Contacts of the helix formed by residues 546 - 552 (chain A) in PDB entry 3EPZ
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 546 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A ILE* 4.0 9.2 - - - +
532A GLU* 4.2 12.1 - - + -
544A ARG 4.1 4.5 + - - +
545A PHE* 1.3 78.2 - - - +
547A GLU* 1.3 64.8 + - - +
548A ASP* 3.1 24.2 + - - +
549A SER* 3.0 24.1 + - - +
550A LEU 3.7 2.3 + - - -
552A ARG* 5.6 0.3 + - - -
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Residues in contact with GLU 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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524A TYR* 2.8 40.2 + - - +
528A ILE* 3.7 33.0 - - + +
531A ILE* 5.6 0.4 - - - -
532A GLU* 4.1 11.0 + - - +
546A THR* 1.3 73.9 - - - +
548A ASP* 1.3 57.5 + - - +
550A LEU* 3.2 5.4 + - - +
551A LEU* 3.0 36.9 + - + +
598A GLN 4.8 1.4 - - - +
599A ALA* 3.4 43.9 - - + +
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Residues in contact with ASP 548 (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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546A THR* 3.1 13.6 + - - +
547A GLU* 1.3 77.8 - - - +
549A SER* 1.3 63.7 + - - +
551A LEU* 4.3 7.9 - - - +
552A ARG* 3.0 42.4 + - - +
596A ARG* 2.7 56.9 + - - +
599A ALA* 4.9 8.8 - - - +
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Residues in contact with SER 549 (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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504A GLU* 3.3 27.3 + - - -
508A ILE* 4.3 9.8 - - - +
544A ARG 4.3 1.7 + - - -
545A PHE* 3.4 18.4 - - - -
546A THR* 3.0 30.8 + - - -
548A ASP* 1.3 78.9 - - - +
550A LEU* 1.3 59.6 + - - +
552A ARG* 4.4 9.9 + - - +
553A HIS* 3.0 29.1 + - - +
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Residues in contact with LEU 550 (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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508A ILE* 4.0 14.5 - - + +
512A VAL* 4.1 10.8 - - + -
524A TYR* 4.3 5.8 - - + -
527A LEU* 3.8 22.4 - - + -
528A ILE* 3.5 28.0 - - + -
531A ILE* 3.9 16.2 - - + -
546A THR 3.7 2.9 + - - +
547A GLU 3.2 8.8 + - - +
549A SER* 1.3 78.2 - - - +
551A LEU* 1.3 65.8 + - + +
553A HIS* 3.0 14.6 + - - +
554A ALA* 3.1 10.6 + - - -
557A VAL* 4.0 19.1 - - + -
584A LEU* 3.9 33.9 - - + -
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Residues in contact with LEU 551 (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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524A TYR* 3.1 30.5 - - + +
547A GLU* 3.0 35.1 + - + +
548A ASP* 3.4 9.6 + - - +
550A LEU* 1.3 79.4 - - + +
552A ARG* 1.3 56.9 + - - +
553A HIS 3.1 1.3 + - - -
554A ALA* 3.2 6.0 + - + +
584A LEU* 4.5 9.2 - - + -
587A LEU* 3.7 23.8 - - + -
592A LEU* 5.6 0.2 - - - -
595A ARG* 2.8 71.4 + - + +
596A ARG* 4.3 3.8 - - + +
599A ALA* 4.4 6.5 - - + +
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Residues in contact with ARG 552 (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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504A GLU* 2.5 36.6 + - - -
546A THR* 5.6 0.4 + - - -
548A ASP* 3.0 38.5 + - - +
549A SER* 4.3 7.8 + - - +
550A LEU 3.3 0.2 + - - -
551A LEU* 1.3 76.1 - - - +
553A HIS* 1.3 75.3 + - + +
554A ALA 3.6 0.2 - - - -
592A LEU* 3.8 33.6 - - + +
595A ARG* 4.3 6.0 + - - -
596A ARG* 4.0 22.6 - - - +
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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