Contacts of the helix formed by residues 424 - 432 (chain A) in PDB entry 1TAQ
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 GLU 424 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLU 4.0 12.1 - - - +
422A GLY* 4.2 3.1 + - - +
423A GLU* 1.3 73.1 + - - +
425A ARG* 1.3 61.1 + - + +
427A LEU* 3.6 20.2 - - - +
428A TRP* 3.0 28.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
423A GLU* 3.3 1.2 - - + +
424A GLU* 1.3 76.3 - - + +
426A LEU* 1.3 65.7 + - - +
428A TRP* 3.7 5.7 + - - +
429A LEU* 3.3 27.8 + - - +
721A GLU* 4.1 13.1 + - - +
722A THR 4.0 3.4 + - - -
723A LEU 2.9 29.8 + - - -
724A PHE* 3.6 20.4 + - - +
725A GLY* 3.6 24.6 - - - +
727A ARG* 4.7 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 3.9 31.9 - - + +
380A LEU* 4.3 22.0 - - + -
420A LEU* 3.8 19.3 - - + -
423A GLU* 3.3 36.2 + - + +
425A ARG* 1.3 76.2 - - - +
427A LEU* 1.3 66.8 + - - +
429A LEU* 3.0 16.5 + - + +
430A TYR* 3.0 21.5 + - - +
725A GLY 3.7 23.3 - - - +
726A ARG* 4.9 0.2 - - - -
727A ARG* 4.3 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 4.5 13.2 - - + -
420A LEU* 3.0 49.1 - - + +
421A GLU* 3.3 36.3 - - - +
423A GLU 2.9 22.1 + - - +
424A GLU* 3.6 23.8 - - - +
426A LEU* 1.3 77.4 - - - +
428A TRP* 1.3 61.5 + - - +
430A TYR* 3.7 3.1 - - - +
431A ARG* 3.1 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLU 3.0 19.4 + - - +
425A ARG* 3.8 6.5 - - - +
427A LEU* 1.3 77.5 - - - +
429A LEU* 1.3 83.4 + - + +
431A ARG* 3.9 3.8 - - - +
432A GLU* 2.8 74.2 + - + +
433A VAL* 4.3 7.6 - - + -
724A PHE* 3.9 42.4 - + + -
763A LEU* 4.4 21.8 - - + -
811A TYR* 5.4 6.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A LEU* 4.3 17.7 - - + -
425A ARG 3.3 16.3 + - - +
426A LEU* 3.0 18.1 + - + +
428A TRP* 1.3 87.1 - - + +
430A TYR* 1.3 58.7 + - - +
433A VAL* 2.6 41.7 + - + +
434A GLU* 3.0 8.9 + - - -
724A PHE* 3.7 37.2 - - + +
725A GLY 3.9 3.8 - - - -
726A ARG* 3.8 40.4 - - + +
759A ASP* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A ASP* 2.6 45.8 + - - +
372A ASP 3.4 6.6 + - - -
375A LEU* 3.4 38.1 - - + -
376A LEU* 3.5 20.0 - - + -
379A LEU* 3.7 16.0 - - + +
413A PHE* 3.8 3.6 - - - -
417A TRP* 3.6 33.0 - + - -
420A LEU* 4.5 2.7 - - + -
426A LEU 3.0 7.6 + - - +
427A LEU* 3.7 11.0 - - - +
429A LEU* 1.3 77.0 - - - +
431A ARG* 1.3 68.0 + - + +
434A GLU* 3.4 12.1 + - + -
435A ARG* 2.9 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 4.7 20.8 - - + -
427A LEU* 3.1 23.6 + - - +
428A TRP* 3.9 5.2 - - - +
430A TYR* 1.3 85.0 - - + +
432A GLU* 1.3 76.6 + - - +
435A ARG* 4.6 27.7 + - - +
436A PRO* 3.5 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A TRP* 2.8 65.3 + - + +
431A ARG* 1.3 97.5 - - + +
433A VAL* 1.3 65.5 + - - +
436A PRO* 3.7 11.5 - - - +
763A LEU* 3.7 12.7 - - + +
766A VAL* 4.0 9.0 - - - +
----------------------------------------------------------
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