Contacts of the helix formed by residues 563 - 575 (chain A) in PDB entry 2EZT
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 SER 563 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A SER* 1.3 76.7 - - - +
564A ALA* 1.3 64.6 + - - +
565A ALA* 3.5 9.8 + - - +
566A ASP* 3.1 32.9 + - - +
567A ILE* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A SER* 6.0 1.5 - - - -
562A SER 3.8 1.4 + - - -
563A SER* 1.3 72.1 - - - +
565A ALA* 1.3 57.4 + - - +
567A ILE* 3.5 10.9 + - - +
568A GLU* 3.1 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563A SER* 3.1 8.9 + - - +
564A ALA* 1.3 77.6 - - - +
566A ASP* 1.3 62.7 + - - +
568A GLU* 4.2 3.3 - - - +
569A ALA* 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ARG* 3.7 26.7 + - + +
562A SER* 4.5 3.0 - - - -
563A SER* 3.1 29.8 + - - +
565A ALA* 1.3 77.9 - - - +
567A ILE* 1.3 59.2 + - - +
569A ALA* 3.7 5.2 + - - +
570A PHE* 3.1 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A ARG 3.2 26.9 - - - +
557A LEU* 3.9 10.1 - - - +
558A ASP 3.8 5.2 - - - -
559A SER* 3.6 40.8 - - - +
562A SER* 3.7 10.1 - - - +
563A SER 3.0 17.6 + - - +
564A ALA* 3.8 8.5 - - - +
566A ASP* 1.3 77.2 - - - +
568A GLU* 1.3 61.8 + - - +
570A PHE* 3.3 2.8 + - - +
571A LYS* 2.8 59.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ALA* 3.1 20.7 + - + +
565A ALA* 4.3 4.0 - - - +
566A ASP 3.4 0.2 - - - -
567A ILE* 1.3 81.0 - - - +
569A ALA* 1.3 58.4 + - - +
571A LYS* 3.6 35.4 + - - +
572A GLN* 3.0 31.4 + - - +
577A GLN* 5.8 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A ALA 3.2 18.9 + - - +
566A ASP* 4.0 6.1 - - - +
568A GLU* 1.3 75.3 - - - +
570A PHE* 1.3 57.6 + - - +
572A GLN* 3.9 4.6 - - - +
573A ARG* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A LEU* 3.6 34.5 - - + -
551A PRO* 4.2 6.3 - - + -
554A LYS 3.2 24.9 - - - -
555A LEU* 3.8 11.4 - - + -
556A ARG* 3.5 37.0 - - + +
557A LEU* 3.8 26.2 - - + -
566A ASP 3.1 19.8 + - - +
567A ILE 3.5 2.9 - - - +
569A ALA* 1.3 74.3 - - - +
571A LYS* 1.3 67.9 + - - +
573A ARG* 3.2 0.7 + - - -
574A TYR* 3.0 57.2 + + - +
576A ALA* 4.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A LEU* 3.8 21.7 + - + +
567A ILE* 2.8 38.4 + - - +
568A GLU* 3.6 34.5 + - - +
570A PHE* 1.3 71.8 - - - +
572A GLN* 1.3 57.5 + - - +
575A GLU* 2.9 26.3 + - - -
576A ALA* 2.9 29.7 + - - +
577A GLN* 3.5 36.6 + - + +
579A LEU 4.4 5.6 + - - -
580A GLN* 5.9 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A GLU 3.0 19.4 + - - +
569A ALA* 3.9 5.2 - - - +
571A LYS* 1.3 77.9 - - - +
573A ARG* 1.3 64.2 + - - +
574A TYR 3.5 0.3 + - - -
575A GLU* 3.7 9.9 + - - +
577A GLN* 4.1 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A LYS* 5.5 4.2 - - - +
482A ASP* 4.9 1.0 + - - -
485A GLU* 2.6 44.8 + - - -
547A ASP* 5.1 9.5 - - - +
548A ARG* 3.5 27.7 - - - +
554A LYS* 6.1 0.2 - - - +
569A ALA 2.9 19.7 + - - +
570A PHE 3.2 2.9 + - - +
572A GLN* 1.3 77.9 - - - +
574A TYR* 1.3 99.6 + - + +
575A GLU* 3.8 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 574 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TYR* 2.5 34.3 + - - +
363A LEU* 4.5 2.6 - - - +
374A TYR* 5.8 0.4 - - - -
548A ARG* 3.1 53.1 + - + -
549A PRO 3.8 2.7 - - - -
550A LEU* 3.7 23.8 - - + -
551A PRO* 3.4 27.4 - - + +
570A PHE* 3.0 54.1 + + - +
573A ARG* 1.3 112.1 + - + +
575A GLU* 1.3 72.1 + - - +
576A ALA* 3.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 575 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TYR* 3.3 13.5 - - - -
362A SER* 4.9 4.5 + - - -
363A LEU* 4.1 17.0 - - + +
366A LYS* 2.5 33.0 + - - -
372A GLN* 3.0 26.9 + - - -
374A TYR* 4.5 3.1 + - - -
547A ASP* 4.8 3.5 - - - +
571A LYS 2.9 9.5 + - - -
572A GLN 3.7 6.0 + - - +
573A ARG 3.5 8.7 - - - +
574A TYR* 1.3 79.7 - - - +
576A ALA* 1.3 56.7 + - - +
577A GLN* 3.2 23.7 + - - +
578A ASP 5.2 0.7 + - - -
----------------------------------------------------------
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