Contacts of the helix formed by residues 241 - 273 (chain u) in PDB entry 6AH0
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 ASP 241 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240u LEU* 1.3 74.1 - - - +
242u GLN* 1.3 57.6 + - - +
244u CYS* 3.2 2.4 + - - +
245u TYR* 2.9 25.6 + - - -
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Residues in contact with GLN 242 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240u LEU* 3.1 3.0 - - - +
241u ASP* 1.3 76.1 - - - +
243u VAL* 1.3 57.9 + - - +
245u TYR* 3.0 3.6 + - - +
246u ARG* 2.9 25.3 + - - -
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Residues in contact with VAL 243 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240u LEU* 3.0 10.7 + - - +
242u GLN* 1.3 74.2 - - - +
244u CYS* 1.3 57.0 + - - +
246u ARG* 3.4 2.8 + - - +
247u VAL* 3.0 23.4 + - - -
19w MET* 4.8 9.0 - - - +
22w MET 5.6 0.7 - - - -
23w ALA* 3.8 26.3 - - - +
26w MET* 6.1 0.4 - - - -
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Residues in contact with CYS 244 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240u LEU 2.9 13.2 + - - -
241u ASP* 3.6 4.0 - - - +
243u VAL* 1.3 76.3 - - - +
245u TYR* 1.3 57.3 + - - +
247u VAL* 3.1 4.3 + - - +
248u GLU* 2.9 25.1 + - - -
26w MET* 6.3 3.6 - - - +
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Residues in contact with TYR 245 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241u ASP 2.9 14.2 + - - -
242u GLN* 3.0 3.8 + - - +
244u CYS* 1.3 74.8 - - - +
246u ARG* 1.3 56.3 + - - +
248u GLU* 3.3 2.8 + - - +
249u TRP* 2.9 24.9 + - - -
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Residues in contact with ARG 246 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242u GLN 2.9 14.2 + - - -
243u VAL* 3.8 4.0 - - - +
244u CYS 3.2 0.2 - - - -
245u TYR* 1.3 71.9 - - - +
247u VAL* 1.3 65.9 + - - +
249u TRP* 3.1 3.8 + - - +
250u ALA* 2.9 19.6 + - - -
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Residues in contact with VAL 247 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243u VAL 3.0 15.3 + - - -
244u CYS* 3.1 4.9 + - - +
246u ARG* 1.3 74.3 - - - +
248u GLU* 1.3 63.3 + - - +
250u ALA* 3.0 4.8 + - - +
251u LYS* 2.9 19.8 + - - -
23w ALA* 4.4 16.0 + - - +
26w MET 5.9 0.4 - - - -
27w LEU* 5.2 9.4 - - - +
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Residues in contact with GLU 248 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244u CYS 2.9 13.0 + - - -
245u TYR* 3.6 4.9 - - - +
247u VAL* 1.3 72.1 - - - +
249u TRP* 1.3 63.9 + - - +
251u LYS* 3.0 4.5 + - - +
252u PHE* 2.9 19.1 + - - -
60w LEU* 5.6 11.0 - - - +
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Residues in contact with TRP 249 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245u TYR 2.9 13.8 + - - -
246u ARG* 3.1 4.7 + - - +
248u GLU* 1.3 74.0 - - - +
250u ALA* 1.3 62.1 + - - +
252u PHE* 2.8 14.6 + - - +
253u GLN* 2.9 12.3 + - - -
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Residues in contact with ALA 250 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246u ARG 2.9 13.1 + - - -
247u VAL* 3.0 4.9 + - - +
249u TRP* 1.3 73.8 - - - +
251u LYS* 1.3 61.7 + - - +
253u GLN* 3.4 2.0 + - - +
254u GLU* 2.9 20.8 + - - -
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Residues in contact with LYS 251 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247u VAL 2.9 12.5 + - - -
248u GLU* 3.0 4.2 + - - +
250u ALA* 1.3 74.6 - - - +
252u PHE* 1.3 63.8 + - - +
254u GLU* 3.2 3.7 + - - +
255u ARG* 2.9 18.9 + - - -
61w TYR* 6.2 5.6 - - - +
62w ASP 6.3 0.9 - - - -
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Residues in contact with PHE 252 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248u GLU 2.9 9.4 + - - -
249u TRP* 2.8 8.1 + - - +
251u LYS* 1.3 74.4 - - - +
253u GLN* 1.3 61.3 + - - +
255u ARG* 2.9 14.0 + - - +
256u GLU* 2.9 10.7 + - - -
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Residues in contact with GLN 253 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249u TRP 2.9 14.8 + - - -
250u ALA* 3.8 3.4 - - - +
252u PHE* 1.3 69.7 - - - +
254u GLU* 1.3 63.4 + - - +
256u GLU* 3.1 3.9 + - - +
257u ARG* 2.9 19.9 + - - -
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Residues in contact with GLU 254 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250u ALA 2.9 14.7 + - - -
251u LYS* 3.2 5.4 + - - +
253u GLN* 1.3 74.1 - - - +
255u ARG* 1.3 56.7 + - - +
257u ARG* 3.3 3.3 + - - +
258u LYS* 2.9 24.8 + - - -
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Residues in contact with ARG 255 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251u LYS 2.9 9.4 + - - -
252u PHE* 2.9 9.0 + - - +
254u GLU* 1.3 73.3 - - - +
256u GLU* 1.3 63.4 + - - +
258u LYS* 3.2 2.6 + - - +
259u LYS* 2.9 21.3 + - - -
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Residues in contact with GLU 256 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252u PHE 2.9 12.4 + - - -
253u GLN* 3.1 4.7 + - - +
255u ARG* 1.3 73.3 - - - +
257u ARG* 1.3 63.4 + - - +
259u LYS* 3.3 2.2 + - - +
260u GLU* 2.9 21.3 + - - -
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Residues in contact with ARG 257 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253u GLN 2.9 13.5 + - - -
254u GLU* 3.6 3.8 - - - +
256u GLU* 1.3 77.3 - - - +
258u LYS* 1.3 60.8 + - - +
260u GLU* 3.3 1.5 + - - +
261u GLU* 3.0 19.9 + - - -
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Residues in contact with LYS 258 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254u GLU 2.9 13.8 + - - -
255u ARG* 3.2 4.2 + - - +
257u ARG* 1.3 74.3 - - - +
259u LYS* 1.3 63.0 + - - +
261u GLU* 3.0 5.3 + - - +
262u GLU* 3.0 18.4 + - - -
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Residues in contact with LYS 259 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255u ARG 2.9 17.1 + - - -
256u GLU* 3.7 3.1 - - - +
258u LYS* 1.3 69.2 - - - +
260u GLU* 1.3 63.9 + - - +
262u GLU* 2.9 13.2 + - - +
263u GLU* 2.9 12.3 + - - -
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Residues in contact with GLU 260 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256u GLU 2.9 14.4 + - - -
257u ARG* 3.6 3.6 - - - +
259u LYS* 1.3 73.8 - - - +
261u GLU* 1.3 62.8 + - - +
263u GLU* 3.1 3.2 + - - +
264u LYS* 2.9 21.5 + - - -
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Residues in contact with GLU 261 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257u ARG 3.0 13.5 + - - -
258u LYS* 3.0 4.7 + - - +
260u GLU* 1.3 73.9 - - - +
262u GLU* 1.3 60.7 + - - +
264u LYS* 3.4 1.7 + - - +
265u GLU* 2.9 19.4 + - - -
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Residues in contact with GLU 262 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258u LYS 3.0 8.7 + - - -
259u LYS* 2.9 10.0 + - - +
261u GLU* 1.3 71.5 - - - +
263u GLU* 1.3 64.8 + - - +
265u GLU* 2.9 13.1 + - - +
266u LYS* 3.0 11.1 + - - -
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Residues in contact with GLU 263 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259u LYS 2.9 15.3 + - - -
260u GLU* 3.1 2.4 + - - +
262u GLU* 1.3 70.7 - - - +
264u LYS* 1.3 64.6 + - - +
266u LYS* 3.0 5.4 + - - +
267u GLU* 2.9 18.2 + - - -
144v GLY* 3.5 24.5 - - - +
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Residues in contact with LYS 264 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260u GLU 2.9 13.0 + - - -
261u GLU* 3.7 3.8 - - - +
263u GLU* 1.3 73.7 - - - +
265u GLU* 1.3 62.9 + - - +
267u GLU* 3.1 4.4 + - - +
268u ARG* 2.9 20.4 + - - -
202v GLU* 4.0 23.4 - - - +
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Residues in contact with GLU 265 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261u GLU 2.9 11.3 + - - -
262u GLU* 2.9 9.1 + - - +
264u LYS* 1.3 73.6 - - - +
266u LYS* 1.3 62.5 + - - +
268u ARG* 3.1 3.6 + - - +
269u VAL* 3.0 19.6 + - - -
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Residues in contact with LYS 266 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262u GLU 3.0 12.2 + - - -
263u GLU* 3.0 4.5 + - - +
265u GLU* 1.3 73.0 - - - +
267u GLU* 1.3 63.1 + - - +
269u VAL* 3.0 4.8 + - - +
270u ALA* 2.9 20.1 + - - -
144v GLY* 5.1 5.4 - - - -
145v ILE* 5.8 0.2 - - - -
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Residues in contact with GLU 267 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263u GLU 2.9 12.9 + - - -
264u LYS* 3.1 4.7 + - - +
266u LYS* 1.3 74.6 - - - +
268u ARG* 1.3 60.5 + - - +
270u ALA* 3.2 1.8 + - - +
271u TYR* 2.9 23.6 + - - -
144v GLY 4.2 10.8 + - - -
145v ILE* 4.7 10.1 - - - +
202v GLU 5.2 2.0 - - - -
203v THR* 5.7 2.9 - - - -
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Residues in contact with ARG 268 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264u LYS 2.9 14.1 + - - -
265u GLU* 3.1 3.3 + - - +
267u GLU* 1.3 74.1 - - - +
269u VAL* 1.3 63.5 + - - +
271u TYR* 3.9 1.2 - - - +
272u ALA* 2.9 22.0 + - - -
202v GLU 4.5 10.2 + - - -
203v THR* 5.2 6.1 - - - +
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Residues in contact with VAL 269 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265u GLU 3.0 13.1 + - - -
266u LYS* 3.0 4.2 + - - +
268u ARG* 1.3 76.9 - - - +
270u ALA* 1.3 56.9 + - - +
272u ALA* 3.2 2.3 + - - -
273u GLN* 3.0 24.8 + - - -
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Residues in contact with ALA 270 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266u LYS 2.9 13.1 + - - -
267u GLU* 3.8 1.8 - - - +
269u VAL* 1.3 71.3 - - - +
271u TYR* 1.3 60.5 + - - +
273u GLN* 2.8 20.0 + - - +
274u ILE* 3.1 13.0 + - - -
----------------------------------------------------------
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Residues in contact with TYR 271 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267u GLU 2.9 15.5 + - - -
268u ARG* 4.0 1.1 - - - +
270u ALA* 1.3 75.4 - - - +
272u ALA* 1.3 60.2 + - - +
273u GLN 3.2 1.0 + - - -
274u ILE* 3.8 10.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 272 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268u ARG 2.9 15.5 + - - -
269u VAL 3.6 4.9 - - - -
271u TYR* 1.3 75.9 - - - +
273u GLN* 1.3 57.6 + - - +
274u ILE 3.6 2.8 + - - +
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Residues in contact with GLN 273 (chain u).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269u VAL 3.0 9.8 + - - -
270u ALA* 2.8 13.6 + - - +
272u ALA* 1.3 79.4 - - - +
274u ILE* 1.3 56.0 + - - -
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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