Contacts of the helix formed by residues 2025 - 2046 (chain B) in PDB entry 3AU5
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 GLU2025 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1751B VAL* 4.1 18.9 - - - +
1752B ASP 3.5 18.0 - - - +
1753B LYS* 4.3 11.9 - - - +
1958B PHE* 4.0 24.4 - - + +
1959B ASP 5.9 0.5 + - - -
2008B ASN* 5.2 0.8 + - - -
2023B THR* 4.8 3.3 + - - +
2024B SER* 1.3 93.1 + - - +
2026B VAL* 1.3 56.1 + - - +
2027B VAL* 2.8 11.9 - - - +
2028B ASP* 2.7 47.2 + - - +
2029B VAL* 3.5 4.4 + - + +
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Residues in contact with VAL2026 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2004B ALA* 4.2 18.4 - - + -
2007B ALA 3.6 23.6 - - - +
2008B ASN* 4.4 2.9 - - - -
2009B THR 3.9 2.9 - - - +
2010B TYR* 3.6 40.6 - - + +
2023B THR* 3.1 38.4 - - + +
2024B SER 2.9 3.4 + - - -
2025B GLU* 1.3 75.9 - - - +
2027B VAL* 1.3 70.5 + - + +
2029B VAL* 3.0 20.3 + - - +
2030B ALA* 3.0 13.6 + - - +
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Residues in contact with VAL2027 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2007B ALA 5.9 0.9 - - - +
2025B GLU* 2.8 5.8 - - - -
2026B VAL* 1.3 88.2 - - + +
2028B ASP* 1.3 59.3 + - - +
2030B ALA* 3.4 7.3 + - + +
2031B LYS* 3.0 60.2 + - + +
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Residues in contact with ASP2028 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1752B ASP 4.8 0.7 - - - -
1753B LYS* 3.1 38.2 - - - +
1754B ALA* 3.3 18.4 + - + +
1789B TYR* 4.2 2.4 + - - +
1958B PHE* 4.0 19.1 - - + -
2025B GLU* 2.7 40.2 + - + +
2027B VAL* 1.3 77.2 - - - +
2029B VAL* 1.3 63.3 + - - +
2031B LYS* 3.9 14.0 + - - +
2032B LEU* 3.2 26.2 + - - +
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Residues in contact with VAL2029 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1958B PHE* 3.6 41.5 - - + -
1973B LEU* 4.0 15.7 - - + -
1975B VAL* 4.3 11.4 - - + +
2010B TYR* 3.2 32.3 - - + -
2023B THR* 5.1 7.9 - - + +
2024B SER 5.5 0.7 - - - +
2025B GLU 4.1 6.3 - - - +
2026B VAL* 3.0 15.2 + - - +
2028B ASP* 1.3 76.6 - - - +
2030B ALA* 1.3 60.2 + - - +
2032B LEU* 4.3 1.8 - - - +
2033B MET* 3.1 30.6 + - - +
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Residues in contact with ALA2030 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002B PHE* 4.4 8.0 - - + -
2003B GLY* 6.3 1.1 - - - -
2010B TYR* 3.3 22.2 + - + +
2026B VAL 3.0 10.7 + - - +
2027B VAL* 3.7 10.5 - - + +
2029B VAL* 1.3 76.7 - - - +
2031B LYS* 1.3 60.7 + - + +
2033B MET* 3.4 2.0 + - - +
2034B LYS* 2.9 38.3 + - + +
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Residues in contact with LYS2031 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1753B LYS* 4.7 6.5 - - - +
1754B ALA* 3.4 28.2 + - + +
1756B GLU* 3.0 30.5 + - + +
1789B TYR* 3.6 15.3 - - + +
2027B VAL* 3.0 45.5 + - + +
2028B ASP* 3.9 17.2 + - - +
2030B ALA* 1.3 76.8 - - + +
2032B LEU* 1.3 58.6 + - - +
2034B LYS* 3.1 16.7 + - - +
2035B ALA* 2.8 29.7 + - - +
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Residues in contact with LEU2032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1789B TYR* 3.3 49.3 + - + +
1790B CYS* 4.1 4.3 - - - -
1956B THR* 3.2 42.0 - - + +
1958B PHE* 3.9 8.3 - - + -
1975B VAL* 3.6 16.4 - - + -
2028B ASP 3.2 15.1 + - - +
2029B VAL 4.3 2.0 - - - +
2031B LYS* 1.3 79.8 - - - +
2033B MET* 1.3 56.6 + - - +
2035B ALA* 3.5 1.7 + - - +
2036B TYR* 3.0 62.4 + - + -
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Residues in contact with MET2033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975B VAL* 4.0 22.4 - - + -
1980B VAL* 3.8 27.1 - - + -
1996B TYR* 4.0 20.6 - - + +
1999B ILE* 4.1 10.1 - - + -
2002B PHE* 4.0 30.3 - - + -
2010B TYR* 3.0 34.5 - - - -
2012B ILE* 4.8 3.8 - - + -
2029B VAL* 3.1 21.8 + - - +
2030B ALA 3.7 4.7 - - - +
2031B LYS 3.2 0.8 - - - -
2032B LEU* 1.3 74.0 - - - +
2034B LYS* 1.3 61.3 + - - +
2036B TYR* 3.3 1.7 + - - +
2037B ILE* 2.8 41.3 + - + +
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Residues in contact with LYS2034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2002B PHE* 4.5 16.2 - - + -
2030B ALA* 2.9 27.9 + - + +
2031B LYS* 3.5 14.4 - - - +
2033B MET* 1.3 76.1 - - - +
2035B ALA* 1.3 52.9 + - - +
2037B ILE* 3.2 8.6 + - - +
2038B SER* 2.6 38.1 + - - -
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Residues in contact with ALA2035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1789B TYR* 4.3 12.8 - - + -
1790B CYS* 3.7 21.1 - - - -
2031B LYS 2.8 16.5 + - - +
2032B LEU 3.7 5.6 - - - +
2034B LYS* 1.3 76.1 - - - +
2036B TYR* 1.3 62.3 + - - +
2038B SER* 3.2 7.1 + - - -
2039B MET* 3.0 30.7 + - + +
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Residues in contact with TYR2036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1789B TYR 4.1 1.9 + - - -
1790B CYS* 3.8 16.1 - - + -
1791B PHE* 3.1 40.9 + - - -
1792B LEU* 4.1 9.9 - - + -
1954B GLY 3.2 16.1 + - - -
1955B SER* 4.9 0.2 - - - -
1956B THR* 5.0 1.7 + - - -
1975B VAL* 3.6 14.1 + - + -
1976B SER* 3.2 27.1 - - - -
1977B ALA* 3.4 23.9 - - + +
1996B TYR* 3.4 21.1 - - + +
2032B LEU* 3.0 44.4 + - + +
2033B MET 3.8 0.4 - - - +
2035B ALA* 1.3 75.8 - - - +
2037B ILE* 1.3 62.3 + - - +
2039B MET* 3.3 7.3 + - - +
2040B ILE* 3.3 25.9 + - - +
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Residues in contact with ILE2037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1996B TYR* 3.8 39.0 - - + -
2002B PHE* 3.7 35.4 - - + -
2033B MET* 2.8 32.1 + - + +
2034B LYS* 3.6 6.1 - - - +
2036B TYR* 1.3 70.0 - - - +
2038B SER* 1.3 61.4 + - - +
2040B ILE* 3.0 11.5 + - + +
2041B VAL* 2.9 43.7 + - + +
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Residues in contact with SER2038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2034B LYS 2.6 21.1 + - - -
2035B ALA* 3.2 8.3 + - - -
2037B ILE* 1.3 73.7 - - - +
2039B MET* 1.3 68.2 + - - +
2041B VAL* 3.2 8.5 + - - +
2042B LYS* 3.0 50.3 + - - +
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Residues in contact with MET2039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1741B MET* 4.3 24.5 - - + +
1790B CYS* 5.2 2.9 - - - -
1792B LEU* 3.9 42.4 - - + -
2035B ALA* 3.0 20.6 + - + +
2036B TYR* 3.5 9.6 - - - +
2037B ILE 3.2 0.2 - - - -
2038B SER* 1.3 84.8 - - - +
2040B ILE* 1.3 58.2 + - + +
2042B LYS* 3.1 33.7 - - - +
2043B LYS* 3.0 35.0 + - - +
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Residues in contact with ILE2040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1977B ALA 3.8 12.6 - - - +
1978B ASP 5.2 0.7 - - - +
1996B TYR* 3.5 38.1 - - + -
1997B GLU* 4.8 10.5 - - - +
2036B TYR 3.3 11.7 - - - +
2037B ILE* 3.0 10.2 + - + +
2039B MET* 1.3 76.5 - - + +
2041B VAL* 1.3 66.2 + - + +
2042B LYS 3.1 3.1 + - - -
2043B LYS* 4.2 6.6 - - - +
2044B ARG* 3.2 55.6 + - + +
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Residues in contact with VAL2041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2037B ILE* 2.9 29.4 + - + +
2038B SER* 3.7 9.6 - - - +
2040B ILE* 1.3 80.0 - - + +
2042B LYS* 1.3 62.3 + - + +
2044B ARG* 4.7 5.6 - - - +
2045B TYR* 3.2 50.0 + - + +
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Residues in contact with LYS2042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2038B SER* 3.0 36.0 + - - +
2039B MET* 3.1 29.0 - - - +
2041B VAL* 1.3 84.4 - - + +
2043B LYS* 1.3 63.2 + - - +
2044B ARG 3.1 2.4 + - - -
2045B TYR* 4.1 6.8 - - + +
2046B SER* 3.3 24.8 + - - -
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Residues in contact with LYS2043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1792B LEU* 5.3 17.0 + - - +
2039B MET* 3.0 30.4 + - - +
2040B ILE* 3.4 7.1 + - - +
2042B LYS* 1.3 76.7 - - - +
2044B ARG* 1.3 57.6 + - - +
2046B SER* 3.5 7.4 + - - -
2047B THR* 3.0 24.6 + - - -
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Residues in contact with ARG2044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1518A LEU* 3.7 34.7 - - - +
1997B GLU* 5.3 4.2 - - - +
2040B ILE* 3.2 42.2 + - + +
2041B VAL* 4.7 5.5 - - - +
2042B LYS 3.1 0.2 - - - -
2043B LYS* 1.3 78.1 - - - +
2045B TYR* 1.3 63.9 + - + +
2046B SER 2.9 5.2 - - - -
2047B THR* 2.8 33.6 + - - +
2048B THR* 3.5 7.2 + - - -
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Residues in contact with TYR2045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1654A LYS* 5.7 4.9 + - - -
2041B VAL* 3.2 37.3 + - + +
2042B LYS* 3.6 9.6 + - + +
2044B ARG* 1.3 85.1 - - + +
2046B SER* 1.3 57.8 + - - +
2048B THR* 4.6 9.2 + - - +
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Residues in contact with SER2046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2042B LYS 3.3 16.4 + - - -
2043B LYS* 3.5 9.2 + - - +
2044B ARG 2.9 0.2 - - - -
2045B TYR* 1.3 76.5 - - - +
2047B THR* 1.3 59.2 + - - +
2048B THR 3.3 12.6 + - - +
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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
------------------------------------------------------------
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