Contacts of the helix formed by residues 1997 - 1999 (chain B) in PDB entry 3AU5
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 GLU1997 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1517A CYS* 4.0 8.6 - - - -
1518A LEU* 3.3 45.5 - - + +
1647A LYS* 4.4 7.8 - - - -
1978B ASP* 4.5 5.9 - - - +
1995B GLN* 3.4 29.2 + - - +
1996B TYR* 1.3 86.4 + - - +
1998B HIS* 1.3 78.2 + - + +
1999B ILE 3.7 1.2 + - - -
2040B ILE* 4.8 11.1 - - + +
2044B ARG* 5.3 4.9 - - - +
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Residues in contact with HIS1998 (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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1514A LYS* 2.8 69.2 + - + +
1515A GLU* 4.7 5.6 - - + -
1517A CYS* 3.6 12.2 - - - -
1647A LYS* 4.2 14.4 - - - +
1994B PHE* 5.6 1.3 - - - -
1995B GLN* 3.1 44.0 + - + +
1996B TYR 3.1 0.8 - - - -
1997B GLU* 1.3 94.6 + - + +
1999B ILE* 1.3 59.6 + - - +
2000B LEU* 3.6 7.4 + - - +
2014B VAL* 3.8 24.2 - - + +
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Residues in contact with ILE1999 (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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1980B VAL* 3.3 34.1 - - + -
1994B PHE* 3.4 18.8 - - + +
1995B GLN 3.1 14.1 - - - +
1996B TYR* 3.2 28.6 + - + +
1997B GLU 3.4 1.6 - - - +
1998B HIS* 1.3 75.9 - - - +
2000B LEU* 1.3 65.5 + - - +
2001B SER* 3.6 25.0 - - - +
2002B PHE* 4.1 14.0 - - + -
2012B ILE* 4.0 14.4 - - + -
2013B VAL 3.8 2.7 - - - -
2014B VAL* 4.3 4.3 - - + -
2033B MET* 4.1 5.8 - - + -
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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