Contacts of the strand formed by residues 846 - 852 (chain A) in PDB entry 1Y6A
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 846 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A AAZ 3.3 66.0 - - + -
837A PRO* 3.5 3.6 - - - +
838A LEU* 2.6 42.3 + - + -
839A GLY 2.9 13.4 + - - +
840A ARG 4.2 8.3 - - - +
845A GLN* 1.3 76.3 - - - +
847A ILE* 1.3 58.6 + - - +
864A ALA* 4.5 3.4 - - + -
865A VAL 3.1 13.7 - - - +
866A LYS* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A LEU* 3.0 56.8 - - + -
835A GLY 4.3 5.2 - - - +
836A LYS 3.6 6.7 - - - +
837A PRO* 4.0 9.0 - - + -
838A LEU* 4.0 6.0 - - - +
845A GLN* 3.9 30.7 - - + +
846A VAL* 1.3 79.5 - - - +
848A GLU* 1.3 68.0 + - - +
864A ALA* 3.5 2.8 - - - -
865A VAL* 2.8 52.0 + - + +
867A MET* 3.7 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A AAZ 4.2 5.0 - - - +
835A GLY* 2.6 33.6 + - - +
836A LYS* 2.8 33.7 + - - +
838A LEU* 3.7 18.9 - - + +
847A ILE* 1.3 76.8 - - - +
849A ALA* 1.3 54.3 + - - +
862A THR* 4.1 13.9 - - + +
863A VAL 3.5 6.3 - - - +
916A PHE* 3.6 38.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A LEU* 4.0 13.7 - - + -
833A LYS 3.1 19.5 - - - +
834A LEU* 4.0 7.6 - - + -
835A GLY* 4.1 1.6 - - - +
848A GLU* 1.3 75.8 - - - +
850A ASP* 1.3 63.1 + - - +
851A ALA 4.0 0.4 - - - -
862A THR* 3.2 6.9 - - - +
863A VAL* 2.8 33.5 + - + +
865A VAL* 3.7 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831A ARG 3.5 3.5 - - - +
832A LEU* 3.5 1.6 - - - -
833A LYS* 2.8 50.1 + - + +
849A ALA* 1.3 73.4 - - - +
851A ALA* 1.3 60.9 + - - +
852A PHE 4.2 0.2 + - - -
860A CYS* 5.4 12.3 - - + -
861A ARG 3.5 5.4 - - - +
862A THR* 3.4 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 851 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A PHE* 4.0 13.2 - - + -
831A ARG 3.3 4.7 - - - -
832A LEU* 3.8 20.0 - - + -
849A ALA 4.0 0.4 - - - -
850A ASP* 1.3 73.2 - - - +
852A PHE* 1.3 60.7 + - - +
853A GLY 3.8 0.3 + - - -
854A ILE* 4.0 13.2 + - + -
859A THR 3.6 1.6 - - - +
860A CYS* 3.5 2.7 - - - -
861A ARG* 2.8 39.6 + - - +
863A VAL* 4.0 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 852 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A PHE* 3.3 5.2 - - - -
831A ARG* 2.9 72.4 + - + +
850A ASP 4.2 0.4 - - - -
851A ALA* 1.3 71.5 - - - +
853A GLY* 1.3 65.4 + - - +
854A ILE 3.4 0.2 - - - -
858A ALA* 3.5 42.4 - - + -
859A THR 3.5 13.9 - - - -
860A CYS* 3.9 19.7 - - - +
----------------------------------------------------------
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