Contacts of the helix formed by residues 145 - 169 (chain B) in PDB entry 3QBK
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 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLY 3.7 0.6 + - - +
144B SER* 1.3 89.1 + - - +
146B ALA* 1.3 61.9 + - - +
147B THR* 3.2 6.9 + - - -
148B LYS* 2.9 36.7 + - - +
149B LEU* 3.1 12.1 + - - +
201B ASP* 4.7 2.0 + - - -
62D PRO* 4.0 13.5 - - + +
402D BR 3.5 21.9 - - - +
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Residues in contact with ALA 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASN* 1.3 75.1 - - - +
147B THR* 1.3 63.9 + - - +
149B LEU* 3.1 8.8 + - - +
150B PHE* 2.9 26.9 + - - +
66D LEU* 5.3 10.1 - - + -
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Residues in contact with THR 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASN* 3.2 9.2 + - - -
146B ALA* 1.3 77.6 - - - +
148B LYS* 1.3 58.4 + - + +
150B PHE* 3.7 4.4 + - - +
151B THR* 2.8 35.7 + - - +
62D PRO* 2.5 34.6 + - - +
65D LYS* 4.0 9.6 - - + +
66D LEU* 3.4 36.4 - - - +
69D VAL* 4.7 1.6 - - + -
402D BR 3.7 19.7 - - + -
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER* 3.4 13.2 - - - +
145B ASN* 2.9 22.9 + - - +
147B THR* 1.3 74.9 - - + +
149B LEU* 1.3 61.3 + - - +
151B THR* 3.2 6.0 + - - -
152B ALA* 2.9 32.1 + - - +
193B ILE* 5.0 7.1 - - + +
197B GLU* 2.8 47.2 + - + +
198B TRP* 3.6 11.1 - - - +
200B GLN* 5.7 0.6 + - - -
201B ASP* 3.4 36.1 + - - +
65D LYS* 5.8 0.7 - - - +
402D BR 3.9 22.9 - - + -
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU 3.9 15.5 - - - +
136B LEU* 4.2 25.6 - - + +
139B GLY* 3.9 10.1 - - - -
140B LEU* 4.6 10.1 - - + +
144B SER* 3.1 38.5 + - - +
145B ASN 3.1 13.4 + - - +
146B ALA* 3.1 11.6 + - - +
148B LYS* 1.3 77.9 - - - +
150B PHE* 1.3 57.3 + - - +
152B ALA* 3.5 0.3 + - - +
153B ILE* 2.9 45.8 + - + +
198B TRP* 3.7 20.0 - - + -
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Residues in contact with PHE 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA 2.9 17.6 + - - +
147B THR* 3.8 6.3 - - - +
149B LEU* 1.3 77.2 - - - +
151B THR* 1.3 51.4 + - - +
153B ILE* 4.7 4.3 - - - -
154B THR* 2.6 60.9 + - + +
66D LEU* 4.3 17.7 - - + -
69D VAL* 4.1 15.7 - - + -
70D SER* 4.0 9.4 - - - -
73D LEU* 3.5 28.3 - - + -
133D MET* 3.9 12.8 - - + -
136D LEU* 3.7 30.7 - - + -
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B THR* 2.8 24.7 + - - +
148B LYS* 3.6 7.4 - - - -
150B PHE* 1.3 74.4 - - - +
152B ALA* 1.3 66.6 + - - +
154B THR* 3.2 6.1 + - - -
155B PHE* 3.1 42.6 + - + +
189B VAL* 4.0 14.1 - - + -
193B ILE* 4.6 10.8 - - + -
69D VAL* 3.6 29.8 - - + +
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 4.2 12.3 - - + -
148B LYS 2.9 20.1 + - - +
149B LEU 3.9 1.3 - - - +
151B THR* 1.3 73.4 - - - +
153B ILE* 1.3 58.2 + - + +
156B ASP* 2.9 32.7 + - - +
189B VAL* 5.5 0.7 - - - -
190B VAL* 3.5 13.2 - - + +
193B ILE* 3.7 32.7 - - + +
198B TRP* 3.8 14.6 - - + -
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PRO* 4.1 32.1 - - + +
133B MET* 5.8 1.8 - - + -
135B LEU* 4.3 11.2 - - + -
136B LEU* 4.2 21.1 - - + -
149B LEU* 2.9 37.6 + - + +
150B PHE* 4.1 3.6 - - - +
152B ALA* 1.3 73.1 - - + +
154B THR* 1.3 69.8 + - + +
156B ASP* 3.2 6.2 + - - +
157B ILE* 3.0 44.0 + - + +
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B PHE* 2.6 61.6 + - + +
151B THR* 3.2 9.2 + - - -
153B ILE* 1.3 77.2 - - + +
155B PHE* 1.3 65.6 + - - +
157B ILE* 3.3 8.7 + - + +
158B ALA* 3.0 26.7 + - - +
73D LEU* 3.6 28.2 - - + +
133D MET* 5.3 3.6 - - - -
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Residues in contact with PHE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B THR* 3.1 25.8 + - + +
152B ALA 4.3 1.1 - - - +
154B THR* 1.3 81.7 + - - +
156B ASP* 1.3 59.9 + - - +
158B ALA* 3.3 3.3 + - + -
159B MET* 2.9 24.3 + - - +
186B CYS* 3.4 36.3 - - - +
189B VAL* 3.8 39.3 - - + -
190B VAL* 4.3 3.1 - - + -
69D VAL* 4.0 20.0 - - + -
72D ILE* 4.9 10.3 - - + -
73D LEU* 3.8 25.6 - - + -
76D VAL* 4.1 29.6 - - + -
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 2.4 25.6 + - - -
132B PRO* 3.6 12.0 - - - +
135B LEU* 3.4 19.3 - - + -
152B ALA 2.9 21.4 + - - +
153B ILE* 3.2 5.8 + - - +
155B PHE* 1.3 74.5 - - - +
157B ILE* 1.3 65.9 + - - +
159B MET* 3.1 15.9 + - - +
160B CYS* 3.1 21.3 + - - -
190B VAL* 3.8 10.2 - - + +
222B TRP* 3.1 32.7 - - - -
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ALA* 3.9 14.6 - - + +
132B PRO* 3.6 28.0 - - + -
153B ILE* 3.0 32.2 + - + +
154B THR* 3.6 9.9 - - + +
156B ASP* 1.3 76.9 - - - +
158B ALA* 1.3 59.0 + - - +
160B CYS* 3.2 7.4 + - - +
161B VAL* 2.9 46.7 + - + +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B THR 3.0 14.1 + - - +
155B PHE* 3.5 14.6 - - + +
156B ASP 3.2 0.2 - - - -
157B ILE* 1.3 77.5 - - - +
159B MET* 1.3 53.5 + - - +
161B VAL* 4.6 5.4 - - - +
162B THR* 2.7 42.0 + - + +
186B CYS* 3.8 17.0 - - - -
73D LEU* 5.7 3.1 - - + -
76D VAL* 5.0 10.1 - - + -
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Residues in contact with MET 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B THR* 5.0 0.7 - - - +
155B PHE 2.9 14.5 + - - +
156B ASP* 3.1 40.6 + - - +
158B ALA* 1.3 76.9 - - - +
160B CYS* 1.3 76.4 + - - +
162B THR* 3.2 3.1 + - - -
163B GLY* 3.1 13.7 + - - -
183B SER* 2.8 42.9 + - - +
186B CYS* 3.9 12.3 - - + +
187B PHE* 3.5 38.1 - - + +
190B VAL* 5.4 1.3 - - - -
222B TRP* 4.3 4.3 - - + -
292B RET 3.9 37.3 - - + +
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Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TYR* 3.8 14.2 - - - +
127B TRP* 3.7 26.9 - - + -
128B ALA* 3.7 22.4 - - + +
131B THR* 3.5 23.1 - - - -
156B ASP* 3.1 15.4 + - - -
157B ILE 3.2 6.0 + - - +
159B MET* 1.3 95.8 - - - +
161B VAL* 1.3 58.0 + - - +
163B GLY* 3.4 1.6 + - - -
164B LEU* 3.0 26.9 + - - +
292B RET 5.0 6.4 - - - +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ALA* 4.6 9.9 - - + -
157B ILE* 2.9 32.6 + - + +
158B ALA* 4.1 5.6 - - - +
160B CYS* 1.3 74.6 - - - +
162B THR* 1.3 64.5 + - + +
164B LEU* 3.2 14.4 + - + +
165B ALA* 2.9 26.9 + - + +
129D LEU* 6.0 7.0 - - + -
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Residues in contact with THR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B ALA* 2.7 26.0 + - + +
159B MET 3.2 8.0 + - - -
161B VAL* 1.3 75.8 - - + +
163B GLY* 1.3 60.1 + - - +
165B ALA* 3.4 7.6 - - - +
166B ALA* 2.9 27.0 + - - +
179B TRP* 3.7 36.8 - - + +
182B ILE* 3.9 20.5 - - + +
183B SER* 3.2 19.5 - - - -
80D ALA* 4.4 11.0 - - + -
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TYR* 4.5 5.1 - - - -
159B MET 3.1 15.9 + - - -
160B CYS 3.8 3.8 - - - -
161B VAL 3.2 0.2 - - - -
162B THR* 1.3 76.9 + - - +
164B LEU* 1.3 63.5 + - - +
166B ALA* 3.2 6.7 + - - +
167B ALA* 3.1 21.7 + - - +
183B SER* 4.2 0.9 + - - -
229B TRP* 4.5 4.5 + - - -
292B RET 3.8 32.8 - - - -
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TRP* 3.5 46.4 - - + +
124B TYR* 3.8 17.4 - - + +
125B LEU* 4.0 31.2 - - + -
160B CYS 3.0 13.2 + - - +
161B VAL* 3.4 17.0 - - + +
163B GLY* 1.3 76.7 - - - +
165B ALA* 1.3 62.8 + - - +
167B ALA* 3.1 4.7 + - - +
168B LEU* 2.9 41.6 + - + +
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B VAL* 2.9 15.2 + - + +
162B THR* 3.4 10.5 - - - +
164B LEU* 1.3 77.7 - - - +
166B ALA* 1.3 61.2 + - - +
168B LEU* 3.2 4.6 + - - +
169B THR* 2.8 31.0 + - - -
179B TRP* 3.6 35.9 - - + -
89D LEU* 4.0 15.5 - - + +
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B THR 2.9 9.7 + - - +
163B GLY* 3.4 12.1 - - - +
164B LEU 3.2 0.2 - - - -
165B ALA* 1.3 77.5 - - - +
167B ALA* 1.3 57.9 + - - +
169B THR* 3.4 3.6 + - - -
176B ARG* 2.9 42.8 + - - +
179B TRP* 3.4 30.5 - - + -
180B TYR* 4.1 7.0 - - + +
229B TRP* 4.0 17.7 - - + -
292B RET 5.8 0.2 - - + -
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Residues in contact with ALA 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 3.6 14.7 - - - +
96B MET* 4.8 1.0 - - - +
119B THR* 4.1 7.7 + - + +
124B TYR* 3.4 36.3 - - + -
163B GLY 3.1 6.1 + - - +
164B LEU 3.1 7.8 + - - +
166B ALA* 1.3 79.3 - - - +
168B LEU* 1.3 62.1 + - + +
176B ARG* 3.1 24.2 + - - +
229B TRP* 4.0 3.1 - - - +
234B GLU* 3.5 14.9 - - + +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 4.2 14.6 - - + +
119B THR* 4.6 0.9 - - + -
121B TRP* 3.7 42.8 - - + -
164B LEU* 2.9 37.0 + - + +
165B ALA* 3.6 5.8 - - - +
167B ALA* 1.3 80.2 - - - +
169B THR* 1.3 60.5 + - - +
170B THR* 3.6 7.2 + - - +
21D GLN* 3.0 19.2 + - - -
89D LEU* 3.5 17.8 - - + +
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA 2.8 19.7 + - - -
166B ALA 3.8 6.1 - - - -
167B ALA 3.3 0.8 - - - -
168B LEU* 1.3 75.2 - - - +
170B THR* 1.3 61.6 + - - +
171B SER* 3.9 11.9 - - - +
172B SER 4.0 6.1 - - - +
175B MET* 3.8 29.2 - - + -
176B ARG* 2.8 36.6 + - + +
179B TRP* 2.9 21.7 + - - +
21D GLN* 3.4 11.4 - - - +
87D SER* 4.4 4.4 + - - -
89D LEU* 4.0 10.6 - - - +
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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