Contacts of the helix formed by residues 724 - 730 (chain A) in PDB entry 3AR2
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 724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A GLY* 3.6 28.7 - - - -
439A GLU* 5.4 9.4 - - - +
703A ASP 2.8 24.5 + - - +
704A GLY* 4.4 2.5 - - - -
705A VAL* 4.1 14.0 + - + +
723A GLY* 1.3 75.0 - - - -
725A ALA* 1.3 64.5 + - - +
726A VAL* 3.4 4.2 + - - +
727A ALA* 2.9 22.0 + - - +
728A LYS* 3.0 25.4 + - - +
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Residues in contact with ALA 725 (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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156A GLY 3.3 11.0 + - - +
157A ASP* 5.0 0.2 - - - -
158A LYS* 3.5 36.6 - - + +
213A ASN* 3.9 10.5 - - - +
723A GLY 4.0 0.8 + - - -
724A THR* 1.3 74.1 - - - +
726A VAL* 1.3 52.8 + - - +
728A LYS* 3.1 13.2 + - - +
729A THR* 2.7 38.2 + - - +
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Residues in contact with VAL 726 (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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156A GLY* 3.2 38.6 - - - +
176A ASP* 6.4 0.4 - - + -
213A ASN* 3.7 20.2 - - + +
214A ILE 4.1 8.5 - - - +
215A ALA* 5.7 2.5 - - - -
705A VAL* 3.5 30.5 - - + -
708A ALA* 4.0 15.3 - - + -
724A THR* 3.7 1.1 - - - +
725A ALA* 1.3 74.8 - - - +
727A ALA* 1.3 63.7 + - - +
729A THR* 3.3 3.0 + - - -
730A ALA* 3.1 23.2 + - - +
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Residues in contact with ALA 727 (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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702A GLY 4.5 2.7 - - - +
703A ASP* 3.4 33.0 - - - +
704A GLY 3.7 9.9 - - - +
708A ALA* 5.1 1.3 - - - -
711A LEU* 4.1 14.0 - - + +
719A ALA* 4.0 3.1 - - + -
724A THR* 2.9 20.9 + - - +
726A VAL* 1.3 80.3 - - - +
728A LYS* 1.3 54.8 + - - +
730A ALA* 3.2 12.1 + - - +
731A SER* 2.6 25.8 + - - -
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Residues in contact with LYS 728 (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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334A ARG* 3.3 21.5 + - - +
719A ALA* 3.7 21.3 - - + -
720A MET 3.5 12.3 - - - +
721A GLY* 3.0 34.9 + - - -
723A GLY 4.2 11.3 + - - -
724A THR 3.0 14.8 + - - +
725A ALA* 3.4 12.8 - - - +
727A ALA* 1.3 74.9 - - - +
729A THR* 1.3 64.7 + - - +
731A SER* 3.1 12.3 + - - -
734A VAL* 4.1 19.8 - - + +
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Residues in contact with THR 729 (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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176A ASP* 4.4 13.0 - - - +
178A SER* 5.7 2.5 - - - +
213A ASN* 2.9 28.4 + - - +
334A ARG* 3.3 21.9 + - - +
725A ALA* 2.7 16.8 + - - +
726A VAL* 3.3 6.5 + - - -
728A LYS* 1.3 72.4 - - - +
730A ALA* 1.3 61.5 + - + +
731A SER 3.2 2.6 + - - +
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Residues in contact with ALA 730 (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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708A ALA* 3.8 29.6 - - + +
711A LEU* 3.8 8.9 - - + +
712A LYS* 3.7 41.7 + - + +
726A VAL 3.1 15.8 + - - +
727A ALA 3.7 4.9 - - - +
728A LYS 3.2 0.6 - - - -
729A THR* 1.3 76.0 - - - +
731A SER* 1.3 59.6 + - - +
732A GLU* 3.8 7.4 - - - +
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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