Contacts of the helix formed by residues 547 - 556 (chain A) in PDB entry 4DAJ
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 ASN 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ASN* 4.7 8.1 + - - +
106A LEU* 5.7 3.0 - - - +
490A GLN* 3.3 20.8 + - - +
491A THR* 3.2 20.7 + - - -
543A TYR 3.0 6.3 + - - -
544A ALA 2.6 20.8 - - - +
546A CYS* 1.3 76.6 - - - +
548A LYS* 1.3 64.8 + - - +
549A THR* 3.1 12.9 + - - +
550A PHE* 3.2 47.1 + - + +
551A ARG* 3.3 3.0 + - - -
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Residues in contact with LYS 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 CYS 3.8 3.5 + - - +
547A ASN* 1.3 71.2 - - - +
549A THR* 1.3 63.8 + - - +
551A ARG* 3.0 45.2 - - - +
552A THR* 2.9 32.0 + - + +
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Residues in contact with THR 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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97A GLN* 3.6 30.3 - - + +
98A LEU* 3.3 26.5 - - + -
547A ASN* 3.0 13.8 + - - +
548A LYS* 1.3 77.5 + - - +
550A PHE* 1.3 59.6 + - - +
552A THR* 3.1 7.9 + - - +
553A THR* 2.6 34.8 + - - +
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Residues in contact with PHE 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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88A VAL* 5.0 9.6 - - + -
91A ALA* 5.5 0.9 - - + -
92A PHE* 5.4 7.2 - + + -
98A LEU* 4.0 28.5 - - + +
103A ASN* 4.0 30.7 - - + -
106A LEU* 4.8 15.5 - - + -
543A TYR* 4.1 25.1 - + + -
544A ALA* 3.7 19.1 - - - +
547A ASN* 3.2 46.5 + - + +
549A THR* 1.3 80.1 - - - +
551A ARG* 1.3 57.3 + - - +
553A THR* 4.3 5.4 - - - -
554A PHE* 2.9 57.7 + + + -
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Residues in contact with ARG 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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544A ALA* 3.1 31.1 + - + +
545A LEU* 2.8 33.2 + - + +
546A CYS 4.9 1.4 + - - -
547A ASN 3.4 2.9 - - - +
548A LYS* 3.0 51.7 + - - +
550A PHE* 1.3 78.5 - - - +
552A THR* 1.3 63.2 + - + +
554A PHE* 3.1 3.8 + - - +
555A LYS* 2.9 28.8 + - - +
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Residues in contact with THR 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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548A LYS* 2.9 18.5 + - + +
549A THR* 3.1 12.5 + - - +
551A ARG* 1.3 80.9 - - + +
553A THR* 1.3 64.0 + - - +
555A LYS* 3.7 7.6 + - - +
556A THR* 3.2 30.4 + - - +
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Residues in contact with THR 553 (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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91A ALA* 3.4 34.3 - - + +
94A VAL* 4.8 5.2 - - + -
95A ASN* 3.5 26.0 + - + +
98A LEU* 3.7 19.0 - - + +
549A THR* 2.6 26.3 + - - +
550A PHE 3.9 3.4 - - - -
552A THR* 1.3 78.2 + - - +
554A PHE* 1.3 65.1 + - - +
556A THR* 3.2 18.8 + - - +
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Residues in contact with PHE 554 (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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84A GLY 4.7 1.1 - - - -
87A LEU* 3.3 61.5 - - + +
88A VAL* 3.6 24.9 - - + -
91A ALA* 3.6 17.9 - - + -
540A PRO* 4.8 6.3 - - + -
543A TYR* 5.6 0.4 - - + -
544A ALA* 3.6 32.1 - - + -
550A PHE* 2.9 36.5 + + + +
551A ARG* 3.6 3.8 - - - +
553A THR* 1.3 74.7 - - - +
555A LYS* 1.3 67.6 - - - +
556A THR 2.8 12.0 - - - +
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Residues in contact with LYS 555 (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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551A ARG 2.9 15.7 + - - +
552A THR* 3.8 10.3 - - - +
554A PHE* 1.3 76.9 - - - +
556A THR* 1.3 65.5 + - + +
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Residues in contact with THR 556 (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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552A THR* 3.2 16.4 + - - +
553A THR* 3.2 18.0 + - - +
554A PHE 2.8 12.6 - - - +
555A LYS* 1.3 83.6 - - + +
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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