Contacts of the strand formed by residues 2083 - 2090 (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 SER2083 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2041F LYS 3.7 0.7 - - - +
2042F ILE* 3.4 4.5 - - - +
2043F ASP* 2.6 54.9 + - - -
2044F GLY 4.5 4.2 + - - -
2082F ASN* 1.3 72.7 - - - +
2084F TYR* 1.3 62.7 + - - +
2085F THR* 4.2 7.8 + - - -
2100F SER* 5.6 1.4 + - - -
2101F PHE 4.8 0.2 + - - -
2102F ASN* 3.4 20.4 + - - -
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Residues in contact with TYR2084 (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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2009F ILE* 3.3 9.6 - - + +
2024F VAL* 4.6 16.8 - - + -
2040F TRP* 5.5 2.7 - + + -
2041F LYS 3.5 2.2 - - - -
2042F ILE* 3.7 36.3 - - + -
2071F LEU* 5.2 2.9 - - + -
2073F LEU* 4.9 7.4 - - + +
2077F GLU* 3.6 1.6 + - - +
2078F TYR* 2.5 55.5 + + - -
2081F HIS* 3.4 24.4 - - + +
2082F ASN 3.7 22.2 - - - -
2083F SER* 1.3 74.9 + - - +
2085F THR* 1.3 61.8 + - - +
2100F SER* 3.3 0.9 - - - -
2101F PHE* 3.1 62.6 + + + -
2103F ARG* 4.1 2.7 - - + -
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Residues in contact with THR2085 (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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2009F ILE* 4.2 0.4 - - - -
2040F TRP* 3.3 15.7 - - - -
2041F LYS* 2.7 51.7 + - + +
2083F SER* 4.2 6.2 + - - -
2084F TYR* 1.3 72.2 - - - +
2086F CYS* 1.3 65.3 + - - +
2087F GLU* 3.8 29.2 - - + +
2098F VAL* 3.9 14.8 - - + +
2100F SER* 2.9 22.4 + - - -
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Residues in contact with CYS2086 (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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2007F VAL* 4.3 5.4 - - + +
2009F ILE* 3.9 12.1 - - + +
2026F CYS* 2.0 51.6 - - + -
2028F LEU* 4.6 1.3 - - - -
2038F VAL* 3.9 20.6 - - - -
2039F LYS 3.6 3.6 - - - -
2040F TRP* 4.1 9.4 - - + -
2085F THR* 1.3 74.4 - - - +
2087F GLU* 1.3 64.2 + - - +
2088F ALA 4.0 0.4 + - - -
2097F ILE 4.0 1.4 - - - +
2098F VAL* 3.9 1.0 - - - -
2099F LYS* 2.9 37.2 + - - +
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Residues in contact with GLU2087 (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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2037F ASN 3.7 0.7 - - - +
2038F VAL* 3.2 8.6 - - - +
2039F LYS* 2.8 62.6 + - + +
2041F LYS* 2.8 35.6 + - - +
2085F THR* 3.8 18.8 - - + +
2086F CYS* 1.3 71.6 - - - +
2088F ALA* 1.3 60.9 + - - +
2089F THR* 4.0 1.6 + - - +
2096F PRO* 4.3 17.9 - - + +
2097F ILE 3.5 4.9 - - - +
2098F VAL* 3.7 27.2 - - + +
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Residues in contact with ALA2088 (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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2005F PRO* 4.6 6.3 - - + -
2007F VAL* 3.5 15.3 - - + -
2028F LEU* 3.5 29.8 - - + -
2036F ILE* 4.6 0.9 - - + -
2037F ASN 3.5 4.5 - - - -
2086F CYS 4.0 1.6 + - - -
2087F GLU* 1.3 71.5 - - - +
2089F THR* 1.3 61.9 + - - +
2090F HIS* 4.3 0.7 + - - -
2093F SER* 4.7 0.7 + - - -
2096F PRO* 3.5 0.6 - - - +
2097F ILE* 2.9 61.7 + - + +
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Residues in contact with THR2089 (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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2036F ILE* 3.8 3.5 - - - +
2037F ASN* 2.8 54.3 + - + +
2039F LYS* 5.6 4.9 - - - -
2087F GLU* 4.0 2.6 + - - +
2088F ALA* 1.3 69.6 - - - +
2090F HIS* 1.3 69.5 + - - +
2093F SER* 5.0 4.5 - - - +
2094F THR 6.4 0.2 - - - -
2095F SER 5.8 0.4 - - - -
2096F PRO* 3.3 35.8 - - + +
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Residues in contact with HIS2090 (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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2003F ALA 3.2 14.8 + - - -
2005F PRO* 3.8 15.5 - - + -
2031F PHE* 3.8 7.2 - + - -
2032F TYR 2.9 25.8 + - - -
2033F PRO* 3.1 35.1 - - + +
2035F ASP 3.1 18.0 + - - -
2036F ILE* 3.4 13.8 - - + +
2088F ALA 5.4 0.4 - - - +
2089F THR* 1.3 79.9 - - - +
2091F LYS* 1.3 64.5 + - - +
2092F THR* 3.1 29.1 - - + +
2093F SER* 2.9 40.6 + - - +
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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