Contacts of the helix formed by residues 225 - 246 (chain E) in PDB entry 6CP3
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 PRO 225 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LYS* 5.2 0.7 - - - +
302A TYR* 3.4 24.2 - - + +
19E ALA* 4.1 8.3 - - + -
63E ALA* 3.8 17.5 - - + -
64E MET 3.8 4.7 - - - +
65E ASP* 3.3 48.7 - - - +
66E GLY* 4.2 1.8 - - - +
223E ASN 4.4 0.4 - - - +
224E GLU* 1.3 91.2 - - + +
226E PRO* 1.3 71.6 - - + +
227E GLY 3.2 1.8 - - - +
228E ALA* 2.9 24.4 + - - +
229E ARG* 3.9 1.9 + - - -
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Residues in contact with PRO 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A ASP* 4.4 8.5 - - + -
302A TYR* 4.2 13.2 - - + -
19E ALA* 4.3 14.4 - - + -
225E PRO* 1.3 86.2 - - + +
227E GLY* 1.3 61.3 + - - +
229E ARG* 3.3 31.3 + - - +
230E ALA* 3.0 20.3 + - - +
264E ALA* 3.9 6.4 - - - +
267E GLU* 3.7 29.6 - - + +
268E VAL* 3.5 21.6 - - + +
271E LEU* 4.5 5.6 - - + -
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Residues in contact with GLY 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E ALA* 5.8 0.6 - - - +
62E ILE* 3.7 25.8 - - - +
63E ALA 3.4 15.8 + - - +
64E MET* 3.2 17.6 - - - +
225E PRO* 3.1 2.0 + - - +
226E PRO* 1.3 79.7 - - - +
228E ALA* 1.3 62.3 + - - +
230E ALA* 3.7 3.2 + - - +
231E ARG* 3.4 15.8 - - - +
268E VAL* 3.7 5.3 - - - +
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ALA 3.8 3.8 + - - -
64E MET* 3.7 27.6 - - - +
98E VAL* 3.9 7.5 - - + +
224E GLU* 3.3 33.4 - - + +
225E PRO 2.9 13.1 + - - +
227E GLY* 1.3 76.3 - - - +
229E ARG* 1.3 58.4 + - - +
231E ARG* 2.8 21.8 + - - +
232E VAL* 3.0 16.5 + - - +
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Residues in contact with ARG 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 3.2 37.0 - - - -
302A TYR* 4.5 5.1 - - - +
187E VAL* 3.6 23.2 - - + +
188E GLY* 4.2 25.8 - - - +
220E GLY 4.5 4.0 - - - +
221E GLN 4.0 21.5 - - - +
222E MET* 4.3 6.4 + - - +
224E GLU* 3.8 17.4 + - + +
225E PRO 3.9 1.9 + - - +
226E PRO* 3.3 41.9 + - - +
228E ALA* 1.3 80.6 - - + +
230E ALA* 1.3 58.8 + - - +
231E ARG 3.1 1.5 + - - -
232E VAL* 3.8 12.6 + - + -
260E ARG* 4.9 11.9 + - - +
261E PHE* 3.8 8.8 - - - -
263E GLN* 5.2 4.8 - - - +
264E ALA* 3.6 19.8 - - + +
267E GLU* 3.9 9.5 + - - -
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E PRO 3.0 17.2 + - - +
227E GLY 4.2 2.9 - - - +
228E ALA 3.1 0.4 - - - -
229E ARG* 1.3 78.3 - - - +
231E ARG* 1.3 92.3 + - - +
234E LEU* 4.1 4.7 - - - +
261E PHE* 3.9 20.7 - - + -
264E ALA* 3.5 17.5 - - + +
265E GLY* 4.5 4.0 - - - +
268E VAL* 4.0 16.2 - - + -
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Residues in contact with ARG 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 4.6 8.9 - - - +
49E GLU* 2.5 37.1 + - - +
51E ALA* 5.6 3.6 - - - +
62E ILE* 3.6 23.2 - - - +
64E MET* 4.0 6.7 - - + -
83E ILE* 4.5 1.3 - - + -
98E VAL* 3.7 12.3 - - + -
117E ILE* 4.4 9.4 - - + +
118E HIS* 3.5 25.2 - - - -
227E GLY 3.4 13.2 - - - +
228E ALA 2.8 7.3 + - - +
230E ALA* 1.3 116.7 + - - +
232E VAL* 1.3 60.8 + - - +
233E ALA 3.3 2.7 - - - -
234E LEU* 3.0 16.3 + - - +
235E THR* 2.9 28.1 + - - -
268E VAL* 5.0 4.9 - - - +
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Residues in contact with VAL 232 (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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98E VAL* 3.7 22.7 - - + -
185E THR* 3.7 10.1 - - + +
186E GLY 4.1 1.1 - - - +
187E VAL* 3.8 19.5 - - + -
218E VAL* 3.8 15.4 - - + +
220E GLY* 3.6 41.1 - - - +
224E GLU* 4.7 1.3 - - - +
228E ALA 3.0 20.6 + - - +
229E ARG* 3.8 7.2 + - - +
231E ARG* 1.3 77.0 - - - +
233E ALA* 1.3 63.0 + - - +
235E THR* 3.1 5.5 + - - -
236E GLY 3.0 19.1 + - - -
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Residues in contact with ALA 233 (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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185E THR* 4.1 7.2 - - - -
187E VAL* 3.5 20.7 - - + +
229E ARG 4.6 0.8 + - - -
231E ARG 3.3 0.4 - - - -
232E VAL* 1.3 77.0 - - - +
234E LEU* 1.3 58.5 + - - +
236E GLY* 3.4 1.4 + - - -
237E LEU* 2.9 28.1 + - - +
255E ILE* 4.4 16.2 - - + +
261E PHE* 4.3 14.1 - - + -
292E LEU* 3.9 32.0 - - + +
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Residues in contact with LEU 234 (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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117E ILE* 4.3 16.2 - - + +
118E HIS* 3.9 31.0 - - + +
230E ALA 4.1 7.0 - - - +
231E ARG* 3.0 26.1 + - - +
233E ALA* 1.3 76.5 - - + +
235E THR* 1.3 58.7 + - - +
237E LEU* 3.2 16.1 + - + +
238E THR* 2.9 33.9 + - - -
261E PHE* 5.5 6.7 - - + -
291E LEU* 4.0 14.8 - - + +
292E LEU* 4.1 11.4 - - + -
295E ARG* 3.8 20.4 + - - +
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Residues in contact with THR 235 (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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85E VAL* 3.8 25.2 - - + +
96E ILE* 5.4 2.0 - - + -
97E ASN 4.4 10.5 - - - +
98E VAL* 3.4 21.4 + - - +
117E ILE* 4.4 13.3 - - - +
218E VAL* 4.0 25.6 - - + -
231E ARG 2.9 13.9 + - - -
232E VAL* 3.1 10.3 + - - -
234E LEU* 1.3 75.0 - - - +
236E GLY* 1.3 63.5 + - - +
238E THR* 3.2 3.6 + - - -
239E ILE* 3.0 29.6 + - + +
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Residues in contact with GLY 236 (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 VAL* 3.7 11.8 - - - +
185E THR* 3.4 24.2 - - - -
218E VAL* 4.4 6.8 - - - +
232E VAL 3.0 11.1 + - - -
233E ALA 3.7 2.2 - - - -
235E THR* 1.3 77.4 - - - +
237E LEU* 1.3 56.1 + - - +
239E ILE* 3.4 1.2 + - - -
240E ALA 3.0 22.2 + - - -
253E LEU* 3.4 18.6 - - - +
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Residues in contact with LEU 237 (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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233E ALA 2.9 17.5 + - - +
234E LEU* 3.4 18.8 - - + +
235E THR 3.2 0.2 - - - -
236E GLY* 1.3 78.1 - - - +
238E THR* 1.3 57.0 + - - +
240E ALA* 3.2 6.9 + - + +
241E GLU* 2.9 33.6 + - + +
253E LEU* 4.1 14.5 - - + +
291E LEU 4.4 0.4 - - - +
292E LEU* 3.9 15.5 - - + +
295E ARG* 3.5 59.0 - - + +
296E ILE* 3.6 29.8 - - + -
304E VAL* 5.8 1.3 - - + -
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Residues in contact with THR 238 (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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85E VAL* 4.0 10.8 - - + -
87E VAL* 4.7 1.7 - - + +
115E LYS* 3.8 23.6 - - + -
116E PRO 3.3 20.6 - - - +
117E ILE* 3.3 24.8 - - - -
234E LEU 2.9 16.9 + - - -
235E THR 3.2 4.2 + - - -
237E LEU* 1.3 73.7 - - - +
239E ILE* 1.3 65.7 + - - +
241E GLU* 3.1 9.4 + - + +
242E TYR* 3.0 24.8 + - - +
295E ARG* 3.3 11.2 + - - +
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Residues in contact with ILE 239 (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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85E VAL* 5.1 6.3 - - + -
86E PRO 4.4 13.9 - - - +
87E VAL* 4.7 11.0 - - + -
88E GLY 5.7 3.1 - - - +
91E THR* 4.6 9.2 - - - +
96E ILE* 4.4 20.0 - - + -
183E VAL* 3.8 22.9 - - + -
216E ALA* 4.1 15.7 - - + -
218E VAL* 3.8 25.6 - - + -
235E THR* 3.0 25.2 + - + +
236E GLY 3.8 4.7 - - - +
238E THR* 1.3 74.9 - - - +
240E ALA* 1.3 62.3 + - - +
242E TYR* 3.8 1.8 + - - +
243E PHE* 3.5 30.1 + - + -
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Residues in contact with ALA 240 (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 VAL* 4.3 8.0 - - + +
236E GLY 3.0 14.2 + - - +
237E LEU* 3.3 13.2 - - + +
238E THR 3.1 0.2 - - - -
239E ILE* 1.3 78.1 - - - +
241E GLU* 1.3 57.1 + - - +
243E PHE* 3.2 5.2 + - - +
244E ARG* 2.9 26.3 + - - +
251E VAL* 4.6 8.2 - - + +
253E LEU* 4.2 14.4 - - + -
304E VAL* 3.7 33.1 - - + +
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Residues in contact with GLU 241 (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 ALA* 4.4 10.0 - - - +
120E ASP 4.9 4.0 - - - +
122E PRO* 5.6 1.0 - - - +
237E LEU* 2.9 19.1 + - + +
238E THR* 3.1 10.0 + - + +
240E ALA* 1.3 77.2 - - + +
242E TYR* 1.3 58.2 + - - +
244E ARG* 3.6 28.5 + - - +
245E ASP* 2.9 35.2 + - - +
295E ARG* 2.7 65.8 + - - +
304E VAL* 5.0 0.9 - - + -
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Residues in contact with TYR 242 (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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87E VAL* 3.6 35.4 - - + -
88E GLY* 3.6 29.8 - - - -
112E LYS* 5.6 5.0 - - - +
113E LEU* 4.4 21.2 - - + +
115E LYS* 4.9 17.3 - - + +
238E THR* 3.0 15.5 + - + +
239E ILE 4.3 2.7 - - - +
240E ALA 3.3 0.2 - - - -
241E GLU* 1.3 76.5 - - - +
243E PHE* 1.3 70.6 + + - +
246E GLU* 3.2 61.2 + - + +
247E GLU* 4.0 9.1 + - + +
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Residues in contact with PHE 243 (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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88E GLY* 3.2 45.3 - - - -
89E ARG* 4.3 4.9 - - - -
91E THR* 4.2 3.6 - - - -
92E LEU* 4.0 28.0 - - + -
181E PHE* 4.3 26.2 - + + -
183E VAL* 4.5 11.2 - - + -
239E ILE* 3.5 18.7 + - + +
240E ALA 3.2 6.6 + - - +
242E TYR* 1.3 86.6 - + - +
244E ARG* 1.3 64.5 + - - +
247E GLU* 3.9 25.3 + - - +
248E GLY 3.6 12.1 + - - -
249E GLN* 3.8 12.9 + - - +
251E VAL* 3.7 27.0 - - + +
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Residues in contact with ARG 244 (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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122E PRO* 3.8 21.7 - - - +
240E ALA 2.9 15.7 + - - +
241E GLU* 3.2 28.5 + - - +
243E PHE* 1.3 76.9 - - - +
245E ASP* 1.3 89.5 + - - +
248E GLY* 3.1 30.0 + - - -
249E GLN 4.7 4.0 - - - +
251E VAL* 4.4 3.6 - - - +
295E ARG 3.6 19.9 + - - -
297E THR* 3.0 31.2 + - - +
299E THR* 4.5 6.8 + - - +
301E LYS* 3.8 3.6 - - - +
302E GLY* 3.8 7.7 + - - -
303E SER* 3.6 35.0 - - - +
304E VAL* 3.7 18.0 - - + +
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Residues in contact with ASP 245 (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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122E PRO* 5.6 1.2 - - - +
241E GLU* 2.9 16.7 + - - +
242E TYR* 5.8 0.2 - - - -
244E ARG* 1.3 116.6 + - - +
246E GLU* 1.3 61.1 + - - +
299E THR* 3.7 15.7 + - - +
301E LYS* 3.5 28.1 + - + +
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Residues in contact with GLU 246 (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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113E LEU* 6.1 0.6 - - - +
242E TYR* 3.2 52.7 + - + +
244E ARG 3.2 0.6 - - - -
245E ASP* 1.3 82.0 - - - +
247E GLU* 1.3 73.2 + - + +
248E GLY 3.3 1.9 + - - -
301E LYS* 4.4 8.1 + - - +
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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) + - + + + + + -
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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