Contacts of the helix formed by residues 320 - 347 (chain H) in PDB entry 2R9R
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 320 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316H THR 2.7 22.3 + - - -
317H LEU* 3.0 8.3 + - - -
319H ALA* 1.3 78.4 - - - +
321H MET* 1.3 64.5 + - - +
322H ARG 3.1 3.4 + - - -
323H GLU* 3.1 20.5 + - - -
324H LEU* 2.8 26.0 + - - +
405H ILE* 3.9 23.7 - - - +
408H ASN* 2.8 23.1 + - - +
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Residues in contact with MET 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H LEU* 3.2 13.3 + - - +
318H LYS* 3.4 22.9 - - + +
319H ALA 3.5 2.6 - - - -
320H SER* 1.3 76.4 - - - +
322H ARG* 1.3 63.9 + - - +
324H LEU* 3.3 14.1 + - - +
325H GLY* 2.9 21.1 + - - -
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Residues in contact with ARG 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H SER 3.1 0.8 + - - -
321H MET* 1.3 80.4 - - - +
323H GLU* 1.3 74.2 + - - +
325H GLY* 3.1 4.0 + - - -
326H LEU* 3.0 56.5 + - + +
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Residues in contact with GLU 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319H ALA 3.6 7.4 - - - +
320H SER* 3.3 37.1 - - - +
322H ARG* 1.3 88.3 + - - +
324H LEU* 1.3 63.3 + - - +
325H GLY 3.0 2.0 - - - -
326H LEU* 3.1 11.8 + - + +
327H LEU* 3.0 23.6 + - - +
401H PRO* 3.7 19.6 - - + +
404H VAL* 3.7 28.0 - - + +
405H ILE* 4.0 15.5 - - + -
408H ASN* 4.9 2.5 - - - +
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Residues in contact with LEU 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H LEU* 4.1 43.3 - - + +
320H SER* 2.8 18.0 + - - +
321H MET* 3.5 14.4 - - - +
323H GLU* 1.3 72.7 - - - +
325H GLY* 1.3 61.3 + - - +
327H LEU* 3.4 15.3 - - + +
328H ILE* 3.2 29.6 + - + +
405H ILE* 3.4 31.6 - - + -
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Residues in contact with GLY 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H MET 2.9 14.6 + - - -
322H ARG 3.5 3.8 - - - -
324H LEU* 1.3 75.3 - - - +
326H LEU* 1.3 61.1 + - - +
327H LEU 3.1 1.6 - - - -
328H ILE* 3.2 7.9 + - - +
329H PHE* 2.8 30.7 + - - +
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Residues in contact with LEU 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322H ARG* 3.0 55.0 + - + +
323H GLU* 3.1 13.0 + - + +
325H GLY* 1.3 77.0 - - - +
327H LEU* 1.3 54.7 + - - +
329H PHE* 4.1 8.7 - - + -
330H PHE* 2.7 69.4 + - + -
401H PRO* 4.5 6.1 - - + -
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Residues in contact with LEU 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H GLU 3.0 12.9 + - - +
324H LEU* 3.4 24.9 - - + +
326H LEU* 1.3 77.1 - - - +
328H ILE* 1.3 74.1 + - + +
330H PHE* 4.0 2.4 - - - +
331H LEU* 3.1 32.3 + - + +
397H THR* 4.3 7.7 - - + +
398H ILE* 3.9 44.0 - - + +
401H PRO* 4.1 14.7 - - + +
402H VAL* 4.7 10.8 - - + -
405H ILE* 5.2 4.0 - - + -
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Residues in contact with ILE 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H LEU* 3.2 17.5 - - + +
325H GLY* 3.2 8.6 + - - +
327H LEU* 1.3 87.2 - - + +
329H PHE* 1.3 57.9 + - - +
331H LEU* 3.6 9.7 - - + +
332H PHE* 2.9 30.5 + - + +
500H PGW 3.8 27.9 - - + +
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Residues in contact with PHE 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325H GLY 2.8 17.9 + - - +
326H LEU* 3.5 10.1 - - + +
327H LEU 3.2 0.2 - - - -
328H ILE* 1.3 74.0 - - - +
330H PHE* 1.3 84.8 + + - +
332H PHE* 3.2 18.2 + + - +
333H ILE* 3.0 51.7 + - + +
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Residues in contact with PHE 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H LEU* 2.7 54.3 + - + +
327H LEU 4.0 0.9 - - - +
329H PHE* 1.3 92.4 - + - +
331H LEU* 1.3 62.7 + - - +
333H ILE* 3.1 11.1 + - + +
334H GLY* 2.9 20.8 + - - -
368H MET* 5.2 0.2 - - - +
397H THR* 3.8 26.6 + - + +
400H LEU* 5.0 15.5 - - + -
401H PRO* 4.1 19.5 - - + -
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Residues in contact with LEU 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H LEU* 3.1 25.0 + - + +
328H ILE* 3.6 9.9 - - + +
330H PHE* 1.3 76.1 - - - +
332H PHE* 1.3 53.6 + - - +
334H GLY* 3.2 2.0 + - - +
335H VAL* 2.7 48.6 + - + +
365H VAL* 5.1 8.5 - - + -
368H MET* 4.2 25.5 - - + +
369H THR* 4.8 15.0 - - + -
397H THR* 3.8 22.3 - - + +
398H ILE* 4.4 18.2 - - + -
500H PGW 4.8 18.8 - - + -
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Residues in contact with PHE 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328H ILE* 2.9 17.0 + - + +
329H PHE* 3.2 21.5 - + - +
331H LEU* 1.3 75.9 - - - +
333H ILE* 1.3 84.3 + - + +
335H VAL* 3.3 7.2 + - + +
336H ILE* 3.0 53.9 + - + +
500H PGW 5.2 11.1 - - + +
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Residues in contact with ILE 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H PHE* 3.0 42.7 + - + +
330H PHE* 3.1 11.6 + - + +
332H PHE* 1.3 96.3 - - + +
334H GLY* 1.3 63.0 + - - +
336H ILE* 3.8 3.4 - - - +
337H LEU* 2.9 36.7 + - + +
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Residues in contact with GLY 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H PHE 2.9 13.8 + - - -
331H LEU 3.6 2.2 - - - -
333H ILE* 1.3 77.2 - - - +
335H VAL* 1.3 56.2 + - - +
337H LEU* 3.1 5.9 + - - -
338H PHE* 2.8 48.1 + - - +
368H MET* 4.0 17.9 - - - -
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Residues in contact with VAL 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H LEU* 2.7 30.5 + - + +
332H PHE* 3.6 8.3 - - + +
334H GLY* 1.3 72.1 - - - +
336H ILE* 1.3 60.7 + - + +
339H SER* 2.8 39.4 + - - +
361H PHE* 3.7 36.3 - - + +
364H ALA* 3.8 13.6 - - + +
365H VAL* 3.6 30.1 - - + +
368H MET* 3.9 9.5 - - - -
500H PGW 5.2 8.1 - - + -
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Residues in contact with ILE 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H PHE* 3.0 55.6 + - + +
333H ILE* 4.0 2.9 - - - +
335H VAL* 1.3 79.0 - - + +
337H LEU* 1.3 62.2 + - - +
340H SER* 2.7 38.3 + - - +
357H ILE* 5.7 1.3 - - + -
361H PHE* 4.0 28.7 - - + -
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Residues in contact with LEU 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H ILE* 2.9 28.9 + - + +
334H GLY* 3.5 6.7 - - - +
336H ILE* 1.3 79.7 - - - +
338H PHE* 1.3 81.3 + - + +
340H SER* 3.7 3.7 - - - -
341H ALA* 3.3 22.4 + - + +
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Residues in contact with PHE 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H GLY* 2.8 41.6 + - - +
335H VAL 4.3 0.7 - - - +
337H LEU* 1.3 89.0 - - + +
339H SER* 1.3 64.2 + - - +
340H SER 3.2 1.6 - - - -
341H ALA* 4.0 3.3 - - + +
342H VAL* 3.0 27.7 + - - +
363H TRP* 3.8 6.6 - - + -
364H ALA* 4.7 2.7 - - + -
368H MET* 4.5 4.5 - - + -
386H VAL* 3.9 15.2 - - + +
389H LEU* 3.9 17.7 - - + -
390H CYS* 3.7 50.9 - - + -
393H ALA* 3.7 33.0 - - + -
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Residues in contact with SER 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H VAL 2.8 26.1 + - - -
336H ILE 4.2 0.7 - - - -
338H PHE* 1.3 71.8 - - - +
340H SER* 1.3 63.5 + - - +
342H VAL* 3.3 5.1 - - - +
343H TYR* 3.0 25.6 + - - +
357H ILE* 3.7 13.2 - - - +
360H ALA* 3.2 15.4 + - - +
361H PHE* 3.1 46.2 + - - -
363H TRP* 4.8 0.4 - - - -
364H ALA* 3.4 5.7 - - - +
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Residues in contact with SER 340 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ILE* 2.7 27.7 + - - +
337H LEU* 3.7 5.2 - - - -
339H SER* 1.3 78.6 - - - +
341H ALA* 1.3 64.1 + - - +
343H TYR* 3.1 2.9 + - - +
344H PHE* 3.1 34.6 + - - -
357H ILE* 3.7 30.4 - - - +
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Residues in contact with ALA 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H LEU* 3.3 18.2 + - + +
338H PHE* 3.4 3.1 + - + +
340H SER* 1.3 80.0 - - - +
342H VAL* 1.3 64.0 + - - +
344H PHE* 3.3 6.5 + - - +
345H ALA* 3.0 22.5 + - - +
386H VAL* 3.8 26.0 - - + +
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Residues in contact with VAL 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H PHE 3.0 16.6 + - - +
339H SER 3.3 12.1 - - - +
341H ALA* 1.3 76.6 - - - +
343H TYR* 1.3 68.7 + - - +
345H ALA* 3.3 5.0 + - - -
346H GLU* 3.1 31.7 + - + +
354H PHE* 3.9 28.3 - - + -
360H ALA* 4.0 11.4 - - + -
363H TRP* 3.6 32.5 - - + -
378H PRO* 4.0 17.7 - - + -
383H GLY* 4.2 9.0 - - - +
386H VAL* 3.8 7.5 - - + +
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Residues in contact with TYR 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339H SER 3.0 15.5 + - - +
340H SER 3.1 3.3 + - - +
342H VAL* 1.3 85.4 - - - +
344H PHE* 1.3 92.5 + + - +
346H GLU* 3.3 1.6 + - - +
347H ALA* 2.8 39.3 + - + +
352H SER* 5.2 0.3 + - - -
354H PHE* 3.6 27.5 - - + +
355H PRO 3.8 5.9 + - - -
356H SER* 3.5 35.4 - - - +
357H ILE* 3.7 24.5 - - + -
360H ALA* 5.0 0.7 - - + -
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Residues in contact with PHE 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H SER* 3.1 27.5 + - - +
341H ALA* 4.0 4.9 - - - +
343H TYR* 1.3 103.5 - + - +
345H ALA* 1.3 61.8 + - - +
346H GLU 3.4 0.3 + - - -
347H ALA* 3.5 18.0 + - + +
348H ASP* 4.8 3.6 + - - +
357H ILE* 3.9 24.2 - - + -
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Residues in contact with ALA 345 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341H ALA 3.0 17.7 + - - +
342H VAL* 3.8 4.9 - - - +
343H TYR 3.2 0.2 - - - -
344H PHE* 1.3 77.5 - - - +
346H GLU* 1.3 58.1 + - - +
347H ALA 3.5 0.2 - - - -
348H ASP 5.3 0.7 + - - -
349H GLU* 4.9 1.4 - - - +
380H THR* 3.3 18.9 + - - +
382H GLY* 3.9 10.5 - - - +
383H GLY* 3.7 26.5 - - - +
386H VAL* 4.6 3.8 - - + -
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Residues in contact with GLU 346 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H VAL* 3.1 21.6 + - + +
343H TYR 3.7 1.3 - - - +
345H ALA* 1.3 75.8 - - - +
347H ALA* 1.3 66.7 + - - +
348H ASP 3.3 2.5 - - - -
349H GLU* 3.1 20.7 + - + +
352H SER* 3.2 33.8 - - - +
353H GLN 4.9 0.7 + - - -
354H PHE* 3.5 20.9 - - + -
377H VAL 4.4 0.9 - - - +
378H PRO* 3.3 9.0 - - - +
379H THR* 2.7 35.1 + - - +
380H THR* 2.6 37.3 + - - +
383H GLY* 3.4 9.6 - - - -
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Residues in contact with ALA 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343H TYR* 2.8 35.5 + - + +
344H PHE* 3.5 21.0 + - + +
346H GLU* 1.3 76.2 - - - +
348H ASP* 1.3 63.9 + - - +
349H GLU 3.1 10.4 + - - +
352H SER* 4.8 4.4 - - - -
354H PHE 5.9 0.2 - - - -
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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