Contacts of the helix formed by residues 375 - 398 (chain A) in PDB entry 5CEO
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 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A SER 3.5 7.4 - - - +
374A THR* 1.4 89.9 - - + +
376A GLN* 1.3 61.6 + - - +
377A GLU* 3.2 6.3 - - + +
378A THR* 3.1 23.1 + - + +
379A TYR* 3.0 26.0 + - - +
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Residues in contact with GLN 376 (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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209A THR* 3.6 31.3 - - + +
210A PRO* 4.0 19.8 - - + +
211A SER* 5.9 3.0 - - - -
374A THR 3.7 1.2 + - - +
375A PRO* 1.3 70.5 - - - +
377A GLU* 1.3 55.9 + - - +
379A TYR* 4.7 3.1 - - - -
380A PHE* 3.0 44.8 + - + +
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Residues in contact with GLU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A PRO* 3.2 5.5 - - + +
376A GLN* 1.3 77.2 - - - +
378A THR* 1.4 64.2 + - - +
380A PHE* 4.0 2.6 - - - +
381A LYS* 3.2 29.2 + - + +
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Residues in contact with THR 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A THR* 4.1 11.7 - - + -
375A PRO* 3.1 29.5 + - + +
377A GLU* 1.4 75.7 - - - +
379A TYR* 1.4 64.7 + - - +
381A LYS* 3.1 17.9 + - - +
382A SER* 3.2 21.6 + - - +
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Residues in contact with TYR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A VAL 3.6 21.2 + - - -
210A PRO* 3.7 32.3 - - + -
213A LEU* 3.3 26.0 - - + +
303A LEU 4.5 0.9 + - - -
304A LEU* 3.7 23.2 + - + +
336A PRO* 5.4 1.1 - - + -
371A VAL* 4.2 24.7 - - + -
374A THR* 3.8 18.5 - - + +
375A PRO 3.0 16.1 + - - +
376A GLN 4.2 2.2 - - - +
378A THR* 1.4 74.6 - - - +
380A PHE* 1.3 65.7 + + - +
382A SER* 3.3 9.7 + - - -
383A GLN* 3.1 36.4 + - - +
386A TRP* 4.0 22.6 - + - -
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Residues in contact with PHE 380 (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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207A PRO* 3.5 33.2 - - + -
208A VAL 3.3 33.4 - - - -
209A THR* 3.5 26.2 - - + -
376A GLN* 3.0 38.9 + - + +
377A GLU* 4.3 2.7 - - - +
379A TYR* 1.3 78.9 - + - +
381A LYS* 1.3 62.3 + - - +
383A GLN* 3.6 29.5 - - - +
384A ALA* 3.5 18.7 + - - +
387A ARG* 5.0 3.4 + - - -
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLU* 3.2 19.5 + - + +
378A THR* 3.1 13.4 + - - +
380A PHE* 1.3 72.5 - - - +
382A SER* 1.4 65.0 + - - +
384A ALA* 3.3 17.4 + - - +
385A GLU* 3.4 11.5 + - - +
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Residues in contact with SER 382 (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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334A SER* 4.7 6.1 - - - -
378A THR* 3.2 18.4 + - - +
379A TYR* 3.5 9.3 - - - -
381A LYS* 1.4 78.3 - - - +
383A GLN* 1.4 55.6 + - - +
385A GLU* 3.0 12.6 + - - +
386A TRP* 2.9 59.9 + - - +
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Residues in contact with GLN 383 (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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208A VAL* 4.1 20.6 + - - +
303A LEU 4.1 8.5 + - - -
304A LEU 3.2 30.1 + - - +
305A THR 3.9 11.7 - - - +
306A GLY* 4.4 2.8 - - - +
379A TYR* 3.1 22.6 + - + +
380A PHE* 3.6 29.4 - - - +
381A LYS 3.3 0.2 - - - -
382A SER* 1.4 75.7 - - - +
384A ALA* 1.3 56.0 + - - +
386A TRP* 3.4 15.3 + - + +
387A ARG* 3.1 55.3 + - - +
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Residues in contact with ALA 384 (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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380A PHE 3.5 9.8 + - - +
381A LYS* 3.3 12.4 + - - +
383A GLN* 1.3 76.4 - - - +
385A GLU* 1.3 57.6 + - - +
387A ARG* 3.6 20.6 + - - +
388A GLU* 3.2 32.8 + - - +
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Residues in contact with GLU 385 (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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333A SER* 5.7 0.2 + - - -
334A SER* 2.9 31.0 + - - -
381A LYS 3.4 8.2 + - - +
382A SER* 3.0 15.3 + - - +
384A ALA* 1.3 76.7 - - - +
386A TRP* 1.4 53.7 + - - +
388A GLU* 3.3 9.8 + - + +
389A GLU* 2.9 37.8 + - + +
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Residues in contact with TRP 386 (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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304A LEU* 3.3 42.4 - - + -
305A THR* 4.7 7.2 - - + -
332A PRO* 3.6 31.9 - - + -
334A SER* 2.7 32.0 + - - -
335A CYS* 3.7 23.3 - - + +
336A PRO* 4.0 19.3 - - + -
379A TYR* 4.0 28.7 - + - -
382A SER* 2.9 39.8 + - - -
383A GLN* 3.4 16.6 + - + +
385A GLU* 1.4 73.3 - - - +
387A ARG* 1.3 54.5 + - - +
389A GLU* 3.3 10.2 + - - +
390A VAL* 2.9 40.2 + - - +
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Residues in contact with ARG 387 (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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305A THR* 3.0 34.3 + - - +
306A GLY* 3.9 12.0 + - - -
307A GLU* 3.8 29.6 - - + +
380A PHE* 5.0 3.0 + - - -
383A GLN* 3.1 38.0 + - - +
384A ALA* 3.6 27.0 - - - +
386A TRP* 1.3 73.2 - - - +
388A GLU* 1.4 60.8 + - + +
390A VAL* 3.4 10.7 + - - +
391A LYS* 3.0 28.6 + - - +
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Residues in contact with GLU 388 (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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384A ALA 3.2 18.0 + - - +
385A GLU* 3.3 9.4 + - + +
387A ARG* 1.4 75.7 - - - +
389A GLU* 1.4 63.3 + - - +
391A LYS* 3.2 26.5 + - - +
392A LEU* 3.2 27.3 + - + +
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Residues in contact with GLU 389 (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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330A PRO* 5.9 2.5 - - + -
331A VAL 4.9 2.1 - - - +
332A PRO* 3.5 14.3 - - + +
333A SER* 3.1 46.6 + - - -
334A SER* 4.6 1.7 + - - -
385A GLU* 2.9 20.1 + - + +
386A TRP* 3.4 10.8 - - - +
388A GLU* 1.4 76.1 - - - +
390A VAL* 1.4 60.8 + - + +
392A LEU* 3.6 9.5 - - - +
393A HIS* 3.5 18.0 + - - +
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Residues in contact with VAL 390 (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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301A TRP* 3.8 29.4 - - + +
305A THR* 4.6 3.6 - - + -
307A GLU* 4.5 13.7 - - + -
330A PRO* 3.7 37.0 - - + +
332A PRO* 4.4 9.9 - - + -
386A TRP 2.9 23.8 + - - +
387A ARG* 3.4 18.2 - - - +
389A GLU* 1.4 71.9 - - + +
391A LYS* 1.4 65.3 + - - +
393A HIS* 3.3 2.8 + - - +
394A PHE* 3.0 37.6 + - + -
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Residues in contact with LYS 391 (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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311A LYS* 5.8 4.4 - - - +
387A ARG 3.0 13.6 + - - +
388A GLU* 3.3 22.7 - - - +
390A VAL* 1.4 76.5 - - - +
392A LEU* 1.3 56.1 + - + +
394A PHE* 3.1 11.2 + - - +
395A GLU* 2.9 59.1 + - - +
398A LYS* 5.1 3.6 - - - +
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Residues in contact with LEU 392 (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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388A GLU* 3.2 28.5 + - + +
389A GLU* 3.6 11.4 - - - +
391A LYS* 1.3 82.8 - - + +
393A HIS* 1.3 57.4 + - - +
395A GLU* 3.3 15.8 + - - +
396A LYS* 3.1 26.5 + - - +
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Residues in contact with HIS 393 (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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310A TYR* 6.3 0.2 - - - -
327A LEU* 4.5 12.5 - - + +
328A HIS 4.6 3.7 + - - -
330A PRO* 3.6 46.3 - - + +
389A GLU 3.5 9.6 + - - +
390A VAL 3.3 7.8 + - - +
391A LYS 3.3 0.6 - - - -
392A LEU* 1.3 75.7 - - - +
394A PHE* 1.4 65.9 + + - +
396A LYS* 3.3 29.1 + - - +
397A ILE* 3.4 32.9 + - + +
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Residues in contact with PHE 394 (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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301A TRP* 3.9 11.2 - + - -
307A GLU* 5.6 1.3 - - + -
308A ILE 4.0 8.1 - - - -
310A TYR* 3.4 44.4 - + - -
311A LYS* 3.9 20.9 - - + +
313A VAL* 3.9 13.5 - - + +
329A LEU* 3.6 12.8 - - + -
330A PRO* 3.6 27.1 - - + -
390A VAL* 3.0 28.6 + - + -
391A LYS* 3.1 8.0 + - - +
393A HIS* 1.4 77.8 - + - +
395A GLU* 1.4 50.8 + - - +
397A ILE* 3.1 21.0 + - + +
398A LYS* 2.8 46.5 + - - +
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Residues in contact with GLU 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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391A LYS* 2.9 48.2 + - - +
392A LEU* 3.4 19.2 - - - +
394A PHE* 1.4 74.3 - - - +
396A LYS* 1.4 58.2 + - - +
398A LYS* 3.6 41.2 + - + +
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Residues in contact with LYS 396 (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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392A LEU 3.1 10.7 + - - +
393A HIS* 3.4 25.6 - - + +
394A PHE 3.2 0.4 - - - -
395A GLU* 1.4 76.3 - - - +
397A ILE* 1.4 73.7 + - - +
398A LYS 4.1 3.3 - - - +
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Residues in contact with ILE 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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310A TYR* 5.0 3.6 - - + -
313A VAL* 3.8 26.5 - - + -
317A ALA* 4.7 12.6 - - + +
327A LEU* 4.4 25.6 - - + -
393A HIS* 3.4 42.4 - - + +
394A PHE* 3.1 22.6 + - + +
396A LYS* 1.4 88.8 - - - +
398A LYS* 1.4 59.1 + - - +
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Residues in contact with LYS 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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311A LYS 3.8 15.0 - - - +
312A ASP* 3.7 40.7 + - + +
313A VAL* 4.2 9.4 - - + -
314A ASP 5.6 1.3 - - - +
391A LYS* 5.1 3.3 - - - +
394A PHE* 2.8 35.2 + - - +
395A GLU* 3.6 43.7 + - + +
396A LYS 4.1 3.5 - - - +
397A ILE* 1.4 77.0 - - - +
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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
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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