Contacts of the helix formed by residues 392 - 417 (chain E) in PDB entry 5UQ9
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 ASP 392 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLN* 5.5 0.7 - - - +
379E ALA* 3.8 12.4 - - - +
382E ARG* 2.9 43.0 + - - +
383E ASN* 5.9 0.5 - - - +
386E LEU* 4.0 17.0 - - + +
388E ASN 4.2 0.4 + - - -
389E LEU 3.3 12.1 + - - +
390E LEU 3.3 1.6 - - - -
391E LEU* 1.3 78.9 - - - +
393E ASP* 1.3 55.6 + - - +
394E PHE* 2.9 28.6 + - - +
395E PHE* 3.3 10.4 + - + -
396E LYS* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 393 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D GLN* 3.1 31.1 + - - +
391E LEU 4.0 2.7 + - - +
392E ASP* 1.3 75.9 + - - +
394E PHE* 1.3 57.8 + - - +
396E LYS* 4.2 9.2 - - - +
397E SER* 2.8 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 394 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E GLU* 6.4 0.9 - - + -
328E TYR* 4.0 20.9 - - - -
375E LYS* 3.5 53.8 - - + -
382E ARG* 4.2 17.0 - - - +
392E ASP* 2.9 16.9 + - - +
393E ASP* 1.3 77.9 - - - +
395E PHE* 1.3 77.4 + + + +
397E SER* 2.8 19.4 + - - -
398E ALA* 3.1 13.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 395 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E TYR* 5.0 0.4 - - - -
332E ILE* 3.9 31.9 - - + -
372E PHE* 3.4 31.2 - + - -
375E LYS* 3.7 9.6 - - + -
376E ILE* 3.5 32.1 - - + -
379E ALA* 3.6 24.5 - - + -
389E LEU* 3.5 40.2 - - + +
390E LEU* 5.0 2.0 - - - -
392E ASP* 3.3 13.0 + - + -
394E PHE* 1.3 90.3 - + + +
396E LYS* 1.3 60.6 + - - +
398E ALA* 3.6 4.2 - - - +
399E VAL* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 396 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E LEU* 3.9 13.3 + - - +
391E LEU 5.4 0.7 - - - -
392E ASP 2.7 25.4 + - - +
393E ASP* 4.0 9.9 - - - +
395E PHE* 1.3 73.9 - - - +
397E SER* 1.3 64.5 + - - +
399E VAL* 3.2 5.4 + - + +
400E GLU* 3.0 55.7 + - - +
430E TYR* 3.3 11.5 + - - +
303F LYS* 3.2 22.7 - - + +
304F LEU* 3.6 19.5 - - + -
305F LYS* 2.8 34.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393E ASP 2.8 23.0 + - - -
394E PHE* 2.8 16.6 + - - -
396E LYS* 1.3 78.6 - - - +
398E ALA* 1.3 56.2 + - - +
400E GLU* 3.6 6.8 + - - +
401E ASN* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 398 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328E TYR* 3.6 31.9 - - + +
332E ILE* 3.7 11.2 - - + -
394E PHE* 3.1 21.8 + - + +
395E PHE* 3.6 7.0 - - - +
396E LYS 3.2 0.2 - - - -
397E SER* 1.3 75.4 + - - +
399E VAL* 1.3 65.1 + - - +
401E ASN* 3.4 5.2 + - - +
402E CYS* 3.2 30.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 399 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E ALA* 5.1 8.7 - - + +
332E ILE* 4.1 27.4 - - + -
333E ILE* 5.3 2.7 - - + -
390E LEU* 4.4 13.0 - - + -
395E PHE 2.9 21.5 + - - +
396E LYS* 3.2 6.5 + - + +
398E ALA* 1.3 75.0 - - - +
400E GLU* 1.3 59.9 + - - +
402E CYS* 3.1 6.5 + - - +
403E GLN* 2.9 28.4 + - + +
406E TRP* 4.5 12.6 - - + -
430E TYR* 3.5 44.0 - - + +
304F LEU* 6.0 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 400 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396E LYS* 3.0 39.6 + - - +
397E SER* 3.9 6.7 - - - +
399E VAL* 1.3 77.2 - - - +
401E ASN* 1.3 62.8 + - - +
402E CYS 3.0 1.3 + - - -
403E GLN* 3.2 33.4 + - - +
404E ASP 4.8 0.7 + - - -
430E TYR* 5.1 0.2 - - - +
305F LYS* 2.9 44.0 + - + +
306F GLY 4.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 401 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ARG* 3.4 36.9 + - - +
227E GLU* 5.1 7.9 + - - -
325E LYS* 3.4 33.7 + - - +
397E SER 3.0 18.6 + - - +
398E ALA* 3.7 7.4 - - - +
399E VAL 3.3 0.4 - - - -
400E GLU* 1.3 75.8 - - - +
402E CYS* 1.3 60.9 + - - +
403E GLN 3.7 0.2 - - - -
405E SER* 5.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 402 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E GLU* 6.0 1.3 - - - -
324E ARG* 5.9 1.1 - - - -
325E LYS* 3.2 50.5 - - + +
328E TYR* 3.7 23.6 - - - -
329E ALA* 4.1 9.6 - - + -
398E ALA 3.2 18.8 - - - +
399E VAL 3.1 4.5 + - - +
400E GLU 3.0 0.8 - - - -
401E ASN* 1.3 86.6 - - - +
403E GLN* 1.3 56.6 + - - +
404E ASP 3.6 2.0 - - - -
405E SER* 3.7 4.8 + - - -
406E TRP* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 403 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399E VAL* 2.9 13.9 + - + +
400E GLU* 3.2 37.1 + - - +
401E ASN 3.7 0.2 - - - -
402E CYS* 1.3 75.4 - - - +
404E ASP* 1.3 68.3 + - - +
406E TRP* 3.1 14.8 + - + +
407E ARG* 3.0 58.9 + - - +
430E TYR* 3.6 12.8 + - + -
305F LYS 3.6 9.1 + - - +
306F GLY* 3.1 32.5 + - - -
307F PRO* 4.1 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 404 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ARG 5.6 0.9 - - - +
117C LYS* 5.5 1.4 - - - +
118C ALA* 4.5 11.5 + - + +
400E GLU 4.8 1.4 + - - -
403E GLN* 1.3 79.7 - - - +
405E SER* 1.3 57.7 + - - +
407E ARG* 3.4 8.4 + - - +
408E ARG* 2.8 57.3 + - - +
309F LYS* 3.4 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 405 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E ASP* 2.8 44.6 + - - +
325E LYS* 3.6 30.3 + - - +
401E ASN 5.2 1.0 + - - -
402E CYS 3.7 3.3 + - - -
403E GLN 3.3 0.2 - - - -
404E ASP* 1.3 75.0 - - - +
406E TRP* 1.3 60.9 + - - +
408E ARG* 3.7 11.0 + - - +
409E ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 406 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E ALA* 3.6 27.5 - - + +
329E ALA* 3.5 22.7 - - + -
330E SER* 3.2 28.8 + - - -
333E ILE* 3.5 18.8 - - + -
399E VAL* 4.5 9.9 - - + -
402E CYS 2.9 20.3 + - - +
403E GLN* 3.1 17.2 + - + +
405E SER* 1.3 77.5 - - - +
407E ARG* 1.3 62.8 + - + +
409E ALA* 3.4 1.7 + - - +
410E VAL* 3.1 37.1 + - + +
423E PHE* 3.7 12.1 + + - -
426E ALA* 3.3 22.4 - - + -
427E LEU* 3.3 38.7 - - + +
430E TYR* 4.1 22.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 407 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403E GLN* 3.0 48.5 + - - +
404E ASP* 4.1 8.1 - - - +
406E TRP* 1.3 72.5 - - - +
408E ARG* 1.3 61.0 + - - +
410E VAL* 4.4 1.3 - - - -
411E SER* 2.9 35.9 + - - -
427E LEU* 3.8 23.8 - - + +
430E TYR* 4.4 1.8 - - - -
431E ASP* 2.4 45.3 + - - -
307F PRO* 3.2 29.8 - - - +
414F VAL* 2.5 52.8 + - + +
415F GLN* 4.4 11.9 - - + +
417F GLY* 3.5 4.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 408 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LYS* 3.0 43.8 - - - +
318E SER* 6.0 1.2 - - - -
319E PHE* 4.4 5.2 - - + -
322E ASP* 3.2 37.5 + - - +
404E ASP* 2.8 54.4 + - - +
405E SER* 3.7 9.7 + - - +
406E TRP 3.3 0.2 - - - -
407E ARG* 1.3 77.4 - - - +
409E ALA* 1.3 57.7 + - - +
411E SER* 4.1 3.9 - - - -
412E THR* 2.7 38.1 + - - +
415F GLN* 5.6 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 409 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E LEU* 4.7 8.4 - - + +
319E PHE* 3.7 23.5 - - + -
322E ASP* 4.1 11.0 - - - +
323E ILE* 4.5 7.0 - - + -
326E ALA* 4.0 16.6 - - + -
405E SER 3.0 17.4 + - - +
406E TRP 3.9 3.1 - - - +
408E ARG* 1.3 74.7 - - - +
410E VAL* 1.3 61.8 + - + +
412E THR* 3.4 1.4 + - - -
413E GLY* 3.0 26.3 + - - -
420E MET* 4.1 5.2 - - - +
423E PHE* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326E ALA* 5.7 0.2 - - + -
406E TRP* 3.1 33.8 + - + +
407E ARG 3.9 3.6 - - - +
409E ALA* 1.3 78.0 - - + +
411E SER* 1.3 57.2 + - - +
414E VAL* 2.9 37.9 + - + +
420E MET* 3.3 9.8 - - + +
423E PHE* 4.2 24.9 - - + +
424E THR* 4.0 23.1 - - + -
427E LEU* 4.1 11.4 - - + -
414F VAL* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 411 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407E ARG 2.9 18.8 + - - -
408E ARG* 4.2 3.1 - - - -
410E VAL* 1.3 77.8 - - - +
412E THR* 1.3 62.7 + - - +
414E VAL* 3.5 3.9 + - - +
415E GLN* 3.1 30.0 + - - +
411F SER* 3.8 29.7 + - - +
414F VAL* 3.4 15.8 - - - +
415F GLN* 3.8 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 412 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E VAL* 4.0 17.5 - - + -
310E PHE* 3.9 15.8 - - + -
312E PHE* 4.4 11.0 - - + -
319E PHE* 3.5 32.6 - - + -
408E ARG* 2.7 26.3 + - - +
410E VAL 3.3 0.2 - - - -
411E SER* 1.3 78.0 - - - +
413E GLY* 1.3 57.8 + - - +
415E GLN* 3.4 6.0 + - - +
416E ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 413 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E LEU* 4.1 15.7 - - - +
208E VAL* 5.0 0.9 - - - -
409E ALA 3.0 16.6 + - - -
410E VAL 3.8 0.7 - - - -
412E THR* 1.3 74.0 - - - +
414E VAL* 1.3 59.5 + - - +
416E ALA* 3.3 5.2 + - - -
417E GLY 2.9 24.1 + - - -
418E ILE* 2.9 13.7 + - - +
420E MET* 3.8 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 414 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410E VAL* 2.9 29.0 + - + +
411E SER* 3.8 8.1 - - - +
412E THR 3.3 0.2 - - - -
413E GLY* 1.3 77.1 - - - +
415E GLN* 1.3 61.9 + - + +
417E GLY 3.1 1.2 + - - -
418E ILE 5.2 1.6 - - - +
420E MET* 3.9 11.9 - - + -
424E THR* 4.9 5.2 - - + -
407F ARG* 2.7 58.0 + - + +
410F VAL* 4.2 20.9 - - + -
411F SER* 4.6 4.0 - - - +
414F VAL* 5.7 0.4 - - + -
427F LEU* 3.6 26.7 - - + -
431F ASP* 5.3 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 415 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E PRO* 3.6 18.7 - - - +
310E PHE* 3.7 31.5 - - + +
411E SER* 3.1 18.1 + - - +
412E THR* 3.8 2.0 - - - +
413E GLY 3.4 0.2 - - - -
414E VAL* 1.3 75.9 - - - +
416E ALA* 1.3 59.6 + - - +
404F ASP* 5.5 2.8 - - - +
407F ARG* 3.8 25.0 + - - +
408F ARG* 4.3 7.3 - - - +
411F SER* 3.3 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207E ASP 5.8 1.1 - - - +
208E VAL* 4.1 10.1 - - + -
307E PRO* 3.5 13.5 - - - +
310E PHE* 3.5 30.4 - - + +
412E THR 3.0 17.9 + - - +
413E GLY 3.8 4.0 - - - +
414E VAL 3.2 0.2 - - - -
415E GLN* 1.3 76.8 - - - +
417E GLY* 1.3 60.6 + - - +
418E ILE* 3.9 20.2 - - + +
434F ARG* 4.2 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 417 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307E PRO* 4.1 0.4 - - - -
413E GLY 2.9 4.4 + - - -
414E VAL 3.1 4.8 + - - -
415E GLN 3.3 0.4 - - - -
416E ALA* 1.3 79.5 - - - +
418E ILE* 1.3 61.3 + - - +
407F ARG* 3.3 25.4 - - - -
431F ASP* 3.3 10.8 - - - -
434F ARG* 2.9 27.0 + - - -
435F HIS* 3.2 13.5 - - - -
----------------------------------------------------------
Back to top of page
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