Contacts of the helix formed by residues 242 - 266 (chain B) in PDB entry 4R1Z
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 242 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B VAL* 5.6 12.3 - - + -
117B LEU* 4.3 18.8 - - + -
221B THR* 5.4 0.4 - - - -
241B ASP* 1.3 73.6 - - - +
243B THR* 1.3 60.8 + - - +
245B LEU* 3.8 8.5 - - - -
246B ARG* 3.0 55.1 + - + +
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Residues in contact with THR 243 (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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241B ASP 3.6 18.8 - - - +
242B LEU* 1.3 83.6 - - - +
244B ILE* 1.3 80.6 + - + +
246B ARG* 3.8 3.5 + - - +
247B GLN* 3.6 24.2 + - - +
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Residues in contact with ILE 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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217B GLY* 5.0 7.1 - - - +
221B THR* 3.7 19.3 - - - +
241B ASP* 3.3 40.8 - - - +
243B THR* 1.3 89.9 - - + +
245B LEU* 1.3 65.4 + - - +
247B GLN* 3.9 9.8 + - - +
248B CYS* 3.5 23.1 + - - -
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B THR* 4.6 14.6 - - + +
117B LEU* 4.0 29.6 - - + -
118B LEU* 5.8 0.4 - - + -
217B GLY 4.9 0.4 - - - +
218B ILE* 4.1 30.1 - - + +
221B THR* 3.6 34.8 - - + +
222B VAL* 6.3 0.4 - - + -
241B ASP 3.0 18.2 + - - +
242B LEU* 3.7 9.0 - - - +
243B THR 3.2 0.2 - - - -
244B ILE* 1.3 72.4 - - - +
246B ARG* 1.3 56.2 + - - +
247B GLN 2.7 15.3 + - - -
248B CYS* 2.7 18.4 + - - +
249B ILE* 3.0 30.9 + - + +
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Residues in contact with ARG 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.8 36.4 - - + +
242B LEU* 3.0 40.9 + - + +
243B THR* 4.2 3.8 - - - +
245B LEU* 1.3 77.7 - - - +
247B GLN* 1.3 56.8 + - - +
249B ILE* 3.9 12.2 - - + +
250B SER* 3.1 26.2 + - - -
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B THR* 3.6 17.9 + - - +
244B ILE* 4.0 10.1 - - - +
245B LEU 2.7 5.3 + - - -
246B ARG* 1.3 73.6 - - - +
248B CYS* 1.3 60.4 + - - +
250B SER* 2.9 20.2 + - - +
251B ILE* 3.3 21.6 + - + +
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Residues in contact with CYS 248 (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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214B TYR* 3.4 40.7 - - + +
217B GLY* 3.9 17.9 - - - -
218B ILE* 3.7 12.8 - - + -
244B ILE* 3.5 12.9 + - - +
245B LEU* 2.7 13.5 + - - +
247B GLN* 1.3 69.7 - - - +
249B ILE* 1.3 66.2 + - - +
250B SER 3.0 1.8 - - - -
251B ILE* 3.0 12.9 + - - +
252B ARG* 2.9 24.6 + - - +
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Residues in contact with ILE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 4.5 15.0 - - + +
118B LEU* 3.5 41.5 - - + +
120B ARG* 6.5 0.7 - - + -
218B ILE* 3.6 20.4 - - + -
245B LEU* 3.0 39.2 + - + +
246B ARG* 3.9 9.0 - - - +
248B CYS* 1.3 76.5 - - - +
250B SER* 1.3 51.9 + - - +
252B ARG* 3.6 16.8 - - - +
253B ASP* 2.7 47.3 + - - +
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Residues in contact with SER 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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246B ARG 3.1 16.7 + - - -
247B GLN* 2.9 24.4 + - - +
249B ILE* 1.3 72.1 - - - +
251B ILE* 1.3 67.2 + - - +
252B ARG 3.0 1.9 + - - -
253B ASP* 3.0 10.8 + - - +
254B LYS* 2.9 26.9 + - - +
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Residues in contact with ILE 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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210B SER* 4.9 4.5 - - - +
213B GLN* 5.9 1.3 - - + -
214B TYR* 3.5 35.8 - - + +
247B GLN* 3.3 17.4 + - + +
248B CYS* 3.0 19.5 + - - +
250B SER* 1.3 76.3 + - - +
252B ARG* 1.3 60.9 + - - +
254B LYS* 4.5 4.8 - - - +
255B LEU* 3.6 15.1 + - - +
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Residues in contact with ARG 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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118B LEU* 3.2 31.0 + - - +
120B ARG* 5.1 1.2 - - - +
214B TYR* 3.1 47.0 - - + +
218B ILE* 4.9 3.8 - - + -
248B CYS 2.9 10.8 + - - +
249B ILE* 3.6 20.4 + - - +
250B SER 3.1 0.2 - - - -
251B ILE* 1.3 73.1 - - - +
253B ASP* 1.3 86.6 + - - +
254B LYS 3.0 1.8 - - - -
255B LEU* 2.5 31.9 + - + +
256B LEU* 3.2 31.5 + - + +
305B MET* 3.2 32.4 - - - +
308B GLY* 4.8 9.4 - - - -
311B PHE* 6.3 1.3 - - - -
601B AER 4.7 14.2 - - - +
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Residues in contact with ASP 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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120B ARG* 3.1 34.0 + - - +
249B ILE* 2.7 37.6 + - - +
250B SER* 3.0 11.5 + - - +
252B ARG* 1.3 96.6 + - - +
254B LYS* 1.3 57.4 + - - +
256B LEU* 3.4 10.9 + - - +
257B GLN* 3.0 29.2 + - - +
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Residues in contact with LYS 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 SER 2.9 15.2 + - - +
251B ILE* 4.6 4.7 - - - +
252B ARG 2.6 4.4 + - - -
253B ASP* 1.3 71.6 - - + +
255B LEU* 1.3 57.9 + - - +
257B GLN* 3.7 26.9 - - + +
258B LYS* 3.0 35.5 + - + +
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Residues in contact with LEU 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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197B PHE* 4.7 8.3 - - + -
201B TYR* 4.2 9.0 - - - +
207B GLU* 4.0 46.7 - - + +
210B SER* 5.3 2.2 - - - +
211B MET* 4.2 10.5 - - + -
214B TYR* 4.0 21.5 - - + +
251B ILE 3.6 9.8 + - - +
252B ARG* 2.5 22.6 + - - +
254B LYS* 1.3 70.2 - - - +
256B LEU* 1.3 78.6 - - + +
258B LYS* 3.7 7.2 - - - +
259B LYS* 3.4 28.6 + - + +
311B PHE* 4.9 4.0 - - + -
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Residues in contact with LEU 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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120B ARG* 6.3 0.4 - - - +
197B PHE* 4.1 26.0 - - + -
252B ARG* 3.2 41.5 + - + +
253B ASP* 3.6 9.6 - - - +
255B LEU* 1.3 86.4 - - + +
257B GLN* 1.3 51.3 + - - +
259B LYS* 3.0 8.4 + - - +
260B TYR* 2.7 33.8 + - - +
276B LEU* 5.5 0.2 - - - +
304B LEU* 3.4 47.3 - - + +
305B MET* 4.9 1.1 - - + -
307B VAL* 5.2 1.6 - - + -
308B GLY* 4.3 17.5 - - - +
311B PHE* 5.0 7.2 - - + -
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Residues in contact with GLN 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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120B ARG* 5.0 5.7 + - - -
253B ASP 3.0 19.6 + - - +
254B LYS* 3.8 31.6 - - + +
255B LEU 3.3 0.4 - - - -
256B LEU* 1.3 76.6 - - - +
258B LYS* 1.3 57.6 + - - +
260B TYR* 3.4 26.0 - - - +
261B GLU* 2.9 36.2 + - + +
300B GLU* 4.9 7.3 + - - +
304B LEU* 3.5 25.2 - - - +
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Residues in contact with LYS 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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207B GLU* 3.8 19.6 + - - +
254B LYS* 3.0 23.9 + - + +
255B LEU* 3.7 8.3 - - - +
257B GLN* 1.3 75.7 - - - +
259B LYS* 1.3 60.7 + - + +
261B GLU* 4.3 3.1 - - - +
262B GLU* 3.0 49.4 + - - +
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Residues in contact with LYS 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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197B PHE* 4.0 45.6 - - + +
199B SER* 3.2 32.3 + - - +
201B TYR* 4.2 12.6 + - - -
207B GLU* 3.4 26.7 + - - -
255B LEU* 3.4 20.2 - - + +
256B LEU 3.0 7.0 + - - +
258B LYS* 1.3 76.2 - - + +
260B TYR* 1.3 66.1 + - - +
262B GLU* 3.1 18.8 + - - +
263B HIS* 2.9 34.3 + - + +
276B LEU* 4.2 3.6 - - + -
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Residues in contact with TYR 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 LEU 2.7 16.5 + - - +
257B GLN* 3.2 26.9 + - - +
259B LYS* 1.3 72.6 - - - +
261B GLU* 1.3 66.4 + - + +
263B HIS* 3.3 8.8 + - - +
264B LYS* 3.3 40.4 + - - +
276B LEU* 4.2 21.4 - - + +
280B LEU* 3.6 24.8 - - + +
283B LYS* 3.9 19.6 + - - +
300B GLU* 3.0 48.1 + - + +
303B VAL* 4.2 14.4 - - + -
304B LEU* 3.7 23.3 - - + -
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Residues in contact with GLU 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 GLN* 2.9 17.9 + - + +
258B LYS* 4.3 3.4 - - - +
260B TYR* 1.3 77.4 - - + +
262B GLU* 1.3 68.7 + - - +
263B HIS 3.0 1.4 + - - -
264B LYS* 2.8 45.9 + - - +
265B VAL* 3.1 38.1 + - + +
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Residues in contact with GLU 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 LYS* 3.0 51.3 + - - +
259B LYS* 3.1 19.7 + - - +
261B GLU* 1.3 79.5 - - - +
263B HIS* 1.3 64.8 + - + +
265B VAL* 3.2 19.1 - - + +
266B THR* 3.0 21.1 + - - -
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Residues in contact with HIS 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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197B PHE* 3.4 21.4 + - - +
198B ASN* 4.9 1.8 - - + -
259B LYS* 2.9 32.8 + - + +
260B TYR 3.7 5.8 - - - +
261B GLU 3.0 0.4 - - - -
262B GLU* 1.3 86.0 + - + +
264B LYS* 1.3 57.4 + - - +
265B VAL 3.2 0.2 - - - -
266B THR* 3.2 3.9 + - - -
267B TYR* 2.9 32.3 + - - +
273B ARG* 3.3 14.7 + - - +
274B ASP* 2.8 34.6 + - - -
276B LEU* 3.6 23.9 - - + +
277B ASP* 3.1 23.0 + - - +
280B LEU* 3.9 10.3 - - + -
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Residues in contact with LYS 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 TYR* 3.3 49.0 + - - +
261B GLU* 2.8 42.4 + - - +
263B HIS* 1.3 76.5 - - - +
265B VAL* 1.3 59.9 + - - +
267B TYR* 4.0 17.3 - - + +
280B LEU* 4.1 16.8 - - + +
300B GLU* 4.2 6.6 + - - -
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Residues in contact with VAL 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B GLU* 3.1 31.6 + - + +
262B GLU* 3.2 24.9 - - + +
264B LYS* 1.3 78.9 - - - +
266B THR* 1.3 69.7 + - + +
267B TYR 3.6 2.7 - - - -
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Residues in contact with THR 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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262B GLU 3.0 16.3 + - - -
263B HIS 3.2 5.0 + - - -
265B VAL* 1.3 85.3 - - + +
267B TYR* 1.3 58.3 + - - +
273B ARG* 2.8 33.8 + - - -
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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
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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