Contacts of the helix formed by residues 416 - 428 (chain A) in PDB entry 2EBT
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 416 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 4.2 1.7 - - - -
414A PHE* 4.2 2.9 - - - +
415A ALA* 1.3 82.3 - - + +
417A SER* 1.3 68.2 + - - +
418A ASP* 4.4 6.5 - - + +
419A GLU* 3.2 40.7 + - + +
420A LEU* 3.3 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 2.6 46.6 + - - -
415A ALA 3.8 3.0 + - - -
416A ARG* 1.3 73.7 - - - +
418A ASP* 1.3 63.1 + - - +
420A LEU* 3.2 8.6 + - - +
421A THR* 3.2 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 3.3 7.5 - - + +
417A SER* 1.3 78.7 - - - +
419A GLU* 1.3 67.4 + - + +
421A THR* 3.2 14.0 + - - +
422A ARG* 3.1 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 4.5 19.7 - - + -
415A ALA 6.0 0.2 - - - +
416A ARG* 3.2 31.2 + - + +
418A ASP* 1.3 82.1 - - - +
420A LEU* 1.3 63.7 + - - +
422A ARG* 3.4 18.2 + - - +
423A HIS* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403A TYR* 4.2 25.1 - - + -
404A LYS 4.4 9.6 - - - +
405A CYS* 4.0 25.8 - - + +
414A PHE* 3.4 40.8 - - + -
416A ARG 3.3 6.3 + - - +
417A SER* 3.2 9.2 + - - +
419A GLU* 1.3 77.0 - - - +
421A THR* 1.3 71.6 + - - +
423A HIS* 2.7 18.3 + - + +
424A TYR* 2.8 24.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER* 3.2 13.9 + - - -
418A ASP* 3.4 17.8 - - - +
420A LEU* 1.3 82.1 - - - +
422A ARG* 1.3 63.9 + - - +
424A TYR* 3.2 15.9 + - - +
425A ARG* 3.3 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ASP* 3.1 25.3 + - - +
419A GLU* 3.6 21.4 + - - +
420A LEU 3.1 0.6 - - - -
421A THR* 1.3 78.7 - - - +
423A HIS* 1.3 64.7 + - - +
425A ARG* 2.9 30.7 - - + +
426A LYS* 3.8 4.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ZN 2.0 37.6 - - - -
405A CYS* 3.6 7.6 - - - -
410A CYS* 3.7 7.7 - - - -
412A TRP* 5.1 6.9 - + - +
414A PHE* 3.2 43.6 - + + -
419A GLU 3.1 7.1 + - - +
420A LEU* 2.7 14.7 + - + +
422A ARG* 1.3 75.3 - - - +
424A TYR* 1.3 65.5 + - - +
426A LYS* 2.9 34.7 + - + +
427A HIS* 3.6 9.8 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A CYS* 4.0 22.9 - - - -
406A THR* 3.9 29.4 + - - -
407A TRP* 3.3 31.1 - + - -
420A LEU* 2.8 24.9 + - + +
421A THR* 3.4 14.6 - - - +
423A HIS* 1.3 75.3 - - + +
425A ARG* 1.3 63.4 + - - +
427A HIS* 2.8 25.5 + + - +
428A THR* 3.1 34.6 + - + -
----------------------------------------------------------
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
----------------------------------------------------------
421A THR* 3.3 31.3 + - - +
422A ARG* 2.9 26.9 + - + +
424A TYR* 1.3 77.2 - - - +
426A LYS* 1.3 65.8 + - + +
428A THR* 2.9 30.0 + - - -
429A GLY* 3.0 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ARG 4.4 2.9 - - - +
423A HIS* 3.1 28.0 - - + +
425A ARG* 1.3 80.1 - - - +
427A HIS* 1.3 68.6 - - + +
429A GLY 3.5 3.5 + - - -
430A ALA 2.7 31.2 + - - +
431A LYS* 4.9 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ZN 2.1 35.1 - - - -
405A CYS* 3.6 11.2 - - - -
407A TRP* 3.5 54.5 + + + -
410A CYS* 4.0 8.1 - - + -
423A HIS* 3.2 13.5 + + - -
424A TYR* 2.8 23.9 + + - +
426A LYS* 1.3 74.7 - - + +
428A THR* 1.3 56.4 + - - +
429A GLY 3.0 11.8 + - - +
430A ALA 5.1 0.7 - - - +
431A LYS* 3.2 27.3 + - - +
443A SER* 5.3 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A TRP* 4.4 8.7 - - + -
424A TYR* 3.1 32.9 + - + -
425A ARG* 2.9 28.2 + - - +
427A HIS* 1.3 74.0 - - - +
429A GLY* 1.3 55.3 + - - +
----------------------------------------------------------
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