Contacts of the helix formed by residues 539 - 543 (chain A) in PDB entry 1BF5
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 TRP 539 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A GLU* 5.9 1.8 - - + -
469A ALA* 3.9 8.5 - - + -
470A SER* 3.8 31.9 - - - -
473A TRP* 3.4 58.4 - + + -
487A PHE* 3.6 26.2 + + - +
490A PRO* 3.5 45.8 + - + +
492A CYS* 4.8 1.6 - - - +
537A ILE 3.4 2.2 + - - -
538A PRO* 1.3 68.5 - - - +
540A THR* 1.3 59.5 + - - +
542A PHE* 2.6 40.2 + + - +
543A CYS* 3.0 36.0 + - + +
544A LYS* 4.0 26.5 + - + +
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Residues in contact with THR 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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490A PRO* 5.3 3.5 - - - +
538A PRO* 4.3 10.2 - - - +
539A TRP* 1.3 82.0 + - - +
541A ARG* 1.3 60.4 + - - +
542A PHE 2.9 1.6 + - - -
544A LYS* 3.0 32.5 + - + +
545A GLU* 2.8 32.0 + - + +
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Residues in contact with ARG 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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525A LYS 5.6 0.7 - - - -
526A LEU* 3.2 42.1 + - + +
527A LEU* 4.4 15.4 + - - +
536A LEU 4.9 1.4 + - - -
537A ILE* 4.6 5.2 - - + -
538A PRO* 2.9 42.1 + - + +
540A THR* 1.3 76.0 - - - +
542A PHE* 1.3 59.7 + - - +
545A GLU* 3.7 41.1 + - - +
547A ILE* 4.2 6.8 - - + +
554A PHE* 4.0 14.7 + - - +
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Residues in contact with PHE 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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469A ALA* 4.4 13.9 - - + -
472A LEU* 4.9 8.3 - - + -
473A TRP* 3.7 31.9 - + + -
476A MET* 6.0 1.3 - - + -
498A LEU* 3.9 35.7 - - + -
502A LEU* 4.4 2.0 - - + -
526A LEU* 4.8 2.9 - - + -
537A ILE* 4.7 2.5 - - + -
538A PRO 3.1 8.8 + - - +
539A TRP* 2.6 25.4 + + - +
541A ARG* 1.3 79.8 - - - +
543A CYS* 1.4 56.6 + - + -
544A LYS 3.8 0.4 - - - -
554A PHE* 3.6 40.0 + + - +
555A TRP* 3.0 68.1 + + + +
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Residues in contact with CYS 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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466A SER* 3.7 27.4 - - - -
469A ALA* 3.8 21.8 - - + -
539A TRP* 3.0 40.6 + - + +
542A PHE* 1.4 79.1 - - + +
544A LYS* 1.3 66.9 + - + +
553A PRO* 3.8 17.9 - - - +
555A TRP* 4.4 9.6 - - + -
556A LEU* 4.9 7.7 - - - +
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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