Contacts of the strand formed by residues 805 - 810 (chain F) in PDB entry 5DFV
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 THR 805 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506F GLN* 3.4 13.1 + - - +
507F SER 4.0 0.2 - - - -
508F PRO* 2.6 25.9 + - + +
509F ALA 3.3 4.5 - - - +
510F SER* 4.4 0.2 - - - -
511F LEU* 3.4 29.8 - - + -
521F ILE* 3.3 40.4 - - + +
731F THR* 3.4 3.8 - - - +
732F TYR* 2.7 37.9 + - - +
804F GLY* 1.3 72.1 + - - -
806F LYS* 1.3 61.2 + - - +
807F LEU 3.7 1.2 + - - -
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Residues in contact with LYS 806 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509F ALA 3.1 9.7 + - - +
510F SER* 3.3 15.2 - - - -
511F LEU 3.0 26.0 + - - +
606F PRO* 5.3 6.3 - - - +
730F ALA 3.7 6.7 - - - +
731F THR* 3.9 21.9 + - + +
804F GLY 4.3 0.2 - - - -
805F THR* 1.3 72.7 - - - +
807F LEU* 1.3 65.2 + - - +
808F GLU* 3.7 5.5 + - + +
2034F LYS* 6.3 0.7 - - - +
2057F ASP* 4.2 17.7 + - - -
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Residues in contact with LEU 807 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F LEU* 3.6 17.3 - - + +
513F VAL* 3.8 31.6 - - + -
519F ALA* 4.1 10.5 - - + -
521F ILE* 5.6 2.7 - - + -
721F ILE* 3.5 29.4 - - + -
724F VAL* 4.7 3.6 - - + -
728F ASP* 3.5 22.0 - - + +
729F ALA* 3.8 8.0 - - - +
730F ALA 2.9 24.1 + - - +
732F TYR* 3.7 18.6 - - + -
805F THR 3.7 1.4 + - - -
806F LYS* 1.3 74.8 - - - +
808F GLU* 1.3 66.4 + - - +
809F ILE* 3.9 16.6 - - + -
2058F GLN* 4.6 0.3 - - - +
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Residues in contact with GLU 808 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F LEU 2.7 15.9 + - - +
512F SER* 3.4 22.4 + - - +
513F VAL* 2.8 31.4 + - - +
806F LYS* 3.7 5.3 + - + +
807F LEU* 1.3 78.6 - - - +
809F ILE* 1.3 81.6 + - - +
810F LYS 3.9 0.2 - - - -
2032F TYR* 3.4 15.8 + - - -
2033F PRO* 6.0 0.7 - - - +
2034F LYS* 5.8 1.0 + - - +
2058F GLN* 3.0 19.2 + - - +
2065F TYR* 3.0 28.4 + - - +
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Residues in contact with ILE 809 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513F VAL 3.4 4.9 - - - +
515F LEU* 3.6 38.4 - - + -
724F VAL* 3.1 29.2 - - + -
725F GLU 3.4 13.0 - - - +
726F GLU 4.2 2.9 - - - +
728F ASP 4.2 0.4 - - - -
729F ALA* 3.9 27.1 - - + +
807F LEU* 3.9 24.0 - - + -
808F GLU* 1.3 80.5 + - - +
810F LYS* 1.3 61.7 + - - +
2000F ARG 3.3 3.1 + - - -
2032F TYR* 3.8 1.0 + - - -
2058F GLN* 2.6 27.7 + - - +
2063F SER* 3.6 17.3 - - - +
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Residues in contact with LYS 810 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512F SER* 3.4 39.9 + - - +
513F VAL 2.8 8.9 + - - -
514F SER* 3.2 30.4 + - - +
515F LEU* 3.0 28.1 + - - +
808F GLU* 3.8 1.2 + - - -
809F ILE* 1.3 69.4 - - - +
2000F ARG* 1.3 61.2 + - - +
2032F TYR* 3.2 19.7 - - + +
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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