Contacts of the strand formed by residues 848 - 858 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843B ILE 3.5 0.3 - - - +
844B LYS* 3.4 3.1 - - - -
845B LYS 3.0 32.0 + - - +
846B ASP* 3.1 9.3 - - + +
847B GLY* 1.3 86.4 - - - +
849B ARG* 1.3 70.7 + - - +
850B MET* 3.6 8.8 + - + +
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Residues in contact with ARG 849 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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823B ASP* 2.4 38.5 + - - -
825B LYS* 4.2 21.2 - - - +
842B ARG* 2.6 64.2 + - - +
843B ILE* 3.2 11.8 + - - +
844B LYS* 4.5 10.1 - - + +
847B GLY 5.5 1.6 - - - +
848B LEU* 1.3 81.3 - - - +
850B MET* 1.3 55.3 + - - +
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Residues in contact with MET 850 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842B ARG* 3.1 16.3 - - - +
843B ILE* 3.0 43.5 + - + +
845B LYS* 3.4 44.6 - - + +
846B ASP* 4.9 3.1 - - + +
848B LEU* 4.3 8.3 - - + +
849B ARG* 1.3 74.4 - - - +
851B ASP* 1.3 65.9 + - - +
889B LEU* 4.1 27.8 - - + -
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Residues in contact with ASP 851 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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827B GLN* 4.4 3.8 + - - -
840B LYS* 4.7 9.0 + - + +
841B ALA 3.6 5.0 - - - +
842B ARG* 3.4 26.0 + - - +
850B MET* 1.3 85.3 - - - +
852B ALA* 1.3 64.5 + - - +
889B LEU* 4.3 3.6 - - - +
904B TYR* 4.0 32.5 + - + +
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Residues in contact with ALA 852 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840B LYS* 3.8 4.9 - - - +
841B ALA* 2.8 32.2 + - - +
843B ILE* 4.2 26.7 - - + -
851B ASP* 1.3 80.2 - - - +
853B ALA* 1.3 63.7 + - - +
854B ILE* 5.4 0.2 - - + -
889B LEU* 3.8 13.5 - - + -
901B ALA* 4.9 0.9 - - + -
902B ILE 3.5 14.6 - - - +
904B TYR* 3.6 15.7 - - - +
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Residues in contact with ALA 853 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830B ILE* 5.1 1.1 - - + -
832B GLU* 3.2 26.9 - - - +
838B VAL* 3.9 14.4 - - + -
839B LEU 3.2 8.1 - - - +
840B LYS* 4.4 1.6 - - - +
852B ALA* 1.3 74.8 - - - +
854B ILE* 1.3 66.5 + - - +
901B ALA* 3.4 0.7 - - - -
902B ILE* 2.8 43.2 + - + +
903B GLU 4.3 2.5 - - - +
904B TYR* 4.6 8.3 - - + -
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Residues in contact with ILE 854 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824B ILE* 3.4 43.1 - - + -
826B PHE* 3.9 10.1 - - + -
838B VAL* 3.5 6.1 - - - +
839B LEU* 2.6 51.1 + - + +
841B ALA* 4.0 11.7 - - + -
843B ILE* 4.2 11.2 - - + -
852B ALA 5.4 0.2 - - - -
853B ALA* 1.3 80.5 - - - +
855B LYS* 1.3 62.4 + - - +
856B ARG* 3.7 2.3 + - - +
899B TYR* 3.8 38.4 - - + +
900B LEU 3.2 8.3 - - - +
901B ALA* 4.2 11.0 - - + +
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Residues in contact with LYS 855 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835B PHE* 2.8 43.7 + - + +
836B GLY* 4.8 2.0 - - - -
837B GLN 4.2 10.1 + - - +
838B VAL* 4.0 15.0 - - + +
853B ALA 4.2 0.2 - - - -
854B ILE* 1.3 71.6 - - - +
856B ARG* 1.3 73.0 + - - +
857B MET* 3.6 15.4 + - + +
898B LEU 3.4 2.9 - - - +
900B LEU* 2.7 46.2 + - + +
902B ILE* 5.1 3.3 - - + +
983B PHE* 3.8 37.7 - - + -
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Residues in contact with ARG 856 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829A VAL* 3.4 42.5 + - - +
830A ILE* 4.8 2.6 - - - +
837A GLN* 2.9 25.9 + - - +
837B GLN 5.5 1.0 + - - -
839B LEU* 5.0 7.9 - - + -
854B ILE 3.7 3.2 + - - -
855B LYS* 1.3 83.9 + - - +
857B MET* 1.3 62.2 + - - +
858B LYS 4.2 0.9 + - - -
897B TYR* 3.0 60.2 + - + -
898B LEU 3.6 3.6 - - - -
899B TYR* 3.0 43.4 + - + +
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Residues in contact with MET 857 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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855B LYS* 4.0 14.8 - - + +
856B ARG* 1.3 77.0 - - - +
858B LYS* 1.3 64.2 + - - +
859B GLU* 3.4 1.6 + - - +
869B PHE* 3.8 31.0 - - + +
872B GLU* 3.9 32.3 - - + +
873B LEU* 4.7 4.7 - - + +
876B LEU* 4.3 9.4 - - + -
897B TYR* 3.5 3.8 - - - -
898B LEU* 2.8 49.7 + - + +
900B LEU* 4.3 24.7 - - - -
983B PHE* 3.9 26.5 - - + -
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Residues in contact with LYS 858 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856B ARG 4.2 1.4 + - - -
857B MET* 1.3 71.5 - - - +
859B GLU* 1.3 60.9 + - - +
860B TYR 4.8 9.0 - - - +
869B PHE* 3.5 16.5 - - - +
896B GLY 4.3 0.2 - - - -
897B TYR* 3.6 30.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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