Contacts of the strand formed by residues 848 - 858 (chain A) in PDB entry 1FVR
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 848 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A ILE 3.6 0.3 - - - +
844A LYS* 3.4 3.5 - - - -
845A LYS* 2.8 37.7 + - - +
846A ASP* 3.8 12.6 - - + +
847A GLY* 1.3 85.7 - - - +
849A ARG* 1.3 68.4 - - - +
850A MET* 3.7 3.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823A ASP* 2.6 40.2 + - - +
825A LYS* 4.1 16.4 - - - +
842A ARG* 3.4 47.4 + - + +
843A ILE 3.3 9.2 - - - -
844A LYS* 3.4 31.0 - - - +
847A GLY 5.7 0.9 - - - +
848A LEU* 1.3 78.1 - - - +
850A MET* 1.3 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 850 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A ARG* 3.2 16.0 - - - +
843A ILE* 2.9 48.3 + - + +
845A LYS* 4.0 32.3 - - + +
848A LEU* 4.6 6.5 - - + +
849A ARG* 1.3 75.4 - - - +
851A ASP* 1.3 77.6 + - - +
889A LEU* 3.8 26.0 - - + -
903A GLU* 6.3 0.4 - - + -
974A GLU* 5.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 851 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827A GLN* 4.4 4.0 + - - -
840A LYS* 4.8 7.8 + - + +
841A ALA 3.6 5.8 - - - +
842A ARG* 2.9 32.6 + - - +
850A MET* 1.3 94.1 - - - +
852A ALA* 1.3 66.4 + - - +
889A LEU* 4.5 0.7 - - - +
904A TYR* 3.8 32.6 + - + +
974A GLU* 5.9 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 852 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A LYS* 3.7 4.7 - - - +
841A ALA* 2.8 35.3 + - - +
843A ILE* 3.9 37.5 - - + -
851A ASP* 1.3 78.3 - - - +
853A ALA* 1.3 61.4 + - - +
854A ILE* 5.4 0.7 - - + -
889A LEU* 4.0 5.4 - - + -
901A ALA* 4.8 2.0 - - + -
902A ILE 3.6 13.2 - - - +
904A TYR* 3.7 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 853 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A ILE* 4.9 1.6 - - + -
832A GLU* 3.3 26.7 - - - +
838A VAL* 4.0 12.8 - - + -
839A LEU 3.2 9.2 - - - +
840A LYS* 4.4 3.1 - - - +
852A ALA* 1.3 75.4 - - - +
854A ILE* 1.3 64.2 + - - +
901A ALA* 3.4 4.0 - - - -
902A ILE* 2.8 40.9 + - + +
903A GLU 4.4 2.2 - - - +
904A TYR* 4.2 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 854 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A LEU* 5.9 0.2 - - + -
824A ILE* 3.4 45.3 - - + -
826A PHE* 3.9 8.5 - - + -
838A VAL* 3.5 5.9 - - - -
839A LEU* 2.7 50.2 + - + +
841A ALA* 4.1 11.2 - - + -
843A ILE* 4.3 9.0 - - + -
853A ALA* 1.3 81.4 - - - +
855A LYS* 1.3 63.8 + - - +
856A ARG 3.8 2.0 + - - +
899A TYR* 3.8 39.3 - - + +
900A LEU 3.3 6.5 - - - +
901A ALA* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A PHE* 2.9 42.5 + - + +
836A GLY* 4.9 2.2 - - - -
837A GLN 4.2 9.9 + - - +
838A VAL* 4.0 15.0 - - + +
853A ALA 4.2 0.4 - - - -
854A ILE* 1.3 71.6 - - - +
856A ARG* 1.3 73.2 + - - +
857A MET* 3.6 15.7 + - + +
898A LEU 3.4 2.9 - - - +
900A LEU* 2.9 45.8 + - + +
902A ILE* 5.0 2.6 - - + +
983A PHE* 3.9 36.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A GLN 5.5 1.2 + - - -
838A VAL* 5.9 0.2 - - - +
839A LEU* 5.0 7.2 - - + -
854A ILE 3.8 3.2 + - - -
855A LYS* 1.3 84.1 + - - +
857A MET* 1.3 64.6 + - - +
858A LYS 4.2 0.9 + - - -
897A TYR* 3.0 61.2 + - + -
898A LEU 3.7 3.6 - - - -
899A TYR* 2.9 44.8 + - + +
829B VAL* 3.3 44.8 + - - +
830B ILE* 4.8 1.8 - - - +
837B GLN* 3.5 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A LYS* 4.1 16.2 - - + +
856A ARG* 1.3 78.0 - - - +
858A LYS* 1.3 65.7 + - - +
859A GLU* 3.4 1.6 + - - +
869A PHE* 3.9 28.5 - - + +
872A GLU* 3.5 41.7 - - + +
873A LEU* 5.0 2.9 - - + +
876A LEU* 4.3 8.5 - - + -
897A TYR* 3.4 4.6 - - - -
898A LEU* 2.8 52.4 + - + +
900A LEU* 4.2 21.3 - - - -
983A PHE* 3.9 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856A ARG 4.2 1.0 + - - -
857A MET* 1.3 71.9 - - - +
859A GLU* 1.3 62.4 + - - +
860A TYR* 3.3 11.9 + - + +
869A PHE* 3.7 15.0 - - - +
896A GLY 4.4 0.2 - - - -
897A TYR* 3.4 31.4 - - + +
----------------------------------------------------------
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