Contacts of the helix formed by residues 2014 - 2021 (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 ALA2014 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1967C PHE* 3.9 11.3 - - + -
2004C TYR* 4.1 6.1 - - - +
2009C LYS* 3.2 33.1 - - + +
2010C GLU 6.4 0.2 - - - -
2012C ARG 3.5 0.4 - - - +
2013C GLU* 1.3 75.2 - - - +
2015C ALA* 1.3 53.7 + - - +
2016C ASN 2.7 5.3 + - - -
2017C GLY* 2.6 30.8 + - - -
2018C ASP* 3.3 11.0 + - - +
2048C GLY* 6.1 1.8 - - - -
2052C TYR* 3.2 15.0 + - + +
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Residues in contact with ALA2015 (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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2011C ALA 4.4 14.4 - - - +
2012C ARG 4.1 4.8 + - - +
2013C GLU 3.6 0.4 - - - -
2014C ALA* 1.3 72.5 - - - +
2016C ASN* 1.3 51.1 + - - +
2018C ASP* 3.8 9.2 - - + -
2019C SER* 2.5 42.6 + - - -
2052C TYR* 2.8 28.3 + - + +
2060C ARG* 5.7 2.0 - - - +
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Residues in contact with ASN2016 (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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1967C PHE* 4.9 5.5 - - + -
2012C ARG 3.5 11.4 - - - +
2013C GLU* 2.3 39.7 + - - +
2015C ALA* 1.3 74.4 - - - +
2017C GLY* 1.3 57.6 + - - +
2019C SER* 2.7 21.0 + - - -
2020C ASP* 2.9 29.7 + - - +
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Residues in contact with GLY2017 (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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1967C PHE* 5.0 3.9 - - - -
1970C LYS* 3.4 31.3 - - - -
1971C PRO* 6.5 0.2 - - - -
2014C ALA 2.6 13.4 + - - -
2016C ASN* 1.3 74.5 - - - +
2018C ASP* 1.3 59.2 + - - -
2020C ASP* 4.7 2.2 - - - -
2021C GLY* 2.8 29.0 + - - -
2044C ASP* 3.5 2.3 - - - +
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Residues in contact with ASP2018 (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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1970C LYS* 5.0 2.6 - - - -
2014C ALA* 3.3 10.5 + - - +
2015C ALA* 4.1 8.1 - - + +
2017C GLY* 1.3 74.5 - - - +
2019C SER* 1.3 69.3 + - - +
2022C PRO* 2.9 24.1 - - - +
2044C ASP* 2.7 37.7 - - - +
2045C PHE* 2.9 18.7 - - + +
2047C THR* 4.6 0.5 + - - -
2048C GLY* 2.9 28.8 + - - -
2049C VAL* 3.2 2.3 + - + +
2052C TYR* 3.1 21.1 + - + -
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Residues in contact with SER2019 (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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2015C ALA* 2.5 29.9 + - - -
2016C ASN* 2.7 5.9 + - - -
2018C ASP* 1.3 75.9 - - - +
2020C ASP* 1.3 70.9 + - - +
2045C PHE* 3.3 21.6 - - - -
2064C GLY 4.7 10.5 - - - -
2069C ARG* 2.4 29.6 + - - -
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Residues in contact with ASP2020 (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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2016C ASN* 2.9 25.8 + - - +
2017C GLY* 4.7 2.0 - - - -
2019C SER* 1.3 86.8 + - - +
2021C GLY* 1.3 67.3 + - - +
2022C PRO 2.9 2.9 - - - +
2023C SER* 4.1 3.8 + - - -
2069C ARG* 2.5 25.3 + - - +
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Residues in contact with GLY2021 (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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1970C LYS* 4.8 2.9 - - - -
1988C TYR* 5.3 3.9 + - - -
2017C GLY* 2.8 17.7 + - - -
2020C ASP* 1.3 78.6 - - - +
2022C PRO* 1.3 65.1 - - - +
2023C SER* 3.3 10.4 + - - -
2025C MET* 5.4 1.4 - - - +
2041C SER* 4.0 5.6 - - - -
2044C ASP* 2.9 19.5 - - - -
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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