Contacts of the strand formed by residues 724 - 732 (chain A) in PDB entry 5AMN
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 LEU 724 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PHE* 4.1 10.1 - - + -
721A ARG* 3.0 21.6 + - + +
722A LYS 3.3 1.8 - - - -
723A ASN* 1.3 80.2 - - - +
725A VAL* 1.3 65.3 + - - +
726A LEU* 4.0 17.9 + - + +
741A ALA* 3.8 19.7 - - + -
742A THR 3.5 18.6 - - - +
743A ALA* 4.4 10.1 - - + -
755A VAL* 4.5 3.1 - - + -
757A VAL* 4.2 12.8 - - + -
794A CYS* 4.1 14.8 - - - -
801A LEU* 3.9 28.5 - - + -
803A ILE* 4.3 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 725 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A LYS 5.7 2.5 - - - +
723A ASN 5.2 1.6 - - - +
724A LEU* 1.3 77.5 - - - +
726A LEU* 1.3 72.3 + - - +
741A ALA* 3.3 4.0 - - - +
742A THR* 3.0 52.0 + - + +
752A TYR* 5.0 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 726 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
724A LEU* 4.0 24.9 + - + +
725A VAL* 1.3 82.2 - - - +
727A GLY* 1.3 63.2 + - - +
739A VAL* 4.1 9.9 - - + -
740A LYS 3.8 1.3 - - - -
741A ALA* 3.9 18.2 - - + -
757A VAL* 4.0 18.2 - - + -
759A MET* 4.4 26.0 - - + -
801A LEU* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 727 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A VAL 4.0 0.6 + - - -
726A LEU* 1.3 77.1 - - - +
728A LYS* 1.3 66.4 + - - +
729A THR 4.0 0.3 + - - -
739A VAL* 3.6 9.2 - - - +
740A LYS* 2.5 22.3 + - - -
741A ALA* 4.3 0.4 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
727A GLY* 1.3 74.2 - - - +
729A THR* 1.3 69.4 + - - +
730A LEU* 3.9 11.9 - - - -
739A VAL* 3.6 1.1 - - - -
740A LYS* 2.9 39.5 + - + +
2013A FMT 3.2 40.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 729 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A GLY 4.0 0.2 + - - -
728A LYS* 1.3 83.4 - - - +
730A LEU* 1.3 62.6 + - - +
731A GLY* 3.5 28.5 - - - +
732A GLU* 4.4 9.2 - - + -
737A LYS* 4.1 29.0 + - + +
738A VAL 3.8 6.1 - - - +
739A VAL* 4.1 5.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
728A LYS* 3.5 26.7 + - - -
729A THR* 1.3 73.5 - - - +
731A GLY* 1.3 57.6 + - - +
738A VAL* 2.8 15.1 + - + +
739A VAL 3.9 5.6 - - - +
740A LYS* 3.7 34.5 - - + +
756A ALA* 4.6 1.1 - - + -
806A TYR* 3.9 11.2 - - + -
2013A FMT 4.1 9.4 - - - +
2018A DTQ 3.3 68.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A THR* 3.5 6.0 - - - +
730A LEU* 1.3 80.5 - - - +
732A GLU* 1.3 62.1 + - - -
737A LYS* 3.3 5.7 - - - +
738A VAL* 2.9 30.8 + - - +
2018A DTQ 4.0 11.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729A THR* 4.4 8.3 - - + -
731A GLY* 1.3 74.8 - - - +
733A GLY* 1.3 75.8 + - - +
736A GLY 3.6 5.6 - - - +
737A LYS* 4.0 22.6 + - + +
761A LYS* 2.9 31.7 + - + +
----------------------------------------------------------
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