Contacts of the strand formed by residues 825 - 831 (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 LYS 825 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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823A ASP 3.8 0.2 + - - -
824A ILE* 1.3 74.5 - - - +
826A PHE* 1.3 69.6 + - - +
827A GLN* 3.8 11.4 - - + +
841A ALA* 3.1 6.6 - - - +
842A ARG* 2.9 53.0 + - + +
849A ARG* 4.1 12.6 - - - +
825B LYS* 5.5 17.5 - - + +
826B PHE 5.9 0.7 - - - +
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Residues in contact with PHE 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821A TRP* 3.6 32.1 - + - -
824A ILE* 3.7 32.5 - - + -
825A LYS* 1.3 79.5 - - - +
827A GLN* 1.3 62.3 + - - +
828A ASP 5.2 0.4 - - - +
839A LEU* 3.8 43.5 - - + -
840A LYS 3.9 3.6 - - - +
841A ALA* 4.2 4.3 - - + -
854A ILE* 3.9 11.9 - - + -
899A TYR* 4.2 9.6 - + - -
825B LYS* 5.8 1.2 - - - +
826B PHE* 3.7 36.8 + - + +
827B GLN* 3.4 35.2 - - - -
828B ASP* 4.3 4.3 - - - -
829B VAL* 6.0 0.7 - - + -
839B LEU* 6.3 0.2 - - + -
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Residues in contact with GLN 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825A LYS* 3.8 19.1 - - + +
826A PHE* 1.3 80.5 - - - +
828A ASP* 1.3 64.2 + - + +
840A LYS* 2.8 40.1 + - + +
841A ALA* 3.3 18.8 + - - +
842A ARG* 3.2 35.7 - - + +
851A ASP* 4.4 2.5 + - - +
821B TRP* 3.5 9.9 + - - -
826B PHE* 3.3 21.5 - - - -
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Residues in contact with ASP 828 (chain A).
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* 4.0 0.8 - - - +
827A GLN* 1.3 79.0 - - + +
829A VAL* 1.3 85.3 + - - +
830A ILE* 4.5 5.8 - - + +
839A LEU* 3.3 11.6 - - - +
840A LYS* 2.8 48.2 + - + +
821B TRP* 3.6 13.7 - - + -
826B PHE* 4.2 8.8 - - - -
894B HIS* 3.7 20.3 + - - -
899B TYR* 2.8 23.1 + - - -
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Residues in contact with VAL 829 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ASP* 1.3 89.5 + - - +
830A ILE* 1.3 72.4 + - - +
837A GLN* 3.6 18.4 - - + +
838A VAL 3.4 8.5 - - - +
839A LEU* 3.7 21.8 - - + -
839B LEU* 3.9 27.4 - - + -
856B ARG* 3.4 49.6 + - - +
899B TYR* 4.3 1.0 + - + +
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Residues in contact with ILE 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828A ASP* 4.5 8.5 - - - +
829A VAL* 1.3 83.5 - - - +
831A GLY* 1.3 66.2 + - - +
832A GLU* 4.7 5.4 - - - +
837A GLN* 3.2 11.7 + - - +
838A VAL* 2.6 60.5 + - + +
840A LYS* 4.3 26.0 - - + +
853A ALA* 4.9 0.9 - - + -
904A TYR* 4.1 31.0 - - + -
905A ALA 5.8 0.7 - - - +
856B ARG* 4.9 2.5 - - - +
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Residues in contact with GLY 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830A ILE* 1.3 86.9 - - - +
832A GLU* 1.3 64.5 + - - +
833A GLY 4.1 0.9 - - - -
836A GLY 3.4 8.1 - - - -
837A GLN* 3.6 13.7 - - - +
838A VAL* 4.4 0.2 - - - -
971A LEU* 4.8 3.5 - - - +
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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