Contacts of the strand formed by residues 893 - 900 (chain B) in PDB entry 5LHY
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 893 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954A CYS* 3.9 23.1 - - + +
955A LEU* 5.1 2.7 - - + -
892B PHE* 1.3 91.7 - - - +
894B LYS* 1.3 64.6 + - - +
895B ASN 3.9 2.2 - - - +
896B VAL* 3.5 32.5 - - + -
909B VAL* 3.6 17.3 - - + -
910B GLN 3.8 2.7 - - - +
911B PHE* 3.8 23.8 - - + -
963B SER* 4.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 894 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892B PHE* 3.9 3.7 + - + -
893B VAL* 1.3 76.2 - - - +
895B ASN* 1.3 88.1 + - - +
910B GLN* 2.8 27.8 + - - +
911B PHE 4.0 22.7 + - - +
912B ASN* 4.2 17.0 + - + +
914B GLY* 5.6 3.0 - - - -
961B MET* 5.1 4.0 - - - +
962B PHE 4.2 0.9 - - - -
963B SER* 2.5 41.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 895 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893B VAL* 3.9 0.3 - - - +
894B LYS* 1.3 105.1 - - - +
896B VAL* 1.3 66.0 + - - +
908B TRP* 4.0 14.8 - - + -
909B VAL* 3.4 1.6 - - - -
910B GLN* 2.7 61.5 + - + +
961B MET 3.3 11.0 - - - +
962B PHE* 3.4 26.2 - - + +
963B SER 3.0 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 896 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A LEU* 5.7 2.2 - - + -
893B VAL* 3.5 22.4 - - + -
895B ASN* 1.3 78.6 - - - +
897B GLY* 1.3 59.3 + - - +
898B TRP* 6.0 2.7 - - + -
907B VAL* 5.7 2.2 - - + -
908B TRP* 3.3 13.4 - - - +
909B VAL* 3.8 15.9 - - + -
959B LEU* 4.0 12.8 - - + -
960B LEU* 3.5 6.4 - - - +
961B MET* 2.8 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 897 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896B VAL* 1.3 77.6 - - - +
898B TRP* 1.3 59.7 + - - +
907B VAL* 3.4 3.0 - - - +
908B TRP* 2.5 51.5 + - - +
959B LEU* 3.1 19.5 - - - -
960B LEU* 3.9 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 898 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A TRP* 4.0 34.1 - + - -
896B VAL* 6.0 2.2 - - + -
897B GLY* 1.3 77.0 - - - +
899B ALA* 1.3 61.3 + - - +
900B THR* 3.9 15.9 - - + +
906B ALA 3.2 15.3 - - - +
907B VAL* 3.8 23.1 - - + -
957B SER* 3.3 31.4 + - - -
958B ILE* 3.2 9.9 - - - +
959B LEU* 3.0 69.3 + - + +
961C MET* 3.5 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 899 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B TRP* 1.3 73.6 - - - +
900B THR* 1.3 61.7 + - - +
901B GLN* 3.7 8.6 + - - -
905B GLY* 3.6 1.9 - - - -
906B ALA* 2.9 30.9 + - + +
957B SER 3.6 5.4 - - - -
958B ILE* 4.1 19.5 - - + -
908Q TRP* 4.4 8.5 - - + +
910Q GLN* 6.1 0.2 - - - +
916Q GLN* 3.7 24.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 900 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B TRP* 3.9 22.4 - - + +
899B ALA* 1.3 74.4 - - - +
901B GLN* 1.3 65.6 + - - +
904B SER 3.8 8.3 - - - +
905B GLY* 4.0 9.2 - - - -
906B ALA 5.1 0.9 - - - +
907B VAL* 6.2 1.8 - - + -
955B LEU 3.4 7.1 + - - +
956B SER* 3.3 20.6 - - - -
957B SER* 2.7 37.9 + - - +
958B ILE* 5.0 0.9 - - - +
964C ASN* 5.2 5.7 - - - +
910Q GLN* 5.8 1.2 + - - -
916Q GLN* 5.3 0.2 - - - -
----------------------------------------------------------
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