Contacts of the helix formed by residues 216 - 238 (chain A) in PDB entry 3R1N
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 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLU* 1.3 80.5 + - + +
218A LYS* 4.0 6.5 - - + +
219A TYR* 2.8 26.4 + - + -
220A ASP* 2.4 47.5 + - - +
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Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A THR* 3.6 46.6 - - - +
216A PRO* 1.3 94.1 - - + +
218A LYS* 1.3 72.2 + - + +
220A ASP* 3.2 3.4 + - - +
221A LYS* 3.2 28.7 + - - +
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PRO* 4.6 7.2 - - + -
217A GLU* 1.3 87.4 - - + +
219A TYR* 1.3 62.9 + - - +
221A LYS* 3.6 11.2 + - + +
222A SER* 3.0 22.3 + - - -
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Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 6.1 0.4 - - - -
216A PRO* 2.8 28.5 + - + +
218A LYS* 1.3 75.6 - - - +
220A ASP* 1.3 76.8 + - - +
222A SER* 2.6 28.8 + - - -
223A CYS* 3.2 24.0 + - - -
289A PRO* 3.9 28.9 - - + -
292A ARG* 5.4 1.1 - - - -
342A MET* 2.6 48.3 + - + +
343A ARG* 5.5 0.2 - - - -
344A VAL 5.6 2.5 - - - -
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Residues in contact with ASP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 3.6 24.6 - - + +
165A ARG* 3.9 28.6 + - + +
192A LYS* 4.0 19.8 - - - +
194A THR* 4.7 3.5 - - + +
216A PRO* 2.4 36.8 + - - +
217A GLU* 3.8 5.8 + - - +
219A TYR* 1.3 85.0 - - - +
221A LYS* 1.3 62.4 + - - +
223A CYS* 3.1 22.4 + - - +
224A ASP* 3.6 4.2 + - - -
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Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A HIS* 3.0 73.0 + - + +
161A ASN* 3.1 17.0 - - - +
162A ILE 5.2 0.2 - - - +
163A ALA* 3.8 7.1 - - + +
194A THR* 3.6 24.2 - - - -
217A GLU* 3.2 14.5 + - - +
218A LYS* 3.7 11.0 - - + +
220A ASP* 1.3 77.0 - - - +
222A SER* 1.3 61.4 + - - +
224A ASP* 3.1 15.8 + - - +
225A MET* 3.2 12.0 + - + +
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LYS 3.0 13.4 + - - -
219A TYR* 2.6 24.0 + - - -
221A LYS* 1.3 76.2 - - - +
223A CYS* 1.3 57.1 + - - +
225A MET* 3.7 9.4 - - - -
226A TRP 3.1 16.8 + - - -
289A PRO* 3.4 40.4 - - - +
292A ARG* 2.8 30.6 + - - -
293A LEU 5.8 0.2 - - - -
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Residues in contact with CYS 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 5.0 15.0 - - + +
219A TYR* 3.4 51.6 - - - -
220A ASP* 3.1 11.1 + - - +
222A SER* 1.3 75.2 - - - +
224A ASP* 1.3 66.2 + - - +
225A MET 3.2 0.2 - - - -
226A TRP* 3.4 3.7 + - - +
227A SER* 3.2 22.5 + - - -
292A ARG* 4.4 3.8 - - - +
339A LEU* 4.4 8.1 - - + +
342A MET* 3.9 27.8 - - + -
343A ARG* 6.3 2.0 - - + -
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Residues in contact with ASP 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.3 17.0 - - + +
157A LEU* 5.5 0.2 - - - +
158A HIS* 2.6 30.7 + - + +
163A ALA* 3.6 2.3 - - - +
164A HIS* 3.0 28.8 + - - +
165A ARG* 2.7 30.7 + - - -
167A VAL* 3.9 7.1 + - - +
220A ASP 3.6 4.6 + - - -
221A LYS 3.1 10.1 + - - +
223A CYS* 1.3 76.1 - - - +
225A MET* 1.3 58.2 + - - +
227A SER* 3.1 10.7 + - - -
228A LEU* 3.0 29.6 + - - +
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Residues in contact with MET 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 4.2 8.5 - - - -
158A HIS* 4.3 3.8 - - + -
221A LYS* 3.2 12.1 + - + +
222A SER* 3.7 13.2 - - - +
223A CYS 3.2 0.8 - - - -
224A ASP* 1.3 79.2 - - - +
226A TRP* 1.3 61.6 + - - +
228A LEU* 3.4 26.2 + - + +
229A GLY 3.2 15.8 + - - -
284A LEU* 3.8 27.7 - - + +
292A ARG* 4.4 6.3 - - - -
293A LEU 3.2 21.1 - - - +
294A THR* 3.8 5.4 - - - +
295A ILE* 3.7 37.0 - - - +
298A PHE* 3.6 31.0 - - + -
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Residues in contact with TRP 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A SER 3.1 13.9 + - - +
223A CYS* 3.6 8.3 - - - +
224A ASP 3.2 0.2 - - - -
225A MET* 1.3 75.0 - - - +
227A SER* 1.3 68.1 + - - +
229A GLY* 3.1 2.9 + - - -
230A VAL* 2.9 46.9 + - + +
242A PHE* 4.0 19.1 - + - -
284A LEU 3.8 8.3 - - - -
285A LEU* 3.7 27.3 + - + +
292A ARG* 3.7 32.0 - - - +
335A MET* 4.2 11.0 - - + -
338A ALA* 3.8 19.1 - - + -
339A LEU* 3.9 21.1 - - + -
342A MET* 3.2 36.5 - - + +
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Residues in contact with SER 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG 5.8 0.2 - - - -
167A VAL* 2.7 46.8 + - - +
223A CYS 3.2 12.6 + - - -
224A ASP* 3.1 12.3 + - - -
226A TRP* 1.3 82.3 - - - +
228A LEU* 1.4 54.1 + - - +
230A VAL* 3.2 2.1 + - - +
231A ILE* 2.8 39.6 + - - +
335A MET* 3.9 5.7 - - - +
339A LEU* 3.6 16.1 - - - +
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Residues in contact with LEU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A MET* 3.4 24.0 - - + +
150A ILE* 3.5 34.5 - - + -
151A GLY* 4.3 4.0 - - - +
154A ILE* 4.3 12.6 - - + -
167A VAL* 5.2 4.7 - - + -
224A ASP 3.0 14.1 + - - +
225A MET* 3.5 38.6 - - + +
227A SER* 1.4 76.1 - - - +
229A GLY* 1.3 56.2 + - - +
231A ILE* 3.9 3.3 - - + +
232A MET* 2.9 30.8 + - - +
284A LEU* 4.1 4.0 - - + -
295A ILE* 3.8 18.8 - - + -
298A PHE* 4.2 19.3 - - + -
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Residues in contact with GLY 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A MET 3.2 7.5 + - - -
226A TRP 3.1 7.1 + - - -
228A LEU* 1.3 75.9 - - - +
230A VAL* 1.3 57.6 + - - +
232A MET* 3.8 2.8 - - - +
233A TYR* 3.1 28.4 + - - +
281A ILE* 4.2 7.3 - - - +
284A LEU* 3.6 22.8 - - - +
285A LEU* 3.6 20.4 - - - +
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TRP* 2.9 53.0 + - + +
227A SER 3.6 6.1 - - - +
229A GLY* 1.3 73.5 - - - +
231A ILE* 1.3 64.4 + - - +
233A TYR* 3.3 6.7 + - - +
234A ILE* 3.1 33.6 + - + +
241A PRO* 4.2 15.3 - - + -
242A PHE* 4.0 17.3 - - + -
285A LEU* 3.9 8.3 - - + -
335A MET* 3.6 30.3 - - + -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 4.4 3.1 - - + -
127A PHE* 3.7 21.2 - - + -
147A MET* 4.0 8.3 - - + -
150A ILE* 4.2 13.9 - - + -
167A VAL* 4.8 7.9 - - + -
168A LYS* 4.1 7.9 - - - -
169A PRO* 3.6 40.2 - - + -
172A LEU* 4.2 11.7 - - + -
227A SER 2.8 25.5 + - - +
228A LEU* 4.0 5.8 - - + +
230A VAL* 1.3 73.2 - - + +
232A MET* 1.3 58.2 + - - +
234A ILE* 3.4 2.3 + - + -
235A LEU* 3.0 39.9 + - + +
335A MET* 4.4 8.1 - - + -
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Residues in contact with MET 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A MET* 3.7 26.2 - - + -
228A LEU 2.9 19.0 + - - +
229A GLY 3.8 4.0 - - - +
230A VAL 3.3 0.2 - - - -
231A ILE* 1.3 74.5 - - - +
233A TYR* 1.3 64.5 + - - +
235A LEU* 3.1 6.6 + - - +
236A LEU* 3.1 28.9 + - + +
277A ALA* 3.4 38.4 - - + +
280A LEU* 3.9 21.1 - - + -
281A ILE* 3.8 14.6 - - + -
284A LEU* 4.5 7.6 - - - -
298A PHE* 5.1 0.9 - - - -
303A TRP* 3.4 38.6 - - + -
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Residues in contact with TYR 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLY 3.1 19.3 + - - +
230A VAL 3.3 5.1 + - - +
232A MET* 1.3 73.8 - - - +
234A ILE* 1.3 63.7 + - - +
236A LEU 3.1 10.2 + - - -
237A CYS* 3.4 20.8 + - - -
239A PHE* 3.0 44.7 - + - -
240A PRO 3.6 12.7 + - - -
241A PRO* 3.6 30.2 - - + +
263A TYR* 4.1 10.5 - + - -
264A GLY 2.5 31.1 + - - -
265A PHE* 4.1 6.3 - + - -
266A PRO* 3.8 3.1 - - - +
270A TRP* 3.6 27.6 + + - -
281A ILE* 3.8 26.2 - - + +
285A LEU* 5.1 0.2 - - + -
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Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 3.5 23.8 - - + -
169A PRO* 5.1 8.3 - - + -
230A VAL* 3.1 27.8 + - + +
231A ILE* 3.8 9.0 - - - +
233A TYR* 1.3 76.0 - - - +
235A LEU* 1.3 57.4 + - - +
238A GLY* 2.8 44.5 + - - +
239A PHE 3.6 8.1 - - - +
240A PRO* 3.7 33.7 - - + -
317A THR* 3.5 3.8 - - - +
321A LEU* 4.7 0.7 - - + -
328A TRP* 4.4 17.3 - - + -
331A VAL* 4.4 13.9 - - + -
335A MET* 5.1 3.1 - - - -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 4.6 3.8 - - + -
127A PHE* 3.8 21.3 - - + -
130A ILE* 4.4 10.5 - - + -
138A PHE* 3.2 44.0 - - + -
143A ALA* 4.4 4.7 - - + +
146A ILE* 3.7 31.2 - - + -
147A MET* 3.6 34.5 - - + -
231A ILE* 3.0 22.0 + - + +
232A MET* 3.1 7.1 + - - +
234A ILE* 1.3 77.3 - - - +
236A LEU* 1.3 62.2 + - + +
315A LEU* 4.1 0.3 - - - +
317A THR* 2.7 23.3 + - + +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLU* 4.9 3.4 - - + -
143A ALA* 3.4 31.9 - - + -
232A MET* 3.1 32.2 + - + +
233A TYR 3.1 0.6 + - - -
235A LEU* 1.3 79.9 - - + +
237A CYS* 1.3 58.9 + - - +
269A GLU 4.3 7.6 - - - +
270A TRP* 3.6 33.0 - - + -
273A VAL* 4.0 11.2 - - + +
277A ALA* 3.8 29.2 - - + -
281A ILE* 4.0 2.5 - - + -
303A TRP* 4.1 11.7 - - + -
315A LEU* 3.5 29.2 - - + +
316A HIS 4.9 0.7 + - - -
317A THR* 3.4 4.4 + - - -
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A TYR* 3.4 15.7 + - - -
235A LEU 3.4 0.6 - - - -
236A LEU* 1.3 81.0 - - - +
238A GLY* 1.3 59.3 + - - +
239A PHE* 3.2 50.9 - - + -
269A GLU* 4.0 13.0 - - + +
270A TRP* 3.3 36.6 - - + +
316A HIS 4.3 2.1 - - - +
317A THR* 3.4 11.1 + - - +
320A VAL* 3.6 19.6 - - - +
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Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A ILE* 2.8 26.7 + - - +
237A CYS* 1.3 71.6 - - - +
239A PHE* 1.3 60.2 + - - +
317A THR* 3.8 20.5 - - - +
320A VAL* 3.6 17.4 - - - +
321A LEU* 3.5 22.7 + - - +
324A ASP* 4.5 3.3 - - - +
328A TRP* 5.1 1.9 - - - -
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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
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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