Contacts of the helix formed by residues 332 - 355 (chain A) in PDB entry 2VXO
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 SER 332 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A THR* 3.4 3.2 - - - +
331A THR* 1.3 80.3 + - - +
333A PRO* 1.3 59.7 - - - +
334A GLU* 3.5 9.4 + - - +
335A GLU* 3.0 43.4 + - - +
336A LYS* 2.8 36.1 + - - +
515A LYS* 6.3 0.9 - - - +
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Residues in contact with PRO 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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331A THR 3.3 7.6 - - - +
332A SER* 1.3 82.1 - - - +
334A GLU* 1.3 66.6 + - + +
336A LYS* 3.3 14.8 + - + +
337A ARG* 3.1 32.8 + - - +
445A ILE* 5.1 1.2 - - + +
515A LYS* 6.0 6.1 - - - +
526A TYR* 3.3 42.8 - - + +
693A GLU* 3.7 39.5 - - + +
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Residues in contact with GLU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A SER* 3.3 7.9 + - - +
333A PRO* 1.3 76.9 - - + +
335A GLU* 1.3 64.5 + - + +
337A ARG* 3.2 4.4 + - - +
338A LYS* 3.1 23.1 + - - +
381A ALA* 3.7 35.0 - - + +
382A SER* 5.7 3.5 - - - -
524A ARG* 6.3 0.4 - - - +
526A TYR* 4.6 17.6 + - + +
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.6 44.2 - - + +
324A SER* 4.9 0.5 - - - -
325A LYS* 4.8 21.5 + - - -
330A THR* 3.6 18.6 + - + +
332A SER* 3.0 29.7 + - - +
334A GLU* 1.3 75.4 - - + +
336A LYS* 1.3 65.6 + - - +
337A ARG 3.3 0.2 + - - -
338A LYS* 3.4 1.4 + - - +
339A ILE* 3.0 35.9 + - + +
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 3.7 20.2 - - + -
330A THR* 4.1 11.0 - - + +
331A THR 4.0 20.0 - - - -
332A SER 2.8 20.4 + - - +
333A PRO* 3.5 9.4 - - + +
334A GLU 3.3 0.2 - - - -
335A GLU* 1.3 74.1 - - - +
337A ARG* 1.3 61.2 + - - +
339A ILE* 3.9 0.7 - - - +
340A ILE* 3.1 36.7 + - + +
444A ALA 2.8 26.8 + - - +
445A ILE* 4.8 7.4 - - + +
447A VAL 2.7 29.1 + - - -
449A CYS* 3.5 19.2 - - - -
580A LEU* 3.8 11.6 - - + +
693A GLU* 2.9 19.4 + - - +
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Residues in contact with ARG 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PRO* 3.1 25.5 + - - +
334A GLU* 3.2 7.3 + - - +
336A LYS* 1.3 77.3 - - - +
338A LYS* 1.3 54.0 + - - +
340A ILE* 3.5 5.0 + - - +
341A GLY* 2.7 33.3 + - - -
380A VAL* 3.7 21.7 - - - +
381A ALA 3.3 18.2 + - - +
382A SER 3.4 23.6 + - - -
441A PRO* 4.3 11.7 - - + -
445A ILE* 3.7 22.0 - - + +
524A ARG* 3.9 4.9 - - - +
526A TYR* 4.3 0.4 + - - -
693A GLU* 2.8 43.4 + - - -
1694A XMP 2.9 45.5 + - - +
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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
----------------------------------------------------------
308A THR* 3.9 3.8 + - + -
309A THR* 2.5 32.1 + - - +
310A LEU* 3.9 10.5 - - + -
311A PRO* 3.7 29.6 - - + -
334A GLU 3.1 15.3 + - - +
335A GLU 4.0 2.9 - - - +
337A ARG* 1.3 74.8 - - - +
339A ILE* 1.3 56.2 + - - +
341A GLY* 4.4 1.1 - - - +
342A ASP* 2.7 71.4 + - - +
377A ALA* 6.5 0.9 - - - -
380A VAL* 5.3 9.0 - - + -
381A ALA* 5.3 8.4 - - + +
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 4.6 0.7 - - - +
306A GLY* 3.5 33.7 - - - +
307A THR 3.9 2.2 - - - +
308A THR* 3.8 17.7 - - + +
310A LEU* 5.5 0.2 - - + -
324A SER* 3.5 29.8 - - - +
325A LYS 3.6 11.7 - - - +
327A LEU* 4.0 26.2 - - + -
330A THR* 3.7 16.4 - - - +
335A GLU* 3.0 26.0 + - + +
336A LYS 3.9 3.6 - - - +
338A LYS* 1.3 75.1 - - - +
340A ILE* 1.3 57.6 + - - +
342A ASP* 3.8 0.9 - - - +
343A THR* 2.7 37.7 + - - +
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Residues in contact with ILE 340 (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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272A ASN* 4.3 9.2 - - - +
274A PHE* 4.1 4.9 - - + -
303A PHE* 3.7 26.5 - - + -
327A LEU* 3.7 25.1 - - + -
336A LYS* 3.1 22.5 + - + +
337A ARG* 3.9 3.1 - - - +
339A ILE* 1.3 74.3 - - - +
341A GLY* 1.3 64.9 + - - +
344A PHE* 3.0 25.7 + - + +
440A GLY 4.9 1.3 - - - +
441A PRO* 3.8 32.5 - - + +
444A ALA* 3.5 31.4 - - + -
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Residues in contact with GLY 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 ARG 2.7 22.6 + - - -
338A LYS* 3.6 1.3 - - - -
340A ILE* 1.3 75.0 - - - +
342A ASP* 1.3 63.0 + - - +
344A PHE* 3.4 1.7 + - - +
345A VAL* 3.2 29.5 + - - +
380A VAL* 5.0 2.5 - - - -
387A LEU* 3.8 30.9 - - - +
392A HIS* 4.8 1.3 - - - -
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Residues in contact with ASP 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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308A THR* 2.5 34.1 + - - +
338A LYS* 2.7 48.9 + - - +
339A ILE 3.9 1.8 - - - +
341A GLY* 1.3 72.1 - - - -
343A THR* 1.3 60.5 + - - +
345A VAL* 3.6 1.9 + - - +
346A LYS* 3.2 37.6 + - + +
380A VAL* 6.0 1.4 - - - +
392A HIS* 3.4 29.8 + - - -
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Residues in contact with THR 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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302A SER* 3.6 23.3 - - - +
303A PHE* 3.9 17.5 - - + -
306A GLY* 4.1 7.3 - - - -
307A THR 4.5 3.5 + - - -
308A THR* 5.9 0.2 - - - -
339A ILE* 2.7 34.5 + - - +
340A ILE 3.9 2.5 - - - -
342A ASP* 1.3 73.5 - - - +
344A PHE* 1.3 66.7 + - - +
346A LYS* 3.4 16.7 + - - +
347A ILE* 3.0 48.9 + - + +
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Residues in contact with PHE 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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242A LEU* 3.9 38.4 - - + -
244A SER* 6.5 0.4 - - - -
270A ILE* 4.0 35.4 - - + -
303A PHE* 3.8 16.7 - + + -
340A ILE* 3.0 19.4 + - + +
341A GLY 3.8 2.9 - - - +
343A THR* 1.3 76.8 - - - +
345A VAL* 1.3 67.5 + - + +
347A ILE* 3.7 3.3 - - - +
348A ALA* 2.8 33.7 + - + +
387A LEU* 3.6 30.5 - - + -
388A ILE* 4.8 6.3 - - + -
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Residues in contact with VAL 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 GLY 3.2 17.2 + - - +
342A ASP 4.2 3.4 - - - +
344A PHE* 1.3 87.3 - - + +
346A LYS* 1.3 56.1 + - - +
348A ALA* 4.3 3.4 - - - -
349A ASN* 2.8 29.5 + - - +
387A LEU* 3.8 25.6 - - + +
388A ILE* 4.8 4.5 - - + +
392A HIS* 3.7 31.2 - - + +
395A THR* 2.9 40.2 - - + -
398A ILE* 3.7 14.5 - - + +
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Residues in contact with LYS 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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307A THR 3.6 23.2 + - - +
308A THR* 5.2 3.8 + - - +
342A ASP* 3.2 27.3 + - + +
343A THR* 3.4 17.6 + - - +
345A VAL* 1.3 74.2 - - - +
347A ILE* 1.3 63.7 + - + +
349A ASN* 3.5 2.8 + - - +
350A GLU* 3.1 23.9 + - - +
393A ASN 4.1 19.5 - - - +
394A ASP* 4.3 23.4 - - + +
395A THR* 5.0 1.1 - - + -
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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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270A ILE* 4.0 21.1 - - + -
297A ILE* 4.7 9.4 - - + -
299A ALA* 3.8 11.9 - - + -
302A SER* 4.2 12.3 - - - +
303A PHE* 3.6 28.7 - - + -
343A THR* 3.0 33.3 + - + +
344A PHE* 3.7 3.6 - - - +
346A LYS* 1.3 75.9 - - + +
348A ALA* 1.3 66.8 + - - +
350A GLU* 3.4 5.3 + - + +
351A VAL* 2.9 43.5 + - + +
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Residues in contact with ALA 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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242A LEU* 4.1 27.4 - - + -
270A ILE* 3.9 17.2 - - + +
344A PHE* 2.8 25.6 + - + +
345A VAL* 3.8 6.1 - - - +
347A ILE* 1.3 72.5 - - - +
349A ASN* 1.3 64.3 + - - +
351A VAL* 3.1 5.1 + - - +
352A ILE* 3.0 30.6 + - + +
398A ILE* 4.0 12.1 - - + -
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Residues in contact with ASN 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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345A VAL 2.8 18.5 + - - +
346A LYS 3.8 4.2 + - - +
347A ILE 3.3 0.2 - - - -
348A ALA* 1.3 77.2 - - - +
350A GLU* 1.3 64.7 + - - +
352A ILE* 3.5 5.3 + - - +
353A GLY* 3.2 16.6 + - - -
394A ASP 3.7 15.7 + - - +
395A THR* 3.1 20.1 - - - +
396A GLU* 4.3 2.0 - - - +
397A LEU* 2.9 48.9 + - - +
398A ILE* 3.4 16.9 + - + +
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Residues in contact with GLU 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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346A LYS 3.1 17.9 + - - +
347A ILE* 3.7 6.7 - - - +
348A ALA 3.3 0.2 - - - -
349A ASN* 1.3 79.7 + - - +
351A VAL* 1.3 62.5 + - + +
353A GLY* 3.1 5.2 + - - -
354A GLU* 2.6 57.1 + - - +
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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
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240A LEU* 6.3 0.4 - - + -
268A VAL* 4.3 17.0 - - + -
270A ILE* 5.0 1.8 - - + -
295A LYS* 5.5 1.8 - - + -
297A ILE* 4.1 33.2 - - + -
347A ILE* 2.9 34.3 + - + +
348A ALA* 3.8 5.8 - - - +
350A GLU* 1.3 77.5 - - + +
352A ILE* 1.3 64.8 + - + +
354A GLU* 3.2 27.6 + - + +
355A MET* 3.5 29.9 + - + +
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Residues in contact with ILE 352 (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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240A LEU* 4.5 31.2 - - + -
242A LEU* 5.4 3.6 - - + -
348A ALA* 3.0 20.8 + - + +
349A ASN 3.8 4.7 - - - +
351A VAL* 1.3 77.4 - - + +
353A GLY* 1.3 62.9 + - - +
355A MET* 3.2 18.7 + - - +
356A ASN 4.4 1.2 + - - -
357A LEU* 4.4 17.4 + - + +
362A VAL* 5.2 5.2 - - + -
364A LEU* 4.9 10.5 - - + -
397A LEU* 4.5 16.2 - - + +
398A ILE* 4.2 24.5 - - + -
401A LEU* 4.3 24.9 - - + -
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Residues in contact with GLY 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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349A ASN 3.2 11.5 + - - -
350A GLU* 3.1 9.4 + - - -
352A ILE* 1.3 77.3 - - - +
354A GLU* 1.3 56.5 + - - +
355A MET 3.1 4.9 + - - -
356A ASN* 3.6 8.7 + - - -
397A LEU* 4.3 18.2 - - - +
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 6.1 0.5 - - - +
350A GLU* 2.6 51.0 + - - +
351A VAL* 3.2 22.7 + - + +
353A GLY* 1.3 71.1 - - - +
355A MET* 1.3 62.5 + - + +
356A ASN* 3.3 4.9 + - - +
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Residues in contact with MET 355 (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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240A LEU* 3.9 26.0 - - - -
266A ILE* 3.8 24.7 - - + -
268A VAL* 3.9 11.7 - - + -
295A LYS* 3.5 33.9 - - + -
351A VAL* 3.7 20.6 - - + +
352A ILE* 3.2 10.2 + - - +
353A GLY 3.1 2.6 + - - -
354A GLU* 1.3 77.9 - - + +
356A ASN* 1.3 70.1 + - - +
357A LEU* 3.1 28.4 + - + +
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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