Contacts of the helix formed by residues 329 - 355 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LEU* 6.0 0.8 - - - +
230A SER* 3.5 18.6 + - - +
243A ILE* 5.4 10.3 - - - +
328A LEU* 1.3 73.8 - - - +
330A GLU* 1.3 66.3 + - - +
331A TYR* 3.2 11.3 + - - +
332A GLU* 2.8 61.4 + - - +
333A ARG* 2.8 24.2 + - - +
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Residues in contact with GLU 330 (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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329A ASN* 1.3 73.4 - - - +
331A TYR* 1.3 65.6 + - - +
333A ARG* 3.0 38.7 + - - +
334A ILE* 2.9 42.4 + - + +
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Residues in contact with TYR 331 (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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226A LEU* 5.8 3.4 - - + -
240A GLN* 6.3 2.7 - - + -
243A ILE* 3.6 29.8 - - + -
244A SER* 3.7 25.3 + - - -
247A THR* 3.4 43.5 - - + +
248A ASP* 4.1 7.4 + - - -
329A ASN* 3.2 10.6 + - - +
330A GLU* 1.3 79.7 - - - +
332A GLU* 1.3 66.1 + - + +
334A ILE* 3.6 8.3 + - - +
335A GLY* 3.1 24.3 + - - -
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Residues in contact with GLU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.7 11.0 - - + +
227A PRO 4.9 4.9 - - - +
228A LEU* 3.3 21.5 - - + -
229A LEU* 3.2 12.7 + - + +
230A SER* 2.6 46.6 + - - -
243A ILE* 6.4 0.4 - - + -
328A LEU* 3.3 16.1 - - + +
329A ASN* 2.8 54.6 + - - +
331A TYR* 1.3 79.0 - - + +
333A ARG* 1.3 54.5 + - - +
335A GLY* 3.2 1.3 + - - +
336A LEU* 2.6 36.7 + - - +
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Residues in contact with ARG 333 (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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328A LEU* 4.1 11.6 + - + +
329A ASN 2.8 18.5 + - - +
330A GLU* 3.2 44.2 - - - +
332A GLU* 1.3 73.2 - - - +
334A ILE* 1.3 63.5 + - - +
336A LEU* 3.1 17.8 + - - +
337A GLU* 3.1 10.7 + - - +
203C GLU 5.2 1.6 + - - -
204C VAL* 3.9 29.1 + - - +
241C GLU* 3.1 42.0 + - - +
242C GLU* 3.7 19.8 + - - +
245C TYR* 3.1 54.5 - - + +
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Residues in contact with ILE 334 (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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330A GLU* 2.9 36.8 + - + +
331A TYR* 3.9 7.4 - - - +
333A ARG* 1.3 75.4 - - - +
335A GLY* 1.3 61.6 + - - +
337A GLU* 3.6 2.9 + - - +
338A LYS* 3.4 20.5 + - + +
241C GLU* 3.5 29.8 - - + +
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Residues in contact with GLY 335 (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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223A VAL 4.3 4.0 - - - +
226A LEU* 4.0 16.4 - - - +
251A GLN* 6.1 2.0 - - - -
331A TYR* 3.1 16.5 + - - -
332A GLU 3.2 3.1 + - - -
333A ARG 3.1 0.2 - - - -
334A ILE* 1.3 76.5 - - - +
336A LEU* 1.3 65.0 + - - +
338A LYS* 3.3 7.3 + - - +
339A ALA* 2.9 23.4 + - - +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A VAL* 4.9 0.2 - - + -
226A LEU* 3.6 20.6 - - + +
308A PHE* 3.6 31.2 - - + -
325A LEU* 4.2 15.5 - - + -
328A LEU* 3.7 21.5 - - + -
332A GLU 2.6 20.4 + - - +
333A ARG* 3.1 7.6 + - - +
335A GLY* 1.3 73.5 - - - +
337A GLU* 1.3 57.5 + - - +
339A ALA* 3.0 7.4 + - + +
340A LYS* 2.8 55.4 + - - +
245C TYR* 4.9 15.3 - - + +
248C ASP* 4.4 3.1 - - + +
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Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG 3.1 11.6 + - - +
334A ILE 3.9 4.3 - - - +
336A LEU* 1.3 79.4 - - - +
338A LYS* 1.3 62.8 + - - +
340A LYS* 3.4 10.7 + - - +
341A LYS* 3.0 36.3 + - + +
240C GLN* 3.4 39.7 + - + +
241C GLU* 3.8 26.5 - - + +
244C SER* 3.2 30.9 + - - -
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Residues in contact with LYS 338 (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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223A VAL* 4.0 38.9 - - + +
334A ILE* 3.4 11.0 + - + +
335A GLY* 3.3 10.7 + - - +
336A LEU 3.3 0.4 - - - -
337A GLU* 1.3 76.0 - - - +
339A ALA* 1.3 67.4 + - - +
341A LYS* 3.4 11.2 + - + +
342A GLU* 3.3 19.2 + - - +
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Residues in contact with ALA 339 (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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218A GLY* 5.2 5.8 - - - -
223A VAL 3.4 20.4 + - - +
224A THR* 3.4 24.8 + - - +
226A LEU* 4.9 7.0 - - + -
308A PHE* 5.6 1.1 - - + -
335A GLY 2.9 14.5 + - - +
336A LEU* 3.1 17.0 - - + +
338A LYS* 1.3 79.8 - - - +
340A LYS* 1.3 58.7 + - + +
342A GLU* 3.1 1.0 + - - +
343A LEU* 2.8 29.9 + - - +
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Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A THR* 3.8 21.7 - - - -
304A GLU* 5.3 8.7 - - + +
305A LEU* 3.9 25.7 - - + +
308A PHE* 4.2 9.4 - - + -
336A LEU* 2.8 40.3 + - + +
337A GLU* 3.6 17.7 - - - +
339A ALA* 1.3 73.9 - - - +
341A LYS* 1.3 58.3 + - - +
343A LEU* 3.7 0.8 - - - +
344A ALA* 2.8 34.4 + - - +
244C SER* 2.8 31.2 + - - +
248C ASP* 2.6 31.8 + - - -
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Residues in contact with LYS 341 (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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337A GLU* 3.0 30.3 + - + +
338A LYS* 3.7 10.5 - - - +
339A ALA 3.2 0.4 - - - -
340A LYS* 1.3 77.6 - - - +
342A GLU* 1.3 62.9 + - - +
344A ALA* 3.7 9.1 + - - +
345A GLY* 3.7 7.1 + - - -
240C GLN* 2.8 40.7 + - - +
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Residues in contact with GLU 342 (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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165A ASN* 5.3 1.0 + - - -
221A ALA* 3.9 23.3 - - - +
222A GLY* 5.3 0.9 - - - -
223A VAL* 3.6 25.1 + - + +
224A THR* 4.4 6.8 - - - +
338A LYS 3.3 8.3 + - - +
339A ALA 3.1 6.7 + - - +
341A LYS* 1.3 77.1 - - - +
343A LEU* 1.3 65.3 + - - +
345A GLY* 3.2 4.2 + - - -
346A SER* 3.1 29.6 + - - +
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Residues in contact with LEU 343 (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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165A ASN* 3.7 37.2 - - + +
218A GLY* 3.7 17.3 - - - +
219A GLY* 4.4 0.7 - - - +
224A THR* 3.7 8.2 + - - +
297A PHE* 3.8 13.7 - - + -
305A LEU* 3.7 7.6 - - + -
307A PHE 3.6 11.2 - - - +
308A PHE* 3.6 35.0 - - + -
339A ALA 2.8 18.4 + - - +
340A LYS* 3.7 3.6 - - - +
342A GLU* 1.3 75.9 - - - +
344A ALA* 1.3 66.5 + - - +
346A SER* 3.2 2.4 + - - +
347A ILE* 3.0 40.0 + - + +
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Residues in contact with ALA 344 (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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305A LEU* 3.9 24.1 - - + +
340A LYS 2.8 21.5 + - - +
341A LYS* 3.8 7.4 - - - +
343A LEU* 1.3 72.9 - - - +
345A GLY* 1.3 62.8 + - - +
347A ILE* 3.5 4.6 + - - +
348A GLU* 3.1 22.3 + - - +
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Residues in contact with GLY 345 (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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341A LYS 3.7 5.3 + - - -
342A GLU 3.2 7.2 + - - -
343A LEU 3.2 0.4 - - - -
344A ALA* 1.3 78.1 - - - +
346A SER* 1.3 58.6 + - - +
348A GLU* 3.4 7.0 + - - +
349A LYS* 2.9 28.5 + - - +
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Residues in contact with SER 346 (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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163A PRO* 6.5 0.2 - - - -
165A ASN* 3.7 30.2 + - - +
166A SER* 2.6 28.2 + - - -
342A GLU* 3.1 25.6 + - - +
343A LEU* 3.2 6.3 + - - -
345A GLY* 1.3 76.7 - - - +
347A ILE* 1.3 61.8 + - - +
349A LYS* 3.3 7.0 + - - +
350A GLY 3.2 9.9 + - - -
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Residues in contact with ILE 347 (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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165A ASN 3.8 16.4 - - - +
169A PRO* 3.9 14.3 - - + +
297A PHE* 4.4 2.5 - - + -
305A LEU* 4.3 10.1 - - + -
306A PRO* 3.9 24.5 - - + -
307A PHE* 3.5 37.7 - - + +
343A LEU* 3.0 37.0 + - + +
344A ALA* 3.7 4.0 - - - +
346A SER* 1.3 74.5 - - - +
348A GLU* 1.3 67.5 + - - +
350A GLY* 2.9 4.3 + - - -
351A VAL* 2.9 39.9 + - + +
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Residues in contact with GLU 348 (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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344A ALA 3.1 14.2 + - - +
345A GLY* 3.6 7.2 - - - +
347A ILE* 1.3 79.2 - - - +
349A LYS* 1.3 57.9 + - - +
351A VAL* 4.3 13.7 - - - +
352A SER* 2.7 50.1 + - - -
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Residues in contact with LYS 349 (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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131A ASP* 3.2 24.1 + - - -
134A PHE* 3.7 44.9 - - + +
163A PRO* 6.1 0.4 - - + -
166A SER* 4.2 4.9 - - - +
345A GLY 2.9 15.0 + - - +
346A SER* 3.4 13.0 - - - +
347A ILE 3.1 0.2 - - - -
348A GLU* 1.3 78.0 - - - +
350A GLY* 1.3 55.8 + - - +
352A SER* 3.7 4.8 - - - -
353A PHE* 3.2 24.4 + - - +
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Residues in contact with GLY 350 (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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134A PHE* 4.8 0.7 - - - -
166A SER* 3.5 28.2 - - - -
170A ILE* 3.3 30.5 - - - +
346A SER 3.2 4.0 + - - -
347A ILE 2.9 6.8 + - - -
349A LYS* 1.3 76.9 - - - +
351A VAL* 1.3 65.5 + - - +
352A SER 3.1 1.3 - - - -
353A PHE* 3.2 11.4 + - - +
354A ILE* 3.7 4.2 + - - +
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 3.9 15.6 - - + +
173A GLU* 4.0 22.4 - - + +
306A PRO* 6.1 0.4 - - + -
307A PHE* 5.2 5.2 - - + -
347A ILE* 2.9 32.0 + - + +
348A GLU* 3.8 15.5 - - - +
350A GLY* 1.3 76.1 - - - +
352A SER* 1.3 63.7 + - - +
354A ILE* 3.4 1.9 + - - +
355A ARG* 3.0 56.1 + - - +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLU* 2.7 34.1 + - - -
349A LYS* 3.7 6.5 - - - -
351A VAL* 1.3 79.7 - - - +
353A PHE* 1.3 63.2 + - - +
354A ILE 3.0 1.2 + - - -
355A ARG* 3.2 11.2 + - - +
356A SER* 3.1 28.2 + - - -
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Residues in contact with PHE 353 (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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134A PHE* 4.4 12.1 - + + -
135A LYS* 4.2 16.6 - - + -
138A ALA* 3.4 44.4 - - + -
139A GLY* 3.6 16.2 - - - -
142A LYS* 4.4 8.5 - - + -
170A ILE* 4.3 8.3 - - + -
349A LYS 3.2 12.8 + - - +
350A GLY* 3.2 12.9 + - - +
352A SER* 1.3 77.4 - - - +
354A ILE* 1.3 79.8 + - + +
356A SER* 4.8 4.9 - - - -
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LYS* 3.8 33.8 + - + +
170A ILE* 3.8 23.8 - - + +
173A GLU* 3.9 26.2 - - + +
174A VAL* 3.4 35.7 - - + +
177A LYS* 5.0 19.1 + - + +
350A GLY 3.7 0.8 + - - +
351A VAL 3.4 3.2 + - - +
352A SER 3.1 0.4 - - - -
353A PHE* 1.3 90.2 - - + +
355A ARG* 1.3 55.8 + - + +
356A SER 2.8 25.5 + - - +
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Residues in contact with ARG 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLU* 3.0 34.8 + - + +
176A LYS* 5.2 5.6 - - - +
351A VAL* 3.0 36.8 + - + +
352A SER* 3.2 4.8 + - - +
354A ILE* 1.3 73.7 - - + +
356A SER* 1.3 68.3 + - - +
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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