Contacts of the helix formed by residues 415 - 434 (chain A) in PDB entry 5JZU
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 415 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS* 3.8 21.1 - - + +
333A LEU* 3.4 27.6 - - - +
334A LEU 3.8 2.9 - - - +
335A ASN* 3.7 22.9 - - + +
375A PRO* 4.5 3.8 - - + -
413A ASP 3.5 9.2 - - - +
414A VAL* 1.3 85.1 - - + +
416A ALA* 1.3 62.2 + - - +
418A LEU* 3.2 10.9 + - + +
419A LEU* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A VAL 3.6 2.1 + - - -
415A PRO* 1.3 71.2 - - - +
417A ASP* 1.3 61.9 + - - +
419A LEU* 3.0 10.7 + - - +
420A LYS* 2.8 33.4 + - - +
450A PHE* 3.7 21.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LYS 4.7 1.4 - - - +
331A PRO* 3.8 14.6 - - + +
332A LYS* 3.2 39.2 + - - +
333A LEU* 3.9 9.6 - - + -
415A PRO 3.4 0.2 - - - -
416A ALA* 1.3 80.1 - - - +
418A LEU* 1.3 56.5 + - - +
420A LYS* 3.8 9.2 + - - +
421A LEU* 3.0 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS 4.3 0.4 + - - -
333A LEU* 3.5 49.0 - - + +
375A PRO* 3.6 41.1 - - + +
376A ARG* 4.0 4.7 - - - +
379A TYR* 3.4 43.1 - - + -
408A VAL* 4.4 8.3 - - + -
414A VAL* 5.5 1.1 - - + -
415A PRO* 3.2 12.4 + - + +
416A ALA 3.2 0.6 - - - -
417A ASP* 1.3 77.6 - - - +
419A LEU* 1.3 66.4 + - - +
421A LEU* 3.8 2.0 - - + +
422A SER* 3.0 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A VAL* 5.4 2.5 - - + -
409A ALA* 3.8 37.9 - - + +
414A VAL* 4.6 19.2 - - + +
415A PRO 2.8 14.5 + - - +
416A ALA* 3.3 10.3 - - - +
418A LEU* 1.3 77.0 - - - +
420A LYS* 1.3 63.1 + - - +
422A SER* 4.0 3.5 - - - -
423A LEU* 3.3 35.0 + - + +
445A ARG* 5.8 0.4 - - - +
449A LEU* 4.3 21.3 - - + -
450A PHE* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 2.8 18.6 + - - +
417A ASP* 3.8 8.0 + - - +
419A LEU* 1.3 75.0 - - - +
421A LEU* 1.3 64.6 + - + +
423A LEU* 3.9 0.9 - - - +
424A LYS* 2.9 50.0 + - + +
446A LEU* 4.2 4.0 - - + +
450A PHE* 3.8 43.1 - - + -
453A ASP* 3.0 32.9 + - - +
456A LEU* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A PRO* 4.9 11.7 - - + -
333A LEU* 3.7 28.7 - - + -
379A TYR* 4.1 24.4 + - + +
417A ASP* 3.0 22.1 + - + +
418A LEU* 3.8 4.3 - - - +
420A LYS* 1.3 76.8 - - - +
422A SER* 1.3 62.9 + - - +
424A LYS* 3.8 10.5 - - + +
425A ARG* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TYR* 3.8 19.5 - - - -
405A TYR* 2.9 55.1 + - - +
408A VAL* 3.5 18.6 - - - +
409A ALA* 5.7 0.7 - - - -
418A LEU 3.0 18.8 + - - -
419A LEU* 4.0 3.6 - - - -
421A LEU* 1.3 78.1 - - - +
423A LEU* 1.3 62.7 + - - +
425A ARG 3.7 0.2 + - - -
426A ARG 3.2 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A TYR 4.4 9.2 - - - +
406A GLN* 4.6 7.4 - - + -
409A ALA* 3.9 24.2 - - + -
419A LEU* 3.3 26.6 + - + +
422A SER* 1.3 75.6 - - - +
424A LYS* 1.3 67.0 + - - +
426A ARG* 3.2 15.5 + - - +
427A SER* 3.1 19.1 + - - -
442A THR* 3.5 16.2 - - + +
445A ARG* 4.3 19.5 - - + +
446A LEU* 3.7 26.7 - - + -
449A LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS* 2.9 40.8 + - + +
421A LEU* 3.8 10.5 - - + +
423A LEU* 1.3 77.2 - - - +
425A ARG* 1.3 56.8 + - - +
427A SER* 3.1 7.6 + - - -
428A ASP* 2.9 26.8 + - - +
443A LEU* 6.3 0.4 - - + -
446A LEU* 3.9 9.8 - - + +
455A SER* 5.2 8.2 + - - -
456A LEU* 3.9 27.1 - - + -
459A ASP* 4.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 425 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A TYR* 5.8 2.7 - - - +
386A ASP* 2.7 31.7 + - - -
390A GLU* 4.5 2.8 + - - +
405A TYR* 3.5 32.6 + - + +
421A LEU 3.1 14.8 + - - +
422A SER 4.0 3.8 - - - +
424A LYS* 1.3 76.3 - - - +
426A ARG* 1.3 65.6 + - - +
428A ASP* 3.5 17.8 + - - +
429A ARG* 3.0 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE* 3.1 34.7 + - + +
403A GLU* 4.6 5.5 + - - +
405A TYR* 4.0 12.5 - - + -
406A GLN* 2.7 48.4 + - - +
422A SER 3.2 14.3 + - - +
423A LEU* 3.2 19.8 + - - +
424A LYS 3.1 0.6 - - - -
425A ARG* 1.3 77.9 - - - +
427A SER* 1.3 58.2 + - - +
429A ARG* 3.2 3.5 + - - +
430A GLN* 2.8 59.5 + - + +
438A GLY 4.8 0.6 + - - -
442A THR* 2.8 32.1 + - - +
445A ARG* 5.9 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU 3.1 9.1 + - - -
424A LYS* 3.4 9.6 - - - -
426A ARG* 1.3 79.1 - - - +
428A ASP* 1.3 65.2 + - - +
430A GLN* 3.0 12.1 + - - +
431A GLN* 2.8 29.9 + - - +
439A SER* 2.7 24.7 + - - -
442A THR* 4.1 11.8 - - - +
443A LEU* 3.6 27.4 - - - +
446A LEU* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS 2.9 13.4 + - - +
425A ARG* 3.5 24.5 + - - +
426A ARG 3.3 0.2 - - - -
427A SER* 1.3 76.3 + - - +
429A ARG* 1.3 95.6 + - - +
431A GLN* 3.2 12.0 + - - +
432A PHE* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASP* 4.2 5.7 + - - +
390A GLU* 3.4 20.6 + - - -
398A LEU* 3.5 38.9 - - + +
402A ILE* 5.6 8.7 - - + -
405A TYR* 5.7 3.4 - - + -
425A ARG* 3.0 56.5 + - + +
426A ARG* 3.8 3.6 - - - +
428A ASP* 1.3 105.7 + - - +
430A GLN* 1.3 59.9 + - - +
432A PHE* 3.0 44.0 + - - +
433A LEU* 2.9 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ILE* 4.8 11.7 - - + +
426A ARG* 2.8 52.4 + - + +
427A SER* 3.4 8.9 - - - +
429A ARG* 1.3 76.6 - - - +
431A GLN* 1.3 54.9 + - - +
433A LEU* 3.3 6.0 + - + +
434A GLY 3.0 6.2 + - - -
435A HIS* 2.7 54.7 + - + +
438A GLY* 3.8 19.8 - - - -
439A SER* 3.4 16.8 - - - -
442A THR* 2.8 25.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER* 2.8 16.9 + - - +
428A ASP* 3.4 11.5 - - - +
430A GLN* 1.3 74.5 - - - +
432A PHE* 1.3 65.2 + - - +
434A GLY* 3.3 2.9 + - - -
436A MET* 3.1 38.6 - - + +
439A SER* 3.2 29.8 + - - +
443A LEU* 4.1 12.9 - - - +
459A ASP 5.1 1.0 + - - -
462A VAL* 4.9 5.4 - - - +
463A GLY* 4.4 7.3 - - - +
466A LEU* 3.7 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLU* 5.8 4.7 - - - -
398A LEU* 4.0 23.1 - - + -
428A ASP 3.0 9.5 + - - +
429A ARG* 3.0 45.8 - - - +
431A GLN* 1.3 78.4 - - - +
433A LEU* 1.3 67.7 + - + +
434A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A ASN* 4.1 35.4 - - + +
398A LEU* 3.8 27.8 - - + +
399A ARG* 4.4 14.1 - - + +
402A ILE* 5.7 4.3 - - + -
429A ARG* 2.9 19.0 + - + +
430A GLN* 3.9 6.3 - - + +
431A GLN 3.2 0.2 - - - -
432A PHE* 1.3 85.9 - - + +
434A GLY* 1.3 59.0 + - - +
435A HIS* 3.9 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A GLN 3.0 3.2 + - - -
431A GLN 3.3 8.3 + - - -
432A PHE 3.3 4.4 + - - -
433A LEU* 1.3 79.6 - - - +
435A HIS* 1.3 59.4 + - - +
436A MET* 2.9 27.8 + - - +
----------------------------------------------------------
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