Contacts of the helix formed by residues 388 - 411 (chain A) in PDB entry 5I4V
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 GLU 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A LEU* 5.1 2.7 - - + +
296A GLY* 4.8 11.3 + - - -
299A ASP* 3.0 14.4 + - - +
386A VAL* 4.1 3.1 - - - -
387A GLN* 1.3 84.3 - - + +
389A PRO* 1.3 66.5 - - - +
390A GLY 3.3 2.2 - - - -
391A ARG* 3.1 49.1 + - + +
392A VAL* 3.5 14.4 + - - +
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Residues in contact with PRO 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA* 3.4 32.0 - - + +
386A VAL* 3.9 19.9 - - + +
387A GLN 3.3 10.1 - - - +
388A GLU* 1.3 85.8 - - - +
390A GLY* 1.3 65.6 - - - +
392A VAL* 3.2 2.3 + - + -
393A GLU* 3.2 25.5 + - - +
422B THR* 5.7 9.0 - - + -
423B GLU* 5.3 4.9 - - - +
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Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A GLU 3.3 0.8 - - - -
389A PRO* 1.3 83.6 - - - +
391A ARG* 1.3 60.6 + - - +
393A GLU* 3.7 9.1 + - - +
394A ALA* 3.3 21.8 + - - +
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Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN* 2.8 47.1 + - - +
295A LEU* 4.1 17.5 - - + +
388A GLU* 3.1 47.2 + - + +
389A PRO 3.2 0.8 - - - -
390A GLY* 1.3 76.1 - - - +
392A VAL* 1.3 63.2 + - - +
394A ALA* 3.4 6.7 + - - +
395A LEU* 3.2 30.3 + - + +
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LEU* 4.6 12.8 - - + -
299A ASP* 4.8 3.4 - - - +
303A LEU* 4.3 21.3 - - + -
379A PHE* 3.4 36.9 - - + +
380A SER 3.8 4.3 - - - +
381A ALA* 3.8 14.6 - - + +
386A VAL* 4.1 17.9 - - + -
388A GLU 3.5 14.4 - - - +
389A PRO 3.2 6.2 + - - +
391A ARG* 1.3 75.7 - - - +
393A GLU* 1.3 59.7 + - - +
395A LEU* 3.3 9.6 + - - +
396A GLN* 2.9 25.8 + - - +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A PHE 5.0 0.7 - - - +
381A ALA* 3.3 28.2 - - + +
389A PRO* 3.2 14.8 + - - +
390A GLY* 4.1 7.9 - - - +
392A VAL* 1.3 76.0 - - - +
394A ALA* 1.3 62.5 + - - +
396A GLN* 3.3 12.6 + - - +
397A GLN* 3.2 23.9 + - - +
423B GLU* 4.7 3.0 - - - +
427B LYS* 3.2 36.1 + - - +
492B ARG* 4.5 11.0 + - - +
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Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLY 3.3 15.5 + - - +
391A ARG* 3.7 7.9 - - - +
392A VAL 3.2 0.6 - - - -
393A GLU* 1.3 74.9 - - - +
395A LEU* 1.3 61.9 + - + +
397A GLN* 3.9 7.5 - - - +
398A PRO* 2.9 26.2 - - - +
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Residues in contact with LEU 395 (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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290A PRO 4.6 4.9 - - - +
291A GLY* 3.9 29.2 - - - +
294A GLN* 5.2 7.0 - - + +
295A LEU* 3.6 34.1 - - + -
379A PHE* 3.9 30.5 - - + -
391A ARG* 3.2 15.5 + - + +
392A VAL* 3.3 7.6 + - - +
394A ALA* 1.3 76.7 - - + +
396A GLN* 1.3 65.3 + - - +
397A GLN 3.4 0.3 + - - -
398A PRO* 3.4 8.9 - - + +
399A TYR* 3.0 26.1 - - + -
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Residues in contact with GLN 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 3.0 41.6 - - + +
379A PHE* 2.9 38.7 - - + +
380A SER* 4.0 7.8 + - - -
381A ALA 5.8 0.2 - - - -
392A VAL 2.9 10.4 + - - +
393A GLU* 3.7 13.2 + - - +
394A ALA 3.3 0.2 - - - -
395A LEU* 1.3 76.6 - - - +
397A GLN* 1.3 65.0 + - - +
399A TYR* 3.0 7.8 + - - +
400A VAL* 3.0 21.3 + - + +
425A LEU* 5.4 1.2 - - - +
491B LEU* 3.7 33.3 - - - +
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Residues in contact with GLN 397 (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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393A GLU 3.2 13.9 + - - +
394A ALA* 3.9 6.1 - - - +
396A GLN* 1.3 80.0 - - - +
398A PRO* 1.3 67.8 - - + +
400A VAL* 3.0 11.0 + - + +
401A GLU* 2.8 58.2 + - + +
488B LYS* 5.3 9.5 - - - -
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Residues in contact with PRO 398 (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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224A GLN* 4.9 1.2 + - - +
227A MET* 4.2 11.3 - - + +
394A ALA 2.9 27.6 - - - +
395A LEU* 3.4 14.6 - - + +
397A GLN* 1.3 86.9 - - + +
399A TYR* 1.3 56.5 + - + +
401A GLU* 3.3 13.4 + - + +
402A ALA* 2.7 36.8 + - - +
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Residues in contact with TYR 399 (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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227A MET* 3.3 41.8 - - + -
231A LEU* 4.1 12.1 - - + -
289A VAL* 3.6 10.2 - - + +
290A PRO* 2.6 45.7 + - - +
372A LEU* 3.8 14.1 - - + +
375A ALA* 4.0 14.8 - - + -
376A ILE* 3.6 22.9 - - + +
379A PHE* 3.6 24.0 - + - -
395A LEU* 3.0 28.7 - - + -
396A GLN 3.0 6.5 + - - +
398A PRO* 1.3 81.2 - - + +
400A VAL* 1.3 60.5 + - - +
402A ALA* 3.6 0.4 + - - -
403A LEU* 3.2 22.9 + - - +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A ILE* 4.0 24.7 - - + -
396A GLN* 3.0 26.9 + - + +
397A GLN* 3.4 10.1 - - + +
399A TYR* 1.3 74.7 - - - +
401A GLU* 1.3 66.6 + - + +
403A LEU* 3.1 4.4 + - - +
404A LEU* 3.0 21.8 + - + +
418A PHE* 4.1 12.8 - - + -
422A LEU* 5.0 4.3 - - + -
487B ALA* 4.0 26.5 - - + -
491B LEU* 4.1 22.0 - - + -
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLN* 4.0 11.4 + - - +
397A GLN* 2.8 53.5 + - + +
398A PRO* 3.6 11.1 - - + +
400A VAL* 1.3 75.3 - - + +
402A ALA* 1.3 61.1 + - - +
404A LEU* 3.4 14.0 + - + +
405A SER* 3.1 24.9 + - - -
483B GLN* 5.4 13.0 - - + +
484B GLY* 5.5 10.2 - - - -
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Residues in contact with ALA 402 (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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220A LEU* 4.3 2.3 - - - +
224A GLN* 3.7 23.7 - - + +
227A MET* 3.6 25.1 - - + -
228A ILE* 4.4 8.0 - - + +
372A LEU* 4.2 10.0 - - + +
398A PRO 2.7 19.7 + - - +
399A TYR 3.9 4.0 - - - +
401A GLU* 1.3 73.5 - - - +
403A LEU* 1.3 57.6 + - - +
405A SER* 3.5 1.6 + - - -
406A TYR* 2.8 31.0 + - - +
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Residues in contact with LEU 403 (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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369A GLU* 4.2 7.2 - - + -
372A LEU* 3.7 27.5 - - + +
373A LEU* 4.4 9.4 - - + +
376A ILE* 3.7 23.1 - - + -
399A TYR 3.2 14.3 + - - +
400A VAL 3.1 5.6 + - - +
402A ALA* 1.3 76.7 - - - +
404A LEU* 1.3 66.4 + - - +
406A TYR* 4.4 1.3 - - + -
407A THR* 2.9 39.1 + - + -
418A PHE* 4.2 17.9 - - + -
421A MET* 3.6 37.0 - - + -
422A LEU* 4.6 5.6 - - + -
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Residues in contact with LEU 404 (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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400A VAL* 3.0 12.7 + - + +
401A GLU* 3.5 17.3 - - + +
403A LEU* 1.3 78.0 - - - +
405A SER* 1.3 64.0 + - - +
407A THR* 3.3 2.4 + - - -
408A ARG* 3.1 68.1 + - - +
418A PHE* 3.6 39.7 - - + -
472B GLU* 5.4 1.8 - - - +
483B GLN 4.7 14.6 - - - +
484B GLY* 5.8 3.1 - - - -
487B ALA* 6.0 2.5 - - + -
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Residues in contact with SER 405 (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 VAL 4.8 11.2 + - - +
219A GLN 3.6 19.9 + - - -
220A LEU* 3.5 22.0 - - - -
224A GLN* 3.9 11.0 + - - -
401A GLU 3.1 14.3 + - - -
402A ALA 3.8 1.6 - - - -
404A LEU* 1.3 78.6 - - - +
406A TYR* 1.3 64.5 + - - +
408A ARG* 3.2 4.9 + - - +
409A ILE* 3.1 28.1 + - - +
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Residues in contact with TYR 406 (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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220A LEU* 3.6 18.1 - - + +
228A ILE* 3.7 27.8 - - + -
366A ASP* 2.4 33.6 + - - -
368A ALA* 3.6 19.5 - - + +
369A GLU* 3.7 27.4 - - + -
372A LEU* 4.4 3.6 - - + -
402A ALA 2.8 21.6 + - - +
403A LEU* 3.9 6.1 - - - +
405A SER* 1.3 73.5 - - - +
407A THR* 1.3 60.4 + - - +
409A ILE* 3.3 4.2 + - - +
410A LYS* 2.9 39.2 + - + +
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Residues in contact with THR 407 (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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369A GLU* 3.2 26.2 - - + +
403A LEU* 2.9 40.1 + - + +
404A LEU 3.3 4.9 + - - -
406A TYR* 1.3 80.2 - - - +
408A ARG* 1.3 61.8 + - - +
410A LYS* 3.8 4.8 - - - +
411A ARG* 3.1 29.6 + - - +
414A ASP 5.3 0.5 - - - +
417A ARG* 4.1 16.4 - - + +
418A PHE* 3.8 19.5 + - - +
421A MET* 3.8 13.5 - - - -
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Residues in contact with ARG 408 (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 VAL* 5.6 11.2 - - - +
404A LEU* 3.1 50.2 + - - +
405A SER* 3.8 4.7 - - - +
407A THR* 1.3 78.7 + - - +
409A ILE* 1.3 60.3 + - + +
411A ARG 4.2 3.8 - - - +
412A PRO* 3.3 29.9 - - + +
414A ASP 5.4 0.6 + - - -
415A GLN* 2.5 66.6 + - - +
418A PHE* 4.4 7.8 - - - +
419A PRO* 4.3 7.7 - - - +
472B GLU* 3.2 32.5 + - - -
476B LYS* 4.2 9.1 - - - +
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Residues in contact with ILE 409 (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 VAL 3.9 15.7 - - - +
219A GLN* 3.9 8.1 - - - -
220A LEU* 3.5 45.1 - - + +
405A SER 3.1 16.7 + - - +
406A TYR* 3.7 3.8 - - - +
408A ARG* 1.3 78.1 - - - +
410A LYS* 1.3 67.0 + - - +
412A PRO* 3.5 13.6 - - - +
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Residues in contact with LYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY 4.7 2.2 - - - -
366A ASP* 2.9 33.8 + - - +
369A GLU* 3.5 33.2 - - - +
406A TYR* 2.9 25.5 + - + +
407A THR* 4.0 5.4 - - - +
409A ILE* 1.3 80.2 - - - +
411A ARG* 1.3 93.5 + - + +
412A PRO* 3.7 3.3 - - - +
413A GLN* 5.0 0.2 - - - +
417A ARG* 3.8 12.3 - - - +
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Residues in contact with ARG 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A GLY* 4.6 10.9 + - - -
407A THR 3.1 18.0 + - - +
408A ARG* 4.7 1.7 - - - +
410A LYS* 1.3 117.9 + - + +
412A PRO* 1.3 67.5 - - - +
413A GLN* 3.2 26.7 - - - +
414A ASP* 3.1 26.3 + - + +
417A ARG* 4.0 33.4 - - - +
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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
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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) + - + + + + + -
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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