Contacts of the helix formed by residues 243 - 264 (chain B) in PDB entry 3E8R
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 GLU 243 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B TYR* 3.4 5.9 - - - -
240B GLY 2.9 7.8 + - - +
241B ARG* 2.8 30.5 - - - +
242B GLY* 1.3 80.7 - - - +
244B GLU* 1.3 64.2 + - - +
245B SER* 4.1 11.6 + - - +
246B THR* 2.8 26.3 + - - +
247B THR* 2.9 27.4 + - - -
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Residues in contact with GLU 244 (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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236B TYR* 3.6 11.3 + - - -
243B GLU* 1.3 72.9 - - - +
245B SER* 1.3 55.5 + - - +
247B THR* 3.8 3.1 - - - -
248B THR* 2.7 45.7 + - - +
284B ILE* 4.7 12.3 - - + +
286B LYS* 2.7 43.9 + - - +
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Residues in contact with SER 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLU* 4.1 9.7 + - - +
244B GLU* 1.3 79.5 - - - +
246B THR* 1.3 70.1 + - - +
248B THR* 3.4 4.4 + - - -
249B ASN* 2.9 44.7 + - - +
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Residues in contact with THR 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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239B MET 4.3 6.3 - - - +
240B GLY* 3.2 27.1 + - - +
241B ARG* 4.5 6.0 - - + +
243B GLU* 2.8 27.3 + - - -
244B GLU 3.5 0.2 - - - -
245B SER* 1.3 75.1 + - - +
247B THR* 1.3 66.4 + - - +
249B ASN* 3.4 7.2 + - - +
250B TYR* 3.0 27.2 + - + +
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA* 3.8 17.9 - - + -
235B PHE* 4.1 13.3 - - + -
236B TYR* 3.4 17.1 - - - -
240B GLY* 2.9 28.5 - - - -
243B GLU 2.9 15.6 + - - -
244B GLU 3.8 3.1 - - - -
246B THR* 1.3 78.6 - - - +
248B THR* 1.3 63.9 + - - +
250B TYR* 3.5 5.0 + - - +
251B LEU* 3.4 21.0 + - + +
284B ILE* 3.0 33.0 - - + -
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B GLU* 2.7 33.0 + - - +
245B SER* 3.6 5.6 - - - -
247B THR* 1.3 77.3 - - - +
249B ASN* 1.3 66.5 + - - +
251B LEU* 3.2 5.3 + - - +
252B ILE* 3.0 36.7 + - + +
282B ILE* 3.9 25.0 - - + +
284B ILE* 4.1 14.4 - - - +
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Residues in contact with ASN 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B SER* 2.9 33.4 + - - +
246B THR* 3.4 6.9 + - - +
248B THR* 1.3 78.5 - - - +
250B TYR* 1.3 63.2 + - - +
252B ILE* 3.4 8.9 + - - +
253B GLU* 3.0 37.2 + - + +
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Residues in contact with TYR 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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235B PHE* 3.6 30.1 - + + -
239B MET* 3.4 37.2 - - + +
246B THR* 3.0 19.2 + - + +
247B THR* 3.7 6.3 - - - +
249B ASN* 1.3 75.8 - - - +
251B LEU* 1.3 63.3 + - + +
253B GLU* 3.6 3.8 + - - +
254B LEU* 3.0 45.9 + - + +
257B ARG* 4.9 1.4 + - - -
338B PHE* 5.8 0.9 - + - -
387B THR* 3.9 5.4 - - + +
394B ILE 5.3 2.3 + - - -
396B THR* 4.3 28.8 - - + -
399B ALA* 3.4 24.5 - - + +
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Residues in contact with LEU 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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229B VAL* 3.4 29.2 - - + -
231B ALA* 3.9 25.6 - - + -
235B PHE* 3.9 19.3 - - + -
247B THR 3.4 12.5 + - - +
248B THR 3.2 7.2 + - - +
249B ASN 3.2 1.0 - - - -
250B TYR* 1.3 77.3 - - + +
252B ILE* 1.3 66.7 + - - +
254B LEU* 3.3 3.2 + - + +
255B ILE* 2.9 29.7 + - + +
279B ILE* 4.2 5.4 - - + -
282B ILE* 4.3 14.1 - - + -
284B ILE* 4.7 2.2 - - + -
338B PHE* 3.6 40.4 - - + -
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Residues in contact with ILE 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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248B THR* 3.0 34.1 + - + +
249B ASN* 3.9 10.1 - - - +
251B LEU* 1.3 77.1 - - - +
253B GLU* 1.3 63.9 + - + +
255B ILE* 4.0 1.7 - - - +
256B ASP* 3.0 29.3 + - + +
279B ILE* 3.9 13.1 - - + +
282B ILE* 3.7 18.6 - - + -
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Residues in contact with GLU 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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249B ASN* 3.0 27.3 + - + +
250B TYR* 4.0 4.0 - - - +
252B ILE* 1.3 81.9 - - + +
254B LEU* 1.3 63.7 + - - +
256B ASP* 3.4 6.2 + - - +
257B ARG* 3.0 48.2 + - - +
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Residues in contact with LEU 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 TYR* 3.0 34.8 + - + +
251B LEU* 3.3 5.8 + - - +
253B GLU* 1.3 75.7 - - - +
255B ILE* 1.3 78.6 + - + +
257B ARG* 3.2 18.9 + - - +
258B VAL* 2.9 37.2 + - + +
338B PHE* 4.0 14.6 - - + -
387B THR* 5.9 0.2 - - + -
396B THR 5.0 0.2 - - - +
399B ALA* 3.8 32.5 - - + +
400B ASP* 3.5 19.5 - - - +
403B THR* 3.9 24.9 - - + +
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B LEU* 3.9 26.7 - - + -
229B VAL* 4.3 8.1 - - + -
251B LEU* 2.9 21.9 + - + +
252B ILE 4.1 1.1 - - - +
254B LEU* 1.3 90.8 - - + +
256B ASP* 1.3 58.1 + - - +
258B VAL* 3.4 2.4 + - + +
259B ASP* 2.8 28.5 + - + +
277B ILE* 4.0 18.5 - - + +
278B GLN* 4.7 2.7 - - - -
279B ILE* 3.7 41.3 - - + +
336B HIS* 6.2 1.1 - - + -
338B PHE* 4.3 14.8 - - + -
403B THR* 4.5 8.7 - - + -
407B LEU* 5.0 1.1 - - + -
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Residues in contact with ASP 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 ILE* 3.0 19.9 + - + +
253B GLU* 3.8 7.4 - - - +
254B LEU 3.3 0.2 - - - -
255B ILE* 1.3 78.9 - - - +
257B ARG* 1.3 62.1 + - - +
259B ASP* 3.3 11.9 + - - +
260B ASP* 3.0 40.3 + - - +
473B ARG* 5.8 0.9 + - - -
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Residues in contact with ARG 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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250B TYR* 4.9 2.6 + - - -
253B GLU* 3.0 50.5 + - - +
254B LEU* 3.5 18.5 - - - +
256B ASP* 1.3 76.9 - - - +
258B VAL* 1.3 65.8 + - - +
260B ASP* 3.1 23.1 + - - +
261B ILE* 3.4 16.5 + - - +
396B THR* 3.0 28.1 - - - +
400B ASP* 2.6 44.6 + - - +
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Residues in contact with VAL 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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254B LEU* 2.9 36.7 + - + +
255B ILE* 3.9 4.5 - - - +
257B ARG* 1.3 75.2 - - - +
259B ASP* 1.3 64.4 + - - +
261B ILE* 3.0 16.7 + - + +
262B TYR* 3.1 33.7 + - + -
277B ILE* 3.8 13.7 - - + -
400B ASP* 3.8 20.9 - - + +
403B THR* 4.4 5.2 - - + -
404B THR* 3.5 32.5 - - - +
407B LEU* 4.2 6.7 - - + -
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Residues in contact with ASP 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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255B ILE* 2.8 18.8 + - + +
256B ASP* 3.5 12.1 - - - +
258B VAL* 1.3 75.3 - - - +
260B ASP* 1.3 68.6 + - - +
262B TYR* 3.1 2.9 + - - +
263B ARG* 2.7 57.4 + - - +
276B GLY* 3.3 1.2 - - - -
277B ILE* 3.0 42.2 + - + +
473B ARG* 3.1 28.4 + - - -
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Residues in contact with ASP 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 ASP* 3.0 32.1 + - - +
257B ARG* 3.1 17.0 + - - +
259B ASP* 1.3 77.8 - - - +
261B ILE* 1.3 62.6 + - + +
263B ARG* 3.6 5.4 + - - +
264B ASN* 3.3 37.4 + - - +
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Residues in contact with ILE 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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257B ARG* 3.4 13.0 + - + +
258B VAL* 3.0 10.7 + - + +
260B ASP* 1.3 80.5 - - + +
262B TYR* 1.3 63.3 + - + +
264B ASN* 3.5 4.2 + - - +
265B THR* 2.8 29.7 + - - +
400B ASP* 5.9 6.1 - - + -
401B LEU* 6.2 0.2 - - + -
404B THR* 4.3 26.2 - - + +
448B LYS* 3.3 57.4 - - + +
449B MET* 4.6 6.5 - - + -
450B PHE* 4.6 7.2 - - + -
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Residues in contact with TYR 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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258B VAL* 3.1 44.3 + - + +
259B ASP* 3.7 7.0 - - - +
261B ILE* 1.3 77.8 - - - +
263B ARG* 1.3 63.6 + - - +
265B THR* 3.0 24.4 + - - +
267B TRP* 4.0 22.2 + + - -
275B TYR 3.1 17.2 + - - +
276B GLY* 4.0 9.6 - - - -
277B ILE* 4.8 5.8 - - + -
404B THR* 2.9 23.1 + - + -
407B LEU* 3.1 12.5 - - + +
408B GLY* 2.9 33.4 + - - -
411B PHE* 3.9 38.6 - + + -
450B PHE* 3.4 17.8 - + - -
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Residues in contact with ARG 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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223B ASN* 3.3 20.4 + - - +
224B THR* 2.8 36.6 + - - +
259B ASP* 2.7 49.5 + - - +
260B ASP* 4.1 5.6 - - - +
262B TYR* 1.3 72.7 - - - +
264B ASN* 1.3 65.6 + - - +
265B THR 3.2 0.6 + - - -
273B LYS* 3.5 6.1 - - - +
274B GLY* 2.5 63.1 + - - -
275B TYR 3.3 7.4 - - - -
276B GLY* 3.3 11.9 - - - -
277B ILE 3.7 1.0 + - - +
473B ARG* 3.2 38.5 - - - +
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Residues in contact with ASN 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B ASP* 3.3 24.3 + - - +
261B ILE* 4.2 3.8 - - - +
262B TYR 3.3 0.8 - - - -
263B ARG* 1.3 80.1 - - - +
265B THR* 1.3 60.8 + - - +
266B ALA 3.5 0.3 + - - -
273B LYS* 3.0 27.4 + - - +
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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