Contacts of the helix formed by residues 2015 - 2029 (chain E) in PDB entry 1PDW
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 GLU2015 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2013E GLY 3.8 0.8 + - - -
2014E ALA* 1.3 70.6 - - - +
2016E GLU* 1.3 60.7 + - - +
2017E MSE 2.7 41.9 + - - +
2018E GLU* 3.2 40.8 + - + +
2019E THR* 2.9 23.9 + - - -
2047E SER* 3.6 14.9 + - - +
2048E ARG* 4.1 3.8 - - - +
2073E PRO* 4.6 0.2 - - - +
2074E GLY 3.1 8.5 + - - -
2075E GLY* 3.9 12.1 - - - +
2106E CYS* 5.7 0.7 - - - -
2158E PRO* 4.5 0.2 - - - -
2224F ASP* 2.5 24.0 - - - +
2228F ARG* 2.8 29.9 + - - +
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Residues in contact with GLU2016 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2014E ALA 3.3 1.6 + - - -
2015E GLU* 1.3 70.4 + - - +
2017E MSE 1.3 61.6 + - - +
2019E THR* 4.2 7.0 - - - -
2020E VAL* 2.9 35.3 + - - +
2046E CYS* 3.3 24.8 - - + +
2047E SER* 2.9 21.5 + - - -
2048E ARG* 2.9 38.1 + - - +
2050E VAL* 3.2 32.6 + - + +
2052E ILE* 4.2 6.7 - - + -
2220F VAL* 3.7 13.7 - - + -
2224F ASP* 3.5 16.1 - - - +
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Residues in contact with MSE2017 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2015E GLU* 2.7 22.1 + - - +
2016E GLU* 1.3 73.5 - - - +
2018E GLU* 1.3 63.3 + - - +
2019E THR 3.1 0.4 - - - -
2020E VAL* 4.9 0.7 - - - -
2021E ILE* 3.1 45.6 + - + +
2158E PRO* 3.6 27.4 - - + -
2161E SER* 4.5 0.4 - - - -
2220F VAL* 3.9 14.1 - - + -
2221F ILE* 3.8 22.4 - - + -
2224F ASP* 3.4 39.0 - - + +
2225F VAL* 4.0 7.9 - - + -
2228F ARG* 3.6 13.5 - - - +
2362F PHE* 3.8 22.9 - - - -
2385F LEU* 4.2 6.7 - - + -
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Residues in contact with GLU2018 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2015E GLU* 3.2 23.8 + - + +
2017E MSE 1.3 76.4 - - - +
2019E THR* 1.3 56.9 + - - +
2022E PRO* 3.2 21.1 - - - +
2071E VAL* 5.4 1.4 - - - +
2073E PRO* 4.2 8.4 - - - +
2074E GLY* 2.7 48.3 + - - +
2105E ILE* 3.6 17.2 - - + +
2106E CYS* 3.0 22.4 - - - +
2157E GLY 4.4 0.2 - - - -
2158E PRO* 3.1 37.4 - - + +
2161E SER* 3.6 21.3 - - - +
2164E PHE* 5.2 0.3 - - - -
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Residues in contact with THR2019 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008E VAL* 4.2 20.2 - - + +
2010E LEU* 4.2 22.4 - - + +
2014E ALA* 4.0 8.8 - - - +
2015E GLU 2.9 17.4 + - - -
2016E GLU* 3.7 8.0 - - - -
2017E MSE 3.1 0.4 - - - -
2018E GLU* 1.3 79.1 - - - +
2020E VAL* 1.3 65.4 + - + +
2021E ILE 3.5 0.7 - - - -
2022E PRO* 3.3 8.8 - - - +
2023E VAL* 3.0 29.8 - - + +
2035E VAL* 5.0 5.4 - - + -
2052E ILE* 4.6 10.1 - - + -
2073E PRO* 3.5 20.2 - - + +
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Residues in contact with VAL2020 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2016E GLU 2.9 17.5 + - - +
2017E MSE 4.5 0.7 - - - +
2019E THR* 1.3 76.4 - - + +
2021E ILE* 1.3 60.6 + - + +
2023E VAL* 3.2 5.1 + - - +
2024E ASP* 2.8 29.5 + - - +
2052E ILE* 3.6 27.1 - - + -
2216F GLU* 3.5 47.8 - - + +
2217F MSE 4.3 4.7 - - + +
2220F VAL* 4.0 17.9 - - + -
2250F VAL* 4.2 12.8 - - + -
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Residues in contact with ILE2021 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017E MSE 3.1 17.5 + - + +
2020E VAL* 1.3 74.3 - - + +
2022E PRO* 1.3 65.0 - - + +
2024E ASP* 3.7 0.3 - - - +
2025E VAL* 2.8 32.8 + - + +
2161E SER* 3.6 43.5 - - - +
2162E PHE* 3.9 33.0 - - + +
2165E ALA* 4.4 0.4 - - + -
2217F MSE 3.8 23.6 - - + -
2221F ILE* 3.9 27.6 - - + -
2362F PHE* 4.2 10.5 - - + -
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Residues in contact with PRO2022 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008E VAL* 5.8 0.7 - - + -
2018E GLU* 3.2 30.1 - - - +
2019E THR 3.3 7.9 - - - +
2021E ILE* 1.3 91.7 - - + +
2023E VAL* 1.3 56.5 + - + +
2026E MSE 2.7 54.7 + - + +
2071E VAL* 4.7 7.0 - - + -
2161E SER* 4.7 3.6 - - - +
2164E PHE* 4.0 30.3 - - + -
2165E ALA* 3.8 18.4 - - + -
2168E ILE* 5.2 1.3 - - + -
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Residues in contact with VAL2023 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2008E VAL* 4.0 27.8 - - + -
2019E THR* 3.0 28.9 + - + +
2020E VAL* 3.2 5.3 + - - +
2022E PRO* 1.3 77.2 - - - +
2024E ASP* 1.3 63.9 + - - +
2026E MSE 3.9 6.5 - - - +
2027E ARG* 3.0 64.0 + - - +
2033E VAL* 4.2 5.3 - - + +
2035E VAL* 4.1 17.9 - - + -
2250F VAL* 3.8 15.3 - - + -
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Residues in contact with ASP2024 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2020E VAL 2.8 21.7 + - - +
2021E ILE 3.7 3.1 - - - +
2023E VAL* 1.3 75.4 - - - +
2025E VAL* 1.3 62.6 + - - +
2027E ARG* 3.3 2.8 + - - +
2028E ARG* 2.8 44.0 + - - +
2215F GLU* 2.5 29.0 - - - +
2216F GLU* 3.3 19.3 - - + +
2217F MSE 3.2 20.0 - - + +
2248F ARG* 3.3 22.9 - - - +
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Residues in contact with VAL2025 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2021E ILE* 2.8 25.3 + - + +
2024E ASP* 1.3 73.3 - - - +
2026E MSE 1.3 64.9 + - - +
2028E ARG* 2.9 20.4 + - - +
2029E ALA* 3.1 10.4 + - - +
2162E PHE* 4.2 24.9 - - + +
2165E ALA* 3.7 25.1 - - + -
2166E LEU* 4.2 11.7 - - + -
2169E VAL* 4.0 15.0 - - + -
2181E VAL* 3.9 17.3 - - + +
2185E LEU* 4.4 11.0 - - + -
2217F MSE 4.2 9.2 - - + -
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Residues in contact with MSE2026 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2006E ALA* 3.7 23.6 - - + -
2008E VAL* 3.8 17.9 - - + -
2022E PRO* 2.7 46.7 + - + +
2023E VAL* 4.1 3.8 - - - +
2025E VAL* 1.3 73.1 - - + +
2027E ARG* 1.3 57.6 + - - +
2029E ALA* 3.0 16.4 + - - +
2031E ILE* 3.1 33.1 + - + +
2033E VAL* 3.8 12.6 - - + -
2069E VAL* 4.4 0.9 - - - -
2071E VAL* 3.7 25.1 - - + -
2165E ALA 4.8 4.0 - - - +
2168E ILE* 3.8 27.1 - - + -
2169E VAL* 4.2 20.2 - - + -
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Residues in contact with ARG2027 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2023E VAL* 3.0 39.2 + - - +
2024E ASP 3.7 3.8 - - - +
2026E MSE 1.3 77.2 - - - +
2028E ARG* 1.3 60.9 + - - +
2030E GLY* 3.2 12.1 + - - -
2031E ILE 3.7 11.6 + - - +
2033E VAL* 3.2 39.0 + - + +
2035E VAL* 4.0 4.8 - - - +
2055E ASP* 3.1 32.1 + - - -
2248F ARG* 2.7 47.1 + - + -
2249F ASP* 3.5 25.5 + - - +
2250F VAL* 3.7 3.8 - - - +
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Residues in contact with ARG2028 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2024E ASP* 2.8 29.1 + - - +
2025E VAL* 2.9 14.6 + - - +
2027E ARG* 1.3 77.8 - - - +
2029E ALA* 1.3 58.0 + - - +
2030E GLY* 3.1 4.0 + - - -
2181E VAL* 3.8 22.7 + - + +
2184E PRO* 4.7 15.8 + - - +
2185E LEU* 3.4 29.2 - - - +
2215F GLU* 2.6 33.7 + - - +
2217F MSE 3.9 2.6 - - - +
2248F ARG* 3.4 43.3 - - - +
2358F PRO* 3.9 12.9 - - - +
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Residues in contact with ALA2029 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025E VAL 3.1 6.6 + - - +
2026E MSE 3.0 12.2 + - - +
2028E ARG* 1.3 77.9 - - - +
2030E GLY* 1.3 59.9 + - - +
2031E ILE* 4.0 1.3 - - + -
2169E VAL* 3.7 34.1 - - + -
2173E ASN* 3.4 20.2 + - - +
2177E VAL* 4.1 9.4 - - + +
2181E VAL* 3.5 15.5 - - + +
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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