Contacts of the strand formed by residues 448 - 451 (chain F) in PDB entry 4LQL
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 448 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311F MET* 3.4 16.4 - - - +
329F LEU* 3.9 0.5 - - - +
330F MET* 2.6 53.9 + - + +
332F ASP* 4.0 14.1 + - - +
390F ASP* 3.0 37.4 - - + +
391F ILE 3.1 15.8 + - - -
426F TRP* 4.1 8.1 - - + -
439F TRP* 3.7 13.3 - - - -
446F HIS 4.3 0.2 - - - -
447F HIS* 1.3 74.6 - - - +
449F VAL* 1.3 66.3 + - - +
450F LEU* 4.1 0.4 - - + -
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Residues in contact with VAL 449 (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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311F MET* 3.9 10.3 - - + -
314F LEU* 3.7 30.3 - - + -
315F THR* 4.4 18.6 - - - +
318F LEU* 4.4 22.7 - - + -
327F THR* 5.1 3.4 - - + -
328F ALA 3.8 8.5 - - - +
329F LEU* 5.0 1.8 - - - -
390F ASP* 3.0 8.9 - - - -
391F ILE* 2.6 44.3 + - + +
448F THR* 1.3 76.9 + - - +
450F LEU* 1.3 66.6 + - - +
451F THR* 3.8 9.0 + - - +
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Residues in contact with LEU 450 (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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327F THR 3.7 0.3 - - - -
328F ALA* 2.7 47.6 + - + +
329F LEU 4.2 2.6 + - - +
330F MET* 4.2 25.6 - - + -
388F GLY 6.4 0.4 - - - -
389F TYR 4.1 7.4 - - - +
390F ASP* 4.2 9.4 - - + -
407F VAL* 6.3 1.8 - - + -
409F CYS* 5.1 11.7 - - + -
424F GLN* 5.6 3.1 - - + -
426F TRP* 5.1 13.0 - - + -
448F THR* 4.1 1.4 - - + -
449F VAL* 1.3 71.6 - - - +
451F THR* 1.3 58.9 + - - +
452F LEU* 4.0 17.7 + - + +
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Residues in contact with THR 451 (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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318F LEU* 6.1 0.7 - - - -
326F GLN 3.6 4.7 - - - -
327F THR* 3.6 23.1 - - - -
388F GLY* 3.6 10.3 - - - -
389F TYR* 3.6 22.4 + - - +
449F VAL* 3.8 9.0 + - - -
450F LEU* 1.3 73.4 - - - +
452F LEU* 1.3 59.1 + - - +
453F ALA 2.8 3.4 + - - -
454F LEU* 2.9 40.4 + - - +
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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