Contacts of the helix formed by residues 793 - 801 (chain D) in PDB entry 4X52
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 TYR 793 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793B TYR* 3.4 37.2 - + - -
796B SER* 3.7 21.6 + - - -
803B ASP* 2.6 30.7 + - - +
806B LEU* 4.1 8.7 - - + +
789D THR* 3.5 18.2 - - - +
790D SER* 3.0 19.7 + - - +
792D ALA* 1.3 83.7 - - + +
794D VAL* 1.3 63.1 + - - +
795D GLU 3.3 2.7 - - - -
796D SER* 2.8 24.9 + - - +
797D ILE* 3.2 21.3 + - + +
806D LEU* 3.5 26.4 - - + +
833D TYR* 3.5 24.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 794 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728D TYR* 5.5 1.6 - - - +
730D LEU* 4.2 20.0 - - + -
790D SER 3.8 0.4 + - - -
791D ARG* 3.2 25.5 + - + +
793D TYR* 1.3 77.0 - - - +
795D GLU* 1.3 64.5 + - - +
797D ILE* 3.4 1.9 + - - +
798D CYS* 3.0 38.9 + - - -
839D VAL* 3.6 32.5 - - + -
841D PHE* 3.8 15.9 - - + -
890D VAL* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 795 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ALA* 6.1 2.5 - - + +
795B GLU* 5.6 1.6 - - - +
728D TYR* 3.5 32.5 + - + +
792D ALA 4.9 3.9 + - - +
793D TYR 3.3 0.2 - - - -
794D VAL* 1.3 80.1 - - - +
796D SER* 1.3 62.6 + - - +
798D CYS 3.4 0.3 + - - -
799D SER* 3.0 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 796 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ALA* 3.6 27.0 + - - -
793B TYR* 3.6 22.9 + - - -
792D ALA 5.3 1.0 + - - -
793D TYR* 2.8 26.2 + - - +
795D GLU* 1.3 77.1 - - - +
797D ILE* 1.3 60.6 + - - +
799D SER* 4.2 2.9 - - - -
800D ASN* 2.8 28.6 + - - +
801D ASN 3.8 0.7 + - - +
806D LEU* 5.8 0.5 - - - +
901D GOL 3.1 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 797 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767D LEU* 4.0 0.2 - - - +
787D TYR* 3.9 18.8 - - + +
789D THR* 3.8 28.7 - - + -
793D TYR* 3.2 22.3 + - + +
794D VAL 3.8 3.1 - - - +
796D SER* 1.3 80.7 + - - +
798D CYS* 1.4 61.4 + - - +
801D ASN* 2.8 37.7 + - - +
802D PHE* 3.6 35.2 - - + +
803D ASP* 5.3 3.1 - - + +
806D LEU* 5.4 3.8 - - + -
841D PHE* 3.5 28.0 - - + -
887D PRO* 3.7 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 798 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728D TYR* 3.4 42.3 - - + +
730D LEU* 4.4 3.1 - - - -
762D ILE* 3.8 41.2 - - + +
764D ASN* 2.8 23.4 + - - +
767D LEU* 3.8 2.6 - - - +
794D VAL* 3.0 32.9 + - - +
795D GLU 3.4 0.2 + - - -
797D ILE* 1.4 75.7 - - - +
799D SER* 1.3 58.0 + - - +
841D PHE* 4.0 8.1 - - - -
887D PRO* 4.8 1.6 - - - -
890D VAL* 4.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 799 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792B ALA* 5.8 0.2 - - - +
727D LYS* 3.7 29.4 + - - +
728D TYR* 3.7 19.6 - - - -
764D ASN* 3.2 17.3 + - - +
766D GLU* 4.7 1.9 - - - +
767D LEU* 4.2 6.0 - - - +
795D GLU* 3.0 20.7 + - - +
796D SER* 3.7 2.9 + - - -
798D CYS* 1.3 79.0 - - - +
800D ASN* 1.3 75.2 + - - +
801D ASN 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 800 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790B SER* 4.9 0.6 + - - -
792B ALA* 3.8 13.1 - - - +
837B ASN* 5.6 7.0 + - - +
727D LYS* 3.2 25.1 + - - +
767D LEU* 4.2 6.6 - - - +
796D SER 2.8 18.5 + - - +
799D SER* 1.3 84.4 + - - +
801D ASN* 1.4 61.5 + - - +
882D LYS* 2.8 33.4 + - - +
901D GOL 2.8 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 801 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
767D LEU* 3.7 24.8 + - + +
796D SER 3.9 2.8 - - - +
797D ILE* 2.8 29.9 + - - +
800D ASN* 1.4 84.8 - - - +
802D PHE* 1.3 88.9 + - - +
803D ASP* 3.8 1.7 + - - +
818D ILE* 6.2 0.4 - - - -
882D LYS* 3.1 36.3 + - + +
883D ASP* 5.1 1.0 - - - +
885D VAL* 3.0 29.0 + - - +
887D PRO* 3.7 14.9 - - - +
901D GOL 4.6 4.5 + - - -
----------------------------------------------------------
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