Contacts of the helix formed by residues 2042 - 2056 (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 GLN2042 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2022C PRO* 3.6 10.5 - - + +
2038C GLU 2.9 4.7 + - - +
2039C GLU 3.1 15.0 - - - +
2041C SER* 1.3 82.4 + - - +
2043C PHE* 1.3 65.1 + - + +
2044C ASP 2.9 2.7 + - - -
2045C PHE* 3.1 35.7 + - - +
2046C SER* 3.0 13.9 + - - +
2065C ARG* 4.3 9.3 + - - +
2072C ARG* 3.1 31.6 + - + -
2074C PRO* 4.1 25.1 - - + -
2093C CYS* 5.9 4.0 - - - -
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Residues in contact with PHE2043 (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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1989C ASN* 3.3 20.4 - - + +
1992C VAL* 5.5 1.1 - - + -
1993C GLU* 6.2 7.2 - - + -
2039C GLU* 3.3 20.4 - - + -
2040C MET* 2.7 63.8 + - + +
2042C GLN* 1.3 75.9 - - + +
2044C ASP* 1.3 51.1 + - - +
2046C SER* 2.5 30.5 + - - +
2047C THR* 2.6 32.8 + - + +
2092C GLU* 5.6 6.1 - - + -
2093C CYS* 5.8 6.7 - - - -
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Residues in contact with ASP2044 (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* 2.4 32.7 + - - +
1988C TYR* 4.8 2.1 - - - -
1989C ASN* 3.0 13.0 + - - +
1992C VAL* 5.5 1.9 - - - +
2017C GLY 3.5 11.7 - - - +
2018C ASP* 2.7 25.7 - - - +
2021C GLY* 2.9 27.7 - - - -
2022C PRO* 3.5 10.8 - - + -
2041C SER* 2.7 25.2 + - - +
2042C GLN 2.9 0.8 + - - -
2043C PHE* 1.3 75.3 - - - +
2045C PHE* 1.3 64.6 + - - +
2047C THR* 4.0 2.5 - - - -
2048C GLY 2.8 17.5 + - - -
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Residues in contact with PHE2045 (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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2018C ASP* 2.9 24.2 - - + -
2019C SER* 3.3 28.3 - - - -
2022C PRO* 3.3 33.7 - - + -
2042C GLN* 3.1 25.1 + - - +
2044C ASP* 1.3 79.0 - - - +
2046C SER* 1.3 60.2 + - - +
2049C VAL* 2.4 47.7 + - + +
2064C GLY 3.9 12.6 - - - -
2065C ARG* 3.5 47.8 - - - -
2069C ARG* 5.0 7.4 - - + -
2072C ARG* 6.3 1.1 - - - -
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Residues in contact with SER2046 (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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2042C GLN* 3.0 16.5 + - - +
2043C PHE* 2.5 34.5 + - - +
2045C PHE* 1.3 81.3 - - - +
2047C THR* 1.3 86.3 + - - +
2049C VAL* 4.0 1.2 - - - +
2050C GLN* 3.1 18.5 + - - +
2093C CYS* 6.5 0.4 - - - -
2096C PRO* 4.4 22.2 - - - +
2097C LEU* 6.1 4.5 - - - -
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Residues in contact with THR2047 (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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1992C VAL* 3.6 40.7 - - + +
1993C GLU* 4.5 6.3 - - - +
1996C VAL* 4.3 11.7 - - - -
1997C PRO* 5.0 2.9 - - + -
2018C ASP* 4.6 0.5 + - - -
2043C PHE* 2.6 26.4 + - + +
2044C ASP* 3.2 4.0 + - - -
2046C SER* 1.3 84.1 + - - +
2048C GLY* 1.3 63.1 + - - -
2050C GLN* 2.3 62.6 + - - +
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Residues in contact with GLY2048 (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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1996C VAL* 4.9 4.5 - - - +
2014C ALA* 6.1 2.2 - - - -
2018C ASP* 2.9 22.2 - - - -
2044C ASP 2.8 7.0 + - - -
2047C THR* 1.3 81.0 + - - +
2049C VAL* 1.3 61.9 + - - -
2051C SER* 2.4 32.2 + - - -
2052C TYR* 2.9 12.9 + - - -
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Residues in contact with VAL2049 (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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2018C ASP* 3.2 4.6 + - + +
2045C PHE* 2.4 56.8 + - + +
2046C SER* 4.7 1.3 - - - +
2048C GLY* 1.3 73.5 - - - +
2050C GLN* 1.3 62.7 + - - +
2052C TYR* 3.0 18.9 + - + +
2053C SER* 2.8 22.1 + - - +
2061C PRO* 4.9 17.2 - - + +
2065C ARG* 4.6 18.4 - - - +
2097C LEU* 6.5 0.4 - - + -
2100C LEU* 4.3 23.8 - - + -
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Residues in contact with GLN2050 (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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1996C VAL* 3.1 31.3 + - + +
1997C PRO* 3.3 28.3 - - - +
2000C ARG* 2.2 43.3 + - - +
2046C SER 3.1 10.9 + - - +
2047C THR* 2.3 52.8 + - - +
2049C VAL* 1.3 66.5 - - - +
2051C SER* 1.3 57.4 - - - +
2053C SER* 2.4 28.7 + - - -
2096C PRO* 4.5 17.6 - - + +
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Residues in contact with SER2051 (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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1996C VAL* 3.6 21.5 - - - -
2000C ARG* 3.3 31.0 + - - +
2004C TYR* 5.2 13.7 + - - -
2048C GLY* 2.4 31.3 + - - -
2050C GLN* 1.3 81.0 - - - +
2052C TYR* 1.3 69.6 + - - +
2054C TYR* 4.4 0.3 - - - +
2055C SER* 2.9 21.4 + - - -
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Residues in contact with TYR2052 (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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2004C TYR* 5.2 2.2 - + - -
2010C GLU 3.2 22.0 - - - -
2011C ALA* 4.5 3.5 - - - -
2014C ALA* 3.2 16.9 + - + +
2015C ALA* 2.8 41.4 + - + +
2018C ASP* 3.1 23.5 + - + -
2048C GLY* 2.9 13.2 - - - -
2049C VAL* 3.0 22.9 - - + +
2050C GLN 2.9 0.6 - - - -
2051C SER* 1.3 86.3 + - - +
2053C SER* 1.3 52.8 + - - +
2055C SER* 2.7 13.9 + - - -
2056C SER* 2.4 37.8 + - - -
2060C ARG* 3.1 31.2 - - - +
2061C PRO* 4.4 10.3 - - + -
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Residues in contact with SER2053 (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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2000C ARG* 3.9 5.4 - - - -
2049C VAL 2.8 15.4 + - - -
2050C GLN* 2.4 34.4 + - - -
2052C TYR* 1.3 67.8 - - - +
2054C TYR* 1.3 62.8 + - - -
2056C SER* 2.8 25.0 + - - -
2061C PRO* 5.7 0.2 - - - -
2099C ALA 5.1 2.9 - - - -
2100C LEU* 3.9 35.0 - - - +
2103C HIS* 4.8 6.5 - - - +
2104C MET* 3.6 16.4 - - - +
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Residues in contact with TYR2054 (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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2000C ARG* 3.1 46.0 - - - +
2001C LYS* 5.9 6.3 - - + -
2051C SER 4.4 1.3 - - - +
2052C TYR 3.1 0.2 - - - -
2053C SER* 1.3 79.5 - - - +
2055C SER* 1.3 55.7 + - - +
2056C SER* 3.2 8.3 + - - +
2099C ALA* 5.1 1.7 - - + +
2103C HIS* 2.7 58.2 + + + -
2106C ARG* 5.4 1.6 - - - -
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Residues in contact with SER2055 (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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2010C GLU* 4.2 15.9 + - - -
2011C ALA* 5.5 2.9 - - - +
2051C SER 2.9 9.0 + - - -
2052C TYR* 2.7 40.3 + - - -
2054C TYR* 1.3 73.0 - - - +
2056C SER* 1.3 61.4 + - - +
2057C GLN 3.7 0.7 + - - -
2060C ARG* 2.9 15.2 + - - -
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Residues in contact with SER2056 (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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2052C TYR 2.4 22.4 + - - -
2053C SER 2.8 18.5 + - - -
2054C TYR 3.2 3.6 + - - +
2055C SER* 1.3 73.2 - - - +
2057C GLN* 1.3 73.0 + - - +
2058C ASP* 4.6 2.3 + - - +
2060C ARG* 3.0 7.0 - - - +
2061C PRO* 3.4 14.1 - - - -
2104C MET* 3.2 17.7 - - - +
2107C SER* 4.8 3.8 + - - -
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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