Contacts of the helix formed by residues 247 - 272 (chain A) in PDB entry 6D6U
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 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A TYR 5.1 1.8 - - - -
245A ASP 3.2 9.4 + - - -
246A ALA* 1.3 71.5 - - - +
248A ALA* 1.3 64.0 + - - +
250A ARG* 3.2 4.0 + - - +
251A VAL* 2.9 33.7 + - - +
299A TYR* 3.3 22.8 + - - -
303A ASN* 5.4 5.2 - - - -
320E PHE* 3.0 29.6 - - - -
323E SER* 5.1 2.6 + - - -
324E GLN* 4.8 4.3 + - - +
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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
----------------------------------------------------------
246A ALA 3.5 0.4 - - - -
247A SER* 1.3 81.8 + - - +
249A ALA* 1.3 63.3 + - - +
252A ALA* 2.9 29.5 + - - +
316E THR* 3.8 9.8 - - + +
317E LEU* 6.3 0.9 - - + -
320E PHE* 3.5 41.5 - - + -
324E GLN* 5.8 1.0 + - - +
327E ARG* 4.9 15.9 - - + -
331E MET* 5.1 8.3 - - + -
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.7 34.0 - - + +
246A ALA* 4.0 12.3 + - + +
247A SER 3.3 1.0 - - - -
248A ALA* 1.3 78.3 - - - +
250A ARG* 1.3 56.1 + - - +
252A ALA* 4.4 0.9 - - - -
253A LEU* 3.3 30.0 + - - +
406A Y01 5.7 1.3 - - - +
327E ARG* 5.6 5.3 - - - +
331E MET* 4.7 21.4 - - - +
401E Y01 4.7 9.4 - - + +
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A SER* 2.4 48.6 + - - +
240A PHE* 4.0 10.6 + - - +
242A ILE* 2.3 40.5 + - + +
243A ASN 3.9 5.5 + - - -
244A TYR* 3.6 21.4 - - - +
246A ALA 4.1 6.0 + - - +
247A SER 3.2 7.3 + - - +
248A ALA 3.1 0.2 - - - -
249A ALA* 1.3 78.6 - - - +
251A VAL* 1.3 59.9 + - - +
252A ALA 3.3 1.8 - - - -
253A LEU* 3.3 5.4 + - - +
254A GLY* 2.9 25.6 + - - -
296A LEU* 5.5 0.7 - - - +
298A GLU* 6.0 0.4 - - - -
299A TYR* 3.3 57.4 + - + -
317A ASP* 5.9 3.4 + - - -
321A ARG* 4.8 2.2 - - - +
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Residues in contact with VAL 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A SER* 2.9 21.5 + - - +
248A ALA 4.1 0.7 - - - +
250A ARG* 1.3 75.6 - - - +
252A ALA* 1.3 63.2 + - - +
254A GLY* 3.3 2.1 + - - -
255A ILE* 3.0 44.5 + - + +
296A LEU* 5.0 5.3 - - + +
299A TYR* 3.6 24.9 - - + +
303A ASN* 5.6 2.2 - - - +
316E THR* 5.1 2.5 - - + +
319E TYR* 6.2 0.2 - - + -
320E PHE* 3.8 33.4 - - + -
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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
----------------------------------------------------------
248A ALA 2.9 17.7 + - - +
249A ALA* 4.7 2.7 - - - +
251A VAL* 1.3 77.9 - - - +
253A LEU* 1.3 56.7 + - - +
255A ILE* 3.4 3.7 + - - +
256A THR* 2.8 37.8 + - - +
312E VAL* 4.8 1.3 - - + +
313E GLU* 5.3 6.1 - - + -
316E THR* 3.6 29.5 + - + +
331E MET* 5.1 4.0 - - + -
401E Y01 4.9 20.9 - - + -
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 4.6 19.7 - - + +
236A SER* 6.2 0.4 - - - -
238A VAL* 4.6 4.9 - - + -
239A SER* 3.4 40.4 - - - +
242A ILE* 4.1 12.1 - - + -
249A ALA 3.3 18.6 + - - +
250A ARG 3.3 4.5 + - - +
252A ALA* 1.3 78.9 - - - +
254A GLY* 1.3 62.8 + - - +
256A THR* 3.8 2.4 - - - -
257A THR* 2.9 34.5 + - + +
406A Y01 4.8 12.6 - - + -
401E Y01 3.4 44.6 - - + -
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A SER* 6.4 0.4 - - - -
239A SER* 4.6 2.2 + - - -
250A ARG 2.9 14.3 + - - -
251A VAL 3.7 0.9 - - - -
253A LEU* 1.3 76.5 - - - +
255A ILE* 1.3 61.1 - - - +
257A THR* 2.8 20.2 + - - -
258A VAL* 3.0 16.3 + - - +
296A LEU* 3.7 28.0 - - - -
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Residues in contact with ILE 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A VAL* 3.0 38.0 + - + +
252A ALA 4.0 2.0 - - - +
254A GLY* 1.3 74.4 - - - +
256A THR* 1.3 63.5 + - - +
258A VAL* 3.9 4.1 - - - +
259A LEU* 3.0 46.5 + - + +
296A LEU* 4.3 12.1 - - + +
258B PHE* 6.5 1.1 - - + -
312E VAL* 3.8 16.4 - - + -
316E THR* 4.7 10.1 - - - +
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Residues in contact with THR 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 5.9 0.4 - - + -
252A ALA* 2.8 24.6 + - - +
253A LEU* 3.8 4.9 - - - -
255A ILE* 1.3 77.4 - - - +
257A THR* 1.3 57.2 + - + +
259A LEU* 3.8 3.8 - - - +
260A THR* 2.6 44.9 + - - +
309E SER* 3.9 29.9 + - - -
312E VAL* 3.8 19.7 - - - +
313E GLU* 5.3 1.0 + - - -
401E Y01 4.0 31.3 - - + +
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Residues in contact with THR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 3.7 31.2 - - + +
235A LEU* 4.2 22.4 - - + +
236A SER* 4.2 24.0 - - - +
253A LEU* 2.9 21.8 + - + +
254A GLY* 2.8 23.6 + - - -
256A THR* 1.3 76.5 - - - +
258A VAL* 1.3 59.3 + - - +
260A THR* 3.3 1.3 + - - -
261A MET* 2.9 34.3 + - - +
292A VAL* 4.8 6.9 + - - +
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A GLY 3.0 18.4 + - - +
255A ILE* 3.9 3.6 - - - +
257A THR* 1.3 80.8 - - - +
259A LEU* 1.3 63.8 + - + +
261A MET* 3.3 6.0 + - - +
262A THR* 3.0 33.7 + - - +
289A PHE* 4.3 20.7 - - + -
292A VAL* 4.3 15.7 - - + +
293A PHE* 4.5 16.6 - - + -
296A LEU* 3.7 31.0 - - + -
240B LEU* 5.3 12.1 - - + -
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ILE* 3.0 41.0 + - + +
256A THR* 4.0 3.6 - - - +
258A VAL* 1.3 80.9 - - + +
260A THR* 1.3 58.6 + - - +
262A THR* 3.3 12.1 + - + +
263A THR* 3.0 35.9 + - + +
240B LEU* 5.6 14.4 - - + -
257B VAL* 5.7 1.1 - - + -
258B PHE* 6.4 2.5 - - + -
261B THR* 3.7 25.8 - - + +
308E PHE* 3.5 37.5 - - + -
312E VAL* 4.2 8.3 - - + -
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Residues in contact with THR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 3.6 30.4 - - + +
256A THR* 2.6 33.3 + - - +
257A THR* 3.7 3.8 - - - -
259A LEU* 1.3 75.0 - - - +
261A MET* 1.3 61.6 + - - +
263A THR* 2.8 20.0 + - - -
264A ILE* 2.9 30.1 + - + +
305E ILE* 3.8 32.4 + - + +
308E PHE* 6.1 1.6 - - - -
309E SER* 5.6 0.3 - - - -
401E Y01 5.3 1.4 - - + +
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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
----------------------------------------------------------
229A SER* 3.6 31.6 - - - +
232A ILE* 3.6 30.5 - - + -
233A THR* 4.9 1.3 - - - -
257A THR 2.9 21.5 + - - +
258A VAL 3.7 4.3 - - - +
260A THR* 1.3 73.7 - - - +
262A THR* 1.3 64.4 + - - +
264A ILE* 4.0 4.6 - - + +
265A ASN* 2.9 30.2 + - + +
285A LEU* 4.4 9.4 - - + +
288A CYS* 3.6 28.7 - - + -
289A PHE* 4.0 26.2 - - + +
292A VAL* 3.9 17.0 - - + -
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Residues in contact with THR 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 3.0 19.3 + - - +
259A LEU* 3.4 17.6 - - + +
260A THR 3.2 0.2 - - - -
261A MET* 1.3 76.2 - - - +
263A THR* 1.3 60.1 + - + +
265A ASN* 3.7 4.4 - - - +
266A THR* 3.0 45.3 + - + +
289A PHE* 3.9 18.3 - - - -
240B LEU* 6.0 1.7 - - - +
265B THR* 5.1 16.2 - - + +
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Residues in contact with THR 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 3.0 17.6 + - + +
260A THR* 2.8 22.9 + - - -
262A THR* 1.3 79.6 - - + +
264A ILE* 1.3 61.2 + - - +
266A THR* 2.7 22.1 + - - -
267A HIS* 3.0 15.2 + - - +
261B THR* 6.5 0.7 - - + -
304E PHE* 3.9 31.2 - - + -
305E ILE* 4.2 14.2 - - - +
308E PHE* 5.6 6.5 - - + -
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR 5.4 1.6 - - - +
228A PRO* 4.0 31.2 - - + -
229A SER* 4.1 18.8 - - - +
232A ILE* 4.1 13.2 - - + -
260A THR* 2.9 40.3 + - + +
261A MET* 4.0 4.9 - - - +
263A THR* 1.3 77.2 + - - +
265A ASN* 1.3 58.1 + - - +
267A HIS* 4.4 2.4 - - - +
268A LEU* 2.9 46.4 + - + +
285A LEU* 5.5 0.7 - - + -
301E SER* 6.0 2.0 - - - +
305E ILE* 4.0 22.0 - - + -
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Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A MET* 2.9 21.9 + - + +
262A THR* 3.7 4.7 - - - +
264A ILE* 1.3 76.7 - - - +
266A THR* 1.3 65.2 + - + +
268A LEU* 3.9 0.7 - - - +
269A ARG* 2.9 46.6 + - - +
285A LEU* 3.3 46.6 + - + +
286A MET* 5.2 7.9 - - - +
289A PHE* 5.5 9.4 - - + +
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 3.0 30.1 + - + +
263A THR* 2.7 25.7 + - - -
265A ASN* 1.3 77.6 - - + +
267A HIS* 1.3 58.4 + - - +
269A ARG* 3.6 6.7 - - - +
270A GLU* 3.0 40.2 + - - +
265B THR* 5.6 8.7 - - + -
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Residues in contact with HIS 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A THR 3.0 12.5 + - - +
264A ILE* 4.4 2.2 - - - +
266A THR* 1.3 83.5 + - - +
268A LEU* 1.3 60.0 + - - +
270A GLU* 3.2 16.4 + - + +
271A THR* 2.9 54.0 + - + +
284E ARG* 3.1 54.5 + - + +
293E VAL* 6.2 2.0 - - + -
297E ASP* 3.7 25.0 + - + +
298E LEU* 5.9 0.4 - - - -
301E SER* 4.3 14.6 - - - -
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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
----------------------------------------------------------
224A GLN 4.8 2.9 - - - +
225A THR* 3.8 44.6 - - + +
226A TYR* 5.9 0.2 - - + -
264A ILE* 2.9 26.2 + - + +
265A ASN* 4.0 2.9 - - - +
267A HIS* 1.3 78.6 - - - +
269A ARG* 1.3 60.8 + - - +
271A THR* 3.0 15.4 + - - +
272A LEU* 3.2 24.7 - - + +
281A ILE* 4.0 19.7 - - + -
285A LEU* 3.7 31.4 - - + -
293E VAL* 3.8 18.6 - - + -
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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
----------------------------------------------------------
265A ASN* 2.9 39.5 + - - +
266A THR* 3.6 6.9 - - - +
268A LEU* 1.3 78.6 - - - +
270A GLU* 1.3 62.0 - - + +
271A THR 3.5 0.2 + - - -
272A LEU* 3.7 19.7 + - - +
273A PRO 5.3 0.3 - - - +
279A LYS* 5.1 5.4 - - - +
282A ASP* 3.0 55.0 + - - +
285A LEU* 5.6 1.9 - - + +
286A MET* 5.7 6.1 - - - +
225B TYR* 4.9 7.5 + - - +
228B ILE* 4.8 20.1 + - - +
229B GLN* 3.1 43.3 + - - +
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Residues in contact with GLU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A THR* 3.0 27.7 + - - +
267A HIS* 3.2 19.4 + - + +
269A ARG* 1.3 80.2 - - + +
271A THR* 1.3 61.4 + - + +
272A LEU 3.6 6.1 - - - +
268B THR* 4.0 21.3 - - - +
272B SER* 4.7 14.8 - - - +
284E ARG* 5.6 2.1 + - - +
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Residues in contact with THR 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A HIS* 2.9 50.3 + - + +
268A LEU* 3.0 19.4 + - - +
270A GLU* 1.3 76.4 - - - +
272A LEU* 1.3 65.0 + - - +
273A PRO* 3.7 1.0 - - - +
284E ARG* 5.9 1.1 - - + -
292E TYR 3.7 15.7 + - - +
293E VAL* 3.4 26.5 - - + +
297E ASP* 4.7 15.0 - - + +
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Residues in contact with LEU 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.8 31.6 - - + +
225A THR* 5.2 5.6 - - + -
268A LEU* 3.2 24.1 + - + +
269A ARG* 3.9 14.0 - - - +
270A GLU 3.4 8.8 - - - +
271A THR* 1.3 83.0 + - - +
273A PRO* 1.3 78.0 - - + +
274A LYS* 4.6 0.5 - - - -
279A LYS* 4.4 12.8 - - - +
281A ILE* 3.9 37.2 - - + -
282A ASP* 5.6 1.8 - - - +
285A LEU* 6.4 0.4 - - + -
292E TYR* 4.8 5.6 - - - -
293E VAL* 4.0 19.5 - - + -
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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