Contacts of the helix formed by residues 332 - 355 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B THR* 3.2 7.7 - - - +
331B THR* 1.3 80.8 + - - +
333B PRO* 1.3 65.7 - - - +
334B GLU* 3.5 14.0 + - - +
335B GLU* 3.2 33.5 + - - +
336B LYS* 3.0 24.3 + - - +
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Residues in contact with PRO 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B THR 3.5 5.8 - - - +
332B SER* 1.3 82.4 - - - +
334B GLU* 1.3 64.6 + - - +
336B LYS* 3.7 14.1 - - + +
337B ARG* 3.1 34.4 + - - +
445B ILE* 5.0 1.9 - - + +
515B LYS* 6.4 0.4 - - - +
526B TYR* 3.6 43.7 - - + +
693B GLU* 3.6 40.2 - - + +
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PRO* 5.1 13.4 - - - +
332B SER* 3.3 8.8 + - - +
333B PRO* 1.3 77.3 - - - +
335B GLU* 1.3 62.9 + - + +
337B ARG* 3.3 3.2 + - - +
338B LYS* 3.0 30.2 + - - +
381B ALA* 3.9 37.3 - - + +
382B SER* 6.0 1.4 - - - -
526B TYR* 5.0 8.6 + - + +
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B THR* 6.0 0.7 - - - -
310B LEU* 3.9 31.1 - - + +
311B PRO* 6.0 1.6 - - + -
324B SER* 4.7 3.0 - - - -
325B LYS* 4.6 20.3 + - - +
330B THR* 3.7 18.5 + - + +
332B SER* 3.2 29.3 + - - +
334B GLU* 1.3 76.1 - - + +
336B LYS* 1.3 64.8 + - - +
338B LYS* 4.0 4.7 - - - +
339B ILE* 2.8 39.6 + - + +
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 3.8 20.4 - - + -
330B THR* 3.9 14.5 - - + +
331B THR 3.9 17.9 - - - -
332B SER 3.0 17.3 + - - +
333B PRO* 3.7 9.2 - - + +
334B GLU 3.3 0.4 - - - -
335B GLU* 1.3 76.1 - - - +
337B ARG* 1.3 57.3 + - - +
339B ILE* 3.8 0.9 - - - +
340B ILE* 2.9 41.7 + - + +
444B ALA 2.9 24.8 + - - +
445B ILE* 4.7 7.0 - - + +
447B VAL 2.8 22.0 + - - -
449B CYS* 3.4 20.3 - - - +
580B LEU* 3.9 9.4 - - + +
693B GLU* 2.7 29.4 + - - +
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PRO* 3.1 26.1 + - - +
334B GLU 3.8 3.6 - - - +
336B LYS* 1.3 76.3 - - - +
338B LYS* 1.3 57.5 + - - +
340B ILE* 3.7 6.0 - - - +
341B GLY* 2.7 34.1 + - - -
380B VAL* 4.4 11.5 - - - +
381B ALA* 3.4 25.6 + - - +
382B SER* 3.4 23.6 + - - +
383B GLY 4.1 0.4 - - - +
441B PRO* 4.4 11.2 - - + -
445B ILE* 3.7 22.0 - - + +
524B ARG* 4.1 4.4 - - - +
526B TYR* 4.3 1.8 + - - -
693B GLU* 3.0 42.0 + - - -
1694B XMP 2.8 47.5 + - - +
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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
----------------------------------------------------------
308B THR* 3.8 9.0 + - + -
309B THR* 2.7 36.6 + - - +
310B LEU 4.9 0.4 - - - -
311B PRO* 4.1 28.6 - - + +
334B GLU 3.0 17.6 + - - +
335B GLU* 4.0 4.3 - - - +
337B ARG* 1.3 72.7 - - - +
339B ILE* 1.3 58.1 + - - +
341B GLY* 5.0 1.1 - - - -
342B ASP* 2.7 64.5 + - - +
380B VAL* 6.1 7.0 - - + -
381B ALA* 5.5 11.8 - - + +
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B PHE* 4.6 0.4 - - - +
306B GLY* 3.5 31.6 - - - +
307B THR 3.8 2.0 - - - +
308B THR* 3.8 18.8 - - + +
324B SER* 3.5 28.7 - - - +
325B LYS 3.7 6.1 - - - +
327B LEU* 3.9 28.0 - - + +
330B THR* 3.7 23.1 - - - +
335B GLU* 2.8 26.8 + - + +
336B LYS 3.8 3.1 - - - +
338B LYS* 1.3 75.8 - - - +
340B ILE* 1.3 57.1 + - - +
342B ASP* 4.0 0.5 - - - +
343B THR* 2.8 36.2 + - - +
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ASN* 4.1 15.9 - - - +
274B PHE* 4.0 6.5 - - + -
303B PHE* 3.4 25.0 - - + -
327B LEU* 3.7 24.2 - - + -
336B LYS 2.9 24.8 + - - +
337B ARG* 3.8 4.3 - - - +
339B ILE* 1.3 74.9 - - - +
341B GLY* 1.3 59.4 + - - +
344B PHE* 3.0 29.8 + - + +
440B GLY 4.9 1.3 - - - +
441B PRO* 3.8 26.5 - - + +
444B ALA* 3.5 32.8 - - + -
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ARG 2.7 21.6 + - - -
338B LYS* 3.8 0.4 - - - -
340B ILE* 1.3 76.8 - - - +
342B ASP* 1.3 62.6 + - - +
344B PHE* 3.5 2.0 + - - +
345B VAL* 3.2 28.6 + - - +
380B VAL* 5.9 1.6 - - - -
387B LEU* 4.1 26.7 - - - -
392B HIS* 4.4 4.7 - - - -
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Residues in contact with ASP 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B THR* 2.3 33.8 + - - +
338B LYS* 2.7 47.0 + - - +
339B ILE 4.0 1.6 - - - +
341B GLY* 1.3 70.6 - - - -
343B THR* 1.3 62.9 + - - +
345B VAL* 3.5 2.6 + - - +
346B LYS* 3.1 39.7 + - - +
392B HIS* 3.0 33.4 + - - +
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Residues in contact with THR 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B SER* 4.0 13.9 - - - +
303B PHE* 3.7 30.2 - - + -
306B GLY* 4.2 8.0 - - - -
307B THR 4.4 6.4 + - - -
339B ILE* 2.8 34.5 + - - +
342B ASP* 1.3 73.6 - - - +
344B PHE* 1.3 65.0 + - - +
346B LYS* 3.2 13.2 + - - +
347B ILE* 2.9 42.7 + - + +
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Residues in contact with PHE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.2 35.9 - - + -
243B LEU 6.6 0.2 - - - -
244B SER* 6.3 5.8 - - - -
270B ILE* 3.6 38.5 - - + +
272B ASN* 6.0 2.7 - - + -
303B PHE* 3.6 17.1 - + + -
340B ILE* 3.0 19.9 + - + +
341B GLY* 3.7 5.8 - - - +
343B THR* 1.3 77.0 - - - +
345B VAL* 1.3 65.5 + - + +
347B ILE* 3.8 2.8 - - - +
348B ALA* 2.9 34.4 + - + +
387B LEU* 4.2 22.4 - - + -
388B ILE* 5.4 6.7 - - + -
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLY 3.2 17.5 + - - +
342B ASP 4.1 2.9 - - - +
343B THR 3.3 0.2 - - - -
344B PHE* 1.3 83.8 - - + +
346B LYS* 1.3 57.3 + - - +
348B ALA* 3.5 4.0 + - - +
349B ASN* 2.9 29.3 + - - +
387B LEU* 4.0 21.3 - - + +
388B ILE* 5.0 5.8 - - + +
392B HIS* 3.4 36.3 - - + +
395B THR* 3.6 20.6 - - + -
398B ILE* 3.9 22.7 - - + -
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B THR* 3.5 24.2 + - - +
308B THR* 4.8 2.8 + - - +
342B ASP* 3.1 37.2 + - - +
343B THR* 3.2 11.2 + - - +
345B VAL* 1.3 74.2 - - - +
347B ILE* 1.3 60.9 + - + +
349B ASN* 3.6 3.5 + - - +
350B GLU* 3.0 26.0 + - - +
392B HIS* 6.2 0.9 - - + -
393B ASN 4.2 19.7 - - - +
394B ASP* 4.5 10.0 - - + +
395B THR* 4.0 10.8 - - + -
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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
----------------------------------------------------------
270B ILE* 4.3 13.0 - - + -
297B ILE* 4.4 15.7 - - + -
299B ALA* 3.9 13.5 - - + -
302B SER* 4.1 13.0 - - - +
303B PHE* 3.8 19.3 - - + -
343B THR* 2.9 40.0 + - + +
344B PHE 4.0 2.7 - - - +
346B LYS* 1.3 73.7 - - + +
348B ALA* 1.3 66.6 + - - +
350B GLU* 2.9 12.3 + - + +
351B VAL* 2.8 36.2 + - + +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.2 24.4 - - + +
270B ILE* 3.9 17.6 - - + +
344B PHE* 2.9 21.5 + - + +
345B VAL* 3.5 7.4 - - - +
347B ILE* 1.3 78.0 - - - +
349B ASN* 1.3 63.2 + - - +
351B VAL* 3.0 13.3 + - - +
352B ILE* 3.1 18.5 + - + +
388B ILE* 6.4 0.2 - - + -
398B ILE* 3.7 14.4 - - + -
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Residues in contact with ASN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B VAL 2.9 18.7 + - - +
346B LYS* 3.7 5.8 + - - +
348B ALA* 1.3 74.2 - - - +
350B GLU* 1.3 62.7 + - - +
352B ILE* 3.5 5.3 + - - +
353B GLY* 3.2 16.8 + - - -
394B ASP 3.9 12.7 + - - +
395B THR* 3.3 20.3 - - + +
396B GLU* 4.0 4.6 - - - +
397B LEU* 2.9 43.3 + - - +
398B ILE* 3.1 22.8 + - + +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B LYS 3.0 14.8 + - - +
347B ILE* 2.9 18.1 + - + +
349B ASN* 1.3 77.4 - - - +
351B VAL* 1.3 63.9 + - + +
353B GLY* 3.3 2.6 + - - -
354B GLU* 2.8 52.0 + - - +
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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
----------------------------------------------------------
240B LEU* 5.8 1.1 - - + -
242B LEU* 6.5 0.4 - - + -
268B VAL* 4.2 32.5 - - + -
270B ILE* 5.2 1.3 - - + -
295B LYS* 4.4 7.4 - - - -
297B ILE* 4.0 28.9 - - + -
347B ILE* 2.8 35.4 + - + +
348B ALA* 3.6 8.3 - - - +
350B GLU* 1.3 70.5 - - + +
352B ILE* 1.3 68.0 + - + +
354B GLU* 3.3 12.3 + - + +
355B MET* 3.3 32.8 + - + +
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Residues in contact with ILE 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.9 29.2 - - + -
242B LEU* 5.8 2.9 - - + -
348B ALA* 3.1 17.8 + - + +
349B ASN* 3.8 6.3 - - - +
351B VAL* 1.3 75.8 - - + +
353B GLY* 1.3 61.7 + - - +
355B MET* 3.4 12.7 + - - +
356B ASN 3.5 8.1 + - - -
357B LEU* 3.5 36.0 + - + +
359B PRO* 5.9 1.6 - - + -
362B VAL* 5.7 2.7 - - + -
364B LEU* 5.5 4.5 - - + -
397B LEU* 4.4 16.8 - - + -
398B ILE* 3.8 28.9 - - + -
401B LEU* 4.1 21.8 - - + -
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Residues in contact with GLY 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ASN 3.2 10.8 + - - -
350B GLU* 3.3 5.1 + - - -
351B VAL 3.2 0.8 - - - -
352B ILE* 1.3 76.3 - - - +
354B GLU* 1.3 57.7 + - - +
356B ASN* 3.1 26.6 + - - +
357B LEU 5.8 0.2 - - - -
397B LEU* 3.7 18.8 - - - +
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B GLU* 2.8 53.4 + - - +
351B VAL* 3.3 10.4 + - - +
353B GLY* 1.3 76.0 - - - +
355B MET* 1.3 60.6 + - + +
356B ASN* 3.2 12.5 + - - -
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Residues in contact with MET 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 4.9 3.4 - - - -
266B ILE* 3.7 36.6 - - + -
268B VAL* 4.9 0.9 - - - -
295B LYS* 3.8 29.8 - - + -
351B VAL* 3.3 29.4 + - + +
352B ILE 3.9 1.3 - - - +
353B GLY 3.2 0.6 - - - -
354B GLU* 1.3 78.6 - - + +
356B ASN* 1.3 71.1 + - - +
357B LEU* 3.1 32.5 + - + +
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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