Contacts of the helix formed by residues 246 - 271 (chain A) in PDB entry 5I1U
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 SER 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ARG* 3.9 0.9 - - - -
245A CYS* 1.3 82.6 - - - +
247A THR* 1.3 59.8 + - - +
248A ALA* 3.8 6.4 + - - +
249A GLU* 3.1 29.8 + - - +
250A ALA* 2.9 24.6 + - - +
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Residues in contact with THR 247 (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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223A PHE* 3.3 38.1 - - + -
236A VAL* 4.4 1.3 - - + +
240A ARG* 3.5 33.7 + - - +
245A CYS 3.9 0.2 + - - -
246A SER* 1.3 71.0 - - - +
248A ALA* 1.3 62.8 + - - +
250A ALA* 3.2 4.2 + - - +
251A CYS* 2.9 32.4 + - - -
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Residues in contact with ALA 248 (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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246A SER* 3.3 5.7 + - - +
247A THR* 1.3 80.1 - - - +
249A GLU* 1.3 57.4 + - - +
251A CYS* 3.4 8.7 + - - +
252A ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ARG* 5.6 4.0 + - - -
245A CYS* 3.5 25.4 - - + +
246A SER* 3.1 28.2 + - - +
248A ALA* 1.3 77.3 - - - +
250A ALA* 1.3 57.4 + - - +
252A ALA* 3.2 7.7 + - + +
253A VAL* 2.9 40.4 + - + +
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Residues in contact with ALA 250 (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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236A VAL* 3.6 29.4 - - + +
239A VAL* 4.1 8.7 - - + +
240A ARG* 3.7 22.9 - - + +
245A CYS* 3.8 6.7 - - - -
246A SER 2.9 14.4 + - - +
247A THR 3.2 7.6 + - - +
249A GLU* 1.3 76.6 - - - +
251A CYS* 1.3 61.4 + - - +
253A VAL* 3.3 2.6 + - - +
254A VAL* 3.2 27.9 + - - +
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Residues in contact with CYS 251 (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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1A MET* 4.8 15.3 - - + +
220A VAL* 3.9 21.1 - - + +
223A PHE* 4.5 17.3 - - - -
236A VAL* 3.7 27.6 - - - -
247A THR* 2.9 21.3 + - - +
248A ALA* 3.7 11.0 - - - +
250A ALA* 1.3 75.3 - - - +
252A ALA* 1.3 58.7 + - - +
254A VAL* 3.4 1.7 + - - +
255A TRP* 2.9 31.5 + - - +
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.2 4.2 - - - +
248A ALA 3.0 14.3 + - - +
249A GLU* 3.2 10.5 + - + +
251A CYS* 1.3 75.0 - - - +
253A VAL* 1.3 59.6 + - + +
255A TRP* 4.5 4.7 - - - -
256A ASP* 2.8 48.3 + - - +
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG* 5.7 3.4 - - - +
239A VAL* 3.9 24.7 - - + -
243A ARG* 3.5 46.0 - - - +
249A GLU* 2.9 30.3 + - + +
250A ALA 3.3 7.6 + - - +
252A ALA* 1.3 75.8 - - + +
254A VAL* 1.3 64.1 + - - +
256A ASP* 3.9 4.3 - - - +
257A GLU* 3.1 23.8 + - + +
260A ARG* 5.1 1.2 + - - -
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Residues in contact with VAL 254 (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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216A PHE* 3.6 32.7 - - + +
219A ASP* 5.1 0.9 - - + -
220A VAL* 3.5 24.5 - - + +
235A LEU* 4.0 22.0 - - + -
236A VAL* 3.9 17.0 - - + -
239A VAL* 4.0 24.5 - - + -
250A ALA 3.2 16.0 + - - +
253A VAL* 1.3 74.3 - - - +
255A TRP* 1.3 64.0 + - - +
257A GLU* 3.3 7.6 + - - +
258A ALA* 3.1 17.7 + - - +
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Residues in contact with TRP 255 (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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1A MET* 3.6 21.3 - - + -
5A THR* 3.9 16.6 + - - -
6A SER* 3.9 12.7 + - - -
7A LEU* 3.5 41.2 - - + +
216A PHE 5.9 0.2 - - - -
217A THR* 3.7 40.4 - - + -
220A VAL* 3.9 28.0 - - + +
221A ARG* 3.6 30.5 - - - -
251A CYS 2.9 21.8 + - - +
252A ALA* 4.0 3.6 - - - +
254A VAL* 1.3 73.6 - - - +
256A ASP* 1.3 65.8 + - - +
258A ALA* 3.1 8.0 + - - +
259A GLN* 2.9 26.7 + - + +
304A LEU* 5.6 1.6 - - + -
307A GLU* 4.3 1.3 - - - -
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Residues in contact with ASP 256 (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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252A ALA* 2.8 37.9 + - - +
253A VAL* 3.9 4.8 - - - +
255A TRP* 1.3 84.8 - - - +
257A GLU* 1.3 58.8 + - - +
259A GLN* 3.3 9.5 + - - +
260A ARG* 2.9 44.8 + - - +
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Residues in contact with GLU 257 (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* 4.4 11.2 + - - +
216A PHE* 3.5 27.5 - - + -
253A VAL* 3.1 18.4 + - + +
254A VAL* 3.7 5.8 - - - +
255A TRP 3.2 0.4 - - - -
256A ASP* 1.3 74.7 - - - +
258A ALA* 1.3 64.1 + - - +
260A ARG* 2.7 45.0 + - - +
261A MET* 3.0 39.2 + - + +
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Residues in contact with ALA 258 (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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7A LEU* 3.9 9.0 - - + +
213A ILE* 3.9 8.6 - - + +
216A PHE* 3.9 18.6 - - + -
217A THR* 4.0 22.7 - - + +
254A VAL 3.1 12.5 + - - +
255A TRP* 3.1 11.4 + - - +
257A GLU* 1.3 77.8 - - - +
259A GLN* 1.3 55.9 + - - +
261A MET* 3.3 15.5 + - - +
262A ALA* 2.9 27.0 + - - +
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Residues in contact with GLN 259 (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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6A SER 4.8 0.5 - - - +
7A LEU* 3.5 17.1 - - + +
8A GLU* 2.8 62.5 + - + +
255A TRP* 2.9 16.4 + - + +
256A ASP* 3.5 14.4 - - - +
257A GLU 3.2 0.2 - - - -
258A ALA* 1.3 75.2 - - - +
260A ARG* 1.3 60.5 + - - +
262A ALA* 3.2 6.3 + - - +
263A ASP* 2.9 59.3 + - - +
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Residues in contact with ARG 260 (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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253A VAL 5.1 1.0 + - - -
256A ASP* 2.9 27.5 + - - +
257A GLU* 2.7 56.7 + - - +
259A GLN* 1.3 74.5 - - - +
261A MET* 1.3 58.5 + - + +
263A ASP* 3.3 9.9 + - - +
264A ARG* 3.0 29.4 + - + +
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Residues in contact with MET 261 (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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209A LEU* 3.8 28.6 - - + +
212A ASP* 3.9 26.7 - - + +
213A ILE* 3.6 20.1 - - + +
216A PHE* 3.9 38.4 - - + -
257A GLU* 3.0 35.4 + - + +
258A ALA* 3.5 17.0 - - - +
259A GLN 3.3 0.2 - - - -
260A ARG* 1.3 74.3 - - + +
262A ALA* 1.3 59.5 + - - +
264A ARG* 3.3 4.1 + - - +
265A PHE* 2.9 29.5 + - - +
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Residues in contact with ALA 262 (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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7A LEU* 4.2 14.8 - - + -
8A GLU 4.3 0.7 - - - +
9A LEU* 4.1 22.0 - - + -
213A ILE* 3.5 13.4 - - + +
258A ALA 2.9 14.0 + - - +
259A GLN* 3.5 20.6 - - - +
261A MET* 1.3 75.4 - - - +
263A ASP* 1.3 64.6 + - - +
265A PHE* 3.2 5.9 + - - +
266A CYS* 3.0 28.5 + - - -
300A LEU* 5.9 0.2 - - - -
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Residues in contact with ASP 263 (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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8A GLU* 4.4 3.1 - - - +
259A GLN* 2.9 48.7 + - - +
260A ARG* 3.6 9.2 - - + +
261A MET 3.2 0.2 - - - -
262A ALA* 1.3 75.8 - - - +
264A ARG* 1.3 57.9 + - - +
266A CYS* 3.2 7.2 + - - +
267A ASP* 2.9 38.4 + - - +
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Residues in contact with ARG 264 (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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205A GLN* 2.9 32.3 + - - +
209A LEU* 3.6 21.7 - - + +
260A ARG* 3.0 17.3 + - + +
261A MET* 3.6 7.0 - - - +
263A ASP* 1.3 74.3 - - - +
265A PHE* 1.3 65.9 + - - +
267A ASP* 3.2 14.7 + - - +
268A LEU* 2.9 43.4 + - + +
271A GLN* 5.0 7.9 + - - +
164B ASP* 3.1 36.4 + - - -
166B GLU* 3.7 14.7 + - - +
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Residues in contact with PHE 265 (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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9A LEU* 5.5 1.6 - - + -
11A PHE* 4.6 6.3 - + - -
206A LEU* 3.3 61.1 - - + +
209A LEU* 3.7 13.2 - - + +
210A ALA* 3.8 20.4 - - + -
213A ILE* 4.8 2.0 - - + -
261A MET 2.9 13.4 + - - +
262A ALA* 3.4 11.9 - - - +
264A ARG* 1.3 77.9 - - - +
266A CYS* 1.3 69.3 + - - +
268A LEU 3.3 0.3 + - - -
269A ARG* 2.9 33.5 + - - +
293A ALA 4.4 4.0 - - - -
296A MET* 4.2 5.6 - - + -
297A ALA* 3.8 43.1 - - + -
300A LEU* 4.1 15.3 - - + -
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Residues in contact with CYS 266 (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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9A LEU* 3.9 15.7 - - - -
10A PRO* 3.4 38.4 - - + -
11A PHE* 4.1 11.4 - - - -
262A ALA 3.0 21.0 + - - +
263A ASP* 3.7 6.1 - - - +
265A PHE* 1.3 79.4 - - - +
267A ASP* 1.3 67.0 + - - +
269A ARG* 3.3 11.0 + - - +
270A ASP* 3.0 29.7 + - - +
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Residues in contact with ASP 267 (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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263A ASP* 2.9 26.2 + - - +
264A ARG* 3.2 16.0 + - - +
266A CYS* 1.3 79.0 - - - +
268A LEU* 1.3 62.1 + - + +
270A ASP* 3.2 21.4 + - - +
271A GLN* 3.3 30.8 + - - +
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Residues in contact with LEU 268 (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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202A LEU* 3.4 32.5 - - + +
205A GLN* 3.6 38.1 - - + +
206A LEU* 3.7 12.6 - - + +
209A LEU* 3.8 17.0 - - + -
264A ARG* 2.9 51.3 + - - +
265A PHE 3.6 4.3 - - - +
267A ASP* 1.3 73.2 - - - +
269A ARG* 1.3 66.9 + - - +
271A GLN* 3.0 29.8 + - - +
272A LEU 3.2 8.7 + - - -
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Residues in contact with ARG 269 (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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10A PRO* 6.0 1.6 - - - -
11A PHE* 4.4 19.7 - - - -
206A LEU* 3.9 12.9 - - + +
265A PHE* 2.9 20.2 + - + +
266A CYS* 3.3 15.2 + - - +
268A LEU* 1.3 76.8 - - - +
270A ASP* 1.3 67.4 + - - +
272A LEU* 3.2 25.3 + - + +
273A PRO* 3.9 3.8 - - - +
293A ALA* 3.2 35.1 + - - +
294A ASP* 2.7 33.3 + - - +
297A ALA* 3.7 16.4 - - - +
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Residues in contact with ASP 270 (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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266A CYS* 3.0 20.0 + - - +
267A ASP* 3.3 18.7 - - - +
268A LEU 3.2 0.2 - - - -
269A ARG* 1.3 81.9 - - - +
271A GLN* 1.3 60.9 + - + +
272A LEU 3.4 0.2 - - - -
273A PRO* 3.6 12.1 - - - +
274A ASP* 6.0 0.9 - - - -
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Residues in contact with GLN 271 (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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202A LEU* 3.7 9.9 - - + +
264A ARG* 5.0 6.9 + - - +
267A ASP* 3.3 27.8 + - - +
268A LEU* 3.0 29.8 + - - +
270A ASP* 1.3 77.8 - - + +
272A LEU* 1.3 64.7 + - - +
273A PRO* 3.4 1.8 - - - -
274A ASP* 3.3 12.8 + - + +
275A ALA* 3.1 21.1 + - - +
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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