Contacts of the helix formed by residues 169 - 193 (chain E) in PDB entry 1KYZ
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 ASP 169 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E VAL* 3.8 6.9 - - - +
165E TYR* 2.7 45.9 + - + +
166E HIS* 2.9 11.8 + - - +
167E GLY 3.4 0.2 - - - -
168E THR* 1.3 81.4 - - - +
170E PRO* 1.3 62.3 - - - +
171E ARG* 3.3 17.7 + - - +
172E PHE* 2.9 28.9 + - + +
173E ASN 3.0 16.8 + - - -
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Residues in contact with PRO 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E HIS 4.0 1.3 - - - +
167E GLY 4.7 4.7 - - - +
168E THR 3.8 7.6 - - - +
169E ASP* 1.3 83.3 - - - +
171E ARG* 1.3 66.9 + - - +
173E ASN* 3.6 9.5 + - + +
174E LYS* 3.1 27.9 + - - +
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Residues in contact with ARG 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ASP* 2.8 42.6 + - - -
134E LYS* 4.2 20.6 - - - +
135E VAL* 3.7 17.0 - - - +
169E ASP* 3.3 14.2 + - - +
170E PRO* 1.3 82.0 - - - +
172E PHE* 1.3 69.9 + - - +
174E LYS* 3.3 9.0 + - - +
175E VAL* 3.2 35.9 + - + +
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Residues in contact with PHE 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E MET* 4.8 2.9 - - + -
133E ASP* 3.6 25.6 - - + -
135E VAL* 3.8 17.7 - - + -
136E LEU* 3.8 34.1 - - + -
154E PHE* 5.9 0.9 - + - -
165E TYR* 4.1 17.3 - + - -
166E HIS* 3.8 31.4 - + - -
169E ASP* 2.9 29.5 + - - +
171E ARG* 1.3 85.0 - - - +
173E ASN* 1.3 59.5 + - - +
175E VAL* 2.9 7.1 + - + +
176E PHE* 2.8 49.8 + + + +
1698E FER 3.8 14.1 - - - -
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Residues in contact with ASN 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E HIS* 3.2 44.4 - - + +
169E ASP 3.0 13.2 + - - +
170E PRO* 3.6 13.1 + - + +
171E ARG 3.3 0.2 - - - -
172E PHE* 1.3 76.1 - - - +
174E LYS* 1.3 59.1 + - - +
176E PHE* 3.4 1.4 + - - +
177E ASN* 2.9 63.1 + - - +
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Residues in contact with LYS 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E PRO 3.1 15.3 + - - +
171E ARG* 3.5 11.4 - - - +
173E ASN* 1.3 78.4 - - - +
175E VAL* 1.3 65.7 + - + +
177E ASN* 3.5 5.4 + - - +
178E LYS* 3.1 25.3 + - + +
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Residues in contact with VAL 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ALA 4.7 1.0 - - - +
129E LEU* 3.7 18.4 - - + +
130E MET* 3.7 30.3 - - + +
133E ASP* 4.5 8.7 - - + +
171E ARG* 3.5 33.0 - - + +
172E PHE* 2.9 12.0 + - + +
174E LYS* 1.3 78.2 - - + +
176E PHE* 1.3 63.7 + - - +
178E LYS* 3.7 5.1 - - - +
179E GLY* 3.1 19.6 + - - -
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Residues in contact with PHE 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130E MET* 3.7 29.7 - - + +
136E LEU* 5.0 0.9 - - + -
166E HIS* 3.4 29.2 - + - +
172E PHE* 2.8 38.0 + + + +
173E ASN 3.6 4.5 - - - +
175E VAL* 1.3 73.3 - - - +
177E ASN* 1.3 75.4 + - - +
179E GLY 3.3 1.7 + - - -
180E MET* 3.0 47.8 + - + +
1697E SAH 6.2 3.4 - - - -
1698E FER 3.5 45.5 - + + -
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Residues in contact with ASN 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E HIS* 5.3 0.5 - - - -
173E ASN* 2.9 48.0 + - - +
174E LYS* 3.9 6.2 - - - +
176E PHE* 1.3 88.6 - - - +
178E LYS* 1.3 54.6 + - - +
180E MET* 4.1 3.0 - - - +
181E SER* 2.7 40.8 + - - -
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Residues in contact with LYS 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E LYS* 5.6 8.7 - - - +
120E ASP 5.8 0.2 + - - -
121E GLY 3.5 19.1 + - - -
122E VAL* 5.0 1.4 - - - +
126E ALA* 3.9 14.8 - - + -
129E LEU* 6.4 0.9 - - + -
174E LYS* 3.1 19.7 + - + +
175E VAL* 3.7 6.3 - - - +
177E ASN* 1.3 75.8 - - - +
179E GLY* 1.3 56.8 + - - +
181E SER* 4.2 5.4 - - - +
182E ASP* 3.0 60.4 + - - +
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Residues in contact with GLY 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ALA* 3.7 22.8 - - - +
127E LEU* 2.9 31.7 - - - +
130E MET* 4.5 2.9 - - - -
175E VAL 3.1 12.5 + - - -
176E PHE 3.8 2.7 - - - -
178E LYS* 1.3 79.0 - - - +
180E MET* 1.3 61.0 + - - +
182E ASP* 4.0 1.7 - - - +
183E HIS 3.1 15.4 + - - -
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Residues in contact with MET 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E LEU* 4.8 3.8 - - - -
130E MET* 3.9 24.4 - - - -
176E PHE* 3.0 49.5 + - + +
177E ASN* 4.1 3.1 - - - +
179E GLY* 1.3 75.5 - - - +
181E SER* 1.3 58.3 + - - +
183E HIS* 3.6 9.2 + - - +
184E SER* 3.0 30.5 + - - -
266E TRP* 4.2 29.1 - - + -
269E HIS* 5.7 5.6 - - + +
270E ASP* 6.1 1.3 - - - +
1697E SAH 4.8 20.0 - - + +
1698E FER 4.6 17.7 - - + +
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Residues in contact with SER 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ASN* 2.7 25.9 + - - -
178E LYS* 3.8 6.7 - - - +
180E MET* 1.3 71.5 - - - +
182E ASP* 1.3 69.4 + - - +
184E SER* 3.4 6.7 + - - -
185E THR* 3.1 29.6 + - - -
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Residues in contact with ASP 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E LYS* 5.7 0.9 - - - +
121E GLY 3.8 1.2 - - - +
122E VAL* 3.2 39.8 - - + +
123E SER* 2.9 37.4 + - - +
126E ALA* 4.1 7.2 - - + +
178E LYS* 3.0 52.8 + - - +
179E GLY 4.0 2.7 - - - +
181E SER* 1.3 80.9 + - - +
183E HIS* 1.3 62.6 + - - +
185E THR* 3.4 1.9 + - - -
186E ILE* 3.2 17.9 + - - +
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Residues in contact with HIS 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ASN* 5.9 1.9 + - - -
24A MET* 3.6 28.4 - - + +
123E SER 4.8 0.2 + - - -
124E ILE* 4.0 25.3 - - + +
127E LEU* 3.8 18.3 - - + +
179E GLY 3.1 16.7 + - - +
180E MET* 3.7 10.9 - - - +
182E ASP* 1.3 80.7 - - - +
184E SER* 1.3 61.7 + - - +
186E ILE* 3.4 2.1 + - + +
187E THR* 3.0 35.0 + - - -
266E TRP* 3.3 30.9 - + - -
316E ILE* 6.5 0.7 - - + -
354E PHE 5.6 2.6 + - - -
356E THR* 5.3 2.2 + - - -
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Residues in contact with SER 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E MET 3.0 18.8 + - - -
181E SER* 3.6 7.2 - - - -
182E ASP 3.3 0.2 - - - -
183E HIS* 1.3 77.0 - - - +
185E THR* 1.3 51.4 + - - +
187E THR* 3.4 0.9 + - - -
188E MET* 2.8 39.2 + - - +
213E ALA* 5.7 2.6 - - - +
214E VAL* 3.4 19.2 - - - +
265E LYS* 2.8 25.1 + - - +
266E TRP* 3.7 14.1 - - - -
1697E SAH 3.9 7.5 + - - -
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Residues in contact with THR 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E GLU* 2.8 35.2 - - + +
122E VAL* 4.3 15.2 - - + +
181E SER* 3.1 16.3 + - - -
182E ASP* 3.6 8.8 - - - -
183E HIS 3.3 0.2 - - - -
184E SER* 1.3 76.9 - - - +
186E ILE* 1.3 59.9 - - - +
188E MET* 3.9 4.1 - - - +
189E LYS* 3.1 24.7 + - + +
213E ALA* 5.6 5.5 - - - +
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Residues in contact with ILE 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN* 4.1 5.4 - - - +
114E TYR* 3.8 22.7 - - + -
119E GLU* 3.3 27.3 - - - +
122E VAL* 3.6 15.3 - - + +
123E SER* 3.8 25.1 - - - -
124E ILE* 3.9 16.8 - - + +
182E ASP 3.2 18.5 + - - +
183E HIS* 3.8 4.3 - - + +
185E THR* 1.3 75.2 - - - +
187E THR* 1.3 62.4 + - - +
189E LYS* 3.7 2.8 + - - +
190E LYS* 3.4 21.0 + - - +
354E PHE* 3.8 24.4 - - + -
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Residues in contact with THR 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E HIS* 3.0 35.5 + - - -
184E SER 4.0 2.2 - - - -
186E ILE* 1.3 74.7 - - - +
188E MET* 1.3 62.0 + - - +
190E LYS* 3.4 6.9 + - - +
191E ILE* 2.9 44.1 + - + +
265E LYS* 4.4 4.5 - - - -
266E TRP* 4.2 13.0 - - + -
353E ALA 4.1 6.7 - - - +
354E PHE* 4.6 14.2 + - - +
356E THR* 3.7 26.6 + - + +
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Residues in contact with MET 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E SER 2.8 22.4 + - - +
185E THR* 3.9 4.9 - - - +
187E THR* 1.3 71.2 - - - +
189E LYS* 1.3 65.3 + - - +
191E ILE* 3.2 12.7 + - + +
192E LEU* 3.0 55.7 + - + +
198E PHE* 3.8 11.2 - - + -
214E VAL* 3.8 27.6 - - + -
217E THR* 4.4 21.5 - - + +
218E ILE* 3.9 9.6 - - + -
263E PHE* 3.8 30.7 - - + -
265E LYS* 4.1 12.3 - - - +
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Residues in contact with LYS 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E GLU* 3.6 26.2 - - + +
185E THR* 3.1 17.1 + - + +
186E ILE 3.9 4.5 - - - +
188E MET* 1.3 78.3 - - - +
190E LYS* 1.3 64.0 + - - +
192E LEU* 3.3 9.2 + - - +
193E GLU* 3.0 45.6 + - + +
217E THR* 5.5 3.3 - - + +
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Residues in contact with LYS 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ASP* 4.8 5.5 - - - +
17A GLU* 3.4 20.2 + - - -
186E ILE 3.4 12.0 + - - +
187E THR 3.7 7.4 - - - +
188E MET 3.3 0.2 - - - -
189E LYS* 1.3 79.4 - - - +
191E ILE* 1.3 61.9 + - - +
193E GLU* 3.2 34.0 + - - +
194E THR* 3.7 19.5 + - + -
352E ASN 5.6 0.7 - - - +
353E ALA* 3.3 25.4 - - + -
354E PHE* 3.2 50.4 - - + +
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Residues in contact with ILE 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E THR* 2.9 35.3 + - + +
188E MET* 3.2 33.8 + - + +
190E LYS* 1.3 77.0 - - - +
192E LEU* 1.3 61.0 + - + +
194E THR* 3.0 6.0 + - - -
195E TYR* 2.8 49.1 + - + +
198E PHE* 4.7 1.6 - - + -
263E PHE* 4.7 0.9 - - + -
265E LYS* 4.7 2.7 - - + -
296E ALA* 4.4 11.9 - - + -
353E ALA* 3.4 20.9 - - + -
356E THR* 4.5 3.6 - - + -
358E ILE* 3.5 32.1 - - + -
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Residues in contact with LEU 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E MET* 3.0 42.6 + - + +
189E LYS* 3.7 7.0 - - - +
191E ILE* 1.3 77.5 - - + +
193E GLU* 1.3 60.8 + - + +
194E THR 3.2 1.0 + - - -
195E TYR 4.1 11.7 - - - +
198E PHE* 3.6 24.7 - - + -
217E THR* 3.4 44.2 - - + +
218E ILE* 4.4 5.2 - - + -
221E LYS* 3.7 45.2 + - + +
222E TYR* 4.9 2.0 - - + +
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Residues in contact with GLU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E LYS* 3.0 38.4 - - + +
190E LYS* 3.6 32.5 - - + +
191E ILE 3.1 1.2 - - - -
192E LEU* 1.3 78.4 - - + +
194E THR* 1.3 64.8 + - + +
221E LYS* 5.7 0.4 - - - +
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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