Contacts of the strand formed by residues 572 - 575 (chain I) in PDB entry 2A07
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 VAL 572 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524H GLN* 3.5 46.9 - - + +
525H LEU* 3.5 9.6 - - - +
526H THR* 4.0 15.3 - - + +
564I ARG* 3.4 2.6 - - - +
565I VAL* 2.6 57.4 + - + +
567I ASN* 3.9 25.6 - - - +
569I LYS* 5.3 6.7 - - + -
571I ALA* 1.3 81.5 - - - +
573I TRP* 1.3 59.0 + - - +
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Residues in contact with TRP 573 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517H ILE* 3.7 12.6 - - + +
524H GLN* 3.6 5.2 - - - -
525H LEU 2.7 40.0 + - - +
527H LEU* 4.0 26.7 - - + +
530H ILE* 4.2 12.3 - - + -
556I LEU* 3.5 67.8 - - + +
557I SER* 5.2 4.0 - - - -
562I PHE 3.9 10.5 - - - -
563I VAL 3.6 5.8 - - - -
564I ARG* 3.5 64.1 - - + +
571I ALA* 5.2 6.3 + - - +
572I VAL* 1.3 76.9 - - - +
574I THR* 1.3 61.4 + - - +
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Residues in contact with THR 574 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517H ILE* 4.2 3.0 - - - +
523H ARG* 3.6 18.8 + - - +
524H GLN* 4.8 9.6 - - - +
562I PHE* 3.5 8.7 - - - +
563I VAL* 2.8 50.2 + - + +
565I VAL* 3.6 24.0 - - + -
573I TRP* 1.3 75.7 - - - +
575I VAL* 1.3 80.0 + - - +
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Residues in contact with VAL 575 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514H ARG* 4.2 17.5 - - + +
517H ILE* 3.6 35.6 - - + +
518H MET* 5.1 6.7 - - + +
523H ARG 4.8 0.2 + - - -
561I CYS 3.4 6.3 - - - +
562I PHE* 3.9 15.3 - - + -
574I THR* 1.3 91.4 + - - +
576I ASP* 1.3 66.1 + - - +
577I GLU* 3.2 26.5 + - - +
580I TYR* 4.3 19.3 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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