Contacts of the strand formed by residues 2028 - 2033 (chain B) in PDB entry 1D1Z
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 SER2028 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2020B LEU* 3.6 14.9 - - - +
2023B THR* 2.7 37.6 + - - +
2025B LEU* 3.1 23.8 + - - +
2026B ASP 3.4 0.4 - - - -
2027B GLY* 1.3 78.5 - - - +
2029B TYR* 1.3 61.5 + - - +
2045B VAL* 3.3 2.1 - - - -
2046B LEU* 2.9 28.3 + - - -
2100B TYR* 3.2 18.5 - - - +
2102B VAL* 4.6 0.7 - - - -
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Residues in contact with TYR2029 (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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2006B VAL* 3.8 24.2 - - + +
2020B LEU* 3.6 6.1 - - - +
2027B GLY 3.4 11.2 - - - -
2028B SER* 1.3 77.5 - - - +
2030B LEU* 1.3 64.0 + - - +
2043B LEU* 4.3 7.9 - - + -
2044B CYS 3.1 12.6 - - - +
2045B VAL* 4.2 1.6 - - + -
2084B ILE* 3.7 23.9 - - + +
2088B GLN* 3.3 21.1 + - - -
2098B LEU* 3.7 46.7 - - + -
2099B GLN 3.8 2.9 - - - -
2100B TYR 3.0 36.6 + - - -
2101B PRO* 3.6 18.5 - - + +
2102B VAL* 3.0 26.4 + - - +
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Residues in contact with LEU2030 (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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2006B VAL* 3.6 19.3 - - - +
2008B HIS* 4.1 9.9 - - - +
2011B ILE* 5.0 2.0 - - + -
2016B GLY* 3.6 31.4 - - - +
2019B LEU* 3.9 26.0 - - + -
2020B LEU* 3.9 17.0 - - + -
2029B TYR* 1.3 76.2 - - - +
2031B LEU* 1.3 73.4 + - - +
2032B ARG* 4.1 15.5 - - + +
2043B LEU* 3.6 7.9 - - - +
2044B CYS* 2.9 44.0 + - + -
2102B VAL* 4.3 8.3 - - + +
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Residues in contact with LEU2031 (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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2004B VAL* 4.5 2.2 - - + -
2006B VAL* 2.9 19.8 + - + +
2007B TYR* 3.3 26.2 - - + -
2008B HIS* 2.8 26.9 + - - +
2030B LEU* 1.3 78.0 - - - +
2032B ARG* 1.3 62.0 - - - +
2041B TYR* 4.0 24.9 - - + -
2042B CYS 3.4 22.0 - - - +
2043B LEU* 3.8 17.7 - - + +
2056B VAL* 4.3 10.8 - - + -
2080B ILE* 4.4 29.8 - - + -
2083B LEU* 6.3 0.9 - - + -
2084B ILE* 5.2 5.8 - - + -
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Residues in contact with ARG2032 (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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2007B TYR* 4.2 1.6 - - - -
2008B HIS 3.5 15.3 - - - +
2011B ILE* 4.3 9.2 - - + +
2012B SER 4.0 8.7 - - - -
2013B ARG* 3.4 50.0 + - - +
2016B GLY* 4.7 6.0 - - - -
2017B GLU* 5.0 1.0 + - - +
2030B LEU* 4.1 11.2 - - + -
2031B LEU* 1.3 75.5 - - - +
2033B ASP* 1.3 77.8 + - - +
2035B GLU* 4.2 1.0 - - - +
2041B TYR* 3.2 11.7 - - - +
2042B CYS* 2.7 47.6 + - + +
2044B CYS* 3.4 18.5 - - - -
2053B THR* 3.9 17.8 + - - +
5002B SO4 2.8 43.2 + - - -
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Residues in contact with ASP2033 (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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2007B TYR* 2.6 32.7 + - - -
2008B HIS 4.2 1.4 + - - -
2009B GLY* 4.1 0.9 - - - -
2010B LYS* 3.0 34.7 + - - +
2011B ILE 4.6 8.1 + - - +
2032B ARG* 1.3 95.9 + - - +
2034B SER* 1.3 68.8 + - - +
2035B GLU* 3.5 3.3 + - - +
2040B VAL 4.0 4.9 - - - +
2041B TYR* 3.4 9.8 - - - -
2042B CYS 4.6 0.2 - - - -
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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