Contacts of the strand formed by residues 544 - 548 (chain C) in PDB entry 3A8P
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 544 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539C THR 3.6 1.0 - - - +
540C LEU* 3.5 5.3 - - - -
541C LYS* 2.9 36.2 + - - +
542C GLY 3.4 0.6 + - - -
543C CYS* 1.3 81.7 + - - +
545C LEU* 1.3 62.8 + - - +
546C LEU* 3.8 14.2 + - + +
565C ALA* 3.9 20.4 - - + -
566C LEU 3.6 10.1 - - - +
567C PHE* 3.5 36.6 - - + +
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Residues in contact with LEU 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C LEU* 6.1 0.7 - - + -
538C VAL* 4.0 9.4 - - + -
539C THR 3.4 0.7 - - - +
540C LEU* 3.6 26.2 - - + -
544C THR* 1.3 72.0 - - - +
546C LEU* 1.3 61.6 + - - +
547C PHE* 3.5 16.8 - - + -
565C ALA* 3.3 5.2 - - - +
566C LEU* 2.8 51.6 + - + +
568C ALA* 4.9 5.8 - - + -
588C LEU* 4.0 27.4 - - + -
598C PHE* 4.2 21.3 - - + -
609C TRP* 4.0 24.9 - - + -
613C ILE* 4.5 11.9 - - + -
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Residues in contact with LEU 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A PHE* 4.0 17.5 - - + -
537C TRP 3.5 2.4 - - - +
538C VAL* 3.2 6.2 - - - -
539C THR* 2.9 49.7 + - - +
541C LYS* 4.5 24.7 - - + -
544C THR* 4.1 15.9 - - + +
545C LEU* 1.3 72.1 - - - +
547C PHE* 1.3 62.3 + - - +
548C TYR* 3.7 28.8 - - + +
562C PRO* 4.0 9.9 - - + -
564C CYS 4.0 0.2 - - - -
565C ALA* 3.6 25.8 - - + -
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Residues in contact with PHE 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513C PHE* 3.6 37.2 - + + -
536C TYR* 3.6 40.2 - + + -
537C TRP 3.8 2.7 - - - -
538C VAL* 4.0 10.1 - - + -
545C LEU* 3.5 31.2 - - + -
546C LEU* 1.3 75.0 - - - +
548C TYR* 1.3 58.2 + - - +
562C PRO* 3.5 2.0 - - - +
563C ARG* 2.7 33.4 + - - +
564C CYS* 3.0 32.2 + - - +
565C ALA* 4.8 0.4 - - - -
566C LEU* 4.0 13.7 - - + -
598C PHE* 3.6 30.1 - + - -
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Residues in contact with TYR 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C TYR* 3.5 10.3 - - - +
537C TRP* 2.8 51.5 + + + +
539C THR* 3.8 23.5 + - + -
546C LEU* 3.7 31.0 - - + +
547C PHE* 1.3 72.4 - - - +
549C GLU* 1.3 62.9 + - - +
550C THR 3.2 18.3 + - - +
561C ALA 3.8 14.6 - - - -
562C PRO* 3.4 45.5 - - + +
563C ARG 4.6 1.3 - - - +
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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