Contacts of the helix formed by residues 6 - 39 (chain A) in PDB entry 1PV7
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 6 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A TYR* 3.0 25.9 + - - +
3A TYR* 3.7 8.3 - - - +
4A LEU 4.5 0.5 - - - +
5A LYS* 1.3 82.3 - - - +
7A THR* 1.3 63.5 + - - +
8A ASN* 3.1 5.3 + - - +
9A PHE* 2.4 50.0 + - - +
10A TRP* 3.6 14.9 + - - +
136A SER* 3.7 22.2 + - - +
138A PHE* 5.3 2.8 - - - +
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Residues in contact with THR 7 (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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5A LYS 3.7 0.8 + - - -
6A ASN* 1.3 76.5 - - - +
8A ASN* 1.3 81.6 + - - +
10A TRP* 3.4 4.3 + - - +
11A MET* 3.0 40.3 + - + +
187A ALA* 4.8 10.5 - - + -
188A LYS 4.9 6.1 - - - +
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Residues in contact with ASN 8 (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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6A ASN* 3.1 4.6 + - - +
7A THR* 1.3 81.6 - - - +
9A PHE* 1.3 65.4 - - - +
11A MET* 4.2 5.9 - - - +
12A PHE* 2.9 30.3 + - + +
132A VAL* 4.5 15.5 - - + +
135A ARG* 6.0 0.6 - - - +
136A SER* 4.6 19.5 - - - -
187A ALA 5.0 0.9 - - - +
188A LYS* 3.5 17.4 + - - +
189A THR* 2.6 37.5 + - - +
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Residues in contact with PHE 9 (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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3A TYR* 2.6 22.7 - - + -
4A LEU* 3.4 11.0 - - + -
6A ASN* 2.4 46.8 + - - +
8A ASN* 1.3 63.8 - - - +
10A TRP* 1.3 101.0 + + - +
12A PHE* 5.5 0.2 - - - -
13A GLY* 2.5 42.7 + - - +
136A SER* 5.3 1.6 + - - +
138A PHE* 4.4 29.2 - + + -
139A GLU 5.6 0.7 - - - -
142A ARG* 4.6 24.0 - - + -
143A ALA* 4.9 9.2 - - + -
146A PHE* 5.1 16.2 - + + -
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Residues in contact with TRP 10 (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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4A LEU* 3.0 66.6 - - + -
5A LYS 5.8 1.1 - - - -
6A ASN 3.6 7.2 + - - +
7A THR* 3.4 6.0 + - - +
9A PHE* 1.3 115.1 - + - +
11A MET* 1.3 86.6 + - + +
13A GLY* 3.7 0.7 - - - -
14A LEU* 3.0 27.8 + - + +
146A PHE* 5.2 12.1 - + - -
161B MET* 5.9 2.2 - - - -
165B ASN* 5.2 5.3 - - - +
168B PHE* 3.0 52.4 - + + +
171B TRP* 4.7 15.3 - + + -
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Residues in contact with MET 11 (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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7A THR* 3.0 34.0 + - + +
8A ASN* 3.7 7.2 - - - +
10A TRP* 1.3 104.2 - - + +
12A PHE* 1.3 73.0 + - + +
14A LEU* 3.0 22.6 - - + +
15A PHE 3.1 3.6 + - - -
183A LEU 5.9 0.2 - - - +
184A LEU* 3.7 29.3 - - + +
187A ALA* 4.0 31.9 - - + +
171B TRP* 5.0 16.4 - - + +
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Residues in contact with PHE 12 (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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8A ASN* 2.9 20.6 + - + +
9A PHE* 5.5 0.2 - - - -
11A MET* 1.3 79.6 - - + +
13A GLY* 1.3 54.1 + - - +
14A LEU 2.5 17.4 + - - -
15A PHE* 2.5 29.6 + + + -
16A PHE* 2.7 15.3 + - - +
74A LYS* 5.8 2.7 - - + -
77A LEU* 4.9 8.3 - - + -
128A PHE* 3.2 41.1 - + - -
129A ILE* 3.2 41.3 - - + -
132A VAL* 3.6 18.2 - - + -
184A LEU* 4.3 17.3 - - + -
185A PHE* 5.9 6.1 - + - -
187A ALA 5.0 4.3 - - - -
188A LYS* 5.9 7.9 - - + -
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Residues in contact with GLY 13 (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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9A PHE* 2.5 31.3 + - - -
10A TRP* 3.7 0.7 - - - -
12A PHE* 1.3 71.3 - - - +
14A LEU* 1.3 57.8 + - - +
16A PHE* 3.8 7.2 - - - +
17A PHE 3.5 9.4 + - - -
143A ALA* 4.9 12.9 - - - +
146A PHE* 2.6 41.4 - - - -
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Residues in contact with LEU 14 (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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10A TRP* 3.0 23.8 + - + +
11A MET* 3.0 13.3 + - + +
12A PHE 2.5 4.0 + - - -
13A GLY* 1.3 73.0 - - - +
15A PHE* 1.3 58.4 + - - +
16A PHE 2.9 1.1 - - - -
17A PHE* 2.4 40.3 + - + +
18A PHE* 3.0 24.2 + - + -
146A PHE* 3.5 27.8 - - + -
180A LEU* 6.2 0.7 - - + -
184A LEU* 3.6 25.4 - - + -
172B LEU* 6.4 2.5 - - + -
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Residues in contact with PHE 15 (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 MET 3.1 3.9 + - - +
12A PHE* 2.5 33.2 + + + +
14A LEU* 1.3 74.4 - - - +
16A PHE* 1.3 62.8 + - - +
18A PHE* 3.6 4.8 + - + +
19A TYR* 3.3 21.9 + + - +
77A LEU* 4.0 24.9 - - + -
80A ILE* 6.1 1.8 - - + -
81A THR* 3.7 18.6 - - - -
84A LEU* 6.3 1.8 - - + -
125A VAL* 3.7 37.9 - - + -
129A ILE* 3.9 8.5 - - + -
181A ALA* 4.0 26.2 - - + -
184A LEU* 3.5 25.9 - - + +
185A PHE* 4.5 8.7 - + - -
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Residues in contact with PHE 16 (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 PHE 2.7 11.2 + - - +
13A GLY 3.8 6.7 - - - +
14A LEU 2.5 3.8 + - - -
15A PHE* 1.3 70.4 - - - +
17A PHE* 1.3 55.0 + - - +
19A TYR* 2.7 28.0 + - - +
20A PHE* 3.0 30.6 - + - -
125A VAL* 3.8 7.2 - - + -
126A GLU* 4.1 28.7 - - + -
129A ILE* 3.2 53.6 - - + -
140A PHE* 4.9 9.0 - + + -
143A ALA* 3.2 24.9 - - + +
144A ARG* 3.3 37.5 - - + -
147A GLY* 3.3 15.9 - - - -
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Residues in contact with PHE 17 (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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13A GLY 3.7 9.6 - - - +
14A LEU* 2.4 26.7 + - + +
16A PHE* 1.3 74.7 - - - +
18A PHE* 1.3 107.2 + + - -
19A TYR 3.3 1.2 + - - -
20A PHE* 3.7 1.9 + - - +
21A PHE* 3.6 28.5 + + - -
146A PHE* 4.0 13.7 - + + +
147A GLY* 3.2 13.4 - - - -
149A VAL* 3.5 31.4 - - + -
150A GLY* 3.4 31.5 - - - -
153A LEU* 4.4 10.8 - - + -
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Residues in contact with PHE 18 (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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14A LEU* 3.0 36.9 + - + +
15A PHE* 3.9 6.5 - - + +
17A PHE* 1.3 116.7 - + + +
19A TYR* 1.3 65.7 + - - +
21A PHE* 3.8 15.8 + + + +
22A ILE* 3.6 20.1 + - - +
176A CYS* 4.2 26.0 - - + -
177A ALA* 4.9 10.9 - - - +
180A LEU* 3.1 42.8 - - + -
181A ALA* 6.1 0.7 - - - +
184A LEU* 5.0 3.1 - - + -
179B ILE* 4.0 20.2 - - + -
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Residues in contact with TYR 19 (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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15A PHE* 3.3 14.3 + + - +
16A PHE* 2.7 22.1 + - - +
18A PHE* 1.3 73.3 - - - +
20A PHE* 1.3 77.7 + + + +
22A ILE* 3.0 10.4 + - + +
23A MET* 2.8 28.5 + - + +
80A ILE* 4.7 2.3 - - + +
84A LEU* 4.0 20.6 - - + -
117A CYS 2.7 23.7 + - - -
118A PHE* 3.6 25.1 - + - -
121A GLY* 3.0 24.9 - - - -
122A ALA* 3.2 28.8 + - + -
125A VAL* 4.2 27.8 - - + -
126A GLU* 6.0 2.9 - - + -
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Residues in contact with PHE 20 (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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16A PHE* 3.0 38.1 - + - -
17A PHE 3.9 2.7 - - - +
19A TYR* 1.3 87.8 - + + +
21A PHE* 1.3 56.2 + - - +
23A MET* 3.9 16.6 - - + -
24A GLY* 2.3 36.2 + - - -
125A VAL* 6.5 0.2 - - + -
126A GLU* 5.6 4.9 - - + -
144A ARG* 2.9 49.6 - - - -
147A GLY 3.6 6.1 - - - +
148A CYS* 3.6 18.2 - - - -
150A GLY 3.8 3.1 - - - -
151A TRP* 3.3 49.0 - + + +
1E YIO 4.8 2.5 - - - -
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Residues in contact with PHE 21 (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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17A PHE* 3.6 40.8 + + - -
18A PHE* 4.0 16.8 - + - +
19A TYR 3.0 1.4 + - - -
20A PHE* 1.3 79.5 - - - +
22A ILE* 1.3 69.3 + - + +
24A GLY* 3.3 0.6 - - - -
25A ALA* 2.9 22.5 + - - +
150A GLY* 3.6 25.6 - - - -
153A LEU* 3.8 23.3 - - + -
154A GLY* 4.2 19.0 - - - -
157A ILE* 5.3 12.8 - - + -
172A LEU 5.2 2.5 - - - -
173A GLY* 5.4 6.1 - - - +
176A CYS* 4.2 25.1 - - - -
179B ILE* 6.2 4.7 - - + -
183B LEU* 6.2 3.8 - - + -
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Residues in contact with ILE 22 (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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18A PHE 3.6 14.6 - - - +
19A TYR* 3.0 3.5 + - + +
21A PHE* 1.3 82.7 - - + +
23A MET* 1.3 60.5 + - - +
25A ALA* 3.9 3.9 - - - +
26A TYR* 2.8 25.6 + - - +
84A LEU* 4.2 26.7 - - + -
87A PHE* 3.7 31.2 - - + -
118A PHE* 3.1 32.5 - - + -
173A GLY* 3.8 11.9 - - - +
174A SER* 5.2 0.9 - - - -
177A ALA* 3.0 36.8 - - + -
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Residues in contact with MET 23 (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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19A TYR* 2.8 20.9 + - + +
20A PHE* 3.7 22.2 - - + +
22A ILE* 1.3 72.5 - - - +
24A GLY* 1.3 72.5 + - - +
26A TYR* 3.0 6.3 + - + -
27A PHE* 2.9 26.7 + - + +
118A PHE* 3.6 39.6 - - + +
122A ALA* 5.1 9.6 - - + -
144A ARG* 5.4 0.2 - - - +
151A TRP* 3.5 20.4 - - + -
1E YIO 3.0 52.9 - - - +
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Residues in contact with GLY 24 (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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20A PHE 2.3 28.8 + - - -
21A PHE* 2.9 1.7 + - - -
23A MET* 1.3 68.6 - - - +
25A ALA* 1.3 68.9 + - - +
28A PRO* 3.1 23.3 - - - +
151A TRP* 3.4 22.5 - - - -
155A ALA* 5.0 12.1 - - - -
158A VAL* 4.5 3.4 - - - -
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Residues in contact with ALA 25 (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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21A PHE 2.9 15.8 + - - +
22A ILE* 3.9 4.7 - - - +
24A GLY* 1.3 71.4 - - - +
26A TYR* 1.3 60.9 + - - +
29A PHE* 2.5 36.7 + - + +
87A PHE* 5.1 8.5 - - + -
155A ALA 5.3 0.2 - - - +
158A VAL* 3.5 29.8 - - + +
169A VAL* 4.1 21.5 - - + -
170A PHE* 5.7 0.7 - - + -
173A GLY* 5.6 6.3 - - - -
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Residues in contact with TYR 26 (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 ILE 2.8 24.5 + - - +
23A MET* 3.0 6.5 + - + +
25A ALA* 1.3 76.2 - - - +
27A PHE* 1.3 95.2 + + + +
29A PHE* 3.5 4.5 - - - +
30A PHE* 2.8 41.1 + + - +
52A ILE* 3.4 30.0 - - - +
87A PHE* 4.2 24.6 - + + -
91A PHE* 4.4 19.2 - + - -
114A LEU* 6.3 0.4 - - + -
115A GLY* 3.8 29.8 + - - -
118A PHE* 3.7 36.3 - + + -
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Residues in contact with PHE 27 (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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23A MET* 2.9 15.8 + - + +
25A ALA 3.2 0.6 + - - -
26A TYR* 1.3 95.9 - + + +
28A PRO* 1.4 81.4 - - + +
30A PHE* 3.0 3.2 - - - +
31A PRO* 3.0 23.3 - - + +
49A PHE* 5.2 11.8 - + - -
151A TRP* 4.4 15.0 - + + -
240A ASP* 4.0 31.4 - - - -
241A GLN* 5.1 9.4 - - + -
261A PHE* 6.4 0.7 - + - -
319A LYS* 6.2 0.9 - - - -
1E YIO 4.6 13.7 - - - -
2E GAL 4.2 17.5 - - - -
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Residues in contact with PRO 28 (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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24A GLY* 3.1 22.4 - - - +
25A ALA* 5.1 0.4 - - - -
27A PHE* 1.4 101.5 - - + +
29A PHE* 1.3 66.6 + - - +
30A PHE 2.8 2.1 + - - -
31A PRO* 2.9 18.1 - - + +
32A ILE* 3.6 11.9 + - + +
151A TRP* 4.7 8.5 - - + -
155A ALA* 5.5 7.6 - - + -
158A VAL* 5.5 6.7 - - + -
261A PHE* 3.9 32.3 - - + -
262A GLY* 6.5 1.3 - - - -
265A THR* 5.0 15.5 - - + +
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Residues in contact with PHE 29 (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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25A ALA* 2.5 28.6 + - + +
26A TYR* 3.5 2.9 - - - +
28A PRO* 1.3 77.0 - - - +
30A PHE* 1.3 53.0 + - - +
32A ILE* 3.1 9.3 + - - +
33A TRP* 2.3 77.6 + + + +
91A PHE* 5.1 3.1 - + - -
158A VAL* 4.5 12.6 - - + +
162A PHE* 3.3 33.2 - + - -
166A ASN* 4.2 8.1 - - + -
169A VAL* 3.9 29.6 - - + -
170A PHE* 3.0 42.8 - + - -
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Residues in contact with PHE 30 (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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26A TYR* 2.8 36.1 + + - +
27A PHE* 3.0 9.6 - - - +
28A PRO 2.8 3.4 + - - -
29A PHE* 1.3 72.6 - - - +
31A PRO* 1.3 72.5 - - + +
33A TRP* 2.9 18.0 + + - +
34A LEU* 2.8 51.1 + - + +
48A ILE* 3.4 24.9 - - + -
49A PHE* 3.9 20.9 - + - -
52A ILE* 3.3 29.8 - - + -
91A PHE* 4.6 13.9 - + - -
95A PHE* 4.8 12.1 - + - -
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Residues in contact with PRO 31 (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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27A PHE* 3.0 12.1 - - + +
28A PRO* 2.9 16.4 - - + +
30A PHE* 1.3 95.5 - - + +
32A ILE* 1.3 63.3 + - - +
34A LEU* 3.3 13.5 - - + +
35A HIS 3.0 17.2 + - - -
45A THR* 6.1 0.7 - - + -
49A PHE* 3.6 24.2 - - + -
241A GLN 3.8 11.0 - - - +
242A GLN* 5.3 3.6 - - + -
244A ALA* 4.3 19.1 - - + -
245A ASN* 3.5 25.9 + - - +
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Residues in contact with ILE 32 (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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28A PRO 3.6 9.7 + - - +
29A PHE* 3.1 10.4 + - - +
31A PRO* 1.3 76.9 - - + +
33A TRP* 1.3 69.8 + - - +
35A HIS* 3.3 9.9 + - - -
36A ASP* 3.3 24.3 + - - +
37A ILE 3.9 1.4 + - - -
162A PHE* 3.1 33.5 - - + -
244A ALA* 5.3 3.8 - - + -
245A ASN* 3.7 12.8 - - - +
248A THR* 4.3 15.3 - - + +
258A THR* 3.3 41.3 - - + +
261A PHE* 4.8 16.4 - - + -
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Residues in contact with TRP 33 (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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29A PHE* 2.3 66.5 + + + +
30A PHE* 3.1 9.4 - + - +
32A ILE* 1.3 66.3 - - - +
34A LEU* 1.3 83.5 + - + +
37A ILE* 2.8 59.8 + - + +
38A ASN* 2.9 31.9 + - - -
91A PHE* 3.4 50.3 - + - -
92A ILE* 4.7 2.9 - - - +
95A PHE* 3.2 39.9 - + + -
96A GLY* 4.0 4.9 - - - -
99A LEU* 4.6 0.9 - - + -
162A PHE* 4.5 0.9 - - - -
166A ASN* 3.9 5.6 - - - +
170A PHE* 4.0 6.4 - + - -
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Residues in contact with LEU 34 (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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30A PHE* 2.8 36.8 + - + +
31A PRO* 3.3 11.2 - - + +
33A TRP* 1.3 97.6 - - + +
35A HIS* 1.3 57.4 + - - +
38A ASN* 2.3 48.5 + - + +
40A ILE* 3.0 38.4 - - + -
45A THR* 3.9 12.8 - - + -
48A ILE* 3.7 29.6 - - + -
49A PHE* 4.5 6.1 - - + -
99A LEU* 5.1 2.2 - - + -
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Residues in contact with HIS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO 3.0 10.1 + - - +
32A ILE* 3.3 8.4 + - - +
34A LEU* 1.3 88.6 - - - +
36A ASP* 1.3 76.1 + - - +
37A ILE 2.7 10.6 + - - -
39A HIS* 2.7 19.2 + - - -
40A ILE* 3.4 20.1 - - - +
42A LYS* 6.5 0.7 - - - -
245A ASN* 3.8 32.0 - - + +
248A THR* 5.6 8.7 - - + +
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 3.3 28.9 + - + +
35A HIS* 1.3 96.3 + - - +
37A ILE* 1.3 67.1 + - + +
39A HIS* 4.3 15.1 + - - -
162A PHE* 4.5 5.2 - - + -
163A THR* 6.2 0.5 - - - +
248A THR* 5.1 8.8 - - - +
254A GLY* 5.3 8.3 - - - +
258A THR* 4.3 8.3 + - - -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 2.8 39.1 + - + +
35A HIS 2.7 4.4 + - - -
36A ASP* 1.3 80.2 - - + +
38A ASN* 1.3 65.2 + - - +
39A HIS* 3.6 5.5 + - - -
100A GLN* 4.3 4.2 + - - +
162A PHE* 3.1 40.6 - - + -
166A ASN* 2.8 41.5 - - + +
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Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 2.9 55.2 + - - -
34A LEU* 2.3 39.6 + - + +
37A ILE* 1.3 81.5 - - - +
39A HIS* 1.3 71.1 + - - +
40A ILE* 2.4 8.4 + - + +
96A GLY* 4.1 13.7 - - - -
99A LEU* 4.7 8.9 - - + +
100A GLN* 3.1 34.2 + - - +
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Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A HIS* 2.7 16.9 + - - +
36A ASP* 4.3 15.7 + - - -
37A ILE 5.1 3.4 + - - -
38A ASN* 1.3 77.2 - - - +
40A ILE* 1.3 63.3 + - - +
41A SER* 3.7 1.9 + - - -
44A ASP* 4.9 1.6 - - - +
100A GLN* 4.9 10.3 - - - +
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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