Contacts of the helix formed by residues 564 - 573 (chain A) in PDB entry 4EGA
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 564 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A CAS 3.9 10.7 - - - +
562A VAL* 4.4 1.0 - - - +
563A PHE* 1.3 72.0 - - - +
565A PRO* 1.3 71.1 - - - +
566A VAL* 3.5 10.1 + - - +
567A GLU* 2.8 47.4 + - + +
568A LYS* 2.9 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A HIS* 4.8 0.7 - - - -
257A ILE* 3.9 33.2 - - + +
260A VAL* 4.1 15.7 - - + -
318A CAS 3.1 32.5 - - + -
322A MET* 3.4 15.6 - - + +
563A PHE* 3.6 7.4 - - + +
564A ASP* 1.3 95.3 - - - +
566A VAL* 1.3 55.2 + - - +
568A LYS* 4.5 1.1 - - + -
569A ALA* 3.0 24.8 + - - +
577A LEU* 3.2 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A CAS 3.2 33.9 - - + -
321A GLN* 3.7 25.6 - - + -
322A MET* 3.5 16.2 - - + -
564A ASP* 3.4 7.8 + - - +
565A PRO* 1.3 79.6 - - - +
567A GLU* 1.3 67.9 + - - +
569A ALA* 3.4 3.3 + - - +
570A GLU* 3.1 31.1 + - + +
574A TYR* 4.2 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A ASP* 2.8 34.8 + - + +
566A VAL* 1.3 79.8 - - - +
568A LYS* 1.3 57.3 + - + +
570A GLU* 3.5 5.5 + - - +
571A GLU* 3.0 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A VAL 5.2 3.4 - - - -
563A PHE* 3.8 39.7 - - + +
564A ASP 2.9 21.9 + - - +
565A PRO 3.9 3.1 - - - +
567A GLU* 1.3 78.1 - - + +
569A ALA* 1.3 52.8 - - - +
571A GLU* 3.0 16.9 + - - +
572A PHE* 2.6 57.1 + - + +
577A LEU* 4.0 17.5 - - + -
595A ASP* 2.4 43.5 + - - -
598A MET* 4.1 8.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
322A MET* 4.7 0.4 - - + -
565A PRO 3.0 17.9 + - - +
566A VAL 3.4 1.8 + - - +
568A LYS* 1.3 76.8 - - - +
570A GLU* 1.3 57.3 + - - +
573A GLY* 2.6 39.1 + - - -
574A TYR* 3.2 53.8 + - + -
577A LEU* 3.9 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 5.1 2.7 + - - -
566A VAL* 3.1 24.6 + - + +
567A GLU* 4.0 4.9 - - - +
569A ALA* 1.3 74.5 - - - +
571A GLU* 1.3 64.2 + - - +
573A GLY 4.5 1.2 + - - -
574A TYR* 3.4 33.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A GLU* 3.0 25.2 + - - +
568A LYS* 3.0 23.3 + - - +
570A GLU* 1.3 79.7 - - - +
572A PHE* 1.3 80.3 + - + +
595A ASP* 4.0 6.8 - - - +
765A ARG* 3.5 46.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LYS* 2.6 41.5 + - + +
571A GLU* 1.3 104.1 - - + +
573A GLY* 1.3 61.3 + - - +
576A ALA* 3.4 22.1 - - + +
577A LEU* 5.4 5.6 - - + +
595A ASP* 4.6 11.9 - - + -
598A MET* 4.4 20.9 - - + -
599A ILE* 3.7 37.2 - - + -
602A LEU* 4.1 17.6 - - + +
765A ARG* 3.7 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A ALA* 2.6 24.3 + - - +
570A GLU 4.4 1.2 + - - -
571A GLU 3.8 0.8 - - - -
572A PHE* 1.3 73.4 - - - +
574A TYR* 1.3 60.7 + - - -
575A ASP 3.6 1.6 - - - -
576A ALA* 4.0 4.0 - - - -
577A LEU* 3.1 29.3 + - - +
805A GOL 3.2 16.4 - - - -
----------------------------------------------------------
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