Contacts of the helix formed by residues 378 - 406 (chain C) in PDB entry 3D5K
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 THR 378 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA* 3.5 29.4 - - + +
224B THR* 4.3 7.0 - - + -
225B ARG* 3.1 29.7 + - - +
22C GLN 5.1 0.4 - - - +
23C ALA* 3.7 25.1 - - + -
374C ALA 2.7 23.7 + - - +
375C ALA 3.3 0.9 + - - -
377C GLY* 1.3 83.9 - - - +
379C PHE* 1.3 61.5 + - - +
380C THR 3.4 2.5 - - - -
381C GLU* 3.4 7.7 - - - +
382C GLN* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ARG* 3.3 35.9 - - - -
375C ALA* 3.0 32.5 + - + +
376C ARG 4.6 0.2 + - - -
378C THR* 1.3 75.9 + - - +
380C THR* 1.3 60.5 + - - +
382C GLN* 3.4 31.6 - - + +
383C LEU* 2.9 36.4 + - + +
431C ASP* 3.8 24.2 - - + -
434C ASN* 3.7 25.6 - - + -
435C GLN* 3.7 32.8 - - + +
438C SER* 3.9 17.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C ARG 4.4 11.4 + - - -
378C THR 3.4 1.0 - - - +
379C PHE* 1.3 76.7 - - - +
381C GLU* 1.3 76.6 + - + +
383C LEU* 4.0 3.4 - - - +
384C GLN* 3.1 25.7 + - + +
435C GLN* 4.1 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B ARG 5.4 0.4 - - - +
221B ALA* 4.4 9.9 - - + -
377C GLY 3.2 26.6 - - - +
378C THR* 3.4 13.4 - - - +
380C THR* 1.3 90.1 + - + +
382C GLN* 1.3 56.5 + - - +
384C GLN* 3.4 6.5 + - - +
385C ALA* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ALA* 3.5 31.1 + - + +
221B ALA* 3.7 10.5 - - + +
222B GLN* 4.0 11.9 + - - +
225B ARG* 2.9 39.6 + - - +
378C THR 3.1 17.0 + - - +
379C PHE* 3.4 16.4 - - + +
380C THR 3.3 0.2 - - - -
381C GLU* 1.3 73.7 - - - +
383C LEU* 1.3 59.1 + - - +
385C ALA* 3.3 7.8 + - - +
386C GLN* 3.0 27.2 + - - +
431C ASP* 3.7 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C PHE* 2.9 18.1 + - + +
380C THR* 4.0 4.0 - - - +
382C GLN* 1.3 76.0 - - - +
384C GLN* 1.3 54.1 - - - +
386C GLN* 3.2 4.8 + - - +
387C ARG* 2.8 38.4 + - + +
428C LEU* 3.7 20.6 - - + +
431C ASP* 3.7 17.7 - - + +
432C ARG* 3.6 42.2 - - + +
435C GLN* 2.8 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C THR* 3.1 19.5 + - + +
381C GLU* 3.7 7.0 - - - +
382C GLN 3.3 0.2 - - - -
383C LEU* 1.3 73.3 - - - +
385C ALA* 1.3 60.3 + - - +
387C ARG* 3.6 21.6 + - - +
388C ASP* 3.1 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B GLU* 3.6 12.8 - - - +
217B ARG* 3.8 22.7 - - + +
218B ALA* 3.6 30.1 - - - +
381C GLU 3.0 16.8 + - - +
382C GLN 3.3 4.9 + - - +
384C GLN* 1.3 76.2 - - - +
386C GLN* 1.3 57.5 + - - +
388C ASP* 3.6 7.8 + - - +
389C LEU* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 386 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ALA* 3.6 18.6 - - + +
382C GLN* 3.0 16.3 + - - +
383C LEU* 3.6 5.8 - - - +
385C ALA* 1.3 75.8 - - - +
387C ARG* 1.3 58.2 + - - +
389C LEU* 3.2 27.9 + - - +
390C VAL* 2.9 32.9 + - - +
424C ALA* 3.1 24.9 + - - +
427C GLN* 3.5 17.6 - - - +
428C LEU* 3.7 25.1 - - + -
431C ASP* 3.4 25.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 387 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASP* 5.6 10.1 + - - +
383C LEU* 2.8 22.8 + - + +
384C GLN* 3.6 24.2 + - - +
385C ALA 3.4 0.2 - - - -
386C GLN* 1.3 73.8 - - - +
388C ASP* 1.3 59.6 + - - +
390C VAL* 3.3 7.6 + - - +
391C LYS* 3.0 28.3 + - - +
428C LEU* 3.8 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 388 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLN* 4.3 4.7 + - - +
214B GLU* 3.6 33.2 - - + +
217B ARG* 5.7 0.7 + - - -
384C GLN* 3.1 39.3 + - - +
385C ALA* 3.8 2.3 - - - +
387C ARG* 1.3 76.1 - - - +
389C LEU* 1.3 60.9 + - - +
391C LYS* 4.0 10.2 - - - +
392C ALA* 3.1 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 389 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B THR* 3.3 36.8 - - - +
214B GLU* 3.9 8.9 - - + +
215B GLY* 4.0 19.3 - - - +
218B ALA* 5.8 0.2 - - + -
385C ALA 3.0 15.5 + - - +
386C GLN* 3.2 34.7 + - - +
388C ASP* 1.3 75.0 - - - +
390C VAL* 1.3 59.7 + - - +
392C ALA* 3.5 1.4 + - - -
393C SER* 2.9 45.2 + - - +
424C ALA* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLN 2.9 19.0 + - - +
387C ARG* 3.3 8.9 + - - +
389C LEU* 1.3 75.9 - - - +
391C LYS* 1.3 57.5 + - - +
393C SER* 3.4 4.1 + - - -
394C ASP* 3.0 30.7 + - + +
421C LEU* 3.5 7.2 - - + +
424C ALA* 3.6 34.1 - - + +
425C GLN* 3.9 28.3 - - + +
428C LEU* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B GLN* 6.2 2.2 - - - +
387C ARG 3.0 17.0 + - - +
388C ASP* 4.0 11.2 - - - +
390C VAL* 1.3 78.0 - - - +
392C ALA* 1.3 60.1 + - - +
394C ASP* 3.6 6.0 + - - +
395C GLU* 3.2 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 4.6 5.1 - - - +
210B GLN* 3.5 37.4 - - + +
211B THR* 4.0 21.2 - - + +
214B GLU* 5.1 0.4 - - + -
388C ASP 3.1 20.0 + - - +
389C LEU 3.9 2.5 - - - +
391C LYS* 1.3 73.7 - - - +
393C SER* 1.3 60.5 + - - +
395C GLU* 3.4 8.7 + - - +
396C TYR* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B THR* 3.9 8.9 - - - +
389C LEU* 2.9 37.1 + - - +
390C VAL* 3.8 4.9 - - - -
392C ALA* 1.3 76.7 - - - +
394C ASP* 1.3 56.7 + - - +
396C TYR* 3.3 10.1 + - - +
397C TYR* 2.9 28.9 + - - +
417C ALA 4.6 1.0 - - - +
420C SER* 4.1 15.6 + - - -
421C LEU* 3.7 30.6 - - - +
424C ALA* 4.4 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C VAL* 3.0 19.3 + - + +
391C LYS* 3.8 7.2 - - - +
392C ALA 3.2 0.2 - - - -
393C SER* 1.3 74.0 - - - +
395C GLU* 1.3 65.1 + - + +
397C TYR* 3.3 8.8 + - - +
398C GLN* 3.1 38.8 + - - +
421C LEU* 3.5 27.3 - - + +
425C GLN* 6.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 3.4 48.0 + - - +
391C LYS* 3.2 35.4 + - + +
392C ALA* 3.4 4.7 + - - +
394C ASP* 1.3 75.9 - - + +
396C TYR* 1.3 61.8 + - - +
398C GLN* 3.4 18.7 + - - +
399C LEU* 3.3 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.7 24.7 - - + +
207B ARG* 4.5 12.3 - - + +
208B GLN* 3.0 45.0 + - + -
211B THR* 4.4 18.6 - - + -
412B LEU* 3.7 1.4 - - - +
415B LEU* 4.9 4.3 - - + -
392C ALA 2.9 18.4 + - - +
393C SER* 3.4 8.1 - - - +
394C ASP 3.2 0.2 - - - -
395C GLU* 1.3 76.8 - - - +
397C TYR* 1.3 61.3 + - - +
399C LEU* 3.6 2.4 + - - -
400C ALA* 3.1 17.7 + - - +
413C THR* 3.5 18.2 + - + +
416C ASP* 2.7 31.8 + - - +
417C ALA* 3.7 26.9 - - + -
420C SER* 4.9 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 397 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C THR* 3.9 24.5 - - + +
185C TYR* 5.7 2.0 - + - -
188C SER* 5.0 7.4 + - - -
393C SER 2.9 16.9 + - - +
394C ASP* 3.3 11.9 + - - +
396C TYR* 1.3 77.8 - - - +
398C GLN* 1.3 70.1 + - + +
400C ALA* 3.3 0.5 + - - +
401C ASP* 2.8 49.0 + - + +
414C LEU* 3.5 25.8 - - + -
417C ALA* 3.6 16.8 - - + +
418C GLN* 3.7 34.2 + - + -
421C LEU* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ASP* 3.1 35.1 + - - +
395C GLU* 3.7 24.6 + - - +
396C TYR 3.4 0.4 - - - -
397C TYR* 1.3 88.6 - - + +
399C LEU* 1.3 62.9 + - + +
401C ASP* 3.9 4.3 - - - +
402C LYS* 3.2 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 399 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ALA* 4.0 34.8 - - + +
204B LEU* 3.9 20.6 - - + +
207B ARG* 3.8 24.7 - - + +
395C GLU 3.3 18.0 + - - +
396C TYR* 4.0 1.1 - - - +
398C GLN* 1.3 74.8 - - + +
400C ALA* 1.3 59.5 + - - +
402C LYS* 3.4 25.6 + - - +
403C ARG* 3.0 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.9 7.1 - - + +
396C TYR* 3.1 19.7 + - + +
397C TYR 3.6 3.8 - - - +
399C LEU* 1.3 74.9 - - - +
401C ASP* 1.3 64.0 + - - +
403C ARG* 3.4 5.1 + - - +
404C TYR* 3.1 24.3 + - - +
409C ASP* 5.5 1.8 - - - +
410C ASN 5.6 0.3 - - - +
413C THR* 4.0 18.5 - - + -
414C LEU* 3.9 27.4 + - + +
417C ALA* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C SER* 4.4 3.3 + - - -
397C TYR* 2.8 36.0 + - + +
398C GLN* 3.9 5.8 - - - +
400C ALA* 1.3 75.6 - - - +
402C LYS* 1.3 62.2 + - - +
404C TYR* 3.6 1.4 + - - +
405C ARG* 3.2 51.7 + - - +
414C LEU* 3.4 29.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398C GLN 3.2 16.3 + - - +
399C LEU* 3.6 26.5 - - - +
400C ALA 3.3 0.2 - - - -
401C ASP* 1.3 81.1 + - - +
403C ARG* 1.3 60.6 + - - +
405C ARG* 3.8 4.4 + - - +
406C THR* 2.7 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 403 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B SER* 4.0 23.7 + - - -
204B LEU* 3.4 27.8 - - - +
205B ASP* 5.5 0.6 + - - -
399C LEU* 3.0 24.4 + - + +
400C ALA* 4.1 4.0 - - - +
402C LYS* 1.3 81.0 - - + +
404C TYR* 1.3 59.2 + - - +
406C THR* 4.0 4.5 - - - -
407C GLY 3.1 3.8 + - - -
408C VAL* 2.9 61.7 + - + +
409C ASP* 3.1 46.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 404 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C THR* 3.8 4.1 - - + +
195C SER* 6.0 1.1 - - - -
201C ALA* 3.4 20.1 - - + +
205C ASP* 3.0 40.1 + - - +
400C ALA 3.1 16.1 + - - +
401C ASP 4.0 3.1 - - - +
402C LYS 3.4 0.4 - - - -
403C ARG* 1.3 74.0 - - - +
405C ARG* 1.3 99.9 + - - +
406C THR 3.1 1.8 - - - -
407C GLY* 3.0 20.1 + - - -
409C ASP* 4.0 14.1 - - - +
410C ASN* 4.4 8.1 - - - +
411C TYR* 3.6 45.5 - + + -
414C LEU* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 405 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C SER* 2.9 44.4 + - - +
191C LEU* 3.9 24.8 + - + +
192C THR* 3.0 33.3 + - - +
195C SER* 5.5 2.0 - - - -
401C ASP* 3.2 35.6 + - - +
402C LYS* 4.3 4.5 - - - +
403C ARG 3.6 0.2 - - - -
404C TYR* 1.3 100.3 - - - +
406C THR* 1.3 60.3 + - - +
411C TYR* 4.9 0.8 - - - -
414C LEU* 4.7 3.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 406 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402C LYS* 2.7 27.9 + - - +
403C ARG* 4.1 0.4 - - - -
404C TYR 3.1 0.6 - - - -
405C ARG* 1.3 78.1 - - - +
407C GLY* 1.3 57.5 + - - +
408C VAL* 3.7 24.0 - - + +
----------------------------------------------------------
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