Contacts of the helix formed by residues 823 - 831 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750C SER* 3.9 21.2 - - - +
786C PHE* 3.8 4.0 - - - -
821C ALA* 3.4 16.0 - - - +
822C LYS* 1.4 110.2 + - - +
824C ALA* 1.3 65.5 + - - +
825C ILE* 4.1 11.2 - - + +
826C TYR* 3.1 16.7 + - + +
875C SER* 4.7 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 824 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746C HIS 5.4 0.4 + - - -
747C PHE* 3.9 11.9 - - + +
750C SER* 3.3 6.9 + - - +
751C MET* 3.5 24.9 - - + -
786C PHE* 3.4 46.5 - - + -
823C ASP* 1.3 69.0 - - - +
825C ILE* 1.3 57.1 + - - +
827C SER* 3.2 3.1 + - - -
828C HIS* 3.0 24.8 + - - +
840C MET* 3.3 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 825 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750C SER* 3.0 40.9 + - - +
751C MET* 3.4 19.9 - - - -
752C LYS 5.3 1.3 - - - +
754C PHE* 3.9 19.1 - - + -
823C ASP* 4.1 10.1 - - + +
824C ALA* 1.3 76.0 - - - +
826C TYR* 1.4 55.7 + - + +
828C HIS* 3.5 12.2 + - + +
829C LYS* 2.9 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 826 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808C GLU* 4.8 4.0 - - - -
810C ASN* 3.1 30.1 + - - -
814C TYR* 4.4 5.9 + - - -
821C ALA* 3.7 16.4 - - + -
823C ASP* 3.1 19.6 + - + +
825C ILE* 1.4 77.9 - - + +
827C SER* 1.4 68.3 + - - +
829C LYS* 3.3 10.7 - - + +
830C TYR* 3.1 62.6 + + + -
869C ASP* 5.3 2.3 + - - +
875C SER* 3.8 27.8 - - - +
876C VAL* 3.9 31.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 827 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786C PHE* 3.9 8.4 + - - -
787C TYR* 3.4 7.1 - - - -
788C ALA* 2.8 33.1 + - - +
808C GLU* 4.6 12.0 + - - +
819C TYR 5.3 1.4 + - - -
821C ALA* 3.9 17.6 - - - +
823C ASP 3.6 2.0 + - - -
824C ALA 3.2 8.1 + - - -
826C TYR* 1.4 81.4 - - - +
828C HIS* 1.3 62.2 + - - +
830C TYR* 3.5 3.5 + - - +
831C CYS* 3.1 24.9 + - - +
840C MET* 4.2 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 828 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751C MET* 3.9 9.6 - - + -
754C PHE* 3.5 37.7 - + - -
788C ALA* 3.9 9.8 - - - +
824C ALA 3.0 16.8 + - - +
825C ILE* 3.6 12.3 - - + +
827C SER* 1.3 77.4 - - - +
829C LYS* 1.3 67.4 + - + +
831C CYS* 3.3 18.4 + - - +
835C ALA* 5.1 11.6 - - + +
838C VAL* 4.5 8.2 - - + +
840C MET* 3.9 7.9 - - + -
893C TYR* 2.7 27.7 + + - -
895C GLU* 4.3 12.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 829 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809C THR* 4.7 2.3 + - - +
825C ILE* 2.9 27.9 + - + +
826C TYR* 3.3 20.9 - - + +
828C HIS* 1.3 80.9 - - + +
830C TYR* 1.4 88.2 + - + +
831C CYS 3.3 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 830 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808C GLU* 3.4 24.0 - - - +
809C THR* 3.0 48.5 + - - +
810C ASN* 3.5 29.8 - - - -
813C LYS* 5.4 3.8 + - - -
826C TYR* 3.1 63.9 + + + +
827C SER 3.8 3.4 - - - +
828C HIS 3.3 0.2 - - - -
829C LYS* 1.4 104.2 + - + +
831C CYS* 1.3 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 831 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788C ALA* 3.9 12.1 - - + +
789C THR* 4.0 16.8 - - - -
808C GLU* 5.0 2.2 - - - -
809C THR* 4.6 0.6 - - - +
827C SER 3.1 17.3 + - - +
828C HIS* 3.6 12.5 - - - +
829C LYS 3.3 5.3 - - - +
830C TYR* 1.3 75.2 - - - +
832C PRO* 1.3 65.8 - - - +
833C TYR* 3.5 34.9 + - - +
838C VAL* 3.6 27.1 - - + -
----------------------------------------------------------
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