Contacts of the helix formed by residues 823 - 831 (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 ASP 823 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746D HIS 6.0 0.2 - - - -
750D SER* 3.9 22.3 - - - +
786D PHE* 3.8 3.4 - - - -
821D ALA* 3.4 16.9 - - - +
822D LYS* 1.4 108.6 + - - +
824D ALA* 1.3 65.5 + - - +
825D ILE* 4.1 10.3 - - + +
826D TYR* 3.1 19.0 + - + +
875D SER* 4.6 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 824 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746D HIS 5.4 0.4 + - - -
747D PHE* 4.0 12.3 - - + +
750D SER* 3.3 6.3 + - - +
751D MET* 3.5 24.9 - - + -
786D PHE* 3.4 45.6 - - + -
823D ASP* 1.3 70.7 - - - +
825D ILE* 1.4 56.7 + - - +
827D SER* 3.2 3.3 + - - -
828D HIS* 2.9 25.1 + - - +
840D MET* 3.3 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 825 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750D SER* 3.0 43.6 + - - +
751D MET* 3.4 19.9 - - - -
754D PHE* 3.8 19.5 - - + -
823D ASP* 4.1 8.7 - - + +
824D ALA* 1.4 74.9 - - - +
826D TYR* 1.4 59.9 + - + +
828D HIS* 3.5 11.3 + - + +
829D LYS* 2.9 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 826 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808D GLU* 4.8 2.0 - - - -
810D ASN* 3.1 28.8 + - - -
814D TYR* 4.2 6.6 + - - -
821D ALA* 3.8 15.3 - - + -
823D ASP* 3.1 19.5 + - + +
825D ILE* 1.4 77.4 - - - +
827D SER* 1.4 67.5 + - - +
829D LYS* 3.3 19.7 + - - +
830D TYR* 3.1 62.1 + + + +
869D ASP* 5.2 2.3 + - - -
875D SER* 3.8 29.8 - - - +
876D VAL* 3.9 32.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 827 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786D PHE* 3.8 7.4 + - - -
787D TYR* 3.4 6.9 - - - -
788D ALA* 2.8 35.2 + - - +
819D TYR 5.1 2.9 + - - -
821D ALA* 3.7 18.0 + - - +
823D ASP 3.5 2.2 + - - -
824D ALA 3.2 8.3 + - - -
826D TYR* 1.4 80.4 - - - +
828D HIS* 1.3 61.9 + - - +
830D TYR* 3.5 3.9 + - - +
831D CYS* 3.1 24.8 + - - +
840D MET* 4.1 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 828 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751D MET* 3.9 14.1 - - + -
754D PHE* 3.4 36.6 - + - -
788D ALA* 3.8 9.3 - - - +
824D ALA 2.9 17.0 + - - +
825D ILE* 3.6 12.6 - - + +
826D TYR 3.2 0.2 - - - -
827D SER* 1.3 76.5 - - - +
829D LYS* 1.4 67.9 + - + +
831D CYS* 3.3 18.6 + - - +
835D ALA* 5.1 16.3 - - + +
838D VAL* 4.5 8.8 - - + +
840D MET* 3.9 3.1 - - + -
893D TYR* 2.7 28.2 + + - -
895D GLU* 5.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 829 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809D THR* 4.6 1.9 + - - +
825D ILE* 2.9 42.4 + - + +
826D TYR* 3.3 37.7 - - - +
828D HIS* 1.4 81.1 - - + +
830D TYR* 1.4 78.7 + - + +
831D CYS 3.3 5.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 830 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808D GLU* 3.4 22.0 - - + +
809D THR* 3.0 47.0 + - - +
810D ASN* 3.3 33.2 + - - -
813D LYS* 5.3 3.0 + - - -
826D TYR* 3.1 61.7 + + + +
827D SER* 3.8 4.5 - - - +
829D LYS* 1.4 97.0 - - + +
831D CYS* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 831 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788D ALA* 3.9 12.3 - - + +
789D THR* 4.0 12.3 - - - -
808D GLU* 5.0 2.5 - - - -
809D THR* 4.5 1.0 - - - +
827D SER 3.1 16.3 + - - +
828D HIS 3.3 14.3 + - - +
829D LYS 4.2 4.7 - - - +
830D TYR* 1.3 76.1 - - - +
832D PRO* 1.3 65.6 - - - +
833D TYR* 3.5 34.7 + - - +
838D VAL* 3.6 31.2 - - + -
----------------------------------------------------------
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