Contacts of the helix formed by residues 146 - 168 (chain D) in PDB entry 1WNT
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 HIS 146 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B VAL* 4.0 5.0 - - - +
166B GLU* 4.2 0.4 + - - -
88D LEU 5.7 0.7 - - - -
89D LEU* 3.5 34.0 - - + +
138D CYS* 4.6 6.3 - - + -
143D VAL* 3.4 23.1 + - + +
144D THR 2.7 23.1 + - - -
145D ASN* 1.3 81.5 - - + +
147D SER* 1.3 64.3 + - - +
148D VAL 3.3 3.4 - - - +
149D TYR* 3.7 36.0 - + + +
150D CYS* 3.1 33.6 + - - +
190D THR* 4.5 13.4 + - + -
191D TRP* 4.3 18.3 + + - -
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Residues in contact with SER 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 5.7 1.6 - - - -
159B LEU* 4.4 9.8 - - - +
162B VAL* 3.7 22.3 - - - +
166B GLU* 3.4 16.8 + - - -
90D GLN 3.7 8.3 + - - -
92D PHE* 3.5 36.2 - - - -
95D VAL* 4.0 8.4 - - - +
145D ASN 3.7 1.0 - - - -
146D HIS* 1.3 75.8 - - - +
148D VAL* 1.3 54.4 + - - +
151D SER* 2.3 33.4 + - - -
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Residues in contact with VAL 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ILE* 4.2 5.6 - - + -
88D LEU 4.9 9.5 + - - +
95D VAL* 4.0 25.0 - - + +
99D ALA* 4.2 5.2 - - + +
100D PHE* 3.7 34.1 - - + +
103D SER* 3.3 30.3 - - - +
104D PHE* 3.3 21.7 - - + -
146D HIS 3.3 0.4 - - - -
147D SER* 1.3 79.2 - - - +
149D TYR* 1.3 57.2 + - - +
151D SER* 3.1 6.7 + - - -
152D THR* 2.8 32.4 + - - +
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Residues in contact with TYR 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D VAL 3.8 22.4 - - - -
87D ALA* 4.1 11.0 - - + -
88D LEU 5.0 5.4 + - - +
89D LEU* 4.4 17.7 - - + -
103D SER* 5.7 0.7 - - - -
107D ASN* 3.9 8.5 - - - +
136D SER* 4.3 6.5 - - - -
138D CYS* 3.8 13.0 - - + -
146D HIS* 3.7 31.1 + + + +
147D SER 3.6 0.2 - - - -
148D VAL* 1.3 80.3 - - - +
150D CYS* 1.3 61.0 + - - +
152D THR* 2.3 26.4 + - - -
153D LYS* 2.8 39.2 + - + +
186D MET* 2.9 34.5 - - + +
3245D NAP 3.3 20.7 + + - -
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Residues in contact with CYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B MET* 3.5 21.5 - - + +
162B VAL* 4.2 4.9 - - + -
138D CYS* 2.0 61.3 - - - +
141D ARG 3.9 6.3 - - - -
142D ALA* 4.4 0.2 - - - -
143D VAL 4.1 8.5 - - - -
146D HIS* 3.1 31.4 + - - +
149D TYR* 1.3 78.3 - - - +
151D SER* 1.3 51.7 + - - +
153D LYS* 3.2 2.1 + - - +
154D GLY* 2.5 35.3 + - - -
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Residues in contact with SER 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.1 8.2 - - - +
112B ILE* 5.9 0.7 - - - +
155B ALA* 3.7 23.1 - - - +
158B MET* 4.3 4.7 - - - +
159B LEU* 3.6 18.7 - - - +
100D PHE* 5.8 0.2 - - - -
104D PHE* 3.9 17.0 - - - -
147D SER 2.3 27.4 + - - -
148D VAL* 3.1 8.0 + - - -
150D CYS* 1.3 72.6 - - - +
152D THR* 1.3 62.4 + - - +
154D GLY 4.3 0.4 - - - +
155D ALA* 2.8 29.5 + - - +
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Residues in contact with THR 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D SER* 3.8 22.7 - - - +
104D PHE* 3.8 32.1 - - + -
107D ASN* 3.4 31.5 + - + +
108D LEU* 4.8 4.0 - - + +
148D VAL 2.8 21.2 + - - +
149D TYR* 2.3 30.8 + - - -
151D SER* 1.3 73.6 - - - +
153D LYS* 1.3 56.3 + - - +
155D ALA* 2.8 11.1 + - - +
156D LEU* 2.7 35.1 + - - +
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Residues in contact with LYS 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ALA* 3.9 8.1 - - - +
107D ASN* 4.9 5.6 - - + +
134D VAL 3.4 16.2 + - - -
135D SER* 3.2 31.5 + - - -
136D SER* 3.5 12.8 - - - +
138D CYS* 4.6 0.2 - - - -
139D SER* 3.2 30.9 - - - +
149D TYR* 2.8 39.6 + - + +
150D CYS* 3.4 9.0 - - - +
152D THR* 1.3 84.3 + - - +
154D GLY* 1.3 64.3 + - - +
156D LEU* 3.3 12.4 + - + +
157D ASP 3.3 12.6 + - - -
3245D NAP 2.8 32.7 + - - -
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Residues in contact with GLY 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B GLY* 4.2 13.0 - - - +
158B MET* 4.0 11.0 - - - -
139D SER* 3.5 20.8 - - - -
150D CYS 2.5 20.5 + - - -
151D SER 3.9 1.1 - - - -
153D LYS* 1.3 69.4 - - - +
155D ALA* 1.3 66.1 + - - +
157D ASP* 3.4 6.4 + - - +
158D MET* 3.4 17.3 + - - +
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 4.5 0.9 - - + -
151B SER* 3.8 26.3 + - - +
155B ALA* 4.0 7.0 - - + +
104D PHE* 5.1 0.2 - - + -
108D LEU* 3.6 29.2 - - + -
151D SER 2.8 15.5 + - - +
152D THR* 2.9 14.4 - - - +
154D GLY* 1.3 75.9 - - - +
156D LEU* 1.3 49.5 + - - +
158D MET* 3.0 5.9 + - - +
159D LEU* 2.7 34.0 + - - +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ASN 5.6 1.3 - - - +
107D ASN 4.2 11.9 - - - +
108D LEU* 4.1 19.0 - - + +
111D VAL* 4.2 15.7 - - + -
133D ASN* 4.0 34.5 - - + +
134D VAL 3.8 22.7 - - - +
135D SER* 3.9 13.7 - - - +
152D THR 2.7 15.1 + - - +
153D LYS* 3.4 20.6 - - + +
154D GLY 3.3 0.2 - - - -
155D ALA* 1.3 72.4 - - - +
157D ASP* 1.3 52.3 + - - +
159D LEU* 3.1 10.7 + - + +
160D THR* 2.7 38.7 + - - +
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Residues in contact with ASP 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D SER* 2.7 28.1 + - - -
139D SER* 2.3 27.9 + - - +
140D GLN* 2.9 20.9 + - - +
153D LYS 3.3 4.4 + - - -
154D GLY* 3.7 7.0 - - - +
155D ALA 3.3 0.2 - - - -
156D LEU* 1.3 74.8 - - - +
158D MET* 1.3 62.0 + - - +
160D THR* 3.3 8.5 + - - -
161D LYS* 3.1 34.3 + - - +
176D ALA* 4.4 1.7 - - - +
178D ASN* 3.2 7.3 + - - -
234D THR* 3.8 20.1 - - + +
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Residues in contact with MET 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B CYS 3.1 20.2 - - - +
139B SER 3.3 26.9 - - - +
140B GLN* 3.6 15.3 - - - +
141B ARG 3.6 0.4 - - - -
142B ALA* 3.4 34.1 - - + +
150B CYS* 3.7 30.5 - - + +
151B SER* 4.4 2.2 - - - -
154B GLY* 3.9 7.4 - - - -
154D GLY 3.4 6.8 + - - +
155D ALA 3.0 8.0 + - - +
157D ASP* 1.3 80.1 - - - +
159D LEU* 1.3 62.0 + - - +
161D LYS* 3.2 18.0 + - + -
162D VAL* 2.9 30.4 + - - +
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Residues in contact with LEU 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 4.0 15.0 - - + -
147B SER* 4.1 14.1 - - - +
151B SER* 3.7 19.4 + - - +
108D LEU* 3.1 33.0 - - + +
111D VAL* 4.2 9.4 - - + -
112D ILE* 3.7 36.1 - - + -
155D ALA 2.7 16.3 + - - +
156D LEU* 3.1 14.3 + - + +
158D MET* 1.3 77.6 - - - +
160D THR* 1.3 63.7 + - - +
162D VAL* 3.2 4.1 + - - -
163D MET* 2.9 34.4 + - + +
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Residues in contact with THR 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ASN* 3.1 17.2 + - - +
156D LEU 2.7 23.7 + - - -
157D ASP* 3.4 11.0 - - - -
159D LEU* 1.3 74.9 - - - +
161D LYS* 1.3 58.9 + - - +
163D MET* 3.4 2.6 + - - +
164D ALA* 2.8 27.2 + - - +
174D VAL* 3.4 28.8 - - + +
175D ASN* 3.7 26.2 - - - -
176D ALA* 3.8 16.1 - - - +
232D GLY* 4.2 6.7 - - - -
233D SER 4.3 3.8 - - - +
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Residues in contact with LYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A TRP 5.2 1.3 - - - +
243A ALA* 3.8 37.5 - - + +
140B GLN* 5.0 7.6 - - - +
142B ALA* 3.8 6.3 - - + +
140D GLN* 5.4 2.0 - - - +
157D ASP* 3.1 25.3 + - - +
158D MET* 3.2 20.8 + - + +
160D THR* 1.3 76.3 - - - +
162D VAL* 1.3 58.7 + - - +
164D ALA* 3.5 8.2 - - - +
165D LEU* 3.0 27.9 + - - +
232D GLY* 3.4 24.8 + - - +
233D SER* 4.7 1.4 - - - +
234D THR* 3.7 26.9 + - - +
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 5.9 0.2 - - - -
142B ALA* 3.3 20.9 - - + -
143B VAL 3.3 27.4 - - - +
147B SER* 3.7 35.0 - - - +
150B CYS* 4.1 14.6 - - + -
158D MET 2.9 20.4 + - - +
159D LEU* 3.9 4.5 - - - +
161D LYS* 1.3 73.7 - - - +
163D MET* 1.3 61.0 + - - +
165D LEU* 3.3 2.7 + - + +
166D GLU* 2.9 45.0 + - + +
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Residues in contact with MET 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 3.5 44.2 - - + -
111D VAL* 4.8 2.7 - - - -
115D SER* 3.5 32.3 - - - +
131D ILE* 3.7 22.4 - - + -
133D ASN* 4.4 9.4 - - - +
159D LEU* 2.9 34.8 + - + +
160D THR 3.5 4.3 - - - +
162D VAL* 1.3 75.8 - - - +
164D ALA* 1.3 62.2 + - - +
166D GLU* 5.0 2.0 - - - -
167D LEU* 2.9 39.4 + - + +
174D VAL* 3.8 19.1 - - + -
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PRO* 4.0 5.7 - - + +
243A ALA* 5.1 3.4 - - + -
160D THR 2.8 21.2 + - - +
161D LYS 3.5 5.2 - - - +
162D VAL 3.3 0.2 - - - -
163D MET* 1.3 72.7 - - - +
165D LEU* 1.3 57.3 + - - +
167D LEU 3.8 0.2 - - - -
168D GLY* 2.8 30.7 + - - -
172D ILE 4.7 1.9 - - - +
174D VAL* 3.7 12.7 - - - +
231D THR* 3.7 16.7 + - + +
232D GLY* 3.5 31.2 - - - +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PRO* 3.8 24.9 - - + +
243A ALA* 5.7 0.9 - - + +
244A CYS* 4.2 26.2 - - + -
142B ALA* 3.8 27.6 - - + +
143B VAL* 4.1 1.8 - - - -
144B THR* 4.0 30.1 - - - +
161D LYS 3.0 16.6 + - - +
162D VAL* 3.9 3.4 - - + +
164D ALA* 1.3 76.1 - - - +
166D GLU* 1.3 68.0 + - + +
168D GLY* 3.6 5.5 + - - -
169D PRO* 3.6 9.0 - - - +
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PRO* 3.5 9.7 - - - +
92B PHE* 2.9 34.5 + - + +
144B THR* 3.8 23.8 - - + +
145B ASN* 2.9 27.4 + - - +
147B SER* 3.4 18.0 + - - -
162D VAL* 2.9 28.7 + - + +
163D MET 4.3 0.7 - - - +
165D LEU* 1.3 76.2 - - + +
167D LEU* 1.3 61.2 + - + +
168D GLY 3.1 0.4 - - - -
169D PRO* 3.0 21.5 - - - +
170D HIS* 4.1 7.6 + - - -
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 4.4 13.0 - - + -
93B LEU* 4.5 12.6 - - + -
119D ALA* 4.2 24.7 - - + -
123D ILE* 4.0 27.4 - - + -
131D ILE* 4.4 9.4 - - + -
163D MET* 2.9 43.5 + - + +
164D ALA 3.8 0.2 - - - -
166D GLU* 1.3 77.9 - - + +
168D GLY* 1.3 59.0 + - - +
169D PRO* 3.4 0.7 - - - -
170D HIS* 2.8 29.7 + - + +
172D ILE* 3.5 29.9 + - + +
174D VAL* 4.4 4.5 - - + -
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Residues in contact with GLY 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A PRO* 3.1 22.1 - - - +
206A LEU* 3.9 14.1 - - - +
164D ALA 2.8 20.7 + - - -
165D LEU 3.6 1.5 + - - -
166D GLU 3.1 0.4 - - - -
167D LEU* 1.3 74.9 - - - +
169D PRO* 1.3 65.1 - - - +
170D HIS 3.1 4.3 + - - -
171D LYS* 3.1 16.5 + - - +
172D ILE 4.1 7.0 - - - -
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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