Contacts of the helix formed by residues 325 - 351 (chain F) in PDB entry 3IYD
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 PRO 325 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323F ASN 4.4 1.8 - - - +
324F LYS* 1.3 94.5 - - + +
326F TRP* 1.3 63.8 + - + +
328F GLU* 4.7 5.9 + - + +
329F LYS* 4.2 12.0 - - - +
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Residues in contact with TRP 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F CYS* 3.9 6.1 - - + +
296F LYS* 3.5 21.8 - - + +
297F MET* 3.5 37.7 - - + -
298F PRO* 4.2 11.7 - - + +
301F ASN* 3.3 43.7 - - + +
305F LEU* 5.3 0.2 - - + -
319F ALA* 4.3 18.2 - - + -
322F MET* 4.0 19.7 - - + -
324F LYS* 3.4 31.4 - - + +
325F PRO* 1.3 83.8 - - + +
327F SER* 1.3 74.8 + - - +
328F GLU 3.2 2.5 - - - -
329F LYS* 3.3 20.5 + - + +
330F LEU* 3.2 18.7 - - + +
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Residues in contact with SER 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F ALA 3.2 27.6 - - - -
320F ILE* 3.4 36.5 + - - +
323F ASN* 3.8 2.3 - - - -
324F LYS* 2.6 38.4 + - - -
326F TRP* 1.3 84.8 - - - +
328F GLU* 1.3 64.0 + - - +
329F LYS 3.1 8.8 + - - -
330F LEU* 3.7 9.0 + - - +
331F HIS* 3.7 3.5 + - - -
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Residues in contact with GLU 328 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320F ILE* 4.5 11.1 - - - +
323F ASN* 5.6 2.6 - - - -
324F LYS 3.8 6.4 + - - +
325F PRO 5.1 4.5 - - - +
326F TRP 3.2 1.0 - - - -
327F SER* 1.3 88.7 + - - +
329F LYS* 1.3 63.1 + - - +
330F LEU 3.8 0.2 - - - -
331F HIS* 3.2 32.8 + - - +
332F ASP* 5.6 1.7 - - - +
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Residues in contact with LYS 329 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLN 4.3 5.5 + - - -
295F CYS* 3.2 53.5 - - + +
296F LYS* 5.1 4.0 - - + -
325F PRO 4.2 7.4 - - - +
326F TRP* 3.4 26.0 - - + +
327F SER 3.1 1.0 - - - -
328F GLU* 1.3 82.5 - - - +
330F LEU* 1.3 62.5 + - - +
331F HIS 3.0 6.3 + - - -
332F ASP* 3.3 24.0 + - - +
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Residues in contact with LEU 330 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F CYS* 4.4 8.5 - - + -
295F CYS* 3.9 18.8 - - + -
297F MET* 3.9 27.1 - - + -
315F TRP* 5.8 3.6 - - + -
316F PHE* 3.5 32.6 - - + -
319F ALA* 3.9 26.0 - - + -
320F ILE* 4.0 12.8 - - + -
326F TRP* 3.2 22.9 - - + +
327F SER* 3.7 11.5 + - - +
329F LYS* 1.3 76.1 - - - +
331F HIS* 1.3 58.5 + - - +
332F ASP 3.1 1.6 - - - -
333F VAL* 3.3 6.6 + - + +
334F SER* 2.9 30.5 + - - -
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Residues in contact with HIS 331 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F PHE* 6.4 0.6 - + - -
320F ILE* 3.5 37.1 - - + +
327F SER 3.7 12.3 + - - -
328F GLU* 3.2 36.0 + - - +
329F LYS 3.0 1.3 - - - -
330F LEU* 1.3 79.2 - - - +
332F ASP* 1.3 64.3 - - - +
333F VAL 3.2 2.7 + - - -
334F SER* 3.5 19.5 + - - -
335F GLU* 5.4 1.9 + - - +
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Residues in contact with ASP 332 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLN* 4.3 14.5 + - - +
328F GLU 5.6 1.2 - - - +
329F LYS* 3.3 16.7 + - - +
330F LEU 3.1 1.0 - - - -
331F HIS* 1.3 86.8 - - - +
333F VAL* 1.3 60.5 + - - +
335F GLU* 5.6 0.4 - - - -
336F GLU* 5.2 3.5 - - - +
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Residues in contact with VAL 333 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290F LEU* 3.7 41.5 - - + +
291F CYS* 5.5 1.3 - - + -
294F GLN* 3.8 12.1 - - - +
295F CYS* 4.2 3.6 - - - -
316F PHE* 5.0 0.7 - - + -
330F LEU* 3.4 26.9 - - + +
331F HIS 3.2 0.2 - - - -
332F ASP* 1.3 78.5 - - - +
334F SER* 1.3 67.4 + - - +
335F GLU* 3.1 4.7 - - - +
336F GLU* 3.0 34.0 + - + +
337F VAL* 2.9 33.3 + - + +
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Residues in contact with SER 334 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F PHE* 3.6 27.8 - - - -
330F LEU 2.9 16.4 + - - -
331F HIS* 3.5 18.5 + - - -
333F VAL* 1.3 79.2 - - - +
335F GLU* 1.3 64.5 + - - +
337F VAL* 3.9 2.5 - - - +
338F HIS* 3.0 29.6 + - - +
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Residues in contact with GLU 335 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331F HIS 5.7 1.6 - - - +
332F ASP 6.5 0.2 - - - -
333F VAL* 3.1 1.7 - - - -
334F SER* 1.3 84.4 - - - +
336F GLU* 1.3 64.5 + - + +
338F HIS* 3.6 5.8 + - - +
339F ARG* 3.3 28.2 + - - +
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Residues in contact with GLU 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 5.1 0.7 - - - -
290F LEU* 3.3 33.7 - - + +
294F GLN* 4.9 1.6 + - - +
332F ASP 5.2 2.5 - - - +
333F VAL* 3.0 25.8 + - + +
335F GLU* 1.3 78.3 - - + +
337F VAL* 1.3 60.2 + - - +
339F ARG* 3.6 5.3 + - - +
340F ALA* 3.1 28.5 + - - +
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Residues in contact with VAL 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 3.9 33.8 - - + +
290F LEU* 5.2 1.8 - - + -
291F CYS* 6.3 1.3 - - + -
313F ASP* 6.1 0.9 - - - +
315F TRP* 4.3 18.4 - - + -
316F PHE* 3.9 33.7 - - + -
333F VAL* 2.9 38.9 + - + +
334F SER 3.9 3.6 - - - +
336F GLU* 1.3 76.1 - - - +
338F HIS* 1.3 61.5 + - - +
340F ALA* 3.2 2.6 + - - +
341F LEU* 2.9 30.7 + - + +
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Residues in contact with HIS 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F ASP* 3.9 21.7 + - - +
334F SER 3.0 19.3 + - - +
335F GLU* 3.8 6.7 - - - +
336F GLU 3.3 0.2 - - - -
337F VAL* 1.3 77.4 - - - +
339F ARG* 1.3 69.0 + - + +
341F LEU* 3.1 6.6 + - + +
342F GLN* 3.0 47.7 + - + +
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Residues in contact with ARG 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F GLN* 4.0 0.5 + - - -
335F GLU 3.3 16.2 + - - +
336F GLU* 4.0 5.6 - - - +
337F VAL 3.3 0.2 - - - -
338F HIS* 1.3 86.7 - - + +
340F ALA* 1.3 59.7 + - - +
341F LEU 3.1 1.3 + - - -
342F GLN* 4.4 15.6 + - - +
343F LYS* 3.5 36.5 + - - +
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Residues in contact with ALA 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F GLN* 3.3 39.5 + - - +
286F LEU* 5.6 7.9 - - + -
287F ILE* 3.6 28.6 - - + +
290F LEU* 6.5 0.4 - - + -
336F GLU 3.1 20.2 + - - +
337F VAL 3.5 1.3 - - - +
338F HIS 3.2 0.4 - - - -
339F ARG* 1.3 75.4 - - - +
341F LEU* 1.3 57.2 + - - +
344F LEU* 3.3 13.0 - - - +
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Residues in contact with LEU 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287F ILE* 5.4 6.1 - - + -
306F PHE* 5.9 2.0 - - + -
310F GLU 5.0 3.6 - - - +
311F THR 3.3 17.7 - - - +
312F SER* 4.6 1.1 - - - -
313F ASP* 3.3 27.8 - - - +
315F TRP* 4.5 19.7 - - + +
337F VAL* 2.9 20.7 + - + +
338F HIS* 3.5 6.7 - - + +
339F ARG 3.1 0.4 - - - -
340F ALA* 1.3 81.1 - - - +
342F GLN* 1.3 67.2 + - - +
343F LYS 3.4 0.9 - - - -
344F LEU* 3.2 16.7 + - + +
345F GLN* 3.1 46.5 + - - +
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Residues in contact with GLN 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338F HIS* 3.0 34.8 + - + +
339F ARG* 4.4 13.1 + - - +
341F LEU* 1.3 81.4 - - - +
343F LYS* 1.3 62.7 + - - +
345F GLN* 3.2 24.5 + - - +
346F GLN* 3.6 5.7 + - - +
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Residues in contact with LYS 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283F GLN* 3.8 19.5 - - - +
339F ARG* 3.5 24.5 + - - +
341F LEU 3.4 0.2 - - - -
342F GLN* 1.3 79.9 - - - +
344F LEU* 1.3 61.6 + - - +
346F GLN* 3.3 33.6 - - - +
347F ILE* 3.8 11.8 + - + +
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Residues in contact with LEU 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F VAL* 4.0 20.6 - - + -
283F GLN* 3.6 27.3 - - + +
284F GLU* 3.6 26.5 - - + +
287F ILE* 6.4 0.4 - - + -
310F GLU 4.3 5.2 - - - +
311F THR 5.6 0.4 - - - +
340F ALA 3.3 18.6 + - - +
341F LEU* 3.2 21.4 + - + +
342F GLN 3.1 0.6 - - - -
343F LYS* 1.3 77.8 - - - +
345F GLN* 1.3 68.4 + - + +
346F GLN 3.3 0.5 + - - -
347F ILE* 3.4 14.8 + - + +
348F GLU* 3.5 8.4 + - - +
355F ILE* 3.5 31.4 - - + -
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Residues in contact with GLN 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F THR* 3.0 35.7 + - + +
312F SER* 4.1 7.1 + - - +
341F LEU* 3.1 27.8 + - + +
342F GLN* 3.2 13.5 + - - +
344F LEU* 1.3 76.2 - - + +
346F GLN* 1.3 61.0 + - - +
348F GLU* 3.2 17.8 + - - +
349F GLU* 2.9 30.8 + - - +
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Residues in contact with GLN 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342F GLN 3.6 5.3 + - - +
343F LYS* 3.3 29.8 + - - +
344F LEU 3.1 0.2 - - - -
345F GLN* 1.3 80.4 - - - +
347F ILE* 1.3 60.0 + - + +
349F GLU* 3.5 5.5 + - - +
350F GLU* 3.0 31.6 + - + +
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Residues in contact with ILE 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F MET* 3.7 30.1 - - + +
279F ARG* 3.8 33.0 - - + +
280F VAL* 3.6 31.2 - - + +
283F GLN* 5.3 4.3 - - + -
343F LYS* 4.0 14.6 - - + +
344F LEU* 3.4 13.2 + - + +
345F GLN 3.3 0.4 - - - -
346F GLN* 1.3 76.0 - - + +
348F GLU* 1.3 65.5 + - - +
350F GLU* 3.2 12.0 + - - +
351F THR* 3.0 26.4 + - + +
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Residues in contact with GLU 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242F HIS* 3.6 31.5 + - + +
280F VAL* 5.8 0.4 - - - +
311F THR* 3.6 31.2 + - - +
344F LEU 3.5 8.9 + - - +
345F GLN* 3.5 16.7 - - - +
347F ILE* 1.3 79.8 - - - +
349F GLU* 1.3 56.8 + - - +
351F THR* 2.9 19.5 + - - -
352F GLY* 2.9 14.4 + - - -
353F LEU 3.5 17.6 + - - +
354F THR* 4.5 1.9 - - - +
355F ILE* 3.4 38.6 + - + +
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Residues in contact with GLU 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F ILE* 3.4 27.9 - - - +
236F LYS 4.0 9.5 - - - +
238F LYS* 3.3 32.7 - - - +
242F HIS* 4.5 7.1 - - - -
345F GLN 2.9 16.4 + - - +
346F GLN* 3.8 6.5 - - - +
348F GLU* 1.3 74.3 - - - +
350F GLU* 1.3 64.9 + - - +
351F THR 3.4 0.5 + - - -
352F GLY* 3.7 10.2 + - - +
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Residues in contact with GLU 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F GLU* 3.1 20.2 - - - +
276F MET* 3.4 33.6 - - - +
279F ARG* 5.3 0.5 + - - -
346F GLN* 3.0 21.3 + - + +
347F ILE* 3.2 14.4 + - - +
349F GLU* 1.3 79.3 - - - +
351F THR* 1.3 60.4 + - + +
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Residues in contact with THR 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F TYR* 4.4 7.0 - - + +
138F PRO* 3.6 17.0 - - - +
139F GLU* 3.2 23.7 - - - +
235F ILE* 5.6 1.2 - - - +
276F MET* 3.7 23.3 - - + -
347F ILE* 3.0 16.1 + - + +
348F GLU* 2.9 14.4 + - - -
349F GLU 4.2 0.4 - - - -
350F GLU* 1.3 81.2 - - - +
352F GLY* 1.3 65.0 + - - -
353F LEU* 3.3 32.4 + - - +
358F VAL* 5.6 8.1 - - + +
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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