Contacts of the strand formed by residues 716 - 721 (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 ASP 716 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522F SER* 5.6 1.6 - - - -
551F ARG* 3.1 38.3 + - - +
710F GLY* 3.1 5.4 - - - -
711F SER 3.0 30.5 + - - +
715F THR* 1.3 77.9 + - - +
717F PHE* 1.3 63.7 + - - +
718F THR* 4.0 12.5 + - - -
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Residues in contact with PHE 717 (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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522F SER* 3.2 5.5 - - - -
523F CYS* 2.7 48.3 + - + +
562F VAL* 4.2 3.4 - - + -
563F SER* 4.0 1.3 - - - -
596F SER* 3.6 27.6 - - - -
598F MET* 3.7 49.1 - - + -
601F TRP* 3.9 9.5 - - + +
694F ALA* 3.9 12.6 - - + -
709F SER 3.6 4.9 - - - +
710F GLY* 3.4 25.6 - - - -
711F SER* 3.4 17.7 - - - -
712F GLY 3.2 28.7 - - - -
715F THR 3.8 4.3 - - - -
716F ASP* 1.3 78.2 + - - +
718F THR* 1.3 61.8 + - - +
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Residues in contact with THR 718 (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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520F THR* 3.7 16.2 - - - +
521F ILE 3.4 12.3 - - - +
522F SER* 4.3 6.6 - - - +
601F TRP* 4.0 7.5 + - - -
708F GLY* 3.5 2.9 - - - -
709F SER* 2.8 47.5 + - - +
716F ASP* 4.0 10.6 + - - -
717F PHE* 1.3 76.2 + - - +
719F LEU* 1.3 62.0 + - - +
720F ASN* 3.7 21.1 - - - +
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Residues in contact with LEU 719 (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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519F ALA 3.6 0.9 - - - +
520F THR* 3.2 4.9 - - - -
521F ILE* 2.8 43.6 + - + +
601F TRP* 3.5 60.1 - - + -
613F LEU* 5.5 2.0 - - + -
614F ILE* 4.4 13.7 - - + -
706F PHE* 4.8 9.0 - - + -
707F SER 3.3 23.3 - - - +
718F THR* 1.3 73.9 - - - +
720F ASN* 1.3 70.8 + - - +
721F ILE* 4.9 6.1 - - + -
732F TYR* 4.0 27.1 - - + -
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Residues in contact with ASN 720 (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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518F ARG* 3.4 34.5 + - - +
519F ALA 3.3 2.0 - - - -
520F THR* 3.2 24.2 - - - +
705F ARG 3.3 3.7 - - - +
706F PHE* 3.6 1.9 - - - -
707F SER* 2.9 48.4 + - - +
708F GLY* 6.0 0.4 - - - -
709F SER* 5.0 5.5 + - - -
718F THR* 3.7 23.6 - - - +
719F LEU* 1.3 76.6 - - - +
721F ILE* 1.3 63.1 + - - +
722F HIS* 4.1 0.4 - - + -
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Residues in contact with ILE 721 (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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517F GLN 3.8 1.9 - - - +
518F ARG* 3.4 2.3 - - - +
519F ALA* 2.9 39.5 + - + +
521F ILE* 5.6 5.2 - - + -
705F ARG* 3.5 10.1 - - - +
706F PHE* 3.5 28.5 - - + -
719F LEU* 4.9 7.4 - - + +
720F ASN* 1.3 75.0 - - - +
722F HIS* 1.3 66.1 + - - +
724F VAL* 3.9 15.9 - - + +
728F ASP* 3.4 23.6 - - + +
732F TYR* 3.4 36.1 - - + +
807F LEU* 3.5 21.3 - - + -
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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