Contacts of the strand formed by residues 2065 - 2074 (chain F) in PDB entry 5DFV
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 TYR2065 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1050E HIS* 5.6 0.2 - - - -
808F GLU* 3.0 37.1 + - - +
2030F ASN* 3.2 1.9 + - - -
2031F PHE* 2.8 45.3 + - + +
2032F TYR* 3.7 30.1 - + - -
2033F PRO 4.2 1.3 - - - -
2034F LYS* 3.4 62.6 + - + +
2055F TRP* 4.6 3.1 - - + -
2056F THR* 3.5 19.5 - - - +
2057F ASP 4.9 2.2 - - - -
2058F GLN* 3.3 34.7 + - + +
2064F THR* 1.3 72.3 - - - +
2066F SER* 1.3 69.8 + - - +
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Residues in contact with SER2066 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050E HIS* 3.1 33.5 - - - -
1052E PHE* 3.6 7.4 - - - -
2028F LEU 3.4 5.2 - - - -
2029F ASN* 3.5 12.4 - - - -
2030F ASN 2.9 17.5 + - - -
2031F PHE* 3.7 2.9 - - - -
2055F TRP* 3.5 2.6 - - - -
2056F THR* 2.7 45.8 + - - -
2065F TYR* 1.3 82.2 + - - +
2067F MET* 1.3 60.0 + - - +
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Residues in contact with MET2067 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052E PHE* 3.5 5.3 - - - -
2026F CYS 3.8 0.7 - - - +
2027F PHE* 3.7 0.9 - - - -
2028F LEU* 2.7 57.1 + - + +
2031F PHE* 3.8 17.0 - - + -
2036F ILE* 3.6 29.6 - - + +
2038F VAL* 3.8 20.4 - - + +
2053F ASN* 3.8 20.0 - - - +
2054F SER 3.3 12.1 - - - +
2055F TRP* 3.8 31.6 - - + +
2066F SER* 1.3 76.0 - - - +
2068F SER* 1.3 73.8 + - - +
2069F SER* 3.8 4.0 - - - -
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Residues in contact with SER2068 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052E PHE* 3.4 16.2 - - - +
1064E SER* 3.0 26.8 + - - -
2025F VAL* 4.9 2.4 - - - +
2026F CYS 3.4 4.9 - - - -
2027F PHE* 3.7 20.6 - - - -
2052F LEU 3.8 1.7 - - - +
2053F ASN* 3.5 1.4 - - - -
2054F SER* 3.0 34.5 + - - -
2067F MET* 1.3 75.0 - - - +
2069F SER* 1.3 59.9 + - - +
2070F THR* 4.2 9.7 + - - -
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Residues in contact with SER2069 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2025F VAL* 3.7 0.7 - - - -
2026F CYS* 3.0 34.9 + - - -
2028F LEU* 5.0 0.9 - - - -
2038F VAL* 3.9 17.5 - - - +
2040F TRP* 3.1 20.6 + - - -
2051F VAL* 3.0 15.1 - - - +
2053F ASN* 2.6 33.4 + - - +
2067F MET* 3.8 4.8 - - - -
2068F SER* 1.3 73.6 - - - +
2070F THR* 1.3 60.2 + - - +
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Residues in contact with THR2070 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027E LEU* 5.2 9.0 - - + +
1064E SER* 4.9 3.1 + - - -
2023F SER* 4.1 13.0 - - - -
2024F VAL 3.4 9.0 - - - +
2025F VAL* 4.0 16.8 - - + +
2050F GLY 4.1 0.3 - - - +
2051F VAL* 3.2 7.8 - - - -
2052F LEU* 3.0 40.5 + - - +
2068F SER* 4.1 10.4 + - - -
2069F SER* 1.3 74.4 + - - +
2071F LEU* 1.3 63.9 + - - +
2072F THR* 3.5 23.5 + - - +
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Residues in contact with LEU2071 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022F ALA 3.9 1.0 - - - +
2023F SER* 3.3 1.2 - - - -
2024F VAL* 2.7 54.7 + - + +
2040F TRP* 3.9 40.7 - - + -
2042F ILE* 3.9 30.7 - - + -
2047F ARG 5.1 1.8 - - - +
2049F ASN* 3.9 25.8 - - + +
2050F GLY 3.6 16.4 - - - +
2051F VAL* 3.9 15.7 - - + -
2070F THR* 1.3 71.4 - - - +
2072F THR* 1.3 60.3 + - - +
2073F LEU* 4.1 13.9 + - + +
2084F TYR* 5.2 1.6 - - + -
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Residues in contact with THR2072 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029E LYS* 5.1 14.5 - - - +
2016F GLN* 5.4 0.7 - - - +
2021F GLY* 6.3 0.9 - - - -
2022F ALA 3.5 6.3 - - - +
2023F SER* 3.1 22.1 + - - +
2049F ASN 3.5 16.5 - - - +
2050F GLY* 3.6 10.1 + - - +
2052F LEU* 6.2 0.6 - - - +
2070F THR* 3.5 15.1 + - - +
2071F LEU* 1.3 72.1 - - - +
2073F LEU* 1.3 70.9 + - - +
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Residues in contact with LEU2073 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2021F GLY* 4.4 0.7 - - - -
2022F ALA* 2.8 35.1 + - + +
2024F VAL* 5.9 3.6 - - + -
2042F ILE* 4.1 25.4 - - + -
2049F ASN* 4.6 11.4 - - + +
2071F LEU* 4.4 16.6 - - + +
2072F THR* 1.3 83.1 - - - +
2074F THR* 1.3 91.0 + - - +
2077F GLU* 4.3 24.7 - - + +
2078F TYR* 3.5 30.7 - - + +
2084F TYR* 4.9 6.1 - - + -
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Residues in contact with THR2074 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2020F GLY 4.1 6.7 - - - +
2021F GLY* 5.2 0.2 - - - -
2022F ALA* 3.7 0.2 - - - +
2073F LEU* 1.3 94.0 - - - +
2075F LYS* 1.3 64.3 + - - +
2076F ASP* 3.9 14.2 - - - +
2077F GLU* 3.1 25.5 + - - +
2078F TYR 3.2 4.0 + - - -
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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