Contacts of the strand formed by residues 988 - 991 (chain A) in PDB entry 5WRZ
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 GLU 988 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A MET* 4.6 5.5 - - - +
891A PHE* 3.4 27.7 - - + -
896A TYR* 3.6 15.9 - - + -
897A PHE 3.5 4.5 - - - -
903A LYS* 2.9 25.1 + - - +
907A TYR* 5.4 0.9 + - - -
949A LYS* 3.3 4.3 - - - +
950A GLY* 2.7 33.7 + - - +
984A LEU* 3.4 25.0 - - + +
987A ASN* 1.3 70.4 - - - +
989A TYR* 1.3 65.7 + - - +
990A ILE* 4.2 4.7 - - + -
1101A 7U3 3.2 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 989 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A ARG* 3.2 31.2 + - - -
860A LEU* 3.7 35.7 - - + -
895A ILE 3.6 1.0 - - - +
896A TYR* 3.4 4.0 - - - -
897A PHE* 2.8 50.4 + - + +
899A ASP* 2.7 40.9 + - + +
926A LEU* 3.8 28.9 - - + -
929A MET* 4.2 1.6 - - - -
948A VAL 3.4 3.1 - - - -
949A LYS* 3.5 28.3 - - + -
987A ASN* 3.5 21.7 + - + -
988A GLU* 1.3 77.2 - - - +
990A ILE* 1.3 62.5 + - - +
991A VAL 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 990 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A PHE* 3.4 36.6 - - + -
894A GLY* 3.7 17.3 - - - -
895A ILE 3.3 9.6 - - - +
896A TYR* 3.6 32.8 - - + -
947A SER* 3.3 6.6 - - - -
948A VAL* 2.8 52.7 + - + +
950A GLY 4.6 0.2 - - - +
988A GLU* 4.2 7.2 - - + +
989A TYR* 1.3 87.3 - - - +
991A VAL* 1.3 65.0 + - - +
992A TYR* 3.5 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 991 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A GLY* 3.1 3.1 - - - -
895A ILE* 2.7 51.3 + - + +
897A PHE* 4.4 4.5 - - + -
924A VAL* 3.9 21.8 - - + -
925A ALA 4.1 2.7 - - - +
926A LEU* 4.4 1.3 - - + -
946A HIS 4.7 1.8 - - - -
947A SER* 4.0 12.3 - - - -
989A TYR 4.3 0.2 - - - -
990A ILE* 1.3 77.7 - - - +
992A TYR* 1.3 65.5 + - - +
993A ASP 3.7 10.8 - - - +
996A GLN* 3.8 30.1 - - + +
997A VAL* 3.9 28.0 - - + -
----------------------------------------------------------
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