Contacts of the helix formed by residues 329 - 356 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D SER* 3.4 28.4 + - - +
243D ILE* 5.3 10.5 - - - +
328D LEU* 1.3 75.0 - - - +
330D GLU* 1.3 54.3 + - - +
331D TYR* 3.2 11.8 + - - +
332D GLU* 2.8 46.1 + - - +
333D ARG* 2.7 38.2 + - - +
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Residues in contact with GLU 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329D ASN* 1.3 73.4 - - - +
331D TYR* 1.3 66.8 + - - +
333D ARG* 2.9 39.0 + - - +
334D ILE* 2.8 45.1 + - + +
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Residues in contact with TYR 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D LEU* 6.1 3.4 - - + -
229D LEU* 5.5 1.1 - - + -
240D GLN* 6.6 0.2 - - + -
243D ILE* 3.6 27.1 - - + -
244D SER* 4.0 16.5 + - - -
247D THR* 3.6 41.2 - - + +
329D ASN* 3.2 12.9 + - - +
330D GLU* 1.3 81.3 - - - +
332D GLU* 1.3 69.5 + - + +
334D ILE* 3.0 10.0 + - + +
335D GLY* 2.9 25.1 + - - -
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Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D LEU* 3.8 11.8 - - + +
227D PRO 3.8 6.9 - - - +
228D LEU* 3.0 21.4 - - + -
229D LEU* 2.8 17.1 + - + +
230D SER* 2.6 47.8 + - - -
327D PRO 4.3 0.2 - - - +
328D LEU* 3.6 15.5 - - + -
329D ASN* 2.8 38.0 + - - +
331D TYR* 1.3 81.8 - - + +
333D ARG* 1.3 59.9 + - - +
335D GLY* 3.6 0.8 - - - +
336D LEU* 2.8 32.1 + - - +
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Residues in contact with ARG 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328D LEU* 2.9 41.8 + - + +
329D ASN* 2.7 18.1 + - - +
330D GLU* 3.1 48.5 + - - +
332D GLU* 1.3 72.5 - - - +
334D ILE* 1.3 62.6 + - + +
336D LEU* 3.4 7.1 + - + +
337D GLU* 3.2 19.6 + - - +
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Residues in contact with ILE 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D GLU* 2.8 40.1 + - + +
331D TYR* 3.4 10.3 - - + +
333D ARG* 1.3 76.3 - - - +
335D GLY* 1.3 65.0 + - - +
337D GLU* 3.2 16.1 + - + +
338D LYS* 3.2 26.0 + - + +
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Residues in contact with GLY 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D VAL 4.3 2.8 - - - +
226D LEU* 3.9 18.2 - - - +
331D TYR* 2.9 16.0 + - - -
332D GLU 3.1 3.3 + - - -
334D ILE* 1.3 78.7 - - - +
336D LEU* 1.3 56.8 + - - +
338D LYS* 3.2 10.6 + - - +
339D ALA* 2.8 28.4 + - - +
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D LEU* 3.4 18.5 - - + +
308D PHE* 3.6 27.6 - - + -
325D LEU* 3.9 16.6 - - + -
328D LEU* 3.5 22.9 - - + -
332D GLU 2.8 16.4 + - - +
333D ARG* 3.5 9.4 - - + +
335D GLY* 1.3 74.9 - - - +
337D GLU* 1.3 60.3 + - - +
339D ALA* 4.2 2.7 - - + -
340D LYS* 2.8 72.4 + - + +
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Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D ARG 3.2 9.5 + - - +
334D ILE* 3.2 18.3 + - + +
336D LEU* 1.3 77.6 - - - +
338D LYS* 1.3 61.7 + - + +
340D LYS* 3.5 9.0 + - - +
341D LYS* 3.2 57.7 + - - +
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Residues in contact with LYS 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D VAL* 3.7 45.2 - - + +
334D ILE* 3.2 17.8 + - + +
335D GLY* 3.3 13.2 - - - +
337D GLU* 1.3 77.0 - - + +
339D ALA* 1.3 66.4 + - - +
341D LYS* 3.2 17.6 + - - +
342D GLU* 3.3 14.1 + - - +
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Residues in contact with ALA 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D GLY* 5.1 6.3 - - - -
223D VAL* 3.5 23.3 + - - +
224D THR* 3.6 23.9 + - - +
226D LEU* 4.8 7.4 - - + -
308D PHE* 5.4 1.3 - - + -
335D GLY 2.8 17.7 + - - +
336D LEU* 3.6 11.9 - - + +
338D LYS* 1.3 73.2 - - - +
340D LYS* 1.3 58.9 + - + +
341D LYS 3.2 0.5 + - - -
342D GLU* 3.2 1.0 + - - +
343D LEU* 2.8 34.1 + - - +
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Residues in contact with LYS 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D THR* 4.3 13.7 - - - +
304D GLU* 3.0 39.4 + - - +
305D LEU* 3.6 24.2 - - + +
308D PHE* 4.5 4.7 - - + -
336D LEU* 2.8 60.7 + - + +
337D GLU* 3.7 8.3 - - - +
339D ALA* 1.3 73.0 - - - +
341D LYS* 1.3 58.2 + - + +
343D LEU* 4.5 0.2 - - - -
344D ALA* 3.0 30.1 + - - +
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Residues in contact with LYS 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D GLU* 3.2 43.9 + - + +
338D LYS* 3.2 11.2 + - - +
340D LYS* 1.3 78.9 - - + +
342D GLU* 1.3 65.4 + - - +
344D ALA* 3.5 5.7 + - - +
345D GLY* 3.4 13.9 + - - -
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Residues in contact with GLU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ASN* 5.0 0.7 + - - -
221D ALA* 3.6 27.0 - - - +
222D GLY* 4.9 1.0 - - - -
223D VAL* 3.2 29.3 + - + +
224D THR* 4.2 6.7 - - - -
338D LYS 3.3 8.1 + - - +
339D ALA* 3.2 7.1 + - - +
341D LYS* 1.3 79.9 - - - +
343D LEU* 1.3 58.9 + - - +
345D GLY* 3.2 4.4 + - - -
346D SER* 3.0 32.0 + - - +
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ASN* 3.2 37.9 - - + +
218D GLY 4.0 6.1 - - - +
219D GLY* 4.5 0.4 - - - -
224D THR* 3.5 11.2 + - - +
297D PHE* 3.7 21.1 - - + -
305D LEU* 3.7 19.1 - - + -
307D PHE 3.4 23.1 - - - +
308D PHE* 3.7 18.8 - - + -
339D ALA 2.8 18.0 + - - +
342D GLU* 1.3 74.8 - - - +
344D ALA* 1.3 66.9 + - - +
346D SER* 2.9 3.2 + - - -
347D ILE* 2.8 36.7 + - + +
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Residues in contact with ALA 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D LEU* 3.7 14.3 - - + +
306D PRO* 6.5 0.2 - - - -
340D LYS 3.0 20.6 + - - +
341D LYS* 3.6 7.6 - - - +
343D LEU* 1.3 76.3 - - - +
345D GLY* 1.3 64.1 + - - +
347D ILE* 3.5 5.3 + - - +
348D GLU* 3.1 22.7 + - - +
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Residues in contact with GLY 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D LYS 3.4 5.9 + - - -
342D GLU* 3.2 7.0 + - - -
343D LEU 3.1 0.4 - - - -
344D ALA* 1.3 82.5 - - - +
346D SER* 1.3 56.2 + - - +
348D GLU* 3.4 7.4 + - - +
349D LYS* 3.1 27.4 + - - +
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Residues in contact with SER 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ASN* 3.7 33.3 + - - +
166D SER* 2.6 27.6 + - - -
221D ALA* 6.0 0.5 - - - +
342D GLU* 3.0 22.6 + - - +
343D LEU* 2.9 10.3 + - - -
345D GLY* 1.3 72.4 - - - +
347D ILE* 1.3 65.9 + - - +
349D LYS* 3.5 4.5 + - - +
350D GLY 3.1 10.0 + - - -
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Residues in contact with ILE 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D ASN 3.8 16.2 - - - +
169D PRO* 4.0 15.7 - - + +
297D PHE* 4.5 0.2 - - + -
305D LEU* 4.3 5.4 - - + -
306D PRO* 3.6 29.6 - - + -
307D PHE* 3.4 42.4 - - + +
343D LEU* 2.8 32.8 + - + +
344D ALA* 3.8 4.9 - - - +
346D SER* 1.3 72.4 - - - +
348D GLU* 1.3 67.7 + - - +
350D GLY* 3.2 1.7 + - - -
351D VAL* 2.9 36.0 + - + +
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Residues in contact with GLU 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D ALA 3.1 14.6 + - - +
345D GLY* 3.5 12.3 - - - +
346D SER 3.2 0.2 - - - -
347D ILE* 1.3 76.6 - - - +
349D LYS* 1.3 66.0 + - - +
351D VAL* 2.9 11.1 + - - +
352D SER* 2.5 51.2 + - - +
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Residues in contact with LYS 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ASP* 5.4 4.0 + - - -
132D ASP* 3.9 19.2 + - - -
134D PHE* 3.4 53.0 - - + +
166D SER* 4.2 4.0 - - - +
345D GLY 3.1 13.8 + - - +
346D SER* 3.7 7.4 - - - +
347D ILE 3.4 0.2 - - - -
348D GLU* 1.3 81.0 - - - +
350D GLY* 1.3 62.0 + - - +
352D SER* 3.7 6.7 + - - -
353D PHE* 3.3 16.1 + - - +
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Residues in contact with GLY 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 4.4 2.2 - - - -
166D SER* 3.8 26.0 - - - -
169D PRO* 4.7 0.2 - - - -
170D ILE* 3.3 28.2 - - - +
346D SER 3.1 10.4 + - - -
347D ILE 3.6 3.4 - - - -
348D GLU 3.0 1.0 - - - -
349D LYS* 1.3 77.3 - - - +
351D VAL* 1.3 64.4 + - - +
353D PHE* 3.3 12.0 + - - +
354D ILE* 3.9 2.1 + - - +
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Residues in contact with VAL 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D PRO* 4.2 11.2 - - + +
173D GLU* 3.9 25.5 - - + +
306D PRO* 6.2 0.4 - - + -
307D PHE* 5.5 4.3 - - + -
347D ILE* 2.9 38.5 + - + +
348D GLU* 3.6 9.9 - - - +
350D GLY* 1.3 70.8 - - - +
352D SER* 1.3 60.5 + - - +
354D ILE* 3.1 7.1 + - - +
355D ARG* 2.9 48.9 + - + +
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Residues in contact with SER 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348D GLU* 2.5 40.9 + - - +
349D LYS* 3.8 7.9 - - - -
351D VAL* 1.3 73.0 - - - +
353D PHE* 1.3 59.2 + - - +
354D ILE 2.9 4.9 - - - -
355D ARG* 4.3 5.8 - - - +
356D SER* 2.7 46.8 + - - -
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Residues in contact with PHE 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 4.1 21.3 - + + -
135D LYS* 4.4 11.0 - - - -
138D ALA* 3.6 42.2 - - + -
139D GLY* 3.9 11.2 - - - -
142D LYS* 4.0 22.3 - - + -
170D ILE* 4.3 6.3 - - + -
349D LYS 3.3 10.0 + - - +
350D GLY 3.3 13.3 + - - +
352D SER* 1.3 77.4 - - - +
354D ILE* 1.3 69.9 + - + +
356D SER* 4.1 7.7 - - - +
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Residues in contact with ILE 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LYS* 4.0 21.8 - - + -
170D ILE* 3.8 31.6 - - + +
173D GLU* 3.6 33.9 - - + +
174D VAL* 3.6 22.7 - - + +
177D LYS* 4.8 19.9 + - + +
350D GLY 4.5 1.3 - - - +
351D VAL 3.1 3.2 + - - +
352D SER 2.8 0.8 + - - -
353D PHE* 1.3 97.9 - - + +
355D ARG* 1.3 67.6 + - - +
356D SER 3.0 10.8 - - - +
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Residues in contact with ARG 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D GLU* 2.7 35.2 + - - +
176D LYS* 4.0 16.3 - - - +
351D VAL* 2.9 38.1 + - + +
352D SER* 4.2 3.8 - - - +
354D ILE* 1.3 77.7 - - - +
356D SER* 1.3 60.7 + - - +
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Residues in contact with SER 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352D SER* 2.7 33.5 + - - -
353D PHE* 4.1 7.4 - - - +
354D ILE 3.0 15.2 - - - +
355D ARG* 1.3 74.5 - - - +
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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