Contacts of the strand formed by residues 2009 - 2013 (chain K) in PDB entry 2BT4
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 ILE2009 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2004K LEU* 4.2 20.6 - - + -
2008K PRO* 1.3 71.0 - - - +
2010K MET* 1.3 67.8 + - - +
2011K ILE* 3.5 21.6 + - + -
2044K ALA* 4.6 6.1 - - + -
2050K THR 2.9 15.3 + - - +
2051K VAL* 3.3 6.8 - - + +
2052K ASP 2.8 27.0 + - - -
2073K HIS* 4.2 0.7 - - - -
2074K CYS* 3.4 21.3 - - - -
2075K GLY 3.9 12.8 - - - +
2077K VAL* 4.2 13.0 - - + -
2142K VAL* 4.3 23.1 - - + +
2145K ILE* 4.0 21.8 - - + -
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Residues in contact with MET2010 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2009K ILE* 1.3 74.4 - - - +
2011K ILE* 1.3 59.2 + - - +
2012K LEU* 3.4 29.8 - - + -
2052K ASP* 3.4 17.0 - - - +
2054K ARG* 3.7 33.9 - - - +
2065K TRP 3.6 22.9 - - - +
2068K GLU* 4.3 2.2 - - + -
2069K ALA* 3.8 19.1 - - + +
2073K HIS* 3.4 43.4 - - + +
2075K GLY 3.0 14.6 + - - +
2076K ILE* 3.3 4.7 - - + +
2077K VAL 2.9 24.8 + - - +
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Residues in contact with ILE2011 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2009K ILE* 3.8 20.2 - - + +
2010K MET* 1.3 72.6 - - - +
2012K LEU* 1.3 62.7 + - - +
2013K ASN* 3.7 4.5 + - - +
2040K CYS* 4.3 7.9 - - - -
2051K VAL* 4.1 17.3 - - + -
2052K ASP 2.8 7.7 + - - +
2053K PHE* 3.5 32.2 - - + -
2054K ARG 2.9 26.9 + - - +
2077K VAL* 3.1 35.7 - - + +
2138K TYR* 4.0 21.8 - - + -
2142K VAL* 4.0 16.8 - - + -
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Residues in contact with LEU2012 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2010K MET* 3.4 36.8 - - + -
2011K ILE* 1.3 75.0 - - - +
2013K ASN* 1.3 60.9 + - - +
2054K ARG* 3.6 5.2 - - + -
2062K LEU* 4.4 15.0 - - + +
2065K TRP* 4.0 29.2 - - + -
2066K ILE* 3.6 39.3 - - + +
2076K ILE* 4.2 17.5 - - + -
2077K VAL 2.9 9.5 + - - +
2078K ILE* 3.2 16.1 - - + +
2079K ASN 2.8 31.9 + - - +
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Residues in contact with ASN2013 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2011K ILE* 3.7 8.9 + - - +
2012K LEU* 1.3 79.5 - - - +
2014K GLY* 1.3 59.9 + - - +
2017K LEU* 3.8 9.8 - - + +
2033K LEU* 4.1 7.9 - - + +
2053K PHE* 3.4 30.4 - - - -
2054K ARG 3.0 19.1 + - - +
2055K GLN* 3.3 15.8 - - + -
2056K SER 3.0 25.6 + - - -
2062K LEU* 3.8 7.4 - - - +
2078K ILE* 6.1 0.2 - - - -
2079K ASN* 3.4 4.0 - - - +
2138K TYR* 2.7 36.2 + - - -
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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