Contacts of the helix formed by residues 2033 - 2051 (chain B) in PDB entry 1V9P
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 SER2033 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2032B ILE* 1.3 75.9 - - - +
2034B ASP* 1.3 57.7 + - - +
2035B ALA* 2.8 11.9 + - - +
2036B GLU* 2.7 66.4 + - - +
2037B TYR* 3.2 10.7 + - - +
2039B ARG* 5.5 0.2 + - - -
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Residues in contact with ASP2034 (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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2024B TYR* 3.7 31.1 + - + -
2025B TYR* 5.7 0.5 + - - -
2032B ILE 3.8 1.6 + - - -
2033B SER* 1.3 72.2 - - - +
2035B ALA* 1.3 57.2 + - - +
2037B TYR* 3.9 11.2 - - - +
2038B ASP* 2.8 29.7 + - - +
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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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2033B SER* 2.8 9.1 + - - +
2034B ASP* 1.3 78.5 - - - +
2036B GLU* 1.3 59.8 + - + +
2037B TYR 3.1 2.0 - - - -
2038B ASP* 3.3 9.9 + - - +
2039B ARG* 2.8 36.1 + - - +
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Residues in contact with GLU2036 (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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2031B GLU 5.2 0.2 - - - +
2032B ILE* 3.1 32.6 - - + +
2033B SER* 2.7 48.9 + - - +
2035B ALA* 1.3 75.4 - - - +
2037B TYR* 1.3 57.1 + - - +
2039B ARG* 3.0 38.7 + - - +
2040B LEU* 2.8 37.3 + - + +
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Residues in contact with TYR2037 (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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2017B ILE* 3.6 35.5 - - + +
2020B HIS* 4.7 12.3 - - + -
2021B ASN* 2.7 47.5 + - + +
2024B TYR* 5.9 5.6 - + + -
2025B TYR* 5.5 4.3 - + - -
2032B ILE* 4.6 4.2 - - + +
2033B SER 3.2 8.8 + - - +
2034B ASP* 3.9 17.3 - - - +
2036B GLU* 1.3 72.8 - - - +
2038B ASP* 1.3 64.9 + - - +
2039B ARG 2.9 3.6 - - - -
2040B LEU* 2.6 35.5 + - + +
2041B LEU* 2.9 36.0 + - + +
2060B PRO* 5.4 0.3 - - - +
2065B GLY 5.4 4.2 + - - -
2069B LEU* 3.9 6.2 - - - +
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Residues in contact with ASP2038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2034B ASP* 2.8 24.5 - - - +
2035B ALA* 3.3 10.3 + - - +
2037B TYR* 1.3 88.1 - - - +
2039B ARG* 1.3 56.9 + - - +
2041B LEU* 3.5 10.7 + - - +
2042B ARG* 2.9 41.2 + - + +
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Residues in contact with ARG2039 (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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2033B SER* 5.5 0.2 + - - -
2035B ALA* 2.8 20.1 + - - +
2036B GLU* 3.0 47.5 + - - +
2038B ASP* 1.3 78.2 - - - +
2040B LEU* 1.3 61.6 + - + +
2042B ARG* 3.0 37.2 + - - +
2043B GLU* 3.2 23.0 + - - +
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Residues in contact with LEU2040 (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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2013B LEU* 3.8 22.8 - - + +
2016B LEU* 4.5 15.9 - - + -
2017B ILE* 3.5 29.8 - - + +
2020B HIS* 4.4 11.2 - - + -
2032B ILE* 3.5 31.4 - - + -
2036B GLU* 2.8 22.2 + - + +
2037B TYR* 2.6 20.9 + - + +
2039B ARG* 1.3 71.5 - - + +
2041B LEU* 1.3 54.4 + - - +
2043B GLU* 3.4 7.9 + - - +
2044B LEU* 2.9 27.2 + - - +
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Residues in contact with LEU2041 (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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2017B ILE* 3.6 21.3 - - + -
2037B TYR* 2.9 38.8 + - + +
2038B ASP* 3.9 12.1 - - - +
2040B LEU* 1.3 74.7 - - - +
2042B ARG* 1.3 66.5 + - - +
2044B LEU* 3.5 3.3 - - + +
2045B LYS* 3.1 26.3 + - - +
2060B PRO* 3.7 27.1 - - + +
2061B THR* 4.2 20.5 - - + +
2064B VAL* 4.8 16.4 - - + -
2065B GLY 5.8 1.8 - - - +
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Residues in contact with ARG2042 (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 ASP* 2.9 29.5 + - + +
2039B ARG* 3.0 42.0 + - - +
2040B LEU 3.3 0.2 - - - -
2041B LEU* 1.3 77.6 - - - +
2043B GLU* 1.3 64.4 + - - +
2045B LYS* 3.9 3.9 - - - +
2046B GLU* 3.0 24.5 + - - +
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Residues in contact with GLU2043 (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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2009B ARG* 2.4 36.5 + - - +
2013B LEU* 3.2 24.3 - - + +
2039B ARG 3.2 11.7 + - - +
2040B LEU* 3.5 11.5 - - - +
2041B LEU 3.2 0.2 - - - -
2042B ARG* 1.3 79.1 - - - +
2044B LEU* 1.3 66.1 + - - +
2046B GLU* 3.2 6.3 + - - -
2047B LEU* 2.9 41.2 + - + +
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Residues in contact with LEU2044 (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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2010B ILE* 3.9 20.0 - - + -
2013B LEU* 3.9 22.6 - - + +
2014B ARG* 3.9 9.0 - - + -
2017B ILE* 3.7 19.3 - - + -
2040B LEU 2.9 14.9 + - - +
2041B LEU* 3.3 15.2 + - + +
2043B GLU* 1.3 77.1 - - - +
2045B LYS* 1.3 52.9 + - - +
2047B LEU* 3.1 3.6 + - - +
2048B GLU* 2.8 70.1 + - + +
2059B SER* 3.4 20.0 - - - +
2060B PRO* 3.9 14.6 - - + -
2061B THR* 4.6 1.3 - - + -
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Residues in contact with LYS2045 (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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2041B LEU 3.1 13.2 + - - +
2042B ARG* 3.9 3.6 - - - +
2044B LEU* 1.3 79.1 - - - +
2046B GLU* 1.3 54.3 + - - +
2048B GLU* 3.7 13.3 + - + +
2049B GLU* 2.7 64.5 + - + +
2055B LYS* 5.4 5.0 - - - +
2061B THR* 3.7 30.2 + - + +
2062B GLU* 5.8 1.6 + - - -
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Residues in contact with GLU2046 (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 ARG 3.0 15.6 + - - +
2043B GLU* 3.3 13.2 - - - +
2045B LYS* 1.3 77.0 - - - +
2047B LEU* 1.3 76.9 + - + +
2049B GLU* 3.6 5.4 - - - +
2050B ARG* 3.1 44.6 + - - +
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Residues in contact with LEU2047 (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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2001B MET* 3.9 27.1 - - + -
2006B ALA* 4.8 4.3 - - + +
2009B ARG* 3.4 40.4 - - + +
2010B ILE* 4.3 14.4 - - + -
2013B LEU* 5.3 2.0 - - + -
2043B GLU* 2.9 30.0 + - + +
2044B LEU* 3.8 5.2 - - - +
2046B GLU* 1.3 89.6 - - + +
2048B GLU* 1.3 69.1 + - - +
2049B GLU 3.0 1.6 - - - -
2050B ARG* 3.0 12.3 + - - +
2051B PHE* 2.8 34.5 + - + +
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Residues in contact with GLU2048 (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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2010B ILE* 4.2 17.3 - - + -
2014B ARG* 2.8 29.9 + - - +
2044B LEU* 2.8 42.3 + - + +
2045B LYS* 3.8 10.3 - - + +
2047B LEU* 1.3 71.7 - - - +
2049B GLU* 1.3 60.7 + - - +
2051B PHE 3.2 19.1 - - - +
2052B PRO 3.4 2.3 - - - -
2054B PHE 4.8 1.6 - - - +
2055B LYS* 3.6 29.4 - - + +
2059B SER* 2.8 16.2 + - - -
2061B THR* 2.6 33.4 + - - +
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Residues in contact with GLU2049 (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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2045B LYS* 2.7 52.2 + - + +
2046B GLU* 3.6 5.8 - - - +
2048B GLU* 1.3 78.8 - - - +
2050B ARG* 1.3 59.9 + - - +
2051B PHE 3.1 2.0 + - - -
2052B PRO* 3.5 17.3 - - - +
2055B LYS* 2.7 37.0 + - - -
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Residues in contact with ARG2050 (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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2001B MET* 3.1 50.4 - - - +
2046B GLU* 3.1 40.5 + - - +
2047B LEU* 3.0 8.2 + - - +
2049B GLU* 1.3 75.9 - - - +
2051B PHE* 1.3 90.7 + - + +
2052B PRO* 3.4 6.7 - - - +
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Residues in contact with PHE2051 (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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2001B MET* 3.5 32.3 - - + -
2003B ARG* 4.2 17.7 - - + -
2006B ALA* 3.4 32.1 - - + -
2010B ILE* 5.0 0.9 - - + -
2047B LEU* 2.8 21.1 + - + +
2048B GLU* 3.2 9.6 - - - +
2050B ARG* 1.3 113.9 - - + +
2052B PRO* 1.3 67.4 - - - +
2053B GLU* 3.0 23.5 + - - +
2054B PHE* 3.1 30.8 + + + +
2055B LYS 4.2 0.3 + - - -
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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