Contacts of the helix formed by residues 2006 - 2021 (chain B) in PDB entry 1F5T
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 ASP2006 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2004B LEU 2.3 29.2 + - - +
2005B VAL* 1.3 70.6 - - + +
2007B THR* 1.3 65.0 + - - +
2008B THR* 3.1 9.2 + - - -
2009B GLU* 2.7 51.0 + - - +
2010B MET* 3.4 15.4 + - - +
2106B HIS* 4.2 9.8 - - + +
320E A 5.6 2.9 - - - -
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Residues in contact with THR2007 (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 LEU* 3.8 12.2 - - + +
2006B ASP* 1.3 68.8 + - - +
2008B THR* 1.3 69.3 + - - +
2009B GLU 3.0 1.8 - - - -
2010B MET* 2.8 5.0 + - - -
2011B TYR* 2.8 56.1 + - + +
2044B THR* 4.1 13.2 - - + -
320E A 3.6 26.2 + - - +
321E C 3.2 33.7 + - - +
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Residues in contact with THR2008 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2006B ASP* 3.1 8.6 + - - -
2007B THR* 1.3 76.8 - - - +
2009B GLU* 1.3 56.7 + - - +
2011B TYR* 4.4 1.8 - - - -
2012B LEU* 2.9 32.9 + - + +
2044B THR* 5.5 1.4 - - - +
2048B MET* 3.7 29.6 - - + +
2053B LEU* 3.5 33.0 - - + -
2071B LEU* 4.3 6.5 - - + -
320E A 4.5 13.5 + - - -
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Residues in contact with GLU2009 (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 ASP* 2.7 31.4 + - - +
2007B THR 2.8 2.0 + - - -
2008B THR* 1.3 70.7 - - - +
2010B MET* 1.3 59.1 + - - +
2011B TYR 3.0 1.6 - - - -
2012B LEU* 3.1 6.9 + - - +
2013B ARG* 2.8 32.0 + - - +
2071B LEU* 3.5 26.4 - - + +
2075B VAL* 3.8 22.3 - - + +
2105B GLU 4.4 1.6 - - - +
2106B HIS* 3.0 48.4 + - + +
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Residues in contact with MET2010 (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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253B NI 2.0 38.1 - - + -
2004B LEU* 3.8 23.3 - - + +
2006B ASP 3.4 10.0 + - - +
2007B THR 2.8 9.0 + - - +
2009B GLU* 1.3 74.6 - - - +
2011B TYR* 1.3 59.0 + - - +
2013B ARG* 3.9 20.9 - - - +
2014B THR* 3.0 33.7 + - - +
2034B LEU* 4.0 28.9 - - + +
2102B ASP* 3.1 21.3 - - - +
2105B GLU* 2.6 5.8 - - - +
2106B HIS* 2.7 14.8 - - + +
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Residues in contact with TYR2011 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004B LEU* 4.5 1.1 - - + -
2007B THR* 2.8 34.1 + - + +
2008B THR 3.7 4.5 - - - +
2010B MET* 1.3 76.9 - - - +
2012B LEU* 1.3 65.0 + - - +
2014B THR* 3.3 5.3 + - - +
2015B ILE* 3.0 31.1 + - + +
2030B ILE* 4.1 16.7 - - + +
2034B LEU* 3.4 27.1 - - + -
2036B GLN* 2.6 26.3 + - - -
2040B THR 4.4 0.2 + - - -
2041B VAL* 3.4 33.8 + - + +
2044B THR* 3.4 28.7 + - + -
2045B VAL* 4.1 12.1 - - + -
2048B MET* 3.7 28.9 - - + -
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Residues in contact with LEU2012 (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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2008B THR* 2.9 22.6 + - + +
2009B GLU* 3.6 4.5 - - - +
2011B TYR* 1.3 77.8 - - - +
2013B ARG* 1.3 61.6 + - - +
2015B ILE* 3.3 7.8 + - + +
2016B TYR* 3.0 24.1 + - - +
2048B MET* 3.2 25.8 - - + -
2053B LEU* 4.4 9.9 - - + -
2054B VAL* 4.1 18.8 - - + -
2064B MET* 4.2 7.8 - - + +
2068B GLY* 3.9 18.8 - - - +
2071B LEU* 3.2 43.1 - - + -
2072B ALA* 4.0 16.7 - - + +
2075B VAL* 5.6 0.7 - - + -
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Residues in contact with ARG2013 (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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2009B GLU 2.8 20.4 + - - +
2010B MET* 3.9 16.5 - - - +
2012B LEU* 1.3 74.5 - - - +
2014B THR* 1.3 52.8 + - - +
2016B TYR* 3.2 6.9 + - - +
2017B GLU* 2.7 64.3 + - - +
2072B ALA* 5.0 5.1 - - - +
2075B VAL* 4.3 15.0 - - + +
2076B MET* 3.7 26.9 - - + +
2079B HIS* 3.5 19.5 + - - -
2098B HIS* 3.4 24.5 + - - -
2102B ASP* 3.8 14.8 + - - -
2105B GLU* 2.4 51.3 + - - -
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Residues in contact with THR2014 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2010B MET* 3.0 24.9 + - - +
2011B TYR* 3.7 5.8 - - - -
2013B ARG* 1.3 77.1 + - - +
2015B ILE* 1.3 63.7 + - - +
2017B GLU* 3.5 13.0 + - - +
2018B LEU* 3.0 29.2 + - + +
2030B ILE* 3.7 36.3 - - + -
2033B ARG* 4.4 19.0 + - + +
2034B LEU* 3.8 19.6 - - - +
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Residues in contact with ILE2015 (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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2011B TYR* 3.0 23.0 + - + +
2012B LEU* 3.6 9.9 - - + +
2014B THR* 1.3 75.7 - - - +
2016B TYR* 1.3 66.3 + - - +
2018B LEU* 2.8 22.0 + - + +
2019B GLU* 3.0 15.7 + - + +
2025B PRO* 4.3 16.6 - - + -
2030B ILE* 3.8 21.1 - - + -
2045B VAL* 6.0 2.0 - - + -
2048B MET* 5.4 2.2 - - + -
2054B VAL* 3.8 28.5 - - + -
2062B LEU* 3.8 28.0 - - + +
2064B MET* 3.6 26.0 - - + -
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Residues in contact with TYR2016 (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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2012B LEU 3.0 18.3 + - - +
2013B ARG* 3.6 6.1 - - - +
2015B ILE* 1.3 77.7 - - - +
2017B GLU* 1.3 64.0 + - - +
2019B GLU* 3.3 6.8 + - + +
2020B GLU* 3.0 46.2 + - + +
2064B MET* 3.5 23.6 - - + -
2069B ARG* 4.7 13.2 - - - -
2072B ALA* 4.3 9.2 - - + -
2073B THR* 3.5 33.8 - - + +
2076B MET* 3.7 30.7 - - + -
2080B ARG* 5.3 1.5 + - - -
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Residues in contact with GLU2017 (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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2013B ARG* 2.7 59.0 + - - +
2014B THR* 3.7 12.6 + - - +
2016B TYR* 1.3 73.8 - - - +
2018B LEU* 1.3 63.2 + - - +
2020B GLU* 3.3 15.6 + - - +
2021B GLU* 3.1 32.9 + - - +
2033B ARG* 5.2 6.2 + - - +
2076B MET* 4.0 21.2 - - + +
2079B HIS* 5.3 2.1 - - - -
2098B HIS* 5.2 4.3 - - - -
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Residues in contact with LEU2018 (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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2014B THR* 3.0 27.0 + - + +
2015B ILE* 2.8 17.6 + - - +
2017B GLU* 1.3 70.5 - - - +
2019B GLU* 1.3 61.8 + - - +
2021B GLU* 3.0 17.5 + - - +
2022B GLY 3.1 9.2 + - - -
2023B VAL* 3.5 30.7 + - + +
2025B PRO* 3.6 27.8 - - + -
2026B LEU 4.2 2.5 - - - +
2029B ARG* 3.8 27.8 - - + -
2030B ILE* 4.7 4.3 - - + -
2033B ARG* 3.0 44.2 - - - +
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Residues in contact with GLU2019 (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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2015B ILE* 3.0 14.1 + - + +
2016B TYR* 3.7 8.0 - - + +
2018B LEU* 1.3 74.6 - - - +
2020B GLU* 1.3 64.6 - - - +
2022B GLY* 3.2 13.0 + - - -
2023B VAL 4.3 5.4 + - - -
2025B PRO* 4.4 18.1 - - + +
2062B LEU 4.2 14.7 - - - +
2063B GLN* 5.3 0.9 - - - -
2064B MET* 3.5 19.7 + - - +
2069B ARG* 2.4 37.2 + - - -
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Residues in contact with GLU2020 (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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2016B TYR* 3.0 40.9 + - + +
2017B GLU* 3.4 18.6 - - - +
2018B LEU 3.1 0.2 - - - -
2019B GLU* 1.3 78.3 - - - +
2021B GLU* 1.3 58.1 + - + +
2022B GLY 3.5 0.7 + - - -
2076B MET* 4.4 10.9 - - - +
2080B ARG* 4.0 13.6 + - - -
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Residues in contact with GLU2021 (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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2017B GLU* 3.1 23.2 + - - +
2018B LEU* 3.2 11.4 - - - +
2020B GLU* 1.3 76.3 - - - +
2022B GLY* 1.3 56.2 + - - +
2023B VAL* 3.3 20.3 + - + +
2033B ARG* 3.3 37.1 + - - -
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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