Contacts of the strand formed by residues 729 - 732 (chain A) in PDB entry 1MUK
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 TYR 729 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASN* 5.8 0.3 - - - +
555A LEU* 3.0 24.8 + - - +
584A ILE* 4.3 17.2 + - + +
695A ASN* 2.6 32.9 + - - -
696A SER* 4.3 8.9 - - - -
699A MET* 3.7 42.3 - - + +
703A LEU* 5.6 1.1 - - + -
724A THR 3.6 3.3 + - - +
725A ILE* 3.4 24.3 + - + +
727A ARG 3.7 1.6 - - - -
728A ASN* 1.3 79.3 - - - +
730A VAL* 1.3 60.6 + - - +
731A CYS* 3.8 19.2 - - + -
736A GLY* 3.6 16.9 - - - -
737A LEU 3.6 26.9 - - - -
738A MET* 3.9 20.6 - - + -
771A TYR* 5.5 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 730 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TRP* 4.3 1.6 - - + -
306A TYR* 3.7 19.1 - - + +
555A LEU* 3.2 21.8 - - + +
557A PRO* 4.2 4.5 - - + -
570A LEU* 3.6 37.2 - - + -
729A TYR* 1.3 75.8 - - - +
731A CYS* 1.3 63.4 + - - +
736A GLY* 3.4 0.7 - - - -
737A LEU* 2.8 38.4 + - + +
739A ILE* 3.9 19.7 - - + -
781A TYR* 3.3 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 731 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASN* 4.8 0.4 - - - -
555A LEU 3.2 9.7 + - - -
556A SER* 3.1 15.7 - - - -
557A PRO* 2.5 27.6 - - - +
692A THR* 3.7 29.1 - - - +
695A ASN* 4.1 10.3 - - + +
696A SER* 4.0 22.0 - - - -
729A TYR* 3.8 22.0 - - + -
730A VAL* 1.3 77.1 - - - +
732A GLN* 1.3 57.2 + - - +
735A ASP 3.2 12.8 - - - +
736A GLY* 4.1 0.9 - - - -
781A TYR* 3.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 732 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A PRO* 3.2 29.3 - - + +
558A THR* 4.3 1.8 - - - -
559A SER* 2.7 52.8 + - - -
560A GLY 5.3 1.2 + - - -
688A SER* 4.7 10.4 + - - +
692A THR* 3.7 7.6 - - - +
731A CYS* 1.3 75.6 - - - +
733A GLY* 1.3 70.8 + - - +
734A ASP* 3.1 0.7 + - - +
735A ASP* 2.9 25.0 + - - +
781A TYR* 3.7 3.5 + - - +
782A LEU* 3.5 19.0 - - + +
----------------------------------------------------------
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