Contacts of the helix formed by residues 251 - 272 (chain A) in PDB entry 6I53
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 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 4.1 4.7 - - - +
248A ASN* 2.9 34.7 + - - -
249A ARG 3.3 1.4 - - - -
250A GLU* 1.3 76.2 - - - +
252A VAL* 1.3 53.4 + - - +
253A PRO* 3.3 6.5 - - - -
254A ALA* 2.7 26.6 + - - +
255A ARG* 2.9 22.6 + - - +
304A PHE* 5.0 0.4 - - - -
247B SER* 3.8 29.6 - - - -
303B ASN* 4.8 1.8 - - - -
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Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG 3.7 18.8 + - - +
250A GLU* 3.3 5.7 - - - +
251A SER* 1.3 73.1 - - - +
253A PRO* 1.3 64.0 - - + +
254A ALA 3.1 4.2 + - - -
256A THR* 2.7 31.5 + - - +
304A PHE* 3.7 17.7 - - + -
308A ASN* 3.3 37.9 - - - +
311A THR* 6.0 1.3 - - + -
242E ILE* 4.2 2.2 - - + -
246E ALA* 3.9 15.9 - - + -
249E ALA* 3.7 19.4 - - + +
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Residues in contact with PRO 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLU 4.8 3.1 - - - +
251A SER* 3.6 5.4 - - - -
252A VAL* 1.3 91.6 - - + +
254A ALA* 1.3 55.7 + - - -
256A THR* 4.6 0.7 - - - -
257A VAL* 3.3 20.5 - - - +
247B SER* 6.5 0.2 - - - -
248B ALA* 3.7 24.6 - - + +
246E ALA* 5.4 5.8 - - + -
248E ALA* 3.8 32.5 - - + +
249E ALA* 4.3 15.3 - - + +
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.9 2.9 - - + -
251A SER* 2.7 20.7 + - - +
253A PRO* 1.3 73.7 - - - +
255A ARG* 1.3 63.2 + - - +
256A THR 3.2 1.6 - - - -
257A VAL* 3.2 17.2 + - - +
258A PHE* 3.4 17.9 + - - -
247B SER* 3.4 40.6 - - - +
248B ALA* 4.1 1.1 - - - +
251B VAL* 3.6 15.5 - - + +
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Residues in contact with ARG 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A SER* 2.7 33.0 + - - +
245A PHE* 4.0 4.4 - - - +
247A LEU* 3.7 25.9 + - + -
248A ASN 3.3 18.9 + - - -
249A ARG* 3.7 21.8 - - - +
251A SER* 2.9 17.4 + - - +
254A ALA* 1.3 72.9 - - - +
256A THR* 1.3 64.1 + - - +
258A PHE* 3.7 10.2 + - - +
259A GLY* 3.4 15.6 + - - -
301A LEU* 4.8 1.2 - - - +
303A GLU* 3.7 15.2 + - - -
304A PHE* 3.5 50.0 - - + +
307A VAL* 4.3 3.4 - - - +
393A ASP* 3.3 37.5 + - - -
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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
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252A VAL* 2.7 23.7 + - - +
253A PRO 4.9 0.4 - - - -
254A ALA 3.2 0.6 - - - -
255A ARG* 1.3 78.0 - - - +
257A VAL* 1.3 65.2 + - - +
259A GLY* 3.2 10.8 + - - +
260A VAL* 3.2 35.4 + - + +
301A LEU* 4.8 6.1 - - + -
304A PHE* 3.5 17.4 - - - -
242E ILE* 4.4 4.5 - - + +
249E ALA* 3.7 33.3 - - - +
252E ALA* 4.9 5.8 - - + -
253E LEU* 4.0 16.2 - - + +
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PRO 3.3 25.8 - - - +
254A ALA* 3.2 9.5 + - - +
256A THR* 1.3 79.5 - - - +
258A PHE* 1.3 59.1 + - - +
260A VAL* 5.2 1.1 - - - -
261A THR* 3.0 34.6 + - - +
248B ALA* 6.0 1.8 - - - +
251B VAL* 4.3 8.5 - - + -
252B ALA* 4.9 12.3 - - + -
255B ILE* 3.7 29.7 - - + +
256B THR* 6.0 0.4 - - - +
248E ALA 5.8 0.4 - - - +
252E ALA* 5.0 14.8 - - + -
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Residues in contact with PHE 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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240A LEU* 3.3 23.1 - - + +
241A SER* 5.2 2.0 - - - -
243A VAL* 3.8 29.4 - - + -
244A SER* 3.7 28.5 - - - +
247A LEU* 3.6 24.0 - - + -
254A ALA 3.4 18.6 + - - -
255A ARG* 3.9 5.8 - - - +
256A THR 3.2 0.2 - - - -
257A VAL* 1.3 78.0 - - - +
259A GLY* 1.3 54.7 + - - +
260A VAL 3.2 1.4 + - - -
262A THR* 2.6 39.3 + - + +
251B VAL* 3.6 28.9 - - + -
255B ILE* 3.6 24.9 - - + -
296B LEU* 4.1 19.7 - - + -
299B TYR* 6.0 1.1 - + - -
300B ALA* 5.8 0.7 - - + -
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Residues in contact with GLY 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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241A SER* 5.7 4.0 - - - -
244A SER* 5.4 2.0 + - - -
255A ARG 3.4 5.3 + - - -
256A THR 3.2 4.6 + - - -
258A PHE* 1.3 79.4 - - - +
260A VAL* 1.3 60.8 + - - +
262A THR* 3.9 5.7 + - - -
263A VAL* 3.3 20.4 - - - +
297A VAL 4.4 2.9 - - - +
300A ALA* 5.2 3.8 - - - -
301A LEU* 3.4 37.6 - - - +
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Residues in contact with VAL 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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256A THR* 3.2 25.6 + - + +
257A VAL* 5.0 1.1 - - - +
259A GLY* 1.3 78.9 - - - +
261A THR* 1.3 63.9 + - - +
262A THR 3.3 1.3 - - - -
263A VAL* 3.2 9.7 + - + +
264A LEU* 3.0 23.9 + - - +
301A LEU* 3.7 11.4 - - + -
235E LEU* 5.9 3.1 - - + +
252E ALA 4.2 6.3 - - - +
253E LEU* 3.6 34.8 - - + +
256E THR* 3.7 30.9 - - + +
257E THR* 4.9 4.0 - - - +
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Residues in contact with THR 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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257A VAL* 3.0 27.0 + - - +
258A PHE 4.7 0.2 - - - -
260A VAL* 1.3 78.2 - - - +
262A THR* 1.3 52.8 + - + +
264A LEU* 3.0 13.8 + - + +
265A THR* 2.7 38.1 + - - +
255B ILE* 3.7 22.6 - - + +
258B VAL* 6.2 0.9 - - + -
259B LEU* 3.7 37.5 - - + -
256E THR* 4.9 8.3 + - - +
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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
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237A THR* 3.5 16.2 - - + +
240A LEU* 3.9 33.4 - - + +
241A SER* 3.8 11.5 - - - +
258A PHE* 2.6 26.4 + - - +
259A GLY* 3.9 4.0 - - - -
261A THR* 1.3 75.5 - - + +
263A VAL* 1.3 59.7 + - - +
265A THR* 3.7 9.0 - - - +
266A MET* 3.1 30.7 + - - +
297A VAL* 3.3 21.2 - - - +
255B ILE* 5.3 5.6 - - + -
258B VAL* 6.5 0.2 - - + -
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Residues in contact with VAL 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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259A GLY 3.3 22.2 - - - +
260A VAL* 3.2 10.9 + - + +
262A THR* 1.3 77.0 + - - +
264A LEU* 1.3 52.5 + - - +
265A THR 3.2 0.2 - - - -
266A MET* 3.2 4.2 + - - +
267A THR* 2.7 44.6 + - - +
294A TYR* 3.4 28.2 - - + +
297A VAL* 3.7 22.9 - - + +
298A PHE* 4.9 1.6 - - - +
301A LEU* 5.1 0.2 - - + -
232E ILE* 4.5 9.0 - - + -
235E LEU* 3.7 28.5 - - + -
260E THR* 5.7 1.3 - - + -
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Residues in contact with LEU 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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260A VAL 3.0 11.7 + - - +
261A THR* 3.0 21.2 + - + +
263A VAL* 1.3 76.0 - - - +
265A THR* 1.3 59.8 + - - +
267A THR* 3.8 4.8 - - - -
268A THR* 2.9 34.2 + - - +
259B LEU* 4.9 14.4 - - + -
256E THR* 3.9 20.2 - - + +
259E LEU* 5.0 13.0 - - + -
260E THR* 3.4 40.2 - - + +
263E THR* 4.6 13.9 - - + +
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Residues in contact with THR 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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233A PRO* 5.0 0.4 - - + +
237A THR* 3.4 35.9 - - + +
240A LEU* 6.4 1.1 - - + -
261A THR* 2.7 24.0 + - - +
262A THR* 3.9 3.0 - - - +
263A VAL 3.2 0.2 - - - -
264A LEU* 1.3 73.4 - - - +
266A MET* 1.3 57.7 + - - +
268A THR* 3.3 7.6 + - - -
269A LEU* 3.0 35.6 + - + +
258B VAL* 5.8 3.3 - - - +
259B LEU* 3.6 20.6 - - + +
262B THR* 4.8 20.0 - - + +
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Residues in contact with MET 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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234A CYS* 4.0 25.8 - - - +
237A THR* 3.7 24.5 - - + -
262A THR 3.1 20.1 + - - +
263A VAL* 3.2 2.2 + - - +
265A THR* 1.3 72.7 - - - +
267A THR* 1.3 61.7 + - - +
269A LEU* 3.8 5.2 - - - +
270A SER* 3.0 30.3 + - - -
290A ILE* 3.7 26.5 - - + +
293A CYS* 3.8 12.8 - - + +
294A TYR* 3.6 45.5 - - + +
297A VAL* 4.1 15.3 - - + -
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Residues in contact with THR 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 VAL* 2.7 31.2 + - - +
264A LEU* 3.8 5.8 - - - -
265A THR 3.2 0.2 - - - -
266A MET* 1.3 71.0 - - - +
268A THR* 1.3 64.3 + - - +
270A SER* 3.2 17.5 + - - +
271A ILE* 3.3 32.1 + - + +
294A TYR* 4.2 5.7 - - - -
228E PRO* 5.0 4.0 - - + +
232E ILE* 3.4 35.0 - - + +
260E THR* 3.8 16.7 - - + +
263E THR* 4.6 4.5 - - - +
264E ILE* 4.3 7.2 - - + -
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Residues in contact with THR 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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264A LEU* 2.9 22.4 + - - +
265A THR* 3.3 10.6 + - - -
267A THR* 1.3 79.0 - - - +
269A LEU* 1.3 62.1 + - + +
271A ILE* 4.2 3.7 - - - +
272A SER* 2.9 32.8 + - - +
262B THR* 5.9 5.2 - - + -
263B THR* 6.1 5.4 - - + -
266B THR* 5.1 15.9 - - + +
263E THR* 5.5 4.9 + - - +
267E HIS* 5.8 6.5 - - + +
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Residues in contact with LEU 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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229A GLN 4.5 9.2 - - - +
230A THR* 5.4 3.0 - - + +
233A PRO* 3.4 48.5 - - + +
234A CYS* 3.7 24.5 - - - -
237A THR* 4.1 7.2 - - - +
265A THR* 3.0 25.5 + - + +
266A MET* 4.0 9.6 - - + +
267A THR 3.3 0.2 - - - -
268A THR* 1.3 80.1 - - + +
270A SER* 1.3 60.9 + - - +
272A SER* 3.9 5.7 - - - +
273A ALA* 3.2 28.9 + - - +
290A ILE* 4.6 2.4 - - + +
262B THR* 5.1 6.3 - - + -
266B THR* 5.0 16.6 - - + -
269B ARG* 5.6 3.4 - - - +
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Residues in contact with SER 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 MET 3.0 19.3 + - - -
267A THR* 3.2 13.0 + - - -
269A LEU* 1.3 75.7 - - - +
271A ILE* 1.3 64.4 + - - +
273A ALA* 4.4 5.2 + - - +
274A ARG* 5.2 6.2 + - - +
290A ILE* 3.8 28.6 - - - +
294A TYR* 5.5 4.9 - - - -
223E LEU 4.5 12.6 - - - +
224E GLN* 4.5 6.9 - - - +
228E PRO* 4.8 11.3 - - - +
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Residues in contact with ILE 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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267A THR* 3.3 26.1 + - + +
268A THR* 4.2 4.3 - - - +
269A LEU 3.2 0.6 - - - -
270A SER* 1.3 84.6 - - - +
272A SER* 1.3 59.6 + - - +
273A ALA 3.3 5.7 + - - -
274A ARG* 4.0 5.4 + - - -
275A ASN* 4.6 6.1 + - - +
224E GLN* 3.1 50.0 + - - +
228E PRO* 5.4 2.9 - - + -
263E THR* 4.5 6.3 - - - +
264E ILE* 3.9 37.5 - - + +
267E HIS* 4.0 32.3 - - + +
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Residues in contact with SER 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 2.9 26.3 + - - +
269A LEU* 3.9 7.9 + - - +
271A ILE* 1.3 79.2 - - - +
273A ALA* 1.3 58.6 + - - +
274A ARG 3.5 0.7 - - - -
275A ASN* 3.4 30.5 + - - +
266B THR* 5.4 7.3 - - - +
269B ARG* 4.2 25.7 + - - -
267E HIS* 6.2 3.8 - - - -
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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