6 10.4 + - - +
111E GLN* 3.4 22.1 + - - +
112E LYS 3.2 0.4 - - - -
113E PHE* 1.3 78.4 - - - +
115E ILE* 1.3 59.3 + - - +
117E TYR* 4.0 8.2 - - + +
118E ASN* 3.1 29.4 + - + +
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Residues in contact with ILE 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA 5.2 0.2 - - - +
113B ALA* 5.0 16.2 - - + +
116B SER* 4.0 24.2 - - - +
117B ALA* 4.2 10.5 - - + +
120B LYS* 3.9 27.1 - - + -
111E GLN 3.2 15.2 + - - +
112E LYS* 3.2 11.5 + - + +
114E LEU* 1.3 75.9 - - - +
116E GLN* 1.3 67.0 + - - +
118E ASN* 3.1 5.8 + - - +
119E ARG* 2.9 64.5 + - + +
59G GLY 5.3 7.4 - - - +
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Residues in contact with GLN 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E LYS* 2.4 42.5 + - - +
113E PHE* 4.1 11.4 - - + +
115E ILE* 1.3 91.7 - - - +
117E TYR* 1.3 61.0 + - - +
119E ARG* 4.2 8.8 + - - +
120E ARG* 3.3 40.6 + - - +
57G ASP* 3.4 35.4 - - + +
58G GLY* 5.3 0.3 - - - -
59G GLY 4.9 3.5 + - - +
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Residues in contact with TYR 117 (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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12E GLU* 2.6 41.7 + - - -
64E ILE* 5.0 13.5 - - + -
100E THR* 4.8 16.4 - - + -
113E PHE* 3.0 35.1 + + + +
114E LEU* 4.0 9.4 - - + +
115E ILE 3.2 0.2 - - - -
116E GLN* 1.3 77.3 - - - +
118E ASN* 1.3 62.2 + - - +
120E ARG* 3.7 7.0 + - + +
121E GLN* 3.4 34.1 + - - +
27I HIS* 3.3 2.8 + - - -
65I GLN* 2.7 51.3 + - + +
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Residues in contact with ASN 118 (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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109B GLN* 2.5 36.1 + - - +
112B ALA* 3.5 12.5 - - - +
113B ALA* 3.2 28.5 - - + +
114E LEU* 3.1 21.1 + - + +
115E ILE* 3.1 6.9 + - - +
117E TYR* 1.3 77.7 - - + +
119E ARG* 1.3 63.7 + - - +
121E GLN* 3.3 13.7 + - - +
122E LEU* 3.3 34.4 - - - +
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Residues in contact with ARG 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ALA* 5.8 6.3 - - + +
115E ILE* 2.9 43.2 + - + +
116E GLN* 4.2 8.8 + - - +
118E ASN* 1.3 77.9 - - + +
120E ARG* 1.3 63.1 + - + +
121E GLN 3.4 0.7 + - - -
122E LEU* 3.7 3.4 + - - +
123E LEU* 3.3 31.9 + - + +
145E SER* 6.0 4.6 - - - -
57G ASP* 2.9 42.8 + - - +
59G GLY* 3.4 30.5 + - - +
66G CYS* 3.5 19.2 - - - -
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Residues in contact with ARG 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E PHE* 6.3 0.4 - - - -
116E GLN* 3.3 27.9 + - - +
117E TYR* 4.2 7.0 - - + +
118E ASN 3.3 0.4 - - - -
119E ARG* 1.3 78.2 - - + +
121E GLN* 1.3 61.4 + - - +
123E LEU* 4.1 9.5 - - + +
124E ILE* 3.4 33.5 + - + +
53G GLN* 5.2 10.5 - - - +
57G ASP* 4.9 15.7 + - - +
65I GLN* 3.9 25.2 + - + +
66I GLY* 3.4 25.6 + - - -
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Residues in contact with GLN 121 (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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109B GLN* 3.1 36.7 + - - +
12E GLU* 5.1 4.4 + - - +
117E TYR* 3.4 33.4 + - - +
118E ASN* 3.3 11.7 + - - +
119E ARG 3.2 1.0 - - - -
120E ARG* 1.3 79.6 - - - +
122E LEU* 1.3 62.6 + - + +
124E ILE* 3.8 4.6 + - - +
125E LEU* 3.3 27.7 + - + +
27I HIS* 5.0 11.5 - - + -
65I GLN* 4.8 14.4 - - - +
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Residues in contact with LEU 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR* 5.2 4.7 - - + -
109B GLN* 3.3 34.8 - - + +
110B ALA* 5.4 0.4 - - - +
118E ASN* 3.3 38.9 + - - +
119E ARG* 3.7 4.7 + - - +
120E ARG 3.5 0.2 - - - -
121E GLN* 1.3 77.9 - - + +
123E LEU* 1.3 64.4 + - + +
125E LEU* 3.6 15.8 + - + +
126E LEU* 3.3 21.8 + - - +
138E ILE* 3.8 26.5 - - + +
141E SER* 3.6 30.1 - - - +
142E VAL* 6.2 0.2 - - + -
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Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ARG* 3.3 24.5 + - + +
120E ARG* 4.0 9.4 + - + +
121E GLN 3.4 0.4 - - - -
122E LEU* 1.3 79.5 - - + +
124E ILE* 1.3 65.1 + - + +
126E LEU* 3.4 32.1 + - + +
57G ASP* 5.7 4.9 - - - +
92G SER* 3.5 31.9 - - - +
93G PHE* 3.2 20.4 - - + -
94G GLY* 4.4 12.8 - - - +
139G PRO* 5.9 1.6 - - + -
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Residues in contact with ILE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E ARG* 3.4 23.1 + - + +
121E GLN* 4.3 4.7 - - - +
123E LEU* 1.3 78.1 - - + +
125E LEU* 1.3 60.7 + - - +
126E LEU 3.1 1.8 + - - -
127E GLN 3.9 2.1 + - - -
128E ASN* 3.0 42.7 + - - +
93G PHE* 3.9 17.1 - - + -
63I ILE* 3.8 26.7 - - + +
64I VAL 3.8 22.9 - - - +
65I GLN* 3.9 18.6 - - + -
68I SER* 5.8 3.1 - - - -
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Residues in contact with LEU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B THR* 5.3 1.8 - - - +
109B GLN* 4.5 18.4 - - - +
121E GLN* 3.3 22.6 + - + +
122E LEU* 3.7 8.3 - - + +
123E LEU 3.2 0.6 - - - -
124E ILE* 1.3 76.7 - - - +
126E LEU* 1.3 63.3 + - - +
127E GLN 3.7 0.2 - - - -
128E ASN* 4.3 4.9 - - - +
129E CYS* 3.4 32.6 + - + +
134E GLU* 3.4 29.2 - - + +
138E ILE* 4.1 24.5 - - + -
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E LEU 3.3 11.7 - - - +
123E LEU* 3.5 34.8 - - + +
124E ILE 3.1 1.2 - - - -
125E LEU* 1.3 81.9 - - - +
127E GLN* 1.3 63.0 + - - +
129E CYS* 4.6 0.2 - - - +
130E THR* 3.4 14.7 + - - -
135E ARG* 3.5 29.2 + - + +
138E ILE* 3.8 37.9 - - + -
93G PHE* 5.0 3.1 - - + +
94G GLY* 4.5 11.9 - - - -
95G SER 5.2 0.2 - - - +
139G PRO* 3.7 34.5 - - + -
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Residues in contact with GLN 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ILE 3.9 2.6 + - - -
126E LEU* 1.3 78.7 - - + +
128E ASN* 1.3 63.9 + - - +
130E THR* 2.4 25.9 + - - +
135E ARG* 4.9 3.1 - - - +
93G PHE* 3.2 37.8 - - + -
61I LEU* 5.2 14.7 - - + +
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Residues in contact with ASN 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E ILE* 3.0 40.4 + - - +
125E LEU* 4.7 3.8 - - - +
126E LEU 3.4 0.6 - - - -
127E GLN* 1.3 82.0 - - - +
129E CYS* 1.3 64.3 + - - +
130E THR* 4.3 0.3 + - - -
93G PHE* 5.5 0.8 - - - -
61I LEU* 5.0 9.5 - - - +
63I ILE* 4.3 19.2 - - - +
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Residues in contact with CYS 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ILE* 5.3 8.3 - - - -
125E LEU* 3.4 40.6 + - - +
126E LEU 4.6 0.2 - - - +
127E GLN 3.4 0.2 - - - -
128E ASN* 1.3 84.9 - - - +
130E THR* 1.3 71.1 + - - +
131E ASP* 4.6 4.5 - - + +
134E GLU* 3.7 26.9 - - - +
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Residues in contact with THR 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E LEU 3.4 12.4 + - - -
127E GLN* 2.4 33.3 + - - +
128E ASN 4.2 0.4 - - - -
129E CYS* 1.3 80.1 - - - +
131E ASP* 1.3 59.1 + - - +
132E GLU* 6.2 0.2 - - - -
135E ARG* 4.4 13.0 - - - +
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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