Contacts of the helix formed by residues 539 - 547 (chain A) in PDB entry 1FO4
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 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A LYS 3.7 1.0 + - - -
538A LEU* 1.3 76.8 - - - +
540A PRO* 1.3 69.4 - - - +
541A THR* 2.7 44.8 + - - +
542A TYR* 2.8 42.4 + - + +
543A THR* 3.5 5.2 + - - -
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Residues in contact with PRO 540 (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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538A LEU 3.1 6.5 - - - +
539A ASP* 1.3 91.2 - - - +
541A THR* 1.3 60.7 + - + +
542A TYR 3.1 1.3 + - - -
543A THR* 3.4 22.7 + - - +
544A SER 4.8 1.0 + - - -
990A GLU 4.0 6.5 - - - +
991A ASN* 5.4 1.0 - - - +
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Residues in contact with THR 541 (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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539A ASP* 2.7 33.7 + - - +
540A PRO* 1.3 74.3 - - + +
542A TYR* 1.3 69.7 + - - +
543A THR 3.5 0.4 - - - -
544A SER* 4.8 4.0 + - - -
989A LYS 3.9 16.8 - - - +
990A GLU* 3.3 21.8 - - - +
991A ASN* 4.0 2.5 - - - -
992A CYS* 3.0 36.1 + - - +
993A TRP* 4.3 2.1 + - - -
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Residues in contact with TYR 542 (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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517A PHE* 3.9 14.4 - + - -
521A LEU* 4.1 24.6 - - + +
538A LEU* 4.2 13.4 - - + +
539A ASP* 2.8 27.2 + - + +
541A THR* 1.3 99.5 - - - +
543A THR* 1.3 61.9 + - - +
544A SER 3.5 1.1 - - - -
545A ALA* 3.3 20.2 - - - +
546A THR* 4.1 7.1 - - - +
992A CYS* 3.8 16.8 - - - -
993A TRP* 3.4 35.4 - + - -
1285A HIS* 4.9 1.9 + - - -
1312A LYS* 5.3 5.9 + - - -
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Residues in contact with THR 543 (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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525A LYS* 4.7 15.5 - - + +
537A LYS* 6.0 2.3 - - - -
538A LEU* 4.5 16.7 + - + +
539A ASP 3.5 8.9 + - - -
540A PRO* 3.4 20.2 + - - +
542A TYR* 1.3 72.7 - - - +
544A SER* 1.3 63.6 + - - +
545A ALA 3.0 7.2 + - - -
546A THR* 3.0 27.9 + - - +
547A LEU* 3.8 11.4 - - + +
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Residues in contact with SER 544 (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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540A PRO 4.8 1.2 + - - -
541A THR 4.8 4.7 + - - -
542A TYR 3.5 0.2 - - - -
543A THR* 1.3 78.4 - - - +
545A ALA* 1.3 60.6 + - - +
546A THR 3.1 0.2 - - - -
547A LEU* 3.2 34.2 + - - +
987A PHE* 5.8 0.7 - - - -
991A ASN* 2.9 29.6 + - - +
993A TRP 5.1 2.6 + - - -
994A LYS* 3.1 47.3 + - - +
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Residues in contact with ALA 545 (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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518A LYS* 3.4 35.0 + - + +
521A LEU* 4.0 18.6 - - + -
542A TYR 3.3 15.1 + - - +
543A THR 3.0 1.0 + - - -
544A SER* 1.3 81.3 + - - +
546A THR* 1.3 59.1 + - - +
547A LEU 3.4 1.0 + - - +
993A TRP* 4.0 30.2 - - + +
994A LYS* 4.4 5.8 - - - +
1167A LEU* 4.1 9.2 - - + -
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Residues in contact with THR 546 (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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421A PHE* 6.0 2.4 - - - -
518A LYS* 4.9 0.9 - - - +
521A LEU* 3.8 29.2 - - + -
522A THR* 3.6 36.1 + - - +
525A LYS* 3.6 28.8 + - + +
538A LEU* 3.9 18.2 - - + -
542A TYR 4.1 2.7 - - - +
543A THR 3.0 16.3 + - - +
545A ALA* 1.3 77.8 - - - +
547A LEU* 1.3 63.4 + - - +
548A LEU* 3.8 8.9 + - - +
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Residues in contact with LEU 547 (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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518A LYS* 4.8 6.1 + - - -
525A LYS* 4.3 20.0 - - - +
543A THR* 3.8 16.8 - - + +
544A SER* 3.2 32.6 + - - +
545A ALA 4.6 2.4 - - - +
546A THR* 1.3 80.8 - - - +
548A LEU* 1.3 70.7 + - - +
994A LYS* 4.5 11.3 + - - +
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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