Contacts of the helix formed by residues 547 - 556 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ASN* 5.7 1.6 - - - +
106B LEU* 5.8 1.4 - - - +
490B GLN* 4.3 12.8 + - - +
491B THR* 2.6 38.8 + - - +
543B TYR* 3.0 13.4 + - - +
544B ALA 2.8 18.8 - - - +
545B LEU 3.1 1.9 - - - -
546B CYS* 1.3 83.8 + - - +
548B LYS* 1.3 63.8 + - - +
549B THR* 4.2 15.8 + - - +
550B PHE* 3.2 18.9 + - + +
551B ARG 3.4 3.5 + - - -
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Residues in contact with LYS 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B ALA 4.7 0.9 - - - -
545B LEU 5.0 0.4 + - - -
546B CYS 4.3 0.4 + - - -
547B ASN* 1.3 70.7 - - - +
549B THR* 1.3 66.3 + - - +
551B ARG* 3.0 11.8 + - + +
552B THR* 2.9 26.5 + - - -
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Residues in contact with THR 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN* 4.4 5.6 - - - +
97B GLN* 4.6 13.7 - - + -
98B LEU* 3.3 31.6 - - + -
547B ASN* 3.1 14.3 + - - +
548B LYS* 1.3 78.9 - - - +
550B PHE* 1.3 57.1 + - - +
552B THR* 4.0 3.1 - - - -
553B THR* 2.8 40.8 + - - +
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Residues in contact with PHE 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA* 6.4 0.9 - - - -
98B LEU* 4.7 9.1 - - + +
543B TYR* 4.0 11.0 - - + +
544B ALA* 3.6 25.1 - - + +
547B ASN* 3.2 16.7 + - + +
549B THR* 1.3 79.8 - - - +
551B ARG* 1.3 50.1 + - - +
553B THR* 4.7 3.8 - - - -
554B PHE* 2.8 41.1 + - - +
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Residues in contact with ARG 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B ALA* 4.5 14.3 - - + +
547B ASN 3.4 4.0 + - - +
548B LYS* 3.0 20.7 + - + +
550B PHE* 1.3 76.5 - - - +
552B THR* 1.3 59.8 + - - +
554B PHE* 3.9 2.5 - - - +
555B LYS* 2.9 34.3 + - - +
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Residues in contact with THR 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548B LYS 2.9 17.3 + - - -
549B THR* 4.2 3.4 - - - -
551B ARG* 1.3 73.2 - - - +
553B THR* 1.3 61.8 + - - +
555B LYS* 3.0 37.8 - - - +
556B THR* 3.2 14.4 - - - +
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Residues in contact with THR 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA* 3.8 18.3 - - + +
94B VAL* 4.5 6.7 - - + -
95B ASN* 3.0 31.9 + - + +
98B LEU* 3.8 24.2 - - + -
549B THR* 2.8 25.9 + - - +
550B PHE* 4.4 1.6 - - - -
552B THR* 1.3 75.6 - - - +
554B PHE* 1.3 63.0 + - - +
556B THR* 2.9 24.0 + - - +
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Residues in contact with PHE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 4.6 32.3 - - + +
91B ALA* 5.0 9.6 - - + +
544B ALA* 5.9 3.1 - - + -
550B PHE 2.8 23.1 + - - +
551B ARG* 3.9 2.9 - - - +
553B THR* 1.3 74.2 - - - +
555B LYS* 1.3 67.7 + - - +
556B THR 2.8 14.3 - - - +
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Residues in contact with LYS 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551B ARG 2.9 17.2 + - - +
552B THR* 3.0 37.5 - - - +
554B PHE* 1.3 77.5 - - - +
556B THR* 1.3 69.5 + - + +
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Residues in contact with THR 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LEU* 6.0 0.7 - - - +
552B THR 3.2 17.7 + - - +
553B THR* 2.9 22.1 + - - +
554B PHE 2.8 15.0 + - - +
555B LYS* 1.3 90.4 - - + +
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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