Contacts of the helix formed by residues 102 - 131 (chain E) in PDB entry 1O9R
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 LYS 102 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E LYS* 3.5 7.4 - - - +
101E TYR* 1.3 81.2 - - + +
103E ILE* 1.3 66.5 + - - +
104E HIS* 4.1 6.1 - - + +
105E ASP* 3.1 40.9 + - - +
106E HIS* 3.1 11.4 + - - -
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Residues in contact with ILE 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 3.9 20.2 - - + -
44E LYS 3.1 15.5 + - - +
45E GLY* 3.6 17.0 - - - +
46E PRO* 5.8 0.4 - - + -
47E GLN* 3.5 29.8 - - - +
48E PHE* 3.5 32.8 - - - +
51E VAL* 4.3 16.2 - - + -
101E TYR 4.3 0.9 - - - -
102E LYS* 1.3 71.5 - - - +
104E HIS* 1.3 58.4 + - - +
106E HIS* 3.1 7.0 + - - +
107E LEU* 2.8 48.3 + - + +
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Residues in contact with HIS 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LYS* 3.2 6.7 - - + +
103E ILE* 1.3 78.2 - - - +
105E ASP* 1.3 60.2 + - - +
107E LEU* 3.4 7.8 + - + -
108E ASP* 3.0 48.8 + - - -
158E VAL* 3.8 30.0 - - + +
161E LYS* 6.2 4.9 - - + -
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Residues in contact with ASP 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ILE* 3.7 33.3 - - + +
101E TYR 4.9 0.3 + - - -
102E LYS* 3.1 39.2 + - + +
104E HIS* 1.3 78.4 - - - +
106E HIS* 1.3 65.6 + - - +
108E ASP* 3.3 10.4 + - - +
109E ALA* 3.1 23.6 + - - +
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Residues in contact with HIS 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E GLN* 4.5 1.3 - - + -
39E ALA* 3.5 22.4 - - + +
42E ASN* 3.8 17.5 + - + -
43E LEU* 3.5 30.7 - - + -
96E TYR* 2.8 30.1 + + - +
97E PRO 5.1 0.7 - - - -
100E ILE* 2.9 38.0 + - + +
101E TYR* 3.4 28.4 - - - -
102E LYS 3.1 12.7 + - - -
103E ILE 3.7 4.3 - - - +
105E ASP* 1.3 74.1 - - - +
107E LEU* 1.3 61.4 + - - +
109E ALA 3.2 0.5 + - - -
110E LEU* 2.8 36.8 + - + +
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Residues in contact with LEU 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LEU* 6.4 0.2 - - + -
51E VAL* 4.4 18.4 - - + -
103E ILE* 2.8 39.2 + - + +
104E HIS* 3.8 7.2 - - + +
106E HIS* 1.3 77.4 - - + +
108E ASP* 1.3 57.4 + - - +
110E LEU* 3.8 5.5 - - + +
111E ILE* 2.8 38.2 + - + +
154E LEU* 3.7 35.2 - - + +
157E HIS* 3.8 34.1 - - + +
158E VAL* 3.9 22.0 - - + -
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Residues in contact with ASP 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E HIS* 3.0 44.5 + - - +
105E ASP* 3.8 9.4 - - - +
106E HIS 3.2 0.2 - - - -
107E LEU* 1.3 75.8 - - - +
109E ALA* 1.3 63.9 + - - +
111E ILE* 3.4 9.8 + - - +
112E GLU* 3.1 29.9 + - + +
158E VAL* 4.7 7.3 - - - +
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Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E TYR* 3.5 30.1 - - + +
97E PRO* 4.5 7.4 - - + -
100E ILE* 4.3 6.7 - - + -
105E ASP 3.1 17.1 + - - +
108E ASP* 1.3 74.6 - - - +
110E LEU* 1.3 65.6 + - - +
112E GLU* 3.5 4.4 + - - -
113E ARG* 2.9 44.0 + - - +
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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
----------------------------------------------------------
35E VAL* 3.6 30.3 - - + +
36E THR* 4.3 6.1 - - - -
39E ALA* 3.8 26.7 - - + -
43E LEU* 5.1 0.9 - - + -
55E LEU* 3.9 24.2 - - + -
96E TYR* 3.8 6.1 - - - +
106E HIS* 2.8 30.5 + - + +
107E LEU* 3.8 8.3 - - + +
109E ALA* 1.3 72.0 - - - +
111E ILE* 1.4 59.8 + - - +
113E ARG* 3.2 3.1 + - - -
114E TYR* 2.8 50.2 + - + -
154E LEU* 4.2 19.5 - - + -
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Residues in contact with ILE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 3.7 19.1 - - + +
107E LEU* 2.8 32.8 + - + +
108E ASP* 3.8 9.0 - - - +
110E LEU* 1.4 71.8 - - - +
112E GLU* 1.3 59.6 + - + +
115E GLY* 2.8 28.1 + - - -
151E LEU* 4.0 7.5 - - + +
154E LEU* 3.6 35.9 - - + +
155E GLU* 3.7 30.3 - - + +
158E VAL* 3.8 29.4 - - + -
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Residues in contact with GLU 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 4.6 22.7 + - - +
108E ASP 3.1 16.9 + - - +
109E ALA* 3.6 10.7 - - - +
111E ILE* 1.3 76.6 - - + +
113E ARG* 1.3 72.6 + - + +
115E GLY* 3.9 0.5 - - - -
116E GLU* 3.0 38.0 + - - +
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Residues in contact with ARG 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 3.6 19.1 - - + -
35E VAL* 4.2 14.7 - - + +
93E LEU* 4.2 19.1 - - + -
94E LYS* 3.0 32.8 + - - +
95E ALA 3.0 26.1 + - - -
96E TYR* 3.7 26.8 - - - +
97E PRO* 3.9 6.0 - - - +
109E ALA* 2.9 41.5 + - - +
110E LEU* 3.2 3.9 + - - +
112E GLU* 1.3 88.6 + - + +
114E TYR* 1.3 62.6 + - - +
116E GLU* 3.2 10.5 + - - +
117E VAL* 3.0 33.6 + - - +
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Residues in contact with TYR 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 3.7 31.6 - - + -
36E THR* 2.7 29.7 + - + +
55E LEU* 5.4 0.2 - - + -
58E PHE* 3.2 33.0 - + + +
62E LEU* 3.5 9.1 - - + +
110E LEU* 2.8 45.0 + - + +
113E ARG* 1.3 74.4 - - - +
115E GLY* 1.3 57.6 + - - +
117E VAL* 4.1 0.3 - - - +
118E ALA* 2.8 32.2 + - - +
147E LEU* 4.3 13.7 - - + +
150E SER* 3.9 27.4 - - - -
151E LEU* 4.2 15.0 - - + +
154E LEU* 3.6 24.9 - - + -
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Residues in contact with GLY 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 3.9 21.8 - - - -
111E ILE 2.8 19.9 + - - -
112E GLU 3.9 0.9 - - - -
114E TYR* 1.3 78.4 - - - +
116E GLU* 1.3 63.0 - - - +
118E ALA* 3.8 0.3 - - - +
119E ASN* 2.9 34.3 + - - -
151E LEU* 3.8 12.2 - - - +
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Residues in contact with GLU 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E LYS* 4.3 10.8 - - + +
93E LEU* 3.5 26.8 - - + +
94E LYS* 4.8 6.7 + - - +
112E GLU* 3.0 23.1 + - - +
113E ARG* 3.2 10.3 + - - +
115E GLY* 1.3 77.8 - - - +
117E VAL* 1.4 58.8 + - - +
119E ASN* 3.4 5.8 + - - +
120E MET* 2.9 35.9 + - + +
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Residues in contact with VAL 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E SER* 3.9 26.2 - - - +
29E VAL* 4.1 22.4 - - + +
32E LEU* 3.9 22.0 - - + -
62E LEU* 5.4 0.2 - - + -
93E LEU* 4.0 15.3 - - + -
113E ARG 3.0 16.9 + - - +
114E TYR 4.1 1.1 - - - +
116E GLU* 1.4 72.6 - - - +
118E ALA* 1.3 66.9 + - - +
120E MET* 3.2 8.8 + - + +
121E ILE* 2.9 26.6 + - + +
147E LEU* 3.8 24.0 - - + -
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Residues in contact with ALA 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E TYR 2.8 23.2 + - - +
115E GLY* 3.8 5.6 - - - +
117E VAL* 1.3 72.9 - - - +
119E ASN* 1.4 58.5 + - - +
121E ILE* 3.4 2.6 + - - +
122E ARG* 3.0 34.7 + - - +
144E SER* 5.1 1.9 + - - -
147E LEU* 3.9 29.4 - - + +
148E ASP* 3.6 21.4 - - - +
151E LEU* 4.4 8.1 - - + -
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Residues in contact with ASN 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LYS* 2.9 23.4 + - - +
8C ASN* 3.8 2.1 - - - -
9C ASP* 3.0 40.6 + - - +
115E GLY 2.9 24.7 + - - +
116E GLU* 3.9 5.2 - - - +
118E ALA* 1.4 76.1 - - - +
120E MET* 1.3 63.5 + - - +
122E ARG* 2.9 28.7 + - - +
123E LYS* 3.1 22.7 + - - +
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Residues in contact with MET 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E GLU* 4.3 16.2 - - + +
25E SER* 4.0 30.1 + - - +
28E SER* 3.8 35.9 - - - +
29E VAL* 6.3 0.2 - - + -
92E LYS* 4.2 20.6 - - + -
93E LEU* 5.6 0.7 - - - -
116E GLU* 2.9 24.4 + - + +
117E VAL* 3.2 12.5 + - + +
119E ASN* 1.3 77.1 - - - +
121E ILE* 1.4 60.2 + - + +
123E LYS* 3.2 8.5 + - - +
124E ALA* 3.0 27.0 + - - +
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Residues in contact with ILE 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E SER* 3.5 29.6 - - - +
29E VAL* 4.5 8.3 - - + -
69E ILE* 4.3 10.5 - - + -
117E VAL* 2.9 24.6 + - + +
118E ALA 3.8 3.8 - - - +
120E MET* 1.4 78.6 - - + +
122E ARG* 1.4 61.6 + - - +
124E ALA* 3.1 5.4 + - - +
125E ILE* 3.1 21.8 + - - +
140E PHE* 3.3 42.3 - - + +
143E ALA* 4.0 7.2 - - + -
144E SER* 3.7 19.5 - - - +
147E LEU* 3.5 16.6 - - + -
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Residues in contact with ARG 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ASN* 3.4 23.2 + - - +
9C ASP* 2.9 25.6 + - - -
10C LEU* 3.9 27.3 - - + +
11C PRO* 5.9 0.2 - - - -
72C ARG* 4.4 8.1 - - - +
133C ASP* 5.7 0.4 + - - -
134C PRO* 5.7 5.3 - - + +
135C THR* 4.9 2.8 + - - +
118E ALA* 3.0 21.0 + - - +
119E ASN* 2.9 23.9 + - - +
121E ILE* 1.4 72.6 - - - +
123E LYS* 1.3 63.4 + - - +
125E ILE* 3.3 30.7 + - + +
126E ASP* 3.8 10.7 + - - +
144E SER* 4.2 9.4 + - - +
148E ASP* 2.9 41.4 + - - -
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Residues in contact with LYS 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E ASN 3.1 13.8 + - - +
120E MET* 3.6 9.9 - - - +
122E ARG* 1.3 78.1 - - - +
124E ALA* 1.3 56.7 + - - +
126E ASP* 3.1 10.3 + - + +
127E ASP* 2.8 59.1 + - - +
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Residues in contact with ALA 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ILE* 3.7 20.0 - - + -
25E SER* 4.2 4.3 - - - +
120E MET 3.0 13.3 + - - +
121E ILE* 3.1 10.5 + - - +
123E LYS* 1.3 73.1 - - - +
125E ILE* 1.3 59.6 - - - +
127E ASP* 4.4 4.7 - - - +
128E SER* 2.8 35.7 + - - -
140E PHE* 3.7 32.1 - - + -
----------------------------------------------------------
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Residues in contact with ILE 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PRO* 3.9 27.6 - - + -
135C THR* 3.5 25.1 - - - +
121E ILE 3.1 11.7 + - - +
122E ARG* 3.5 15.3 - - + +
123E LYS 3.2 0.4 - - - -
124E ALA* 1.3 78.5 - - - +
126E ASP* 1.3 65.5 + - - +
129E ASP* 3.0 24.3 + - + +
137E ALA* 3.6 15.2 - - + +
140E PHE* 3.7 21.5 - - + -
141E THR* 3.4 25.8 - - - +
144E SER* 3.8 16.4 - - - +
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Residues in contact with ASP 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C GLY 5.1 5.4 - - - +
134C PRO* 3.6 27.2 - - - +
122E ARG* 4.2 10.3 - - - +
123E LYS* 3.1 9.7 + - + +
125E ILE* 1.3 81.5 - - - +
127E ASP* 1.3 62.1 + - - +
129E ASP* 3.4 4.3 + - - +
130E GLU* 2.8 44.4 + - - +
----------------------------------------------------------
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Residues in contact with ASP 127 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E THR* 5.3 0.7 - - - +
21E ILE* 3.7 24.7 - - + +
123E LYS* 2.8 55.3 + - - +
124E ALA* 4.1 4.2 - - - +
126E ASP* 1.3 79.8 - - - +
128E SER* 1.3 58.1 + - - +
130E GLU* 3.5 11.6 + - - +
131E ALA* 3.0 28.8 + - - +
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Residues in contact with SER 128 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E VAL* 4.2 4.6 - - - +
21E ILE* 4.1 12.4 - - - +
124E ALA 2.8 24.1 + - - -
125E ILE 3.8 3.1 - - - -
127E ASP* 1.3 74.8 - - - +
129E ASP* 1.3 64.9 + - - +
131E ALA* 3.3 11.2 + - - +
132E GLY 3.4 0.2 + - - -
133E ASP* 3.0 25.0 + - - +
136E THR* 3.6 10.7 - - - +
137E ALA* 3.8 22.4 - - - -
140E PHE* 3.3 20.8 - - - -
----------------------------------------------------------
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Residues in contact with ASP 129 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E ILE* 3.0 19.5 + - + +
126E ASP* 3.8 6.1 - - - +
128E SER* 1.3 75.5 - - - +
130E GLU* 1.4 64.3 + - + +
132E GLY* 2.9 21.0 + - - -
133E ASP 4.4 4.3 - - - +
134E PRO* 4.0 24.3 - - - +
137E ALA* 3.8 11.4 - - + +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ASP* 2.8 28.7 + - - +
127E ASP* 4.0 12.4 - - - +
129E ASP* 1.4 81.3 - - + +
131E ALA* 1.3 61.0 + - - +
132E GLY* 3.3 1.0 + - - -
----------------------------------------------------------
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Residues in contact with ALA 131 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E ALA* 3.2 24.9 - - - +
17E THR* 4.1 21.1 - - + -
18E VAL* 3.8 22.0 - - + -
127E ASP 3.0 18.2 + - - +
128E SER 3.7 6.1 - - - +
129E ASP 3.1 0.4 - - - -
130E GLU* 1.3 76.8 - - - +
132E GLY* 1.3 54.1 + - - +
133E ASP 3.6 0.2 - - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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