Contacts of the helix formed by residues 244 - 265 (chain B) in PDB entry 6EBT
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 LEU 244 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B PHE* 3.6 23.6 - - + +
228B ILE* 2.9 18.3 + - + +
230B LYS* 3.6 25.4 - - + +
243B THR* 1.3 71.0 - - - +
245B GLY* 1.3 57.0 + - - +
247B GLU* 3.7 16.1 - - - +
248B PHE* 2.8 44.5 + - + +
345B LEU* 4.9 1.3 - - + -
355B GLU* 3.9 8.7 - - - +
356B LEU* 3.9 24.9 - - + -
440B ALA* 3.8 20.6 - - + -
445B ILE* 3.8 26.7 - - + -
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Residues in contact with GLY 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B SER* 2.8 40.8 + - - -
225B PHE* 3.0 18.2 + - - -
226B ALA* 4.1 2.9 - - - -
243B THR* 3.1 2.8 + - - -
244B LEU* 1.3 77.5 - - - +
246B GLN* 1.3 55.5 + - - +
248B PHE 3.4 0.3 + - - -
249B SER* 2.8 26.0 + - - -
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Residues in contact with GLN 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A THR* 3.9 6.2 - - - +
312A PHE* 3.5 43.7 - - + -
242B LEU* 3.5 10.7 - - + +
243B THR* 2.9 46.3 + - - +
245B GLY* 1.3 73.5 - - - +
247B GLU* 1.3 66.1 + - - +
249B SER* 2.6 24.6 + - - -
250B GLY 3.3 3.6 + - - -
507B LEU* 3.3 30.0 + - - +
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A PHE* 5.1 5.0 - - - +
403A PHE* 4.1 12.3 - - - +
404A GLU* 2.5 32.5 - - - +
230B LYS* 3.1 34.9 + - - -
242B LEU* 4.0 9.7 - - + +
243B THR 3.0 12.6 + - - +
244B LEU* 3.7 12.2 - - - +
246B GLN* 1.3 75.7 - - - +
248B PHE* 1.3 63.5 + - - +
250B GLY* 3.1 12.3 + - - -
251B TYR* 3.6 36.1 + - + +
341B ASP* 5.3 0.4 - - - +
345B LEU* 3.4 19.5 - - - +
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Residues in contact with PHE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LEU* 4.0 31.4 - - + +
221B LYS* 4.0 25.8 - - + -
222B SER* 3.8 15.3 - - - -
225B PHE* 4.4 15.3 - + - -
244B LEU* 2.8 45.4 + - + +
245B GLY 3.8 3.1 - - - +
247B GLU* 1.3 78.2 - - - +
249B SER* 1.3 62.1 + - - +
251B TYR* 3.1 28.4 + + - +
252B VAL* 3.0 25.1 + - - +
342B ILE* 4.4 10.1 - - + -
345B LEU* 5.0 1.3 - - + -
356B LEU* 4.1 27.6 - - + -
435B VAL* 5.3 0.4 - - + -
438B ILE* 4.5 11.0 - - + -
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN* 2.9 27.0 + - - -
312A PHE* 3.8 4.2 - - - -
222B SER* 3.7 11.2 + - - -
245B GLY 2.8 15.6 + - - -
246B GLN* 2.6 22.9 + - - -
248B PHE* 1.3 77.1 - - - +
250B GLY* 1.3 56.3 + - - +
252B VAL* 3.4 9.4 + - - +
253B GLN* 3.0 22.3 + - - +
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Residues in contact with GLY 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ASN* 3.6 17.7 - - - -
312A PHE* 4.2 4.7 - - - -
313A GLU* 3.9 12.9 - - - +
246B GLN 3.3 2.0 + - - -
247B GLU 3.1 9.3 + - - -
248B PHE 3.1 0.8 - - - -
249B SER* 1.3 79.9 + - - +
251B TYR* 1.3 66.5 + - - +
253B GLN* 3.2 3.8 + - - +
254B GLN* 3.0 28.7 + - - +
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Residues in contact with TYR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ALA* 6.1 0.7 - - + -
218B LEU* 4.1 11.2 - - + -
247B GLU* 3.6 33.0 + - + +
248B PHE* 3.1 51.8 + + - +
250B GLY* 1.3 74.8 - - - +
252B VAL* 1.3 64.1 + - - +
254B GLN* 3.1 16.5 + - - +
255B VAL* 3.0 26.0 + - - +
337B LYS* 3.9 10.1 - - - -
338B ILE* 3.7 38.8 - - + +
341B ASP* 2.9 43.2 + - + +
342B ILE* 4.4 10.3 - - + -
345B LEU* 3.9 3.5 - - - +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B HIS* 3.5 30.8 - - + +
218B LEU* 3.5 16.6 - - + +
219B ASP* 3.5 48.0 - - + +
222B SER* 4.4 1.6 - - - -
248B PHE 3.0 14.7 + - - +
249B SER* 3.6 13.2 - - - +
250B GLY 3.2 0.2 - - - -
251B TYR* 1.3 75.7 - - - +
253B GLN* 1.3 63.5 + - - +
255B VAL* 3.2 2.6 + - - -
256B LYS* 2.9 23.3 + - + +
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Residues in contact with GLN 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLU* 5.0 0.2 + - - -
309A PRO* 3.9 19.6 - - - +
310A ASN* 3.9 16.7 + - + +
313A GLU* 3.8 26.4 + - + +
249B SER 3.0 14.2 + - - +
250B GLY 3.5 7.9 - - - +
252B VAL* 1.3 77.5 - - - +
254B GLN* 1.3 58.3 + - - +
256B LYS* 3.0 31.6 + - - +
257B TYR* 2.8 69.8 + - + +
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Residues in contact with GLN 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 3.7 18.6 - - + -
316A ALA* 5.7 1.9 - - - +
317A ALA* 3.4 21.7 - - + +
319A ASP* 3.1 25.7 + - - +
250B GLY 3.0 15.4 + - - +
251B TYR* 3.1 22.1 + - - +
253B GLN* 1.3 76.8 - - - +
255B VAL* 1.3 57.1 + - - +
257B TYR* 3.5 4.4 + - - +
258B ALA* 2.9 27.2 + - - +
261B ARG* 4.6 1.1 + - - +
334B SER* 3.8 32.5 + - - +
337B LYS* 4.1 14.9 + - - +
338B ILE* 3.7 22.3 - - + +
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Residues in contact with VAL 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 3.3 44.2 - - + +
214B LEU* 4.2 11.9 - - + -
215B HIS* 3.6 17.9 - - + +
218B LEU* 3.8 16.2 - - + -
251B TYR 3.0 13.9 + - - +
252B VAL 3.8 4.7 - - - +
254B GLN* 1.3 73.5 - - - +
256B LYS* 1.3 67.0 + - - +
258B ALA* 3.1 6.6 + - - +
259B MET* 3.0 23.4 + - + +
334B SER* 5.8 0.7 - - - -
335B LEU* 4.6 5.6 - - + -
338B ILE* 3.7 19.5 - - + -
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Residues in contact with LYS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A PRO* 5.9 1.0 - - - +
215B HIS* 3.8 24.1 - - + +
252B VAL* 2.9 17.2 + - + +
253B GLN* 3.0 35.8 + - - +
255B VAL* 1.3 78.5 - - - +
257B TYR* 1.3 75.1 + - + +
259B MET* 3.4 8.5 + - - +
260B THR* 3.0 28.5 + - - +
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Residues in contact with TYR 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ARG* 3.8 27.4 - - + -
271A GLU* 2.6 40.4 + - - -
309A PRO* 3.9 6.2 - - - +
313A GLU* 3.7 24.9 - - - -
253B GLN* 2.8 53.2 + - + +
254B GLN* 3.9 2.5 - - - +
256B LYS* 1.3 89.3 - - + +
258B ALA* 1.3 60.6 + - - +
260B THR* 3.2 11.0 + - - -
261B ARG* 2.8 55.9 + - - +
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Residues in contact with ALA 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B LEU* 4.6 6.1 - - + -
254B GLN 2.9 15.4 + - - +
255B VAL* 3.1 13.2 + - - +
257B TYR* 1.3 75.5 - - - +
259B MET* 1.3 57.7 + - - +
261B ARG* 3.1 13.1 + - - +
262B ILE* 2.9 35.8 + - - +
330B THR* 6.1 0.2 - - - -
331B THR* 3.5 37.9 + - + +
334B SER* 5.0 4.7 - - - +
335B LEU* 6.4 0.7 - - + -
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Residues in contact with MET 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.6 45.3 - - + +
211B LEU* 3.7 20.9 - - + +
212B GLN* 3.2 46.2 - - + +
215B HIS* 4.7 8.1 - - - -
255B VAL 3.0 15.6 + - - +
256B LYS* 3.7 9.4 - - - +
258B ALA* 1.3 75.2 - - - +
260B THR* 1.3 63.2 + - - +
262B ILE* 3.4 3.2 + - - +
263B LYS* 2.9 46.0 + - - +
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Residues in contact with THR 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ARG* 3.7 25.6 - - - +
256B LYS* 3.0 19.4 + - - +
257B TYR* 3.4 16.8 - - + -
259B MET* 1.3 76.9 - - - +
261B ARG* 1.3 57.3 + - - +
263B LYS* 3.3 8.8 + - - +
264B ALA* 2.8 30.1 + - + +
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Residues in contact with ARG 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ARG* 3.6 24.5 - - - +
313A GLU* 4.7 3.2 + - - -
319A ASP* 3.4 25.5 + - - +
320A ALA* 3.3 29.5 - - - +
323A GLU* 2.7 46.2 + - + +
254B GLN* 4.6 3.2 + - - +
257B TYR* 2.8 49.1 + - - +
258B ALA* 3.1 9.9 + - - +
260B THR* 1.3 72.9 - - - +
262B ILE* 1.3 63.3 + - - +
264B ALA* 3.2 8.7 + - - +
265B ALA* 3.1 22.3 + - - +
327B ALA* 3.7 16.0 - - + +
330B THR* 3.6 22.3 - - - +
331B THR 5.8 0.2 - - - +
334B SER* 4.8 1.2 + - - -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B VAL* 3.8 28.0 - - + -
207B LEU* 3.7 26.5 - - + -
208B LEU* 4.1 9.6 - - + -
211B LEU* 3.3 34.1 - - + -
258B ALA 2.9 16.2 + - - +
259B MET 3.8 3.6 - - - +
261B ARG* 1.3 76.6 - - - +
263B LYS* 1.3 62.1 + - - +
265B ALA* 3.0 14.6 + - - +
266B MET* 3.4 12.5 + - - +
324B LEU* 4.3 7.8 - - + +
327B ALA* 3.9 19.7 - - + +
328B MET* 4.7 2.9 - - + +
331B THR* 3.5 20.2 - - - +
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Residues in contact with LYS 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B HIS* 5.9 2.9 - - + -
208B LEU* 3.9 36.3 - - + -
212B GLN* 5.6 1.0 + - - -
259B MET* 2.9 37.6 + - - +
260B THR* 3.7 6.7 - - + +
262B ILE* 1.3 75.5 - - - +
264B ALA* 1.3 61.2 + - - +
265B ALA 3.2 0.7 + - - -
266B MET* 3.3 20.8 + - + +
267B PRO* 3.5 8.3 - - - +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A ALA* 4.9 24.8 - - + +
268A ARG* 5.1 5.4 - - - +
323A GLU* 5.6 0.9 - - - +
260B THR* 2.8 20.0 + - + +
261B ARG* 3.2 9.8 + - - +
263B LYS* 1.3 76.0 - - - +
265B ALA* 1.3 56.0 + - - +
266B MET 3.4 0.4 - - - -
267B PRO* 3.4 14.2 - - - +
268B ARG* 3.7 5.9 + - - -
323B GLU* 3.5 9.1 - - - +
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Residues in contact with ALA 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B ARG 3.1 9.7 + - - +
262B ILE 3.0 12.3 + - - +
264B ALA* 1.3 77.2 - - - +
266B MET* 1.3 58.7 + - - +
267B PRO* 3.6 1.6 - - - -
268B ARG* 4.8 0.7 + - - +
269B ILE* 3.6 16.1 + - - +
320B ALA 4.6 0.5 - - - +
323B GLU* 3.4 36.9 - - + +
324B LEU* 3.9 14.6 + - + +
327B ALA* 3.9 18.4 - - + -
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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