Contacts of the helix formed by residues 399 - 422 (chain A) in PDB entry 4KZI
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 399 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 1.3 75.2 - - - +
400A ALA* 1.3 63.7 + - - +
401A GLY* 2.9 15.7 + - - -
402A ASP* 3.0 21.6 + - - +
403A VAL* 3.0 21.8 + - - +
477A ARG* 3.3 17.8 + - - +
581A LEU* 3.7 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASP* 1.3 75.3 - - - +
401A GLY* 1.3 57.0 + - - +
403A VAL* 3.3 1.7 + - - +
404A GLN* 2.9 31.4 + - - +
581A LEU* 3.8 15.9 - - + +
582A VAL* 3.9 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ASP* 2.9 8.3 + - - -
400A ALA* 1.3 74.7 - - - +
402A ASP* 1.3 65.8 + - - +
404A GLN* 3.4 5.1 + - - +
405A GLN* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 4.3 1.3 - - + -
399A ASP* 3.0 29.9 + - - +
401A GLY* 1.3 77.8 - - - +
403A VAL* 1.3 62.9 - - - +
405A GLN* 3.8 9.3 - - - +
406A PHE* 3.1 22.5 + - - +
474A GLN 5.5 3.0 - - - +
477A ARG* 2.7 44.9 + - + +
478A GLY* 3.8 23.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLU* 4.1 15.3 - - + -
399A ASP 3.0 13.6 + - - +
400A ALA* 3.9 6.1 - - - +
401A GLY 3.3 0.2 - - - -
402A ASP* 1.3 72.4 - - - +
404A GLN* 1.3 66.9 + - - +
406A PHE* 3.2 7.0 + - - +
407A TYR* 3.0 49.6 + - + -
478A GLY* 5.1 2.0 - - - -
576A LEU* 3.9 35.0 - - + +
579A GLU* 4.4 0.9 - - - +
581A LEU* 4.2 15.9 - - + +
582A VAL* 3.5 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ALA 2.9 18.7 + - - +
401A GLY* 3.9 5.6 - - - +
403A VAL* 1.3 79.7 - - - +
405A GLN* 1.3 57.6 + - - +
407A TYR* 3.4 9.3 + - - +
408A ASP* 2.8 66.3 + - - +
582A VAL* 3.6 28.1 - - + +
583A PRO* 4.9 4.0 + - - +
585A PRO* 6.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A LYS* 4.6 21.3 - - - +
401A GLY 3.0 18.5 + - - +
402A ASP* 3.8 8.8 - - - +
404A GLN* 1.3 77.0 - - - +
406A PHE* 1.3 63.1 + - - +
408A ASP* 3.1 8.5 + - + +
409A LEU* 2.8 41.8 + - + +
468A LEU* 4.8 3.4 - - + +
470A LEU* 3.7 32.8 - - - +
474A GLN 4.4 10.7 - - - +
475A CYS* 5.7 0.9 - - - -
479A PHE* 5.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ASP 3.1 14.9 + - - +
403A VAL* 3.4 10.8 - - - +
405A GLN* 1.3 77.1 - - - +
407A TYR* 1.3 83.3 + + - +
409A LEU* 3.2 2.8 + - - +
410A LEU* 3.1 46.3 + - + +
478A GLY* 3.8 13.0 - - - -
479A PHE* 3.7 51.3 - + + -
482A TRP* 3.8 17.7 - + - -
572A ARG* 4.0 21.1 - - + -
573A ILE* 4.2 13.5 - - + -
576A LEU* 3.5 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A VAL* 3.0 40.2 + - + +
404A GLN* 3.8 10.8 - - - +
406A PHE* 1.3 98.5 - + - +
408A ASP* 1.3 57.3 + - - +
410A LEU* 3.2 10.1 + - + +
411A SER* 2.7 34.3 + - - -
573A ILE* 4.5 7.7 + - + +
576A LEU* 3.7 20.5 - - + +
577A LYS* 4.1 10.0 + - - +
582A VAL* 3.7 22.9 + - + -
583A PRO 3.9 6.3 - - - -
584A PRO* 3.6 36.3 - - + +
585A PRO* 3.6 24.6 - - + +
588A ILE* 4.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A GLN* 2.8 58.1 + - - +
405A GLN* 3.1 8.8 + - + +
407A TYR* 1.3 72.8 - - - +
409A LEU* 1.3 60.8 + - + +
411A SER* 3.6 6.7 + - - -
412A GLY* 2.9 26.7 + - - -
585A PRO* 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN* 2.8 45.6 + - + +
406A PHE 3.5 4.3 - - - +
408A ASP* 1.3 76.2 - - + +
410A LEU* 1.3 67.3 + - - +
412A GLY* 5.4 0.2 - - - -
413A SER* 3.1 26.5 + - - -
447A PHE* 4.2 5.1 - - + -
464A PHE* 3.9 37.3 - - + -
465A CYS* 5.6 0.2 - - - -
466A SER* 5.4 2.7 - - - +
468A LEU* 3.9 23.8 - - + -
470A LEU* 4.5 4.5 - - + -
479A PHE* 4.1 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A PHE* 3.1 46.0 + - + +
407A TYR* 3.4 15.5 - - + +
409A LEU* 1.3 79.8 - - - +
411A SER* 1.3 55.9 + - - +
413A SER* 3.3 0.3 + - - -
414A LEU* 2.9 25.3 + - - +
443A PHE* 3.2 27.2 - - + -
444A LEU* 4.9 3.4 - - + -
447A PHE* 3.5 42.4 - - + -
479A PHE* 5.1 2.5 - - + -
482A TRP* 4.7 9.2 - - + -
573A ILE* 4.5 15.7 - - + -
588A ILE* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A TYR 2.7 21.1 + - - -
408A ASP* 3.6 8.3 - - - -
409A LEU 3.3 0.2 - - - -
410A LEU* 1.3 70.9 - - - +
412A GLY* 1.3 66.4 + - - +
414A LEU* 3.2 8.7 + - - +
415A GLU* 3.0 29.9 + - - +
585A PRO* 3.3 27.2 - - - +
587A ILE* 5.1 4.6 - - - +
588A ILE* 4.2 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASP 2.9 20.0 + - - -
409A LEU* 4.1 0.9 - - - -
411A SER* 1.3 74.8 - - - +
413A SER* 1.3 58.2 + - - +
415A GLU* 3.4 15.5 + - - +
416A VAL* 2.9 32.2 + - - +
465A CYS* 4.2 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A LEU 3.1 19.8 + - - -
410A LEU 3.6 2.9 - - - -
412A GLY* 1.3 75.3 - - - +
414A LEU* 1.3 60.1 + - - +
416A VAL* 3.3 1.6 + - - +
417A ILE* 2.7 43.5 + - - +
443A PHE* 3.4 9.1 - - - -
447A PHE* 3.1 29.5 - - - -
464A PHE* 6.5 0.2 - - - -
465A CYS* 3.7 21.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU 2.9 11.6 + - - +
411A SER* 3.2 9.6 + - - +
413A SER* 1.3 76.3 + - - +
415A GLU* 1.3 57.4 + - - +
417A ILE* 3.1 6.8 + - + -
418A ARG* 2.9 47.3 + - - +
439A LEU* 5.0 17.7 - - + +
440A GLU* 5.8 1.6 - - + -
443A PHE* 3.4 38.3 - - + -
587A ILE* 3.7 40.4 - - + -
588A ILE* 4.5 4.5 - - + -
591A ILE* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A SER* 3.0 18.2 + - - +
412A GLY* 3.5 19.8 - - - +
414A LEU* 1.3 77.0 - - - +
416A VAL* 1.3 65.0 + - + +
418A ARG* 3.4 12.1 + - - +
419A LYS* 3.2 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A SER* 3.1 35.3 - - - +
412A GLY 2.9 21.1 + - - +
413A SER 3.6 4.5 - - - +
415A GLU* 1.3 78.9 - - + +
417A ILE* 1.3 63.3 + - - +
419A LYS* 3.2 11.9 + - + +
420A TRP* 3.0 21.1 + - - +
450A ARG* 3.5 15.3 - - - +
465A CYS* 3.5 24.2 - - + +
466A SER* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A SER* 2.7 39.6 + - - +
414A LEU* 3.7 9.2 - - + +
416A VAL* 1.3 74.3 - - - +
418A ARG* 1.3 58.0 + - - +
420A TRP* 3.2 23.5 + - + -
421A ALA* 3.0 25.8 + - - +
439A LEU* 4.2 12.6 - - + +
443A PHE* 4.0 17.0 - - + -
446A LEU* 3.9 39.3 - - + -
447A PHE* 4.1 6.3 - - - +
450A ARG* 3.8 26.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 2.9 41.5 + - + +
415A GLU* 3.5 11.2 - - - +
417A ILE* 1.3 77.3 - - - +
419A LYS* 1.3 61.7 + - + +
421A ALA* 3.4 2.8 + - - +
422A GLU* 3.1 23.4 + - - +
427A PHE* 5.5 0.5 - - - -
436A ASP* 3.5 24.4 + - - +
439A LEU* 4.2 35.3 - - + +
440A GLU* 5.2 5.7 + - - +
587A ILE* 4.3 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLU* 3.2 32.3 + - - +
416A VAL* 3.2 13.1 + - + +
418A ARG* 1.3 76.2 - - + +
420A TRP* 1.3 65.7 + - - +
422A GLU* 3.1 38.4 + - - +
423A LYS* 3.5 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A LEU* 4.9 3.0 + - + +
371A ALA* 3.4 33.1 - - + +
372A HIS* 3.7 16.7 - - - +
375A SER* 3.7 20.6 - - - -
416A VAL 3.0 16.6 + - - +
417A ILE* 3.2 26.9 + - + -
419A LYS* 1.3 75.8 - - - +
421A ALA* 1.3 69.9 + - + +
423A LYS* 3.0 21.0 + - - +
424A ILE* 3.5 28.3 + - + +
446A LEU* 4.0 24.9 - - + -
450A ARG* 4.4 11.9 - - - +
504A ALA 4.9 2.3 + - - -
507A SER* 3.7 41.0 + - - -
508A ALA* 3.9 13.5 - - + -
511A LEU* 3.9 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ILE 3.0 16.1 + - - +
418A ARG 3.8 3.8 - - - +
419A LYS 3.3 0.2 - - - -
420A TRP* 1.3 78.4 - - + +
422A GLU* 1.3 58.6 + - - +
424A ILE* 2.8 31.0 + - - +
427A PHE* 3.3 39.5 - - + +
439A LEU* 3.7 12.3 - - + -
511A LEU* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ARG* 3.1 12.6 + - + +
419A LYS* 3.1 32.9 - - - +
420A TRP 3.2 0.4 - - - -
421A ALA* 1.3 78.4 - - - +
423A LYS* 1.3 74.1 + - + +
424A ILE 3.4 3.4 + - - +
427A PHE* 4.1 9.6 - - + -
428A ALA* 4.2 23.0 - - + +
435A GLN* 5.9 2.2 - - - +
----------------------------------------------------------
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