Contacts of the helix formed by residues 248 - 269 (chain B) in PDB entry 3D0E
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 THR 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B PHE* 1.3 77.9 - - - +
249B GLU* 1.3 64.9 + - - +
250B GLU* 3.4 18.8 + - - +
251B ARG* 3.1 24.2 + - - +
252B ALA* 3.0 19.9 + - - +
344B MET* 5.0 0.4 - - - -
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Residues in contact with GLU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE 3.8 0.4 + - - -
248B THR* 1.3 73.3 - - - +
250B GLU* 1.3 65.5 + - - +
252B ALA* 3.5 0.3 + - - +
253B ARG* 2.8 38.8 + - - +
344B MET* 3.9 22.0 - - + -
372B THR 4.3 2.6 - - - +
373B LEU* 3.7 16.6 - - + +
374B SER* 2.7 51.0 + - - -
377B ALA* 3.5 12.6 - - - +
408B PHE* 3.7 13.7 - - + -
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Residues in contact with GLU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B THR* 3.4 20.6 - - - +
249B GLU* 1.3 84.3 + - - +
251B ARG* 1.3 61.3 + - - +
253B ARG* 3.3 28.1 + - - +
254B PHE* 3.1 21.5 + - - +
425B PRO* 5.0 2.6 - - + +
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LEU* 5.6 0.2 - - - +
240B HIS* 4.6 4.9 - - - +
244B GLU* 2.8 39.2 + - - -
247B PHE* 3.2 38.0 - - + +
248B THR* 3.1 21.4 + - - +
250B GLU* 1.3 73.8 - - - +
252B ALA* 1.3 66.4 + - - +
254B PHE* 3.3 4.2 + - - +
255B TYR* 3.1 58.0 + - + -
425B PRO* 3.8 32.5 - - + -
426B PHE* 3.4 31.8 - - - +
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Residues in contact with ALA 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 4.3 3.0 - - + +
248B THR 3.0 11.8 + - - +
249B GLU 3.7 2.7 - - - +
251B ARG* 1.3 76.1 - - - +
253B ARG* 1.3 57.3 + - - +
255B TYR* 3.4 1.7 + - - +
256B GLY* 2.8 29.5 + - - -
340B MET* 3.7 12.0 - - + +
343B MET* 4.0 27.3 - - + +
344B MET* 3.5 35.4 - - + -
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU* 2.8 24.0 + - - +
250B GLU* 3.5 37.9 + - - +
251B ARG 3.2 0.4 - - - -
252B ALA* 1.3 75.0 - - - +
254B PHE* 1.3 56.6 + - - +
257B ALA* 2.9 29.5 + - - +
376B GLU* 5.8 2.2 - - - +
408B PHE* 3.1 67.4 + - + +
409B PHE* 3.7 15.4 - - + -
411B SER* 3.5 24.7 + - - -
412B ILE* 3.9 18.3 - - + +
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Residues in contact with PHE 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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250B GLU 3.1 11.8 + - - +
251B ARG 3.5 8.3 - - - +
252B ALA 3.3 0.4 - - - -
253B ARG* 1.3 77.5 - - - +
255B TYR* 1.3 78.5 + + - +
257B ALA* 3.7 4.7 - - - +
258B GLU* 3.3 55.4 + - - +
287B GLY 3.8 20.6 - - - -
288B HIS* 3.8 9.4 - - - -
412B ILE* 5.8 1.6 - - - -
422B LEU* 3.7 35.8 - - + +
423B LEU 3.5 22.2 - - - -
424B PRO* 3.5 18.2 - - + -
425B PRO* 3.6 20.6 - - + -
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Residues in contact with TYR 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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237B LEU* 3.6 14.4 - - + -
247B PHE* 3.5 33.2 - + - -
251B ARG* 3.1 53.4 + - + -
252B ALA 3.9 3.6 - - - +
254B PHE* 1.3 92.5 - + - +
256B GLY* 1.3 58.1 + - - +
258B GLU* 3.2 4.0 + - - +
259B ILE* 3.0 35.0 + - + +
283B LEU* 3.5 31.3 - - + +
287B GLY 3.8 11.1 + - - -
289B ILE* 3.7 29.1 - - + +
343B MET* 3.9 16.2 - - + -
425B PRO* 5.5 2.0 - - + -
426B PHE* 4.0 7.8 + - - +
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Residues in contact with GLY 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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252B ALA 2.8 21.9 + - - -
253B ARG 3.8 1.3 - - - -
255B TYR* 1.3 74.4 - - - +
257B ALA* 1.3 55.3 + - - +
259B ILE* 3.4 8.6 + - - +
260B VAL* 2.9 38.2 + - - +
336B LEU* 4.3 1.5 - - - +
340B MET* 3.6 24.4 - - - -
409B PHE* 4.1 4.3 - - - -
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Residues in contact with ALA 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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253B ARG 2.9 21.1 + - - +
254B PHE* 3.7 6.1 - - - +
255B TYR 3.4 0.2 - - - -
256B GLY* 1.3 71.6 - - - +
258B GLU* 1.3 58.1 + - - +
260B VAL 3.4 0.3 + - - -
261B SER* 3.0 26.2 + - - -
409B PHE* 3.8 5.8 - - + -
412B ILE* 4.2 12.1 - - + -
414B TRP* 3.3 35.3 - - + -
417B VAL* 3.7 19.4 - - + +
422B LEU* 5.0 2.0 - - + -
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Residues in contact with GLU 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 PHE* 3.3 48.3 - - + +
254B PHE* 3.3 33.4 + - + +
255B TYR 3.2 8.1 + - - +
257B ALA* 1.3 74.6 - - + +
259B ILE* 1.3 64.2 + - - +
261B SER* 3.4 0.9 + - - -
262B ALA* 3.1 19.9 + - - +
288B HIS* 2.8 27.6 + - - -
289B ILE* 2.8 40.7 + - + +
417B VAL* 4.0 9.7 - - + +
420B LYS* 5.5 0.3 - - - -
422B LEU* 5.4 3.6 - - + +
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Residues in contact with ILE 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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237B LEU* 5.1 0.7 - - + -
255B TYR* 3.0 32.8 + - + +
256B GLY* 3.4 5.1 + - - +
258B GLU* 1.3 76.2 - - - +
260B VAL* 1.3 58.0 + - - +
262B ALA* 3.2 7.2 + - - +
263B LEU* 2.9 34.2 + - + +
276B ILE* 3.9 27.8 - - + -
281B LEU* 3.7 39.7 - - + -
289B ILE* 4.3 12.6 - - + -
291B ILE* 4.6 5.2 - - + -
336B LEU* 3.8 26.7 - - + -
339B VAL* 4.5 5.4 - - + -
343B MET* 4.8 4.7 - - + -
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Residues in contact with VAL 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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256B GLY 2.9 28.6 + - - +
257B ALA 3.6 5.2 - - - +
259B ILE* 1.3 76.7 - - - +
261B SER* 1.3 56.0 + - - +
263B LEU* 3.4 1.4 + - - +
264B GLU* 2.8 29.3 + - - +
333B TRP* 4.3 16.9 - - + -
336B LEU* 3.4 27.1 - - + -
400B ALA* 4.4 7.6 - - + +
403B VAL* 4.0 14.6 - - + -
404B MET* 3.6 32.1 - - + -
409B PHE* 4.4 8.5 - - + -
414B TRP* 3.9 8.1 - - + -
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Residues in contact with SER 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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209B HIS* 3.2 26.9 + - - -
211B PHE* 4.2 3.0 - - - -
257B ALA 3.0 14.3 + - - -
258B GLU 3.5 9.4 - - - -
260B VAL* 1.3 78.2 - - - +
262B ALA* 1.3 62.2 + - - +
264B GLU* 3.4 12.2 + - - +
265B TYR* 3.1 17.8 + - - +
404B MET* 6.0 0.2 - - - -
414B TRP* 4.5 7.1 + - - -
417B VAL* 4.0 14.8 - - - -
418B VAL* 4.0 17.7 + - - +
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Residues in contact with ALA 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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209B HIS* 3.6 18.3 - - + +
211B PHE* 4.4 6.3 - - + +
212B LEU* 3.9 13.7 - - + -
258B GLU 3.1 10.6 + - - +
259B ILE 3.5 7.0 - - - +
261B SER* 1.3 77.9 - - - +
263B LEU* 1.3 58.5 + - - +
265B TYR* 3.2 5.0 + - - +
266B LEU* 2.9 34.3 + - - +
291B ILE* 3.6 26.2 - - + -
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Residues in contact with LEU 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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259B ILE* 2.9 36.5 + - + +
260B VAL 3.9 0.2 - - - +
262B ALA* 1.3 72.9 - - - +
264B GLU* 1.3 66.4 + - - +
266B LEU* 4.5 9.4 - - + +
267B HIS* 3.0 34.7 + - - +
273B TYR* 4.3 10.5 - - + -
276B ILE* 4.0 17.7 - - + -
291B ILE* 5.3 2.9 - - + -
332B ASP* 3.8 48.7 - - + +
333B TRP* 3.7 35.9 - - + -
336B LEU* 4.5 4.7 - - + -
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Residues in contact with GLU 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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260B VAL 2.8 19.4 + - - +
261B SER* 3.6 9.6 + - - +
262B ALA 3.3 0.2 - - - -
263B LEU* 1.3 75.7 - - - +
265B TYR* 1.3 58.9 + - - +
267B HIS* 3.9 1.0 - - - +
268B SER* 2.9 32.9 + - - -
333B TRP* 4.3 1.0 - - - -
399B ASP* 4.4 4.8 - - - +
400B ALA* 3.5 21.1 - - + -
401B LYS* 3.4 21.9 + - - +
404B MET* 2.9 34.6 - - + +
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Residues in contact with TYR 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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206B ASN 3.9 2.9 + - - -
207B THR* 3.4 12.3 - - + -
208B ARG* 2.8 37.8 + - - +
209B HIS* 3.5 29.8 - + + -
212B LEU* 3.7 31.9 - - + -
261B SER 3.1 5.2 + - - +
262B ALA 3.2 6.9 + - - +
264B GLU* 1.3 80.3 - - - +
266B LEU* 1.3 63.8 + - + +
268B SER* 2.6 25.8 + - - -
269B ARG* 3.3 40.5 + - + +
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Residues in contact with LEU 266 (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* 4.9 1.1 - - + -
207B THR* 4.2 17.5 - - + -
212B LEU* 3.9 36.8 - - + -
262B ALA 2.9 22.2 + - - +
263B LEU* 4.0 10.5 - - + +
265B TYR* 1.3 79.3 - - + +
267B HIS* 1.3 62.0 + - + +
269B ARG* 3.2 12.0 + - - -
270B ASP 3.2 0.2 + - - -
271B VAL* 2.8 54.0 + - + +
273B TYR* 4.2 25.8 - - + -
291B ILE* 5.2 2.7 - - + -
294B PHE* 4.4 13.2 - - + -
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Residues in contact with HIS 267 (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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263B LEU* 3.0 24.4 + - + +
264B GLU 3.9 0.9 - - - +
266B LEU* 1.3 76.8 - - + +
268B SER* 1.3 61.4 + - - +
270B ASP* 3.0 22.7 + - - +
271B VAL 3.3 19.3 - - - +
272B VAL* 4.5 0.9 - - + -
301B ILE 4.6 2.6 - - - +
329B ARG* 3.5 50.4 + - + +
332B ASP* 2.6 31.6 + - + +
333B TRP* 3.6 20.1 - + - -
399B ASP* 2.8 38.0 + - - +
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Residues in contact with SER 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B GLU* 2.9 18.8 + - - -
265B TYR* 2.6 26.9 + - - -
267B HIS* 1.3 76.0 - - - +
269B ARG* 1.3 62.1 + - - +
270B ASP* 3.2 9.6 + - - +
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Residues in contact with ARG 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ASN* 3.6 38.9 + - - +
207B THR* 4.5 10.4 - - - +
265B TYR* 3.3 48.5 + - + +
266B LEU* 3.2 9.9 + - - +
268B SER* 1.3 79.9 + - - +
270B ASP* 1.3 69.5 + - - +
271B VAL* 3.3 15.9 + - + +
300B GLY 5.2 0.7 + - - -
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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