Contacts of the strand formed by residues 724 - 731 (chain A) in PDB entry 3POZ
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 GLY 724 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A SER* 3.6 1.4 + - - -
721A GLY 3.1 32.8 + - - +
722A ALA 3.3 1.8 - - - -
723A PHE* 1.3 80.4 - - - +
725A THR* 1.3 64.6 + - - -
726A VAL* 5.8 0.7 - - - -
745A LYS* 5.8 1.3 - - - -
746A GLU 3.4 10.5 - - - -
747A LEU 4.4 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A VAL* 3.8 18.6 - - + -
719A GLY 3.3 18.6 - - - +
720A SER* 2.9 19.9 + - - +
723A PHE 4.4 0.4 + - - -
724A GLY* 1.3 71.5 - - - -
726A VAL* 1.3 63.7 + - - +
727A TYR* 3.6 36.8 + - + +
744A ILE 3.6 1.6 - - - +
745A LYS* 3.6 1.0 - - - +
746A GLU* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717A VAL* 3.8 3.5 - - - +
718A LEU* 2.8 30.8 + - + -
719A GLY 2.9 17.4 + - - +
724A GLY 5.8 0.4 - - - -
725A THR* 1.3 78.1 - - - +
727A TYR* 1.3 65.8 + - - +
743A ALA* 4.0 18.4 - - + -
744A ILE 3.2 9.0 - - - +
745A LYS* 3.7 28.7 - - + -
1023A 03P 3.5 57.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A LYS* 3.6 52.3 - - + -
716A LYS* 3.2 17.5 - - - +
717A VAL* 3.8 26.7 - - + -
718A LEU* 3.9 4.4 - - - +
725A THR* 3.6 33.4 + - + +
726A VAL* 1.3 76.2 - - - +
728A LYS* 1.3 65.3 + - - +
743A ALA* 3.2 7.8 - - - +
744A ILE* 2.8 44.7 + - + +
746A GLU* 4.2 17.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 728 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A LYS* 3.8 1.7 - - - -
715A ILE* 2.8 40.3 + - + +
716A LYS* 2.8 44.3 + - + +
718A LEU* 3.7 25.9 - - + +
727A TYR* 1.3 75.2 - - - +
729A GLY* 1.3 58.9 + - - +
742A VAL 3.5 6.3 - - - +
744A ILE* 5.0 0.2 - - - -
792A LEU* 4.3 13.5 - - + +
1000A ALA 4.4 5.8 - - - -
1001A LEU* 3.1 46.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A LYS 3.0 14.8 - - - -
715A ILE* 3.8 8.5 - - - -
727A TYR 4.0 0.6 + - - -
728A LYS* 1.3 77.1 - - - +
730A LEU* 1.3 66.6 + - - +
741A PRO* 3.5 6.6 - - - +
742A VAL* 2.8 39.3 + - - +
744A ILE* 4.3 3.3 - - - +
792A LEU* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A PHE* 3.2 5.0 - - - +
713A LYS* 2.9 35.9 + - + +
715A ILE* 4.3 20.4 - - + +
729A GLY* 1.3 81.7 - - - +
731A TRP* 1.3 62.3 + - - +
732A ILE* 3.9 17.4 + - + +
739A LYS* 4.1 37.2 - - + +
740A ILE 3.3 20.2 - - - +
741A PRO* 3.9 10.3 - - + -
742A VAL* 3.8 4.2 - - - +
1010A VAL 4.8 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A ARG* 3.4 44.4 - - - -
707A LEU* 3.6 35.0 - - + +
711A GLU* 3.2 21.6 + - + +
712A PHE* 4.2 3.1 - - + -
730A LEU* 1.3 72.3 - - - +
732A ILE* 1.3 61.8 + - - +
733A PRO* 3.4 31.9 - - + +
738A VAL 3.5 0.9 - - - +
739A LYS* 3.6 0.9 - - - -
740A ILE* 2.8 57.7 + - + +
742A VAL* 3.7 18.3 - - + +
778A LEU* 4.0 39.3 - - + -
789A ILE* 4.6 5.2 - - + -
1013A ALA* 5.8 0.2 - - + -
1016A TYR* 3.7 21.1 - + - -
1017A LEU* 4.9 3.8 - - + -
----------------------------------------------------------
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