Contacts of the helix formed by residues 329 - 356 (chain B) in PDB entry 1SMK
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 ASN 329 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LEU* 6.2 0.4 - - - +
230B SER* 3.6 26.2 + - - +
243B ILE* 6.0 4.0 - - - +
328B LEU* 1.3 76.1 - - - +
330B GLU* 1.3 64.3 + - - +
331B TYR* 3.3 13.5 + - - +
332B GLU* 2.7 48.7 + - - +
333B ARG* 2.9 24.6 + - - +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B ASN* 1.3 75.8 - - - +
331B TYR* 1.3 63.5 + - - +
333B ARG* 3.1 28.1 + - - +
334B ILE* 2.9 43.1 + - + +
241H GLU* 5.4 4.4 - - - +
242H GLU* 5.4 2.4 - - - +
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 6.2 2.7 - - + -
227B PRO 6.1 0.2 - - - -
229B LEU* 5.4 1.3 - - + -
243B ILE* 3.4 34.4 + - + -
244B SER* 4.2 9.1 + - - -
247B THR* 3.5 37.8 - - + +
329B ASN* 3.3 13.3 + - - +
330B GLU* 1.3 79.4 - - - +
332B GLU* 1.3 69.7 + - + +
334B ILE* 3.3 14.0 + - + +
335B GLY* 2.9 23.1 + - - -
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Residues in contact with GLU 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.7 11.0 - - + +
227B PRO 4.5 5.8 - - - +
228B LEU* 3.2 26.3 - - + +
229B LEU* 3.0 14.0 + - - +
230B SER* 2.5 48.1 + - - -
327B PRO 4.3 0.5 - - - +
328B LEU* 3.5 14.9 - - + +
329B ASN* 2.7 37.9 + - - +
331B TYR* 1.3 80.2 - - + +
333B ARG* 1.3 55.2 + - - +
335B GLY* 3.1 3.6 + - - +
336B LEU* 2.6 35.4 + - - +
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.2 37.6 + - + -
329B ASN* 2.9 9.7 + - - +
330B GLU* 3.1 34.3 + - - +
332B GLU* 1.3 73.9 - - - +
334B ILE* 1.3 65.8 + - - +
336B LEU* 3.2 12.0 + - + +
337B GLU* 3.1 27.0 + - - +
204H VAL* 4.3 21.5 - - - +
241H GLU* 3.5 27.4 + - + +
242H GLU* 3.5 33.1 + - - +
245H TYR* 3.7 41.3 - - + +
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B GLU* 2.9 36.8 + - + +
331B TYR* 3.5 14.6 - - + +
333B ARG* 1.3 76.3 - - - +
335B GLY* 1.3 66.0 + - - +
337B GLU* 3.1 16.3 + - - +
338B LYS* 3.3 23.5 + - + +
241H GLU* 4.0 11.9 - - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL 4.5 2.6 - - - +
226B LEU* 4.0 19.3 - - - +
331B TYR 2.9 15.3 + - - -
332B GLU 3.1 4.0 + - - -
334B ILE* 1.3 80.1 - - - +
336B LEU* 1.3 61.6 + - - +
338B LYS* 3.4 9.7 + - - +
339B ALA* 3.0 24.4 + - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.7 14.1 - - + +
308B PHE* 3.7 26.0 - - + -
325B LEU* 3.9 16.2 - - + -
328B LEU* 3.8 25.1 - - + -
332B GLU 2.6 17.8 + - - +
333B ARG* 3.3 15.9 - - + +
334B ILE 3.1 0.2 - - - -
335B GLY* 1.3 73.1 - - - +
337B GLU* 1.3 61.7 + - - +
339B ALA* 3.3 2.9 + - + +
340B LYS* 2.9 60.8 + - + +
245H TYR* 6.0 1.6 - - + -
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLU* 5.5 0.7 - - - +
333B ARG 3.1 13.6 + - - +
334B ILE* 3.1 9.2 + - + +
336B LEU* 1.3 77.9 - - - +
338B LYS* 1.3 65.6 + - + +
340B LYS* 3.5 29.7 + - - +
341B LYS* 2.9 26.6 + - - +
241H GLU* 4.1 26.8 - - + +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 3.8 40.8 - - + +
334B ILE* 3.3 20.5 + - + +
335B GLY* 3.4 9.8 + - - +
337B GLU* 1.3 78.8 - - + +
339B ALA* 1.3 67.9 + - - +
341B LYS* 3.1 26.6 - - + +
342B GLU* 3.1 10.0 + - - +
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Residues in contact with ALA 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLY* 4.9 6.5 - - - -
223B VAL 3.6 19.0 + - - +
224B THR* 3.7 22.3 + - - +
226B LEU* 4.9 7.4 - - + -
308B PHE* 5.3 0.9 - - + -
335B GLY 3.0 14.4 + - - +
336B LEU* 3.3 17.0 - - + +
338B LYS* 1.3 78.8 - - - +
340B LYS* 1.3 58.9 + - + +
342B GLU* 3.3 1.4 + - - +
343B LEU* 2.8 33.3 + - - +
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B THR* 4.1 13.8 - - - +
304B GLU* 3.3 36.1 + - - +
305B LEU* 3.8 19.2 - - + +
308B PHE* 4.4 7.2 - - + -
336B LEU* 2.9 54.1 + - + +
337B GLU* 3.8 25.9 + - - +
339B ALA* 1.3 74.3 - - - +
341B LYS* 1.3 57.8 + - - +
343B LEU* 4.1 6.5 - - - -
344B ALA* 2.9 33.3 + - - +
244H SER* 5.4 5.7 + - - -
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Residues in contact with LYS 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 2.9 15.9 + - + +
338B LYS* 3.1 20.1 + - + +
340B LYS* 1.3 79.7 - - - +
342B GLU* 1.3 62.3 + - - +
344B ALA* 3.7 12.5 + - - +
345B GLY 4.0 2.9 + - - -
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Residues in contact with GLU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASN* 5.3 1.0 + - - -
221B ALA* 4.2 21.8 - - - +
222B GLY* 5.2 1.0 + - - -
223B VAL* 3.2 28.5 + - + +
224B THR* 4.9 5.8 - - - -
338B LYS 3.1 9.5 + - - +
339B ALA 4.2 1.3 - - - +
341B LYS* 1.3 79.0 - - - +
343B LEU* 1.3 64.1 + - - +
344B ALA 3.3 0.2 - - - -
345B GLY* 3.5 3.3 + - - -
346B SER* 3.3 26.2 + - - +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASN* 3.8 31.2 - - + +
218B GLY 3.6 24.0 - - - +
224B THR* 3.5 17.0 + - - +
297B PHE* 4.0 11.2 - - + -
305B LEU* 3.5 15.7 - - + -
307B PHE 4.1 1.1 - - - +
308B PHE* 3.7 25.8 - - + -
339B ALA 2.8 18.3 + - - +
340B LYS 3.3 0.4 + - - +
342B GLU* 1.3 76.7 - - - +
344B ALA* 1.3 64.9 + - - +
346B SER* 3.2 4.0 + - - -
347B ILE* 3.0 38.5 + - + +
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B LEU* 3.7 15.4 - - + +
340B LYS 2.9 17.8 + - - +
341B LYS* 3.8 7.2 - - - +
342B GLU 3.3 0.2 - - - -
343B LEU* 1.3 76.0 - - - +
345B GLY* 1.3 63.1 + - - +
347B ILE* 3.4 6.7 + - - +
348B GLU* 3.2 21.0 + - - +
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LYS 4.0 4.0 + - - -
342B GLU 3.5 6.3 + - - -
343B LEU 3.2 0.4 - - - -
344B ALA* 1.3 76.2 - - - +
346B SER* 1.3 54.8 + - - +
348B GLU* 2.9 9.2 + - - +
349B LYS* 2.7 36.0 + - - +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASN* 3.7 35.6 + - - +
166B SER* 3.0 23.8 + - - -
342B GLU* 3.3 22.0 + - - +
343B LEU 3.2 9.0 + - - -
345B GLY* 1.3 72.4 - - - +
347B ILE* 1.3 64.3 + - - +
349B LYS* 3.0 17.9 + - - +
350B GLY 3.1 3.8 + - - -
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Residues in contact with ILE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ASN 3.8 12.6 - - - +
169B PRO* 3.8 15.5 - - + +
297B PHE* 4.6 0.4 - - + -
305B LEU* 3.9 13.7 - - + -
306B PRO* 3.6 38.1 - - + -
307B PHE* 3.6 33.7 - - + +
343B LEU* 3.0 32.0 + - + +
344B ALA* 3.6 8.1 - - - +
346B SER* 1.3 74.7 - - - +
348B GLU* 1.3 57.5 + - - +
350B GLY* 3.2 2.6 + - - -
351B VAL* 2.9 44.4 + - + +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ALA 3.2 10.3 + - - +
345B GLY* 2.9 11.0 + - - +
347B ILE* 1.3 76.1 - - - +
349B LYS* 1.3 60.5 + - - +
350B GLY 3.0 1.6 - - - -
351B VAL* 4.3 12.4 - - - +
352B SER* 2.7 56.4 + - - +
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Residues in contact with LYS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 3.9 22.2 - - - +
132B ASP* 5.3 4.4 - - - +
134B PHE* 3.4 48.0 - - + +
166B SER* 4.3 4.9 - - - +
345B GLY 2.7 16.7 + - - +
346B SER* 3.3 14.1 - - - +
348B GLU* 1.3 73.1 - - - +
350B GLY* 1.3 58.9 + - - +
352B SER* 3.2 16.7 + - - -
353B PHE* 3.6 5.0 + - - +
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Residues in contact with GLY 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 4.3 0.9 - - - -
166B SER* 3.9 17.7 - - - -
170B ILE* 3.3 33.7 - - - +
346B SER 3.1 9.3 + - - -
347B ILE 3.7 2.9 - - - -
348B GLU 3.0 0.6 - - - -
349B LYS* 1.3 76.5 - - - +
351B VAL* 1.3 64.6 + - - +
352B SER 3.2 0.2 - - - -
353B PHE* 3.0 18.2 + - - +
354B ILE* 3.7 2.4 + - - +
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Residues in contact with VAL 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B PRO* 3.9 16.8 - - + +
173B GLU* 3.7 28.9 - - + +
306B PRO* 5.9 0.9 - - + -
307B PHE* 5.3 3.4 - - + -
347B ILE* 2.9 33.0 + - + +
348B GLU* 3.8 15.7 - - - +
350B GLY* 1.3 75.6 - - - +
352B SER* 1.3 57.6 + - - +
353B PHE 3.1 0.2 - - - -
354B ILE* 3.2 4.3 + - - +
355B ARG* 2.9 45.4 + - + +
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Residues in contact with SER 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLU* 2.7 39.7 + - - +
349B LYS* 3.2 14.2 + - - -
351B VAL* 1.3 71.7 - - - +
353B PHE* 1.3 63.9 + - - +
354B ILE 3.1 0.4 - - - -
355B ARG* 4.4 3.1 - - - -
356B SER* 3.1 40.6 + - - +
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Residues in contact with PHE 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 3.7 23.1 - + + -
135B LYS* 4.3 12.3 - - + -
138B ALA* 3.5 35.0 - - + -
139B GLY* 3.8 15.0 - - - -
142B LYS* 4.5 11.0 + - + +
170B ILE* 3.9 11.2 - - + -
349B LYS 3.8 9.6 - - - +
350B GLY 3.0 16.4 + - - +
352B SER* 1.3 81.1 + - - +
354B ILE* 1.3 77.0 + - + +
356B SER 4.4 4.7 - - - +
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Residues in contact with ILE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LYS* 3.8 25.4 + - + +
170B ILE* 3.7 31.6 - - + +
173B GLU* 3.5 36.6 - - + +
174B VAL* 3.6 21.8 - - + +
177B LYS* 5.5 10.5 - - + -
350B GLY 3.7 1.5 + - - +
351B VAL 3.2 2.3 + - - +
353B PHE* 1.3 99.3 - - + +
355B ARG* 1.3 67.8 + - - +
356B SER 3.3 7.0 - - - +
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Residues in contact with ARG 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLU* 3.1 28.5 + - - +
176B LYS* 4.6 14.1 - - - +
351B VAL* 2.9 35.6 + - + +
352B SER* 4.4 2.7 - - - -
354B ILE* 1.3 81.3 - - - +
356B SER* 1.3 62.6 + - - +
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Residues in contact with SER 356 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B SER* 3.1 33.5 + - - +
353B PHE 4.4 4.0 - - - +
354B ILE 3.3 10.7 - - - +
355B ARG* 1.3 83.4 - - - +
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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
------------------------------------------------------------
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