Contacts of the helix formed by residues 153 - 179 (chain E) in PDB entry 1HBX
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 153 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E ILE* 3.6 2.8 - - + +
152E ASP* 1.3 81.6 + - - +
154E LYS* 1.3 64.1 + - - +
155E LEU* 2.8 16.7 + - - +
156E ARG* 2.5 59.6 + - + +
157E ARG* 2.9 23.6 + - - +
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Residues in contact with LYS 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E ASP 2.9 4.9 + - - -
153E ASN* 1.3 73.4 + - - +
155E LEU* 1.3 68.7 + - - +
157E ARG* 3.4 20.1 - - - +
158E TYR* 3.0 66.0 + - + -
190E GLU* 4.7 1.1 - - - +
10F G 3.4 22.3 - - - -
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Residues in contact with LEU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153E ASN* 2.8 17.3 + - - +
154E LYS* 1.3 77.6 - - - +
156E ARG* 1.3 67.2 - - + +
158E TYR* 4.0 4.5 - - - +
159E THR* 2.4 38.4 + - - +
8F T 6.1 0.9 - - - +
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Residues in contact with ARG 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E ILE* 4.4 19.0 - - - +
151E ILE* 4.0 28.9 - - + +
153E ASN* 2.5 40.4 + - - +
155E LEU* 1.3 78.2 - - + +
157E ARG* 1.3 70.0 + - - +
159E THR* 2.5 22.6 + - - -
160E THR* 2.9 12.0 + - - -
4X G 5.0 0.8 - - - -
5X G 3.1 43.8 + - - +
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Residues in contact with ARG 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LEU 4.2 1.3 - - - -
179D THR* 3.8 26.5 - - - +
150E PHE* 3.0 35.8 - - - -
151E ILE* 2.7 40.7 + - + +
152E ASP 3.5 17.2 + - - -
153E ASN 2.9 15.9 + - - +
154E LYS* 3.4 21.8 - - - +
156E ARG* 1.3 75.3 - - - +
158E TYR* 1.3 78.5 + - + +
160E THR* 2.9 4.2 + - - +
161E PHE* 2.8 20.6 + - + +
190E GLU* 2.5 36.7 + - - +
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Residues in contact with TYR 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E LYS* 3.0 63.0 + - + +
155E LEU* 4.0 3.8 - - - +
157E ARG* 1.3 82.7 - - + +
159E THR* 1.3 52.6 + - - +
161E PHE* 3.1 15.2 + + + +
162E SER* 2.7 35.0 + - - -
189E SER* 5.8 0.9 - - - -
190E GLU* 2.3 59.1 + - + +
191E THR* 3.5 22.2 + - - -
8F T 5.3 1.1 - - + -
9F A 3.1 25.9 + - + +
10F G 4.5 16.8 - - - +
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Residues in contact with THR 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155E LEU* 2.4 36.4 + - - +
156E ARG* 2.5 15.6 + - - -
158E TYR* 1.3 71.3 - - - +
160E THR* 1.3 55.4 + - - +
162E SER* 2.6 24.1 + - - -
163E LYS* 2.8 25.2 + - + +
7F G 5.5 1.3 - - - +
8F T 4.2 30.6 + - + +
5X G 6.3 0.2 - - - +
6X C 4.8 16.2 - - + +
7X C 5.5 2.0 - - - +
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Residues in contact with THR 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D LEU* 4.6 5.8 - - + -
179D THR* 3.5 18.8 - - + -
151E ILE* 3.6 25.2 - - + +
156E ARG* 2.9 10.0 + - - -
157E ARG 3.4 8.3 - - - +
159E THR* 1.3 75.6 - - - +
161E PHE* 1.3 63.1 + - - +
163E LYS* 2.9 3.8 + - - -
164E ARG* 2.7 42.7 + - + +
4X G 2.7 39.0 + - - +
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Residues in contact with PHE 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LEU* 3.7 13.7 - - + -
179D THR* 3.2 36.8 - - + -
181D THR* 3.4 25.4 - - + -
157E ARG* 2.8 9.2 + - + +
158E TYR* 3.3 16.6 - + + +
160E THR* 1.3 77.9 - - - +
162E SER* 1.3 65.9 + - - +
165E LYS* 3.0 39.4 + - + +
187E VAL* 3.2 36.3 - - + -
188E ALA 4.1 0.2 - - - -
189E SER* 3.8 29.8 - - - -
190E GLU 5.9 0.7 - - - -
195E TYR* 4.0 4.7 - + - -
8F T 5.7 0.7 - - - -
9F A 5.7 4.3 - - - -
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Residues in contact with SER 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E TYR 2.7 9.2 + - - -
159E THR 2.6 16.5 + - - -
161E PHE* 1.3 77.2 - - - +
163E LYS* 1.3 72.3 + - - +
165E LYS* 3.3 4.5 - - - +
166E THR* 3.3 17.2 + - - -
8F T 3.0 65.2 + - - +
9F A 4.4 3.8 - - - -
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Residues in contact with LYS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159E THR* 2.8 28.4 + - + +
160E THR* 2.9 6.5 + - - +
162E SER* 1.3 77.4 + - - +
164E ARG* 1.3 67.2 + - - +
166E THR* 2.8 15.6 + - - -
167E GLY 3.3 6.8 + - - -
5F C 4.8 2.0 - - - +
6F G 3.8 24.0 + - - -
7F G 5.4 5.4 - - - +
8F T 6.6 0.7 - - + -
138H ARG* 5.2 2.6 + - - -
3X A 4.1 21.7 + - + +
4X G 3.2 56.4 + - + +
5X G 3.9 6.4 + - - -
6X C 5.1 3.8 - - - +
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Residues in contact with ARG 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D LYS* 4.0 9.9 - - + +
174D GLU* 3.5 26.7 + - - +
175D LEU* 3.5 29.6 - - + +
178D LEU* 3.5 26.4 - - + +
143E ARG* 3.8 19.1 - - - +
146E ILE* 4.2 10.1 - - - +
148E MET* 5.7 1.0 - - - -
160E THR* 2.7 31.9 + - + +
163E LYS* 1.3 73.6 - - - +
165E LYS* 1.3 64.6 + - - +
167E GLY* 2.9 12.1 + - - -
168E ILE* 3.0 17.6 + - - +
3X A 3.8 38.8 + - - +
4X G 2.9 29.8 + - - +
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Residues in contact with LYS 165 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LEU* 4.3 6.4 - - - +
161E PHE* 3.0 35.9 + - + +
162E SER 3.3 7.2 - - - +
163E LYS 3.0 0.2 + - - -
164E ARG* 1.3 75.2 - - - +
166E THR* 1.3 68.6 + - - +
168E ILE* 3.2 9.5 - - - +
169E MET* 2.9 33.6 + - + +
187E VAL* 4.8 6.7 - - + -
195E TYR* 3.1 41.9 - - + +
8F T 3.4 37.7 + - - -
141H TYR* 4.1 15.6 + - - -
147H TYR* 3.4 26.1 + - - -
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Residues in contact with THR 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E SER* 3.3 6.2 + - - -
163E LYS* 2.8 17.6 + - - -
165E LYS* 1.3 79.6 + - - +
167E GLY* 1.3 65.8 + - - +
169E MET* 2.9 6.8 + - - +
170E LYS* 2.8 20.6 + - + +
7F G 5.3 5.0 + - - +
8F T 5.7 4.9 + - - -
138H ARG* 3.3 37.9 - - + +
139H ASN* 4.5 10.0 + - - +
141H TYR* 3.5 30.2 + - + +
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Residues in contact with GLY 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163E LYS 3.3 4.6 + - - -
164E ARG 2.9 4.8 + - - -
166E THR* 1.3 78.0 - - - +
168E ILE* 1.3 54.0 + - - -
170E LYS* 2.6 29.6 + - - +
171E LYS* 2.7 19.6 + - - +
138H ARG* 4.3 8.7 - - - +
2X T 5.3 4.0 - - - -
3X A 3.2 24.4 + - - -
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ILE* 3.8 18.8 - - + +
171D LYS* 3.8 18.3 - - + +
172D ALA* 3.4 39.3 - - + +
175D LEU* 4.2 16.4 - - + -
183D VAL* 5.1 1.3 - - + -
185D LEU* 4.8 0.7 - - + -
164E ARG 3.0 11.9 + - - +
165E LYS* 3.2 18.4 - - - +
167E GLY* 1.3 70.8 - - - -
169E MET* 1.3 61.4 + - + +
171E LYS* 3.5 10.0 - - - +
172E ALA* 2.8 26.5 + - - +
185E LEU* 3.6 33.0 - - + -
187E VAL* 4.9 2.5 - - + -
3X A 4.6 0.8 + - - -
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Residues in contact with MET 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E LYS* 2.9 31.9 + - + +
166E THR 2.9 12.3 + - - +
167E GLY 2.8 1.4 + - - -
168E ILE* 1.3 75.9 - - + +
170E LYS* 1.3 62.3 + - - +
172E ALA* 3.1 5.4 - - - +
173E TYR* 3.0 21.3 + - - +
185E LEU* 3.2 36.8 - - + -
187E VAL* 4.0 17.9 - - + -
195E TYR* 4.5 15.7 - - + +
197E PHE* 3.8 29.2 - - + +
141H TYR* 3.8 30.2 - - + +
147H TYR* 4.4 16.8 - - - -
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Residues in contact with LYS 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E THR 2.8 10.4 + - - +
167E GLY* 2.6 14.7 + - - +
169E MET* 1.3 69.1 - - - +
171E LYS* 1.3 56.0 + - + +
173E TYR* 2.9 10.1 + - + +
174E GLU* 2.7 70.5 + - + +
137H SER 4.8 4.5 - - - -
138H ARG* 3.4 49.4 - - + +
140H ASP* 5.8 1.3 - - - -
141H TYR* 3.9 8.9 - - + -
1X T 3.4 8.3 + - - -
2X T 2.2 40.4 + - - +
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Residues in contact with LYS 171 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ARG* 5.3 7.1 - - - +
164D ARG* 4.8 11.9 + - - +
168D ILE* 3.9 20.4 - - + +
171D LYS* 4.1 26.5 - - + +
167E GLY* 2.7 20.9 + - - +
168E ILE* 3.5 15.9 - - - +
170E LYS* 1.3 72.6 - - + +
172E ALA* 1.3 56.8 + - - +
174E GLU* 3.9 14.8 + - - +
175E LEU* 2.7 37.5 + - + +
-3F A 2.6 33.7 + - - +
-2F T 3.4 14.6 + - - -
1X T 5.2 5.5 + - - -
2X T 4.7 23.6 + - - +
3X A 6.1 0.2 - - - -
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Residues in contact with ALA 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ILE* 3.3 16.5 - - + +
168E ILE 2.8 15.1 + - - +
169E MET* 3.1 11.0 - - - +
171E LYS* 1.3 76.2 - - - +
173E TYR* 1.3 50.9 + - - +
175E LEU* 4.0 2.2 - - - +
176E SER* 2.6 34.5 + - - -
183E VAL* 4.1 8.1 - - + +
185E LEU* 3.7 18.4 - - + -
197E PHE* 3.5 25.8 - - + -
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Residues in contact with TYR 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D MET* 3.9 18.2 - - + +
169E MET 3.0 4.5 + - - +
170E LYS* 2.9 11.3 + - + +
172E ALA* 1.3 73.8 - - - +
174E GLU* 1.3 67.1 + - + +
176E SER* 2.5 22.3 + - - -
177E THR* 2.9 47.6 + - + +
197E PHE* 3.7 16.2 - + + -
140H ASP* 4.1 26.3 + - + +
141H TYR* 3.6 30.7 - - + -
144H SER* 3.8 26.9 - - - -
146H LEU* 5.2 4.3 - - + -
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Residues in contact with GLU 174 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D MET* 3.8 31.7 - - + +
164D ARG* 3.3 28.2 + - - +
170E LYS* 2.7 65.2 + - + +
171E LYS* 3.9 9.6 + - - +
173E TYR* 1.3 72.6 - - + +
175E LEU* 1.3 61.0 + - - +
176E SER 3.0 1.9 + - - -
177E THR* 3.1 7.5 + - - -
178E LEU* 2.7 39.7 + - + +
1X T 5.0 1.6 - - - +
2X T 4.3 2.3 + - - -
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Residues in contact with LEU 175 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D THR* 5.3 0.2 - - + -
161D PHE* 4.1 17.3 - - + +
164D ARG* 3.2 49.9 - - + +
165D LYS* 4.5 2.9 - - - +
168D ILE* 4.9 9.6 - - + -
187D VAL* 4.3 20.9 - - + -
171E LYS 2.7 23.0 + - - +
172E ALA* 4.0 3.8 - - - +
174E GLU* 1.3 72.9 - - - +
176E SER* 1.3 56.7 + - - +
178E LEU* 4.9 1.3 - - - -
179E THR* 2.7 42.0 + - + +
181E THR* 3.8 7.0 - - - +
183E VAL* 3.7 25.8 - - + -
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Residues in contact with SER 176 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E ALA 2.6 17.4 + - - -
173E TYR* 2.5 28.1 + - - -
175E LEU* 1.3 78.3 - - - +
177E THR* 1.3 56.3 + - - +
180E GLY* 2.7 37.9 + - - -
181E THR* 3.4 13.3 + - - +
183E VAL* 3.8 15.3 - - - -
197E PHE* 3.7 5.9 - - - -
199E THR* 4.2 17.5 - - - -
146H LEU* 6.3 0.9 - - - -
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Residues in contact with THR 177 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D MET* 2.7 32.8 - - - +
149D GLU* 4.8 2.0 - - - -
150D PHE* 3.4 18.8 + - - +
173E TYR* 2.9 51.9 + - + +
174E GLU 3.1 5.2 + - - -
176E SER* 1.3 77.7 - - - +
178E LEU* 1.3 67.5 + - - +
180E GLY* 3.7 5.0 + - - -
146H LEU* 6.3 0.9 - - + -
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Residues in contact with LEU 178 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ILE* 3.9 21.1 - - + -
147D LYS 3.7 20.4 - - - +
148D MET* 3.9 16.2 - - - -
149D GLU 3.8 10.1 - - - +
150D PHE* 3.2 6.4 - - - +
151D ILE* 3.1 47.5 + - + +
157D ARG* 4.4 1.6 - - - +
160D THR* 3.8 23.3 - - + -
164D ARG* 3.9 24.2 - - - +
174E GLU 2.7 22.5 + - - +
175E LEU* 4.3 2.2 - - - +
177E THR* 1.3 78.0 + - - +
179E THR* 1.3 65.8 + - + +
----------------------------------------------------------
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Residues in contact with THR 179 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D PHE* 4.1 6.9 - - - -
151D ILE* 5.6 0.2 - - + -
157D ARG* 3.8 22.4 - - + +
160D THR* 4.4 3.1 - - + -
161D PHE* 3.3 42.8 - - + +
190D GLU* 3.5 17.1 - - - +
175E LEU* 2.7 24.3 + - + +
178E LEU* 1.3 82.7 - - + +
180E GLY* 1.3 65.1 + - - +
181E THR* 2.9 32.4 + - - +
----------------------------------------------------------
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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