Contacts of the helix formed by residues 2012 - 2024 (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 SER2012 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2010B LYS 3.7 1.6 + - - -
2011B ILE* 1.3 80.1 - - - +
2013B ARG* 1.3 65.6 + - - +
2014B GLU* 3.4 9.7 + - - +
2015B THR* 3.0 28.9 + - - -
2016B GLY* 3.0 19.8 + - - -
2032B ARG* 4.0 3.5 - - - -
2035B GLU* 3.6 14.6 - - - -
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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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2012B SER* 1.3 70.4 - - - +
2014B GLU* 1.3 59.7 + - - +
2016B GLY* 3.2 2.1 + - - -
2017B GLU* 2.9 73.2 + - - +
2032B ARG* 3.4 39.3 + - - +
2035B GLU* 2.8 29.3 + - - +
5002B SO4 3.8 1.3 - - - -
4013D ARG* 3.1 49.5 - - - +
4017D GLU* 2.8 34.4 + - - -
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Residues in contact with GLU2014 (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 SER* 3.2 8.7 + - - +
2013B ARG* 1.3 81.6 - - - +
2015B THR* 1.3 63.2 + - - +
2017B GLU* 3.2 6.7 + - - +
2018B LYS* 2.9 55.0 + - + +
2035B GLU* 4.7 0.2 + - - -
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Residues in contact with THR2015 (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 ILE* 4.1 23.8 - - + -
2012B SER* 3.0 27.1 + - - -
2014B GLU* 1.3 77.8 - - - +
2016B GLY* 1.3 64.0 + - - +
2018B LYS* 3.2 6.9 + - + +
2019B LEU* 2.9 33.7 + - + +
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Residues in contact with GLY2016 (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 ILE* 3.9 15.2 - - - +
2012B SER 3.0 13.8 + - - -
2013B ARG 3.6 3.4 - - - -
2015B THR* 1.3 78.4 - - - +
2017B GLU* 1.3 61.4 + - - +
2019B LEU* 3.3 4.4 + - - +
2020B LEU* 3.1 28.8 + - - +
2030B LEU* 3.6 18.4 - - - +
2032B ARG* 4.7 4.9 - - - -
2044B CYS* 6.1 1.6 - - - -
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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* 2.9 62.3 + - + +
2014B GLU* 3.2 6.3 + - - +
2016B GLY* 1.3 75.3 - - - +
2018B LYS* 1.3 60.2 + - + +
2020B LEU* 3.2 3.0 + - - +
2021B LEU* 2.9 38.7 + - + +
2032B ARG* 5.0 2.2 + - - +
2044B CYS* 6.0 1.7 - - + -
2051B ILE* 3.9 49.8 - - + +
2053B THR* 4.4 5.7 + - - -
4013D ARG* 4.8 1.6 + - - -
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Residues in contact with LYS2018 (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 GLU* 2.9 43.9 + - + +
2015B THR* 3.2 6.9 + - - +
2017B GLU* 1.3 77.7 - - + +
2019B LEU* 1.3 62.9 + - - +
2021B LEU* 3.4 17.2 + - + +
2022B ALA* 2.9 23.7 + - - +
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Residues in contact with LEU2019 (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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1010A LYS* 3.8 36.0 - - + +
2008B HIS* 4.8 9.9 - - + +
2011B ILE* 4.1 18.2 - - + -
2015B THR* 2.9 25.6 + - + +
2016B GLY 3.5 4.7 - - - +
2018B LYS* 1.3 77.2 - - + +
2020B LEU* 1.3 63.1 + - - +
2022B ALA* 3.2 15.2 + - - +
2023B THR* 3.3 15.5 + - - +
2030B LEU* 3.9 23.1 - - + -
2102B VAL* 4.4 14.1 - - + -
2104B LYS 5.4 1.1 - - - +
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Residues in contact with LEU2020 (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 GLY 3.1 15.9 + - - +
2017B GLU 3.7 5.4 - - - +
2019B LEU* 1.3 80.5 - - - +
2021B LEU* 1.3 62.2 + - - +
2023B THR* 2.7 28.5 + - - -
2028B SER* 3.6 11.0 - - - -
2029B TYR* 3.6 38.8 - - - +
2030B LEU* 3.9 7.9 - - + +
2044B CYS* 3.6 39.7 - - + +
2045B VAL 4.0 5.6 - - - +
2046B LEU* 3.4 17.8 - - + +
2051B ILE* 4.1 19.5 - - + -
2102B VAL* 4.0 9.6 - - + -
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Residues in contact with LEU2021 (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* 2.9 26.9 + - + +
2018B LYS* 3.9 18.8 - - + +
2020B LEU* 1.3 75.8 - - - +
2022B ALA* 1.3 62.1 + - - +
2024B GLY* 3.0 14.7 + - - -
2046B LEU* 3.9 16.2 - - + -
2049B GLY* 3.8 26.2 - - - +
2051B ILE* 4.0 15.5 - - + -
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Residues in contact with ALA2022 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A TYR* 4.4 12.0 - - + +
1008A HIS* 4.2 0.9 - - - -
1009A GLY* 3.0 21.4 + - - -
1010A LYS* 4.0 18.6 - - + -
2018B LYS 2.9 14.6 + - - +
2019B LEU* 3.2 11.2 + - + +
2021B LEU* 1.3 75.7 - - - +
2023B THR* 1.3 60.3 + - - +
2024B GLY 3.5 0.3 + - - -
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Residues in contact with THR2023 (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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1008A HIS* 2.7 37.6 + - - +
1009A GLY 3.1 22.0 - - - +
1010A LYS* 4.2 3.1 - - + -
1011A ILE* 4.0 13.5 - - + -
2019B LEU 3.5 13.2 - - - +
2020B LEU 2.7 14.8 + - - +
2022B ALA* 1.3 78.5 - - - +
2024B GLY* 1.3 53.1 + - - +
2025B LEU* 3.2 6.4 + - - +
2028B SER* 2.7 28.2 + - - +
2102B VAL* 3.6 26.7 - - + -
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Residues in contact with GLY2024 (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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1007A TYR 5.0 2.5 - - - -
1008A HIS* 3.2 20.7 - - - -
1103A GLU 3.2 12.6 - - - +
1104A LYS* 3.5 4.7 - - - +
2020B LEU 3.5 1.8 + - - -
2021B LEU 3.0 15.7 + - - -
2022B ALA 4.5 0.4 - - - -
2023B THR* 1.3 78.8 + - - +
2025B LEU* 1.3 56.0 + - - +
2046B LEU* 4.3 8.5 - - - -
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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