Contacts of the helix formed by residues 547 - 556 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C ASN* 4.4 12.7 + - - +
106C LEU* 5.6 2.6 - - - +
490C GLN* 2.9 43.4 + - - +
491C THR* 3.4 5.6 + - - +
543C TYR 3.2 10.9 + - - +
544C ALA 3.9 4.4 - - - +
546C CYS* 1.3 83.5 - - - +
548C LYS* 1.3 63.3 + - - +
549C THR* 2.9 16.3 + - - +
550C PHE* 3.0 21.3 + - + +
551C ARG 3.5 4.9 + - - -
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Residues in contact with LYS 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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544C ALA 4.9 1.6 - - - -
545C LEU 5.1 1.2 + - - -
546C CYS 4.0 2.6 + - - -
547C ASN* 1.3 70.7 - - - +
549C THR* 1.3 62.1 + - - +
551C ARG* 2.9 14.3 + - + +
552C THR* 2.9 24.8 + - - -
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Residues in contact with THR 549 (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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95C ASN* 5.4 1.1 - - - +
97C GLN* 5.3 11.4 - - + -
98C LEU* 3.6 26.2 - - + -
547C ASN* 2.9 12.9 + - - +
548C LYS* 1.3 78.7 - - - +
550C PHE* 1.3 55.4 + - - +
551C ARG 3.1 0.2 + - - -
552C THR* 3.2 5.7 + - - -
553C THR* 2.8 39.0 + - - +
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Residues in contact with PHE 550 (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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98C LEU* 4.6 12.0 - - + +
543C TYR* 4.5 20.0 - - + +
544C ALA* 4.6 8.0 - - + +
547C ASN* 3.0 13.6 + - + +
549C THR* 1.3 79.4 - - - +
551C ARG* 1.3 58.5 + - - +
553C THR* 3.8 7.7 - - - -
554C PHE* 2.9 32.6 + - - +
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Residues in contact with ARG 551 (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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544C ALA* 4.1 19.9 + - + +
547C ASN 3.5 1.4 + - - -
548C LYS* 2.9 26.5 + - + +
550C PHE* 1.3 78.0 - - - +
552C THR* 1.3 58.3 + - - +
554C PHE* 3.9 2.7 - - - +
555C LYS* 2.9 32.0 + - - +
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Residues in contact with THR 552 (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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548C LYS 2.9 10.5 + - - -
549C THR* 3.8 7.9 - - - -
551C ARG* 1.3 77.3 - - - +
553C THR* 1.3 60.8 + - - +
555C LYS* 3.9 8.1 + - - +
556C THR* 3.7 21.8 + - - +
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Residues in contact with THR 553 (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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91C ALA* 3.6 32.2 - - + +
94C VAL* 5.9 1.6 - - + -
95C ASN* 3.4 30.9 + - + +
98C LEU* 3.7 8.2 - - + +
549C THR* 2.8 25.9 + - - +
550C PHE* 3.8 8.3 - - - -
552C THR* 1.3 76.6 - - - +
554C PHE* 1.3 62.5 + - - +
556C THR* 3.0 24.1 + - - +
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Residues in contact with PHE 554 (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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87C LEU* 4.5 31.3 - - + +
91C ALA* 5.5 5.2 - - + -
544C ALA* 6.0 4.5 - - + -
550C PHE 2.9 19.9 + - - +
551C ARG* 4.0 2.9 - - - +
553C THR* 1.3 74.6 - - - +
555C LYS* 1.3 67.2 + - - +
556C THR 2.9 13.2 - - - +
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Residues in contact with LYS 555 (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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551C ARG 2.9 19.9 + - - +
552C THR* 4.0 9.2 - - - +
553C THR 3.3 0.2 - - - -
554C PHE* 1.3 77.3 - - - +
556C THR* 1.3 62.8 + - + +
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Residues in contact with THR 556 (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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552C THR 3.7 13.9 + - - +
553C THR* 3.0 18.8 + - - +
554C PHE* 2.9 14.7 - - - +
555C LYS* 1.3 80.9 - - + +
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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