Contacts of the helix formed by residues 241 - 267 (chain A) 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 ASP 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A THR* 3.4 25.0 - - - +
239A ASN 5.4 0.2 - - - -
240A LYS* 1.3 95.3 + - - +
242A LEU* 1.3 72.0 + - - +
243A THR* 3.0 35.3 + - - +
244A ILE* 3.5 27.3 - - + +
245A LEU 3.6 0.3 + - - -
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A VAL* 4.5 23.3 - - + -
114A THR* 5.2 8.1 - - + -
117A LEU* 5.5 4.9 - - + -
221A THR* 6.0 0.7 - - - -
240A LYS* 3.4 22.0 - - + +
241A ASP* 1.3 82.9 + - - +
243A THR* 1.3 65.2 + - - +
244A ILE 3.3 0.2 - - - -
245A LEU* 3.7 21.4 - - + +
246A ARG* 3.2 44.3 + - - +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ASP* 3.0 30.0 + - - +
242A LEU* 1.3 84.0 - - - +
244A ILE* 1.3 74.0 + - + +
246A ARG* 3.8 6.3 + - - +
247A GLN* 3.4 24.2 + - - +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A GLY* 4.6 14.6 - - - +
220A ASP* 6.0 0.9 - - + -
221A THR* 3.6 22.0 - - + -
241A ASP* 3.5 22.6 + - + +
243A THR* 1.3 90.2 - - + +
245A LEU* 1.3 70.3 + - - +
247A GLN* 3.1 19.2 + - - +
248A CYS* 3.0 27.3 + - - -
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A THR* 4.5 20.6 - - + +
117A LEU* 3.7 38.6 - - + -
118A LEU* 5.3 1.3 - - + -
217A GLY 5.1 0.4 - - - -
218A ILE* 4.1 32.1 - - + +
221A THR* 3.1 29.2 - - - +
222A VAL* 4.8 6.3 - - + -
241A ASP 3.6 1.2 + - - -
242A LEU* 3.7 22.7 - - + -
244A ILE* 1.3 82.9 - - - +
246A ARG* 1.3 61.9 + - - +
248A CYS* 3.1 8.7 + - - +
249A ILE* 2.9 33.0 + - + +
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Residues in contact with ARG 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.7 23.7 - - + +
242A LEU* 3.2 52.1 + - - +
243A THR* 4.0 7.4 - - - +
244A ILE 3.2 0.2 - - - -
245A LEU* 1.3 81.2 - - - +
247A GLN* 1.3 61.9 + - - +
249A ILE* 3.2 11.7 + - + +
250A SER* 3.1 24.5 + - - -
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Residues in contact with GLN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A THR* 3.4 12.6 + - - +
244A ILE* 3.1 28.4 + - + +
246A ARG* 1.3 78.6 - - - +
248A CYS* 1.3 59.1 + - - +
250A SER* 2.8 24.2 + - - -
251A ILE* 3.4 19.1 + - + +
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Residues in contact with CYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLN 5.0 0.4 - - - -
214A TYR* 3.4 34.8 - - + +
217A GLY* 3.8 22.0 - - - -
218A ILE* 3.4 23.3 - - + -
244A ILE* 3.0 22.3 + - - -
245A LEU* 3.5 3.6 - - - +
247A GLN* 1.3 76.3 - - - +
249A ILE* 1.3 67.3 + - - +
251A ILE* 3.0 19.1 + - - +
252A ARG* 3.0 12.5 + - - +
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Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.9 22.9 - - + +
118A LEU* 3.7 33.9 - - + +
218A ILE* 3.7 23.6 - - + -
245A LEU* 2.9 35.2 + - + +
246A ARG* 3.5 11.4 - - + +
248A CYS* 1.3 75.9 - - - +
250A SER* 1.3 59.2 + - - +
252A ARG* 3.3 11.1 - - - +
253A ASP* 2.8 45.1 + - - +
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Residues in contact with SER 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG 3.1 11.7 + - - -
247A GLN* 2.8 17.4 + - - +
249A ILE* 1.3 76.3 - - - +
251A ILE* 1.3 71.9 + - - +
253A ASP* 3.0 9.3 + - - -
254A LYS* 2.8 48.7 + - - +
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Residues in contact with ILE 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A SER* 4.5 17.7 - - - +
213A GLN* 6.4 1.6 - - + -
214A TYR* 3.5 33.9 - - + -
247A GLN* 3.5 20.9 - - + +
248A CYS* 3.0 9.5 + - - +
250A SER* 1.3 83.5 + - - +
252A ARG* 1.3 62.4 + - - +
254A LYS* 3.4 13.1 + - - +
255A LEU* 3.0 21.2 + - + +
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Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU 4.5 0.4 + - - -
118A LEU* 2.9 39.9 + - - +
120A ARG* 4.4 2.2 - - - +
214A TYR* 3.5 41.8 - - + +
218A ILE* 4.9 3.4 - - + -
248A CYS 3.0 9.1 + - - +
249A ILE* 3.3 22.7 + - - +
251A ILE* 1.3 78.4 - - - +
253A ASP* 1.3 87.4 + - - +
255A LEU* 3.0 4.4 + - - +
256A LEU* 3.0 38.3 + - + +
305A MET* 3.4 28.6 - - - +
308A GLY* 4.7 12.1 - - - -
309A ASP* 5.7 0.8 + - - -
311A PHE* 5.9 2.2 - - + -
601A AER 4.8 21.0 - - - +
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Residues in contact with ASP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 2.6 37.8 + - - +
249A ILE* 2.8 28.4 + - - +
250A SER* 3.0 12.5 + - - +
252A ARG* 1.3 101.6 + - - +
254A LYS* 1.3 58.6 + - + +
256A LEU* 3.4 7.0 + - - +
257A GLN* 2.8 32.0 + - - +
304A LEU* 5.8 0.3 - - - +
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Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A SER* 2.8 45.7 + - - +
251A ILE* 3.8 11.2 - - + +
253A ASP* 1.3 71.2 - - + +
255A LEU* 1.3 67.5 + - - +
257A GLN* 3.7 7.2 - - - +
258A LYS* 2.9 25.8 + - - +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A PHE* 4.6 2.9 - - + -
201A TYR* 4.4 4.7 - - - +
207A GLU* 3.5 44.4 - - + +
210A SER* 4.5 4.3 - - - +
211A MET* 4.3 11.0 - - + -
214A TYR* 4.0 22.0 - - + +
251A ILE* 3.0 13.4 + - + +
252A ARG* 3.0 12.0 + - - +
254A LYS* 1.3 79.2 - - - +
256A LEU* 1.3 74.6 + - + +
258A LYS* 3.4 5.9 + - - +
259A LYS* 3.2 27.6 + - + +
311A PHE* 4.0 22.0 - - + -
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 5.4 2.0 - - - +
197A PHE* 3.9 26.0 - - + -
252A ARG* 3.0 38.7 + - + +
253A ASP* 3.7 8.7 - - - +
255A LEU* 1.3 86.1 - - + +
257A GLN* 1.3 53.0 + - - +
259A LYS* 3.0 7.5 + - - +
260A TYR* 2.7 36.0 + - - +
276A LEU* 5.4 0.7 - - - +
304A LEU* 3.3 45.1 - - + +
305A MET* 5.1 2.0 - - - -
307A VAL* 4.8 1.8 - - + -
308A GLY* 4.1 21.3 - - - +
311A PHE* 4.5 9.0 - - + -
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Residues in contact with GLN 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 5.2 1.6 + - - -
253A ASP 2.8 23.7 + - - +
254A LYS* 3.3 8.3 + - - +
256A LEU* 1.3 72.8 - - - +
258A LYS* 1.3 57.1 + - - +
260A TYR* 3.6 11.5 - - - +
261A GLU* 3.0 47.9 + - + +
300A GLU* 3.2 27.1 + - - +
304A LEU* 3.3 16.9 - - - +
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Residues in contact with LYS 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A GLU* 4.3 18.5 + - - +
254A LYS 2.9 18.1 + - - +
255A LEU* 3.6 4.7 - - - +
257A GLN* 1.3 75.6 - - - +
259A LYS* 1.3 61.0 + - + +
260A TYR 3.2 0.2 + - - -
261A GLU* 3.2 4.4 + - - +
262A GLU* 2.9 62.2 + - + +
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Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A CYS* 4.6 0.8 - - - -
197A PHE* 3.9 53.7 - - + +
199A SER* 3.1 30.7 + - - +
201A TYR* 4.2 6.8 + - - -
207A GLU* 3.3 31.1 + - - +
255A LEU* 3.2 15.7 + - + +
256A LEU 3.0 6.5 + - - +
258A LYS* 1.3 79.9 - - + +
260A TYR* 1.3 62.8 + - - +
262A GLU* 3.7 18.2 + - - +
263A HIS* 2.9 35.1 + - + +
276A LEU* 3.9 2.0 - - + +
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Residues in contact with TYR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU 2.7 19.7 + - - +
257A GLN* 3.6 19.3 - - - +
258A LYS 3.1 0.2 - - - -
259A LYS* 1.3 73.4 - - - +
261A GLU* 1.3 75.5 + - - +
263A HIS* 3.0 13.7 + - - +
264A LYS* 3.2 49.7 + - - +
276A LEU* 4.2 13.4 - - + +
280A LEU* 3.7 24.2 - - + +
283A LYS* 3.9 17.7 - - + +
300A GLU* 3.6 37.2 + - + +
303A VAL* 4.2 20.6 - - + -
304A LEU* 3.8 23.3 - - + -
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLN* 3.0 35.0 + - + +
258A LYS* 4.0 3.8 - - - +
260A TYR* 1.3 93.6 - - + +
262A GLU* 1.3 61.8 + - + +
263A HIS 3.4 0.2 + - - -
264A LYS* 3.5 22.2 + - - +
265A VAL* 3.2 30.3 + - - +
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Residues in contact with GLU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LYS* 2.9 53.5 + - + +
259A LYS* 3.7 30.1 + - - +
260A TYR 3.1 0.2 + - - -
261A GLU* 1.3 74.7 - - + +
263A HIS* 1.3 68.3 + - + +
265A VAL* 3.4 20.3 - - - +
266A THR* 2.9 18.1 + - - +
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Residues in contact with HIS 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A PHE* 3.3 27.3 + - - +
198A ASN* 5.1 0.4 - - + -
259A LYS* 2.9 30.7 - - + +
260A TYR 3.0 4.6 + - - +
262A GLU* 1.3 85.4 - - + +
264A LYS* 1.3 68.7 + - - +
266A THR* 3.2 3.1 + - - -
267A TYR* 2.8 22.1 + - - +
273A ARG* 3.2 24.5 + - - +
274A ASP* 2.8 35.2 + - - -
276A LEU* 3.9 13.7 - - + +
277A ASP* 3.3 16.3 + - - -
280A LEU* 3.9 14.8 - - + -
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Residues in contact with LYS 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A TYR* 3.2 49.7 + - - +
261A GLU* 3.5 29.3 + - - +
263A HIS* 1.3 77.6 - - - +
265A VAL* 1.3 64.7 + - + +
266A THR 3.0 1.4 + - - -
267A TYR* 3.0 21.5 + - - +
280A LEU* 4.1 19.8 - - + +
283A LYS* 6.0 0.9 - - - -
300A GLU* 5.6 0.8 + - - -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLU* 3.2 22.7 - - - +
262A GLU* 3.4 14.3 + - - +
263A HIS 3.3 0.6 - - - -
264A LYS* 1.3 76.4 - - + +
266A THR* 1.3 74.6 + - + +
267A TYR 3.4 0.4 - - - +
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A GLU 2.9 14.1 + - - +
263A HIS* 3.3 3.1 + - - -
265A VAL* 1.3 92.2 - - + +
267A TYR* 1.3 66.4 + - - +
268A SER* 3.5 6.1 + - - -
273A ARG* 3.0 30.5 + - - -
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Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A HIS 2.8 13.4 + - - +
264A LYS* 3.0 17.7 + - - +
265A VAL 3.4 0.6 - - - +
266A THR* 1.3 79.5 - - - +
268A SER* 1.3 65.7 + - - +
269A ASP* 3.6 30.8 + - - -
271A VAL 4.7 1.1 + - - -
272A GLN* 6.0 0.2 - - - +
273A ARG* 3.9 4.0 - - - +
277A ASP* 3.8 47.3 + - + -
280A LEU* 4.3 14.1 - - + -
281A ARG* 3.3 36.8 + - + +
284A ARG* 2.8 34.7 + - - -
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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
------------------------------------------------------------
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