Contacts of the helix formed by residues 443 - 456 (chain A) in PDB entry 5KE6
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 ARG 443 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ALA* 4.8 18.3 - - + +
422A ARG* 5.0 0.7 - - - +
430A TYR* 3.5 7.9 - - - -
441A PHE* 3.3 5.6 - - - +
442A ALA* 1.3 86.7 - - + +
444A SER* 1.3 65.7 + - - +
445A ASP* 2.8 33.1 + - - +
446A GLU* 3.1 37.2 + - + +
447A LEU 3.3 8.3 + - - -
5B T 3.4 34.4 + - - +
6B G 2.8 48.7 + - - -
7B T 3.8 11.6 + - - +
4C A 3.4 10.7 - - - +
5C C 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR* 3.5 40.2 - - - -
443A ARG* 1.3 71.6 - - - +
445A ASP* 1.3 60.7 + - - +
447A LEU* 3.0 8.3 + - - +
448A THR* 3.0 27.7 + - - -
2C C 4.4 11.2 + - - +
3C C 3.8 38.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ARG* 2.8 45.8 + - - +
444A SER* 1.3 82.5 + - - +
446A GLU* 1.3 63.1 + - - +
448A THR* 3.3 11.6 + - - +
449A ARG* 3.0 35.3 + - - +
5B T 3.8 10.7 - - - +
3C C 4.2 6.0 + - + -
4C A 3.5 37.1 + - + +
5C C 5.0 0.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PHE* 3.9 22.9 - - + +
442A ALA* 3.4 15.0 + - - +
443A ARG* 3.1 40.3 + - + +
445A ASP* 1.3 78.5 - - - +
447A LEU* 1.3 62.6 + - - +
449A ARG* 3.3 14.0 + - - +
450A HIS* 3.0 21.5 + - - +
4B G 4.6 22.7 + - + +
5B T 3.5 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A TYR* 4.0 24.9 - - + -
431A HIS 3.7 20.6 - - - +
432A CYS* 3.6 33.4 - - + +
441A PHE* 3.8 23.2 - - + -
443A ARG 3.3 2.4 + - - -
444A SER* 3.0 10.5 + - - +
446A GLU* 1.3 75.8 - - - +
448A THR* 1.3 61.2 + - - +
450A HIS* 3.2 3.8 + - + -
451A TYR* 2.8 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A SER* 3.0 13.7 + - - -
445A ASP* 3.5 14.2 - - - -
446A GLU 3.3 0.2 - - - -
447A LEU* 1.3 77.0 - - - +
449A ARG* 1.3 62.3 + - + +
451A TYR* 3.3 10.4 + - + +
452A ARG* 3.2 54.9 + - - +
3C C 5.5 2.6 + - - -
4C A 4.4 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A ASP* 3.0 22.1 + - - +
446A GLU* 3.5 14.5 - - - +
447A LEU 3.2 0.2 - - - -
448A THR* 1.3 76.7 - - + +
450A HIS* 1.3 61.8 + - - +
452A ARG* 3.2 19.4 + - - +
453A LYS* 3.4 11.9 + - - +
471A ARG* 3.3 49.5 - - + +
3B G 3.8 16.9 + - - +
4B G 2.7 52.3 + - - -
5B T 3.3 18.5 + - - +
6C A 3.4 10.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A CYS* 3.6 16.6 - - + -
437A CYS* 3.3 4.3 - - - -
439A TRP* 3.8 27.8 - + + +
441A PHE* 3.4 33.9 - + + -
446A GLU 3.0 7.3 + - - +
447A LEU* 3.5 8.3 - - + +
449A ARG* 1.3 76.3 - - - +
451A TYR* 1.3 63.7 + - - +
453A LYS* 2.8 45.0 + - + +
454A HIS* 3.1 13.8 + + - -
502A ZN 2.0 37.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A HIS 4.1 1.2 + - - -
432A CYS* 3.6 25.7 - - - -
433A ASP* 2.8 40.1 + - - +
434A TRP* 4.2 19.3 - + - -
447A LEU* 2.8 48.0 + - + +
448A THR* 3.3 9.6 + - + +
450A HIS* 1.3 73.3 - - - +
452A ARG* 1.3 58.6 + - + +
454A HIS* 3.1 13.2 + + - +
455A THR* 3.0 32.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A THR* 3.2 34.3 + - - +
449A ARG* 3.2 13.3 + - - +
450A HIS 3.1 1.4 - - - -
451A TYR* 1.3 75.6 - - + +
453A LYS* 1.3 60.6 + - - +
455A THR* 3.4 10.8 - - - +
456A GLY* 2.8 29.3 + - - -
457A HIS* 3.9 36.0 + - + +
459A PRO* 3.6 23.7 - - - +
460A PHE* 4.2 8.3 - - - -
470A SER* 3.1 36.6 + - - -
471A ARG* 5.5 1.2 - - - +
4C A 4.8 11.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A ARG 3.4 8.6 + - - +
450A HIS* 2.8 38.3 + - + +
452A ARG* 1.3 78.6 - - - +
454A HIS* 1.3 60.9 + - + +
456A GLY* 4.0 3.8 + - - -
2B A 5.0 7.2 - - - +
3B G 3.2 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A CYS* 3.6 3.1 - - - -
434A TRP* 3.3 69.7 + + + -
437A CYS* 4.1 8.5 - - + -
450A HIS* 3.1 26.3 + + - -
451A TYR* 3.1 13.5 + + - +
453A LYS* 1.3 81.7 - - + +
455A THR* 1.3 60.0 + - - +
502A ZN 2.1 36.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 455 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A TRP* 4.1 20.2 - - + -
451A TYR* 3.0 21.0 + - + +
452A ARG* 3.4 5.9 - - - +
454A HIS* 1.3 79.9 - - - +
456A GLY* 1.3 61.4 + - - +
457A HIS* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 456 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A ARG 2.8 14.5 + - - -
453A LYS 4.0 3.8 + - - -
454A HIS 3.5 2.4 - - - -
455A THR* 1.3 75.9 - - - +
457A HIS* 1.3 64.4 + - - +
458A ARG* 3.3 22.5 + - - +
----------------------------------------------------------
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