Contacts of the helix formed by residues 235 - 261 (chain A) in PDB entry 1SL1
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 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A PHE* 1.3 72.1 - - - +
236A THR* 1.3 64.6 + - - +
237A LYS* 3.7 8.3 + - - +
238A ALA* 3.1 35.4 + - + +
239A ILE* 3.2 13.9 + - - +
453A ALA 5.9 0.2 - - - -
454A ALA* 2.8 20.4 + - - +
459A HIS* 3.2 40.2 + - + +
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Residues in contact with THR 236 (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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234A PHE* 3.0 18.4 + - - -
235A ASP* 1.3 70.2 - - - +
237A LYS* 1.3 65.0 + - - +
239A ILE* 3.1 5.4 + - - +
240A GLU* 3.0 40.5 + - - +
407A LEU* 3.8 18.8 - - + +
410A VAL* 3.3 32.6 - - + +
414A GLY* 5.4 1.2 - - - -
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP* 3.3 7.0 + - - +
236A THR* 1.3 78.7 - - - +
238A ALA* 1.3 61.8 + - - +
240A GLU* 3.3 17.8 + - - +
241A GLU* 3.1 45.5 + - + +
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ASP* 3.1 37.7 + - + +
237A LYS* 1.3 76.5 - - - +
239A ILE* 1.3 60.5 + - + +
241A GLU* 3.3 16.0 + - - +
242A LEU* 2.9 25.6 + - - +
450A GLN* 5.6 2.6 + - - +
454A ALA* 5.1 4.9 - - + -
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Residues in contact with ILE 239 (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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234A PHE* 3.3 29.6 - - + -
235A ASP 3.2 2.9 + - - +
236A THR 3.1 7.4 + - - +
238A ALA* 1.3 77.1 - - + +
240A GLU* 1.3 61.4 + - - +
242A LEU* 3.2 19.5 + - + +
243A TYR* 2.8 26.7 + - + +
399A SER* 3.9 24.0 + - - +
406A TRP* 4.1 17.5 - - + -
407A LEU* 3.8 23.1 - - + -
450A GLN 4.3 7.4 - - - +
451A CYS* 4.6 0.9 - - - -
454A ALA* 3.5 27.8 - - + -
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Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 3.0 33.7 + - - +
237A LYS* 3.5 20.2 - - - +
238A ALA 3.3 0.2 - - - -
239A ILE* 1.3 75.6 - - - +
241A GLU* 1.3 59.3 + - + +
243A TYR* 3.2 11.3 + - + +
244A VAL* 3.0 31.5 + - - +
407A LEU* 3.8 20.7 - - + +
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Residues in contact with GLU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LYS* 3.1 31.0 + - + +
238A ALA* 3.6 14.6 - - - +
239A ILE 3.2 0.2 - - - -
240A GLU* 1.3 75.0 - - + +
242A LEU* 1.3 65.4 + - - +
244A VAL* 3.4 9.8 + - - +
245A GLU* 3.1 23.5 + - - +
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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
----------------------------------------------------------
238A ALA 2.9 14.0 + - - +
239A ILE* 3.4 25.1 - - + +
241A GLU* 1.3 76.9 - - - +
243A TYR* 1.3 56.9 - - - +
245A GLU* 3.3 10.1 + - - +
246A LEU* 2.9 51.6 + - + +
395A ARG* 6.0 0.4 - - + -
399A SER* 5.0 7.9 - - - +
447A TYR* 3.9 21.5 - - + +
450A GLN* 3.5 44.2 - - + +
451A CYS* 4.2 24.7 - - - -
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Residues in contact with TYR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE 2.8 13.7 + - - +
240A GLU* 3.3 13.5 - - + +
242A LEU* 1.3 75.5 - - - +
244A VAL* 1.3 69.6 + - + +
246A LEU* 3.3 5.9 + - - +
247A ALA* 2.9 34.9 + - + +
250A ARG* 4.6 1.0 + - - -
396A ILE* 3.8 24.9 - - + -
399A SER* 5.2 2.9 - - - +
400A ALA* 3.7 28.3 - - + -
401A GLU* 2.6 36.9 + - + +
407A LEU* 4.5 7.6 - - + -
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLU 3.0 19.3 + - - +
241A GLU* 3.7 9.4 - - - +
242A LEU 3.3 0.2 - - - -
243A TYR* 1.3 79.3 - - + +
245A GLU* 1.3 64.7 + - - +
247A ALA* 3.4 5.3 + - - +
248A ALA* 3.1 25.2 + - + +
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Residues in contact with GLU 245 (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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241A GLU 3.1 11.4 + - - +
242A LEU* 3.5 11.5 - - - +
244A VAL* 1.3 81.5 - - - +
246A LEU* 1.3 63.3 + - - +
248A ALA* 3.4 7.1 + - - +
249A ARG* 3.1 22.0 + - + +
447A TYR* 3.5 30.1 + - + +
450A GLN* 3.8 20.6 + - - +
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Residues in contact with LEU 246 (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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242A LEU* 2.9 42.9 + - + +
243A TYR* 3.8 4.5 - - - +
245A GLU* 1.3 76.1 - - - +
247A ALA* 1.3 58.5 + - - +
249A ARG* 3.3 5.8 + - - +
250A ARG* 2.8 28.4 + - - +
392A ILE* 3.8 15.9 - - + +
395A ARG* 3.9 22.4 - - + +
396A ILE* 3.6 31.6 - - + +
399A SER* 4.5 4.7 - - - +
447A TYR* 3.7 47.8 - - + +
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Residues in contact with ALA 247 (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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243A TYR* 2.9 28.1 + - + +
244A VAL* 3.8 6.1 - - - +
246A LEU* 1.3 76.6 - - - +
248A ALA* 1.3 62.3 + - - +
250A ARG* 3.2 23.2 + - - +
251A SER* 3.0 27.7 + - - -
396A ILE* 4.0 5.5 - - - +
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Residues in contact with ALA 248 (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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244A VAL* 3.1 19.1 + - + +
245A GLU* 3.6 7.0 - - - +
247A ALA* 1.3 76.5 - - - +
249A ARG* 1.3 62.4 + - - +
251A SER* 3.3 7.1 + - - -
252A GLU* 3.1 24.2 + - - +
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A GLU* 3.1 12.0 + - + +
246A LEU* 3.7 8.1 - - - +
248A ALA* 1.3 79.4 - - - +
250A ARG* 1.3 58.0 + - - +
252A GLU* 3.9 20.9 - - - +
253A LEU* 3.0 50.5 + - + +
256A LYS* 5.4 5.9 - - - +
385A LEU* 4.7 6.3 - - - +
388A GLU* 2.7 37.5 + - - +
392A ILE* 3.3 25.6 - - + -
447A TYR* 4.7 7.9 - - - +
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Residues in contact with ARG 250 (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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243A TYR* 4.6 1.4 + - - -
246A LEU 2.8 14.7 + - - +
247A ALA* 3.4 20.9 + - - +
248A ALA 3.1 0.2 - - - -
249A ARG* 1.3 75.2 - - - +
251A SER* 1.3 67.1 + - - +
253A LEU* 3.2 4.0 + - - +
254A LEU* 2.9 24.0 + - + +
389A TYR* 3.6 32.1 - - + +
392A ILE* 4.3 13.9 - - + +
393A GLN* 2.7 41.5 + - - +
396A ILE* 3.7 20.4 - - + +
401A GLU* 3.1 40.0 + - - -
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Residues in contact with SER 251 (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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247A ALA 3.0 14.5 + - - -
248A ALA* 3.7 9.5 - - - -
250A ARG* 1.3 78.0 + - - +
252A GLU* 1.3 52.6 + - - +
254A LEU* 2.8 12.9 + - - +
255A ARG* 2.7 35.0 + - - +
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Residues in contact with GLU 252 (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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248A ALA 3.1 13.6 + - - +
249A ARG* 3.9 25.1 - - - +
251A SER* 1.3 79.3 - - - +
253A LEU* 1.3 61.8 + - - +
255A ARG* 2.7 45.6 + - - +
256A LYS* 3.1 41.1 + - + +
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Residues in contact with LEU 253 (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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249A ARG* 3.0 46.1 + - - +
250A ARG* 3.6 4.7 - - - +
251A SER 3.2 0.2 - - - -
252A GLU* 1.3 75.5 - - - +
254A LEU* 1.3 58.4 + - - +
256A LYS* 3.5 6.9 + - + +
257A LEU* 3.0 36.0 + - + +
385A LEU* 4.1 26.0 - - + +
388A GLU* 3.3 44.2 - - + +
389A TYR* 3.8 27.8 - - + +
392A ILE* 3.7 14.8 - - + -
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Residues in contact with LEU 254 (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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250A ARG* 2.9 14.6 + - + +
251A SER* 2.8 13.4 + - - +
253A LEU* 1.3 74.7 - - - +
255A ARG* 1.3 54.1 + - - +
257A LEU* 4.7 1.8 - - - -
258A THR* 2.7 63.2 + - + +
334A PHE 4.3 3.1 - - - +
335A ASN* 5.3 0.2 - - - -
336A PRO* 3.4 32.8 - - + -
389A TYR* 4.1 16.1 - - + +
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Residues in contact with ARG 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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251A SER 2.7 16.4 + - - +
252A GLU* 2.7 43.6 + - - +
254A LEU* 1.3 72.7 - - - +
256A LYS* 1.3 80.4 + - - +
258A THR* 2.9 18.1 + - - -
259A GLU* 3.2 21.9 + - + +
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Residues in contact with LYS 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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249A ARG* 5.4 5.2 - - - +
252A GLU* 3.1 41.7 + - + +
253A LEU* 3.8 9.2 - - + +
255A ARG* 1.3 92.0 - - - +
257A LEU* 1.3 59.0 + - - +
259A GLU* 3.1 8.6 + - - +
260A THR* 3.0 31.7 + - - +
385A LEU* 4.2 28.7 - - + -
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Residues in contact with LEU 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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253A LEU 3.0 19.6 + - - +
254A LEU 4.0 1.8 - - - +
256A LYS* 1.3 78.7 - - - +
258A THR* 1.3 58.2 + - - +
260A THR* 4.4 3.1 - - - -
261A PHE* 2.8 40.5 + - + +
334A PHE* 3.8 13.3 - - + -
336A PRO* 3.7 27.1 - - + -
382A ALA* 3.7 36.8 - - + +
385A LEU* 3.8 21.3 - - + +
386A ILE* 3.7 31.6 - - + +
389A TYR* 4.5 2.7 - - + -
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Residues in contact with THR 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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254A LEU* 2.7 53.1 + - + +
255A ARG* 2.9 16.5 + - - -
257A LEU* 1.3 70.9 - - - +
259A GLU* 1.3 62.3 + - - +
261A PHE 2.8 22.8 - - - +
262A GLY* 3.8 5.9 - - - -
333A VAL* 4.1 17.9 - - + -
334A PHE* 3.9 17.7 - - + +
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ARG* 3.2 19.9 + - + +
256A LYS* 3.1 11.4 + - - +
258A THR* 1.3 81.9 + - - +
260A THR* 1.3 65.2 + - - +
261A PHE 4.4 1.6 - - - -
262A GLY* 4.4 2.6 + - - -
378A GLU* 5.2 4.3 - - - +
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Residues in contact with THR 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LYS 3.0 16.9 + - - -
257A LEU* 3.8 6.8 - - - +
259A GLU* 1.3 81.0 + - - +
261A PHE* 1.3 88.6 + - + +
262A GLY 3.9 1.6 + - - -
378A GLU* 3.4 39.5 + - + +
379A LYS* 4.0 18.1 + - + +
382A ALA* 4.3 10.6 - - + +
385A LEU* 5.9 2.1 - - - +
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 2.8 29.2 + - + +
258A THR* 2.8 21.6 - - - +
260A THR* 1.3 79.2 - - + +
262A GLY* 1.3 63.9 + - - +
333A VAL* 6.1 0.2 - - - +
334A PHE* 3.5 38.0 + + + +
345A LYS* 3.9 40.4 - - + +
346A LEU* 4.5 14.1 - - + -
379A LYS* 3.7 37.9 - - + -
382A ALA* 3.9 29.8 - - + -
386A ILE* 3.9 22.0 - - + -
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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) + - + + + + + -
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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