Contacts of the helix formed by residues 400 - 425 (chain H) in PDB entry 2ACL
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 LEU 400 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G GLU* 3.4 40.2 - - + +
397G TYR* 4.2 29.0 - - + -
398G ALA* 4.5 13.5 - - + +
401G GLU* 6.1 1.3 - - - +
398H ASP* 2.7 2.2 - - - -
399H PRO* 1.3 85.7 - - + +
401H MET* 1.3 58.0 + - - +
403H PRO* 2.8 21.7 - - + +
404H ARG* 2.9 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 401 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H LEU* 3.6 46.9 - - + +
349H LEU* 4.2 6.5 - - + -
391H VAL* 4.2 16.6 - - + +
395H HIS* 3.9 35.0 - - + +
398H ASP* 3.0 29.5 + - + +
400H LEU* 1.3 78.3 - - - +
402H PHE* 1.3 65.3 + - - +
404H ARG* 3.6 9.8 - - - +
405H MET* 2.9 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 402 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401G GLU* 5.6 0.2 - - - -
415G PHE* 4.6 15.3 - + - -
416G ALA* 4.0 13.7 - - + -
384H VAL* 3.7 23.8 - - + -
385H GLU* 5.1 2.5 - - - -
387H LEU* 4.3 13.7 - - + -
388H HIS* 3.1 67.3 - + + +
391H VAL* 4.3 10.6 - - + +
398H ASP 4.6 0.4 + - - -
399H PRO 4.0 6.3 + - - +
401H MET* 1.3 79.6 - - - +
403H PRO* 1.4 68.9 - - + +
405H MET* 3.5 4.8 + - - +
406H LEU* 3.2 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 403 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397G TYR* 4.0 31.2 - - + -
401G GLU* 5.2 0.7 - - - +
415G PHE* 3.4 35.0 - - + -
419G LEU* 4.2 11.0 - - + -
399H PRO 3.4 8.3 - - - +
400H LEU* 2.8 30.3 - - + +
402H PHE* 1.4 86.0 - - + +
404H ARG* 1.3 62.5 + - - +
405H MET 2.7 6.9 + - - -
406H LEU* 3.1 1.9 + - + +
407H MET* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 404 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390G GLU* 4.9 8.3 - - - +
394G GLU* 3.2 24.2 + - - +
397G TYR* 4.7 12.9 - - + +
347H LEU* 4.1 26.1 - - + +
398H ASP* 3.8 23.1 + - - +
400H LEU* 2.9 54.0 + - - +
401H MET* 3.6 11.1 - - - +
403H PRO* 1.3 76.6 - - - +
405H MET* 1.3 60.5 + - - +
407H MET* 4.2 3.3 - - - +
408H LYS* 3.5 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 405 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H LEU* 4.0 19.5 - - + -
349H LEU* 4.0 21.8 - - + -
353H GLU* 4.2 20.0 - - + +
357H LEU* 4.3 19.2 - - + +
387H LEU* 3.2 41.7 - - + -
391H VAL* 3.7 22.4 - - - -
401H MET* 2.9 24.5 + - - +
402H PHE* 3.6 5.2 - - - +
403H PRO 2.7 1.4 + - - -
404H ARG* 1.3 75.5 - - - +
406H LEU* 1.3 57.4 + - - +
407H MET 3.1 1.3 - - - -
408H LYS* 2.7 38.9 + - + +
409H LEU 3.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416G ALA* 4.2 18.4 - - + -
419G LEU* 4.5 17.5 - - + -
420G LEU* 4.0 26.4 - - + +
357H LEU* 5.2 2.5 - - + -
360H ILE* 4.6 12.3 - - + -
384H VAL* 4.2 14.4 - - + -
387H LEU* 4.8 4.5 - - + -
402H PHE* 3.2 50.2 + - + +
403H PRO* 3.1 5.6 + - + +
405H MET* 1.3 77.8 - - - +
407H MET* 1.3 57.7 + - + +
409H LEU* 2.7 48.2 + - + +
410H VAL* 3.8 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 407 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373G ILE* 4.2 11.0 - - - -
393G ARG* 5.0 12.3 - - - +
397G TYR* 3.0 32.5 - - + +
419G LEU* 3.6 36.3 - - + +
422G LEU* 3.3 35.0 - - + -
403H PRO 3.0 15.8 + - - +
404H ARG* 4.2 5.8 - - - +
406H LEU* 1.3 78.7 - - - +
408H LYS* 1.3 55.8 + - - +
410H VAL* 2.6 46.9 + - + +
411H SER* 3.2 6.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 408 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340H PHE* 3.6 27.6 - - + -
343H ALA* 4.5 21.5 - - - +
344H MET* 3.7 28.0 - - - +
347H LEU* 4.5 13.0 - - + +
357H LEU* 4.6 11.0 - - + -
404H ARG* 3.5 23.1 + - - +
405H MET* 2.7 25.5 + - - +
407H MET* 1.3 74.6 - - - +
409H LEU* 1.3 60.7 + - - +
411H SER* 3.2 12.3 + - - +
412H LEU* 3.1 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420G LEU* 4.0 22.2 - - + -
423G PRO* 4.2 15.3 - - + +
294H GLU* 4.8 2.4 - - - +
357H LEU* 3.9 26.7 - - + -
360H ILE* 3.6 25.8 - - + -
361H SER* 4.1 30.5 - - - +
380H GLN* 4.7 3.1 - - - +
406H LEU* 2.7 23.9 + - + +
408H LYS* 1.3 78.2 - - - +
410H VAL* 1.3 61.5 + - - +
412H LEU* 3.4 24.7 - - + +
413H ARG* 3.7 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 410 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393G ARG* 5.9 3.4 - - - +
422G LEU* 3.6 17.5 - - + +
423G PRO* 3.4 37.0 - - + -
426G ARG* 3.7 43.5 - - + +
406H LEU 4.6 1.3 - - - +
407H MET* 2.6 38.4 + - + +
409H LEU* 1.3 67.6 - - - +
411H SER* 1.3 65.5 + - - +
412H LEU 3.0 2.0 + - - -
413H ARG* 3.0 17.5 + - - +
414H THR* 3.8 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 411 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379G ASP* 3.9 16.6 + - - -
426G ARG* 4.8 4.8 + - - +
340H PHE* 4.2 21.3 - - - -
407H MET 3.2 7.7 + - - -
408H LYS* 3.2 16.3 + - - +
410H VAL* 1.3 79.9 - - - +
412H LEU* 1.3 56.2 + - - +
414H THR* 3.1 31.5 + - - -
415H LEU* 3.2 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 412 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294H GLU* 3.8 34.1 - - + +
297H LEU* 3.7 37.6 - - + +
298H LEU* 4.2 24.5 - - + -
340H PHE* 3.9 19.7 - - + -
357H LEU* 5.7 0.2 - - + -
361H SER* 4.8 0.9 - - - +
408H LYS* 3.1 19.7 + - + +
409H LEU* 3.4 29.2 - - + +
410H VAL 3.0 0.8 + - - -
411H SER* 1.3 73.9 - - - +
413H ARG* 1.3 60.9 + - - +
414H THR 3.1 2.0 - - - -
415H LEU* 3.8 5.5 - - + +
416H SER* 2.9 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 413 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423G PRO* 3.3 42.3 + - + +
424G ALA* 4.0 1.4 - - - +
426G ARG* 4.5 4.7 - - + -
427G SER* 3.2 39.0 + - - +
430G LEU* 3.7 3.8 - - - +
294H GLU* 3.3 30.6 + - - -
364H SER* 4.0 4.9 + - - -
366H ASP* 2.6 33.6 + - - +
367H ARG* 3.5 20.2 - - - +
409H LEU* 3.9 13.5 + - - +
410H VAL 3.0 7.9 + - - +
412H LEU* 1.3 75.8 - - - +
414H THR* 1.3 61.2 + - - +
416H SER* 3.6 6.0 - - - -
417H SER* 3.1 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 414 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426G ARG* 3.4 32.1 + - - +
430G LEU* 3.6 18.4 - - + +
410H VAL 4.0 1.2 + - - -
411H SER* 3.1 12.5 + - - -
412H LEU 3.1 0.2 - - - -
413H ARG* 1.3 76.0 - - - +
415H LEU* 1.3 61.3 + - + +
416H SER 3.0 1.1 - - - -
417H SER* 2.7 24.5 + - - -
418H VAL* 2.8 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 415 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H LEU* 3.2 28.5 - - + -
333H PHE* 3.7 6.9 - - + -
336H PRO* 3.8 36.8 - - + +
337H ILE* 4.0 19.5 - - + +
340H PHE* 3.5 40.2 - - + -
411H SER* 3.2 15.2 + - - +
412H LEU* 3.9 9.6 - - + +
413H ARG 3.5 0.2 - - - -
414H THR* 1.3 79.6 - - + +
416H SER* 1.3 57.4 + - - +
418H VAL* 3.1 9.1 + - - +
419H HIS* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 416 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H THR* 4.9 1.4 + - - -
293H ILE* 3.7 24.8 - - - +
294H GLU* 4.3 16.1 + - - -
297H LEU* 4.4 0.6 - - - +
412H LEU 2.9 19.3 + - - -
413H ARG* 3.6 11.0 - - - -
415H LEU* 1.3 79.0 - - - +
417H SER* 1.3 55.9 + - - +
419H HIS* 3.5 10.1 + - - +
420H SER* 3.1 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 417 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430G LEU* 3.6 30.9 + - - +
434G GLU* 4.8 8.3 + - - -
413H ARG 3.1 13.9 + - - -
414H THR* 2.7 15.7 + - - -
416H SER* 1.3 70.1 - - - +
418H VAL* 1.3 65.3 + - - -
420H SER* 3.0 24.1 + - - -
421H GLU* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 418 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H GLN* 3.9 2.9 - - - +
332H GLU* 3.2 30.5 - - + +
333H PHE* 3.3 24.7 - - + -
336H PRO* 5.0 9.6 - - + -
414H THR* 2.8 28.0 + - + +
415H LEU* 3.5 9.4 - - - +
417H SER* 1.3 76.2 - - - +
419H HIS* 1.3 61.8 + - - +
421H GLU* 3.3 19.0 + - - +
422H GLN* 3.0 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 419 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H L05 3.4 25.6 + + - -
293H ILE* 3.4 28.2 - - + +
333H PHE* 3.5 22.9 - + + -
415H LEU 2.8 17.2 + - - +
416H SER 3.6 7.2 + - - +
418H VAL* 1.3 74.6 - - - +
420H SER* 1.3 63.8 + - - +
422H GLN* 3.1 8.2 + - + +
423H VAL* 2.9 42.8 + - + +
441H TRP* 3.3 56.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 420 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434G GLU* 5.7 1.2 + - - -
441G LEU* 6.1 1.4 - - - +
416H SER 3.1 13.9 + - - -
417H SER* 3.0 19.3 + - - -
419H HIS* 1.3 80.6 - - - +
421H GLU* 1.3 62.6 + - - +
423H VAL* 3.1 17.7 + - - +
424H PHE* 3.3 8.8 + - - +
443H VAL* 6.0 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 421 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ARG* 4.7 7.1 + - - +
434G GLU* 6.0 2.4 - - - +
438G PHE* 5.0 19.3 - - + -
330H GLN* 4.3 2.9 - - - +
332H GLU* 4.6 11.7 - - - +
417H SER* 3.1 22.2 + - - +
418H VAL* 3.7 19.7 - - - +
420H SER* 1.3 76.5 - - - +
422H GLN* 1.3 55.0 + - - +
424H PHE* 2.7 32.3 + - + +
425H ALA* 2.9 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 422 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H L05 3.4 31.7 - - + +
328H GLY 4.3 0.8 + - - -
329H LEU* 3.2 7.4 - - - +
330H GLN* 2.6 66.0 + - - +
333H PHE* 4.1 16.7 - - + -
418H VAL 3.0 11.0 + - - +
419H HIS* 3.3 13.2 - - + +
421H GLU* 1.3 78.4 - - - +
423H VAL* 1.3 61.2 + - - +
425H ALA* 3.3 18.0 + - - +
426H LEU* 3.5 7.4 + - - +
429H GLN* 4.0 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 423 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H L05 5.0 6.3 - - + -
419H HIS* 2.9 44.1 + - + +
420H SER* 3.1 11.8 + - - +
422H GLN* 1.3 75.7 - - - +
424H PHE* 1.3 58.8 + - - +
426H LEU* 3.2 26.2 - - - +
427H ARG* 4.6 2.1 + - - +
433H LEU* 4.5 5.8 - - + -
441H TRP* 3.9 35.4 - - + +
442H ASP* 3.7 25.0 - - - +
443H VAL* 5.3 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 424 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 3.5 33.2 - - + -
302C ARG* 4.8 13.0 - - + -
305C TRP* 4.0 23.6 - + - -
437G PHE* 4.1 6.3 - + - -
438G PHE* 3.7 43.5 - + + -
441G LEU* 4.5 11.9 - - + -
420H SER 3.3 8.3 + - - +
421H GLU* 2.7 14.1 + - + +
423H VAL* 1.3 74.2 - - - +
425H ALA* 1.3 57.9 + - - +
426H LEU 2.7 15.1 + - - -
427H ARG* 3.0 38.2 + - - +
428H LEU* 3.8 22.8 - - + +
443H VAL* 6.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 425 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 4.5 4.1 - - + +
302C ARG* 3.3 41.1 - - - +
330H GLN* 3.9 1.1 - - - +
421H GLU 2.9 7.1 + - - +
422H GLN* 3.3 20.6 + - - +
424H PHE* 1.3 80.8 - - - +
426H LEU* 1.3 56.5 + - - +
427H ARG 3.3 0.7 - - - -
428H LEU* 3.7 10.6 + - - +
429H GLN* 3.0 32.7 + - - +
----------------------------------------------------------
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