Contacts of the strand formed by residues 843 - 850 (chain A) in PDB entry 3ZJU
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 THR 843 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A VAL* 1.3 79.8 - - - +
844A VAL* 1.3 64.6 + - - +
845A ARG* 3.1 12.0 + - - -
859A VAL* 4.2 1.3 - - - -
860A GLY* 2.6 46.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A ARG* 4.3 13.5 - - - +
839A LEU* 4.3 17.9 - - + -
842A VAL 5.4 0.7 - - - +
843A THR* 1.3 72.6 - - - +
845A ARG* 1.3 61.2 + - - +
846A LYS* 3.4 23.6 - - - +
847A VAL* 3.4 19.5 - - + -
857A LEU* 4.2 15.3 - - + -
858A VAL 3.5 6.7 - - - +
859A VAL* 4.1 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A THR* 3.1 14.6 + - - +
844A VAL* 1.3 73.0 - - - +
846A LYS* 1.3 63.6 + - + +
858A VAL* 2.8 23.3 + - + +
859A VAL 4.6 4.3 - - - -
860A GLY* 3.2 38.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A VAL* 3.4 4.9 - - - +
845A ARG* 1.3 81.6 - - + +
847A VAL* 1.3 76.0 + - - +
848A ILE* 5.2 9.2 - - + +
858A VAL* 3.2 47.6 + - + +
56B C 4.1 35.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822A GLU* 4.8 3.6 - - - +
826A ARG* 3.2 33.7 - - - +
844A VAL* 3.4 19.3 - - + -
846A LYS* 1.3 86.6 - - - +
848A ILE* 1.3 71.4 + - - +
849A TYR* 4.1 3.1 + - + +
855A LEU* 3.2 34.5 - - + -
856A ASN 3.4 10.3 - - - +
857A LEU* 4.0 11.7 - - + -
858A VAL* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A LYS* 5.2 10.8 - - + -
847A VAL* 1.3 79.4 - - - +
849A TYR* 1.3 64.6 + - - +
850A VAL* 5.3 1.8 - - + -
854A LEU* 3.7 4.9 - - + +
855A LEU* 3.4 3.3 - - - +
856A ASN* 2.7 45.5 + - + +
858A VAL* 4.8 5.2 - - + -
19B G 4.2 11.9 - - + +
56B C 3.5 68.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A VAL* 4.8 4.0 - - + +
820A ALA 4.2 10.0 + - - -
822A GLU* 3.5 41.7 + - + +
825A VAL* 3.7 34.3 - - + +
847A VAL* 4.1 2.8 + - + -
848A ILE* 1.3 77.3 - - - +
850A VAL* 1.3 71.0 + - - +
851A PRO* 3.5 34.7 - - + +
852A GLY* 3.6 14.9 + - - -
854A LEU 3.2 15.7 - - - -
855A LEU* 4.1 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A ILE* 5.3 2.2 - - + -
849A TYR* 1.3 77.7 - - - +
851A PRO* 1.3 77.8 - - + +
852A GLY 3.1 0.9 + - - -
853A LYS* 3.0 42.6 + - + +
854A LEU* 2.9 25.8 + - + +
19B G 4.0 36.6 - - + +
----------------------------------------------------------
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