Contacts of the strand formed by residues 897 - 900 (chain A) in PDB entry 5A7R
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 VAL 897 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A MET* 3.7 3.7 - - - +
716A THR* 4.7 3.1 - - - +
717A ARG 2.9 14.9 + - - +
718A LEU* 3.3 22.6 - - + -
719A HIS 3.0 24.8 + - - +
852A PHE* 6.0 0.7 - - + -
865A VAL* 3.7 6.1 - - + +
867A THR* 4.2 19.3 - - + -
886A GLN* 4.6 3.8 - - + +
887A ILE* 4.5 21.8 - - + +
890A ALA* 3.5 32.1 - - + -
895A ARG 4.4 1.1 - - - +
896A ASP* 1.3 74.3 - - - +
898A VAL* 1.3 72.6 + - - +
899A TYR* 4.0 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 4.0 17.7 - - + -
461A MET* 3.9 21.1 - - + -
719A HIS* 3.3 19.5 - - + -
733A MET* 3.7 32.1 - - + -
864A ALA* 4.0 6.3 - - + -
865A VAL 2.8 12.5 + - - +
866A ALA* 3.5 2.0 - - - -
867A THR* 2.9 27.9 + - - +
897A VAL* 1.3 77.9 - - - +
899A TYR* 1.3 59.2 + - - +
900A PHE* 3.7 29.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A LEU* 4.1 13.0 - - + -
719A HIS 2.9 11.0 + - - +
720A VAL* 3.3 13.7 - - + +
721A THR* 3.0 29.2 + - - +
867A THR* 3.6 12.8 - - + -
868A GLY* 3.3 27.9 + - - -
869A ASN* 2.6 32.1 + - - -
879A ALA* 4.2 7.6 + - - +
882A LYS* 5.8 0.9 - - - +
883A ALA* 3.7 29.4 + - + +
886A GLN* 4.0 9.2 - - + -
887A ILE* 6.0 1.8 - - + -
897A VAL* 4.0 6.9 - - + -
898A VAL* 1.3 71.6 - - - +
900A PHE* 1.3 75.2 + - - +
901A THR* 3.7 13.7 - - + -
911A ILE* 3.7 23.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 5.0 3.4 - - + -
721A THR* 3.5 26.7 - - + -
723A GLU 3.6 13.0 - - - -
724A GLY 3.8 14.1 - - - +
725A THR 3.8 9.4 - - - -
726A ILE* 3.9 18.2 - - + -
729A ASN* 3.6 40.6 - - + -
730A GLY* 5.0 0.2 - - - -
866A ALA* 4.2 10.3 - - + -
867A THR 2.9 19.7 + - - +
868A GLY* 3.3 19.4 - - - -
869A ASN* 4.0 2.6 + - - -
898A VAL* 3.7 31.0 - - + -
899A TYR* 1.3 72.3 - - - +
901A THR* 1.3 59.7 + - - +
902A PHE 3.3 3.7 + - - +
1964A AR6 4.1 19.6 + - + -
----------------------------------------------------------
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