Contacts of the helix formed by residues 2072 - 2076 (chain C) in PDB entry 5Y3R
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 ARG2072 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2022C PRO* 6.0 3.4 - - + +
2023C SER 5.7 2.5 - - - +
2038C GLU* 4.9 11.9 - - + +
2042C GLN* 3.1 31.6 + - + -
2045C PHE* 6.3 0.8 - - - -
2065C ARG* 4.7 10.6 + - - +
2068C ARG* 4.1 9.1 - - - +
2069C ARG* 4.8 11.1 - - + +
2070C GLU* 2.2 47.6 + - + +
2071C GLN 1.3 71.1 - - - +
2073C ASP* 1.3 51.9 + - - +
2074C PRO* 3.4 21.7 - - + +
2075C THR* 2.1 53.9 + - + +
2076C VAL* 2.5 38.4 + - - +
2128C PHE* 3.1 30.6 - - - -
2143C ARG* 4.4 5.5 - - - +
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Residues in contact with ASP2073 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2034C SER 4.6 1.8 - - - +
2035C THR* 3.5 18.4 - - - +
2038C GLU* 4.8 4.8 + - - +
2039C GLU* 3.0 58.4 - - + +
2072C ARG* 1.3 71.8 - - - +
2074C PRO* 1.3 62.7 - - + +
2076C VAL* 2.6 55.9 + - - +
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Residues in contact with PRO2074 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2039C GLU* 5.0 2.2 - - + +
2042C GLN* 4.1 22.2 - - + -
2072C ARG* 3.4 27.4 - - + -
2073C ASP* 1.3 94.9 - - + +
2075C THR* 1.3 57.6 + - - -
2076C VAL 3.8 3.0 + - - +
2077C HIS* 5.1 0.9 - - - +
2091C HIS* 3.2 36.1 + - + +
2093C CYS* 4.2 7.9 - - + -
2139C PRO* 3.9 15.8 - - - +
2143C ARG* 3.5 18.7 + - - +
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Residues in contact with THR2075 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2070C GLU* 3.0 34.7 - - - +
2071C GLN* 3.0 12.2 - - - +
2072C ARG* 2.1 65.7 + - + +
2074C PRO* 1.3 74.1 - - - +
2076C VAL* 1.3 59.5 + - - +
2077C HIS* 3.8 4.0 + - - +
2135C ASN* 5.5 5.0 - - - +
2136C PRO* 5.7 4.5 - - - +
2139C PRO* 5.0 6.5 - - + +
2140C LEU* 5.6 2.9 - - + -
2143C ARG* 3.7 13.2 - - - +
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Residues in contact with VAL2076 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2034C SER 5.5 5.2 - - - +
2035C THR* 5.8 4.3 - - + -
2038C GLU* 5.8 1.6 - - - +
2071C GLN* 3.3 41.7 - - + +
2072C ARG 2.5 24.7 + - - +
2073C ASP* 2.6 48.9 + - - +
2074C PRO* 4.4 1.7 - - - +
2075C THR* 1.3 71.9 - - - +
2077C HIS* 1.3 62.0 + - - +
2079C ASP* 3.1 24.1 - - + +
2135C ASN* 6.0 0.2 - - - -
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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