Contacts of the strand formed by residues 886 - 891 (chain B) in PDB entry 1ED8
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 886 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772B LYS* 4.3 14.1 - - - +
773B ALA* 3.8 27.1 - - + +
774B THR* 3.8 3.4 - - - -
775B TYR* 3.8 20.6 - - + +
833B ALA* 3.7 24.2 - - + -
885B GLY* 1.3 76.1 - - - +
887B THR* 1.3 61.4 - - - +
901B SER* 3.4 2.3 - - - -
902B TYR* 2.8 45.1 + - + +
905B SER 6.1 0.2 - - - +
910B GLN* 4.0 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 887 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773B ALA* 3.9 3.4 - - - -
774B THR 3.1 25.7 + - - +
776B HIS* 3.7 4.4 + - - +
777B GLY* 3.2 21.5 + - - -
778B ASN* 2.6 32.0 + - - +
877B VAL* 5.3 1.8 - - + -
881B THR* 5.3 1.1 - - + -
883B ALA* 3.7 31.0 - - + +
885B GLY 4.1 1.8 + - - +
886B LEU* 1.3 80.3 - - - +
888B GLN* 1.3 65.9 + - - +
899B VAL* 4.3 4.7 - - + -
900B MET 3.1 11.9 - - - +
901B SER* 4.0 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 888 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771B PRO* 2.8 37.7 + - - +
772B LYS 3.4 15.8 + - - -
773B ALA* 4.0 3.8 - - + +
777B GLY 4.6 2.0 - - - +
778B ASN* 4.3 4.3 - - - +
782B PRO 5.9 0.2 - - - +
784B VAL* 4.0 17.6 - - + +
835B PRO* 3.1 40.3 - - + +
836B CYS* 4.6 2.8 + - - -
887B THR* 1.3 77.7 - - - +
889B ALA* 1.3 73.3 + - - +
890B LEU* 3.9 13.9 + - + +
898B MET 3.7 0.5 - - - +
899B VAL* 3.1 6.9 - - - -
900B MET 2.9 31.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 889 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777B GLY 4.7 1.6 + - - -
778B ASN* 4.1 19.8 - - - +
781B LYS 5.2 2.5 - - - +
782B PRO 4.3 2.7 + - - +
783B ALA* 3.4 14.8 - - + +
784B VAL* 2.9 28.6 + - - +
888B GLN* 1.3 78.1 - - - +
890B LEU* 1.3 59.0 + - - +
897B VAL* 3.7 22.0 - - + -
898B MET 3.4 4.7 - - - -
899B VAL* 3.9 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 890 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B TYR* 4.0 20.6 - - + -
783B ALA* 4.1 2.0 - - - -
784B VAL* 3.4 11.4 - - + +
786B CYS* 4.0 26.5 - - - -
835B PRO* 3.9 13.5 - - + -
836B CYS* 4.0 9.0 - - - +
839B ILE* 4.9 3.4 - - + -
888B GLN* 4.0 22.2 - - - +
889B ALA* 1.3 75.6 - - - +
891B ASN* 1.3 64.1 + - - +
892B THR* 3.8 0.6 + - - +
896B ALA 3.7 0.2 - - - +
897B VAL* 3.2 7.1 - - - -
898B MET* 2.7 47.2 + - + +
900B MET* 3.8 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 891 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B TYR* 3.0 22.3 + - - -
783B ALA* 3.4 38.7 + - - +
784B VAL 2.9 7.5 + - - +
785B THR* 3.2 27.3 + - + +
890B LEU* 1.3 69.6 - - - +
892B THR* 1.3 64.8 + - - +
895B GLY* 6.0 2.6 - - - -
896B ALA 3.6 4.8 - - - +
897B VAL* 4.3 10.2 - - - +
----------------------------------------------------------
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