Contacts of the strand formed by residues 837 - 845 (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 GLN 837 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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856A ARG* 3.5 26.9 + - - +
897A TYR* 4.8 7.0 + - - -
829B VAL* 3.9 10.3 - - + +
830B ILE 3.3 13.9 - - - +
831B GLY* 3.7 16.6 - - - +
835B PHE 3.6 3.3 + - - +
836B GLY* 1.3 72.9 - - - -
838B VAL* 1.3 64.8 + - - +
855B LYS* 4.2 10.9 + - - +
856B ARG 5.5 0.7 + - - -
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Residues in contact with VAL 838 (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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829B VAL* 3.5 6.3 - - - +
830B ILE* 2.8 53.4 + - + +
832B GLU* 3.9 16.6 - - + +
835B PHE* 3.9 23.8 - - + +
836B GLY 3.9 7.6 - - - +
837B GLN* 1.3 80.8 - - - +
839B LEU* 1.3 63.8 + - - +
853B ALA* 3.9 17.7 - - + -
854B ILE 3.5 17.7 - - - +
855B LYS* 4.0 14.6 - - + +
902B ILE* 4.7 4.3 - - + -
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Residues in contact with LEU 839 (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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826A PHE* 6.3 0.2 - - + -
829A VAL* 3.9 20.2 - - + -
839A LEU* 3.9 27.8 - - + -
826B PHE* 3.6 45.8 - - + -
828B ASP 3.4 5.2 - - - +
829B VAL* 3.9 17.9 - - + -
838B VAL* 1.3 75.2 - - - +
840B LYS* 1.3 62.4 + - - +
841B ALA 3.5 0.5 + - - -
853B ALA* 3.2 3.3 - - - -
854B ILE* 2.6 52.1 + - + +
856B ARG* 5.0 7.6 - - + -
899B TYR* 4.6 7.0 - - + -
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Residues in contact with LYS 840 (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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895A ARG* 5.9 3.1 - - - +
826B PHE* 3.7 1.6 - - - -
827B GLN* 2.8 55.1 + - + +
828B ASP* 2.7 36.0 + - + +
830B ILE* 4.2 20.8 - - + +
838B VAL 3.8 2.4 + - - -
839B LEU* 1.3 72.8 - - - +
841B ALA* 1.3 63.2 + - - +
851B ASP* 4.7 9.9 + - + -
852B ALA 3.8 6.3 - - - +
853B ALA* 4.4 2.2 - - - +
904B TYR* 3.5 46.6 - - + +
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Residues in contact with ALA 841 (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* 4.5 0.2 - - + -
825B LYS 2.9 21.5 - - - +
826B PHE* 3.9 7.4 - - + -
827B GLN* 3.3 17.2 + - - +
839B LEU 3.5 2.2 + - - +
840B LYS* 1.3 78.7 - - - +
842B ARG* 1.3 61.3 + - - +
843B ILE* 5.2 0.7 - - + -
851B ASP* 3.6 3.8 - - - +
852B ALA* 2.8 34.9 + - - +
854B ILE* 4.0 27.1 - - + -
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Residues in contact with ARG 842 (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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823B ASP 3.5 0.5 - - - +
824B ILE* 3.5 2.3 - - - +
825B LYS* 2.9 42.2 + - + +
827B GLN* 3.2 30.5 - - + +
841B ALA* 1.3 75.8 - - - +
843B ILE* 1.3 63.7 + - - +
849B ARG* 2.6 64.1 + - - +
850B MET* 3.1 17.2 + - - +
851B ASP* 3.4 18.1 + - - +
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Residues in contact with ILE 843 (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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819B LEU* 4.3 15.9 - - + -
823B ASP 3.6 6.1 - - - +
824B ILE* 4.3 11.4 - - + -
842B ARG* 1.3 80.0 - - - +
844B LYS* 1.3 59.8 + - - +
845B LYS* 4.3 12.8 - - + -
848B LEU 3.5 0.3 - - - +
849B ARG* 3.2 12.0 + - - -
850B MET* 3.0 44.3 + - + +
852B ALA* 4.2 13.2 - - + -
854B ILE* 4.2 23.8 - - + -
889B LEU* 4.0 36.3 - - + +
901B ALA* 4.2 14.1 - - + -
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Residues in contact with LYS 844 (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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819B LEU* 4.1 14.5 - - - +
823B ASP* 3.6 45.4 + - + +
843B ILE* 1.3 78.5 - - - +
845B LYS* 1.3 59.2 + - - +
846B ASP 4.4 0.3 + - - -
847B GLY* 4.2 29.6 - - - +
848B LEU 3.4 9.2 - - - +
849B ARG* 4.5 11.0 - - + +
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Residues in contact with LYS 845 (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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817B PRO* 3.9 25.6 - - + +
819B LEU* 5.3 1.6 - - + -
843B ILE* 4.0 8.2 - - + -
844B LYS* 1.3 74.7 - - - +
846B ASP* 1.3 92.1 + - - +
847B GLY 3.3 0.9 - - - -
848B LEU* 3.0 20.9 + - - +
850B MET* 3.4 32.6 - - + +
881B HIS* 4.9 7.1 + - - -
888B LEU 4.1 4.9 + - - -
889B LEU* 3.4 55.1 + - + +
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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