Contacts of the helix formed by residues 1950 - 1967 (chain B) in PDB entry 5WBY
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 ARG1950 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1911B PHE 3.0 19.4 + - - -
1912B ASP* 2.8 28.7 + - - +
1915B HIS* 3.5 43.4 + - + -
1948B THR* 3.3 17.6 - - + +
1949B PRO* 1.3 79.0 - - + +
1951B PRO* 1.4 71.8 - - + +
1952B LEU 3.4 1.5 + - - -
1953B VAL* 3.4 10.8 + - + +
1954B GLY 3.2 18.2 + - - -
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Residues in contact with PRO1951 (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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1915B HIS* 5.7 2.9 - - + -
1948B THR 5.2 0.9 - - - +
1949B PRO 3.1 10.0 - - - +
1950B ARG* 1.4 83.6 - - + +
1952B LEU* 1.3 62.1 + - + +
1954B GLY* 4.6 0.9 - - - +
1955B ARG* 3.1 47.9 + - - +
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Residues in contact with LEU1952 (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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1914B GLY 3.9 0.7 - - - +
1915B HIS* 3.5 30.3 - - + +
1917B PRO* 4.1 13.7 - - + -
1920B ASN* 3.4 54.8 + - + +
1950B ARG* 3.4 0.4 - - - +
1951B PRO* 1.3 82.3 - - + +
1953B VAL* 1.3 64.0 + - - +
1955B ARG* 3.9 29.5 + - - +
1956B LEU* 3.9 12.1 + - - +
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Residues in contact with VAL1953 (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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1910B TRP* 3.6 37.8 + - + +
1911B PHE* 4.5 11.4 - - + +
1914B GLY* 3.4 7.0 - - - +
1915B HIS* 3.2 35.7 - - + +
1920B ASN* 5.0 0.2 - - - -
1948B THR* 4.2 13.9 - - + +
1950B ARG* 3.4 20.1 + - + +
1952B LEU* 1.3 75.8 - - - +
1954B GLY* 1.3 66.1 + - - +
1956B LEU 3.3 3.3 + - - -
1957B ILE* 3.2 35.2 + - + +
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Residues in contact with GLY1954 (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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1945B ARG 5.4 1.1 - - - -
1946B ILE 5.5 0.4 - - - -
1948B THR* 4.6 14.6 - - - -
1950B ARG 3.2 12.7 + - - -
1951B PRO* 4.0 1.6 - - - -
1953B VAL* 1.3 79.6 - - - +
1955B ARG* 1.3 63.4 + - - +
1957B ILE* 3.2 9.9 + - - +
1958B HIS* 3.0 39.3 + - - -
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Residues in contact with ARG1955 (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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1951B PRO* 3.1 34.4 + - - +
1952B LEU* 3.9 30.4 - - - +
1953B VAL 3.3 0.2 - - - -
1954B GLY* 1.3 75.1 - - - +
1956B LEU* 1.3 57.3 + - - +
1958B HIS* 3.6 7.8 + - - +
1959B GLN* 3.1 25.9 + - + +
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Residues in contact with LEU1956 (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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1910B TRP* 3.8 23.8 - - + +
1920B ASN* 4.1 7.9 - - - +
1923B LEU* 4.0 24.5 - - + +
1924B VAL* 3.8 35.0 - - + +
1927B VAL* 4.4 21.1 - - + -
1952B LEU 3.9 9.5 + - - +
1953B VAL 3.3 8.8 + - - +
1954B GLY 3.2 0.6 - - - -
1955B ARG* 1.3 76.4 - - - +
1957B ILE* 1.3 60.9 + - - +
1959B GLN* 3.3 23.0 + - - +
1960B LEU* 2.8 28.1 + - + +
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Residues in contact with ILE1957 (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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1910B TRP* 3.4 26.0 - - + -
1911B PHE* 3.8 26.7 - - + -
1942B LEU* 4.0 20.9 - - + +
1945B ARG* 3.6 26.5 - - + +
1946B ILE* 4.7 2.2 - - - -
1948B THR* 4.2 1.1 - - - +
1953B VAL* 3.2 27.1 + - + +
1954B GLY* 3.2 8.3 + - - +
1956B LEU* 1.3 76.3 - - - +
1958B HIS* 1.3 62.8 + - + +
1960B LEU* 3.4 1.8 + - - +
1961B LEU* 3.0 49.5 + - + +
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Residues in contact with HIS1958 (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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1946B ILE* 3.1 27.5 + - + -
1954B GLY* 3.0 25.3 + - - +
1955B ARG* 3.8 6.6 - - - +
1957B ILE* 1.3 84.0 - - + +
1959B GLN* 1.3 54.9 + - - +
1961B LEU* 3.9 1.0 - - - +
1962B THR* 2.6 39.6 + - - +
1990B ALA* 3.4 29.0 + - + +
1993B LYS* 4.5 25.9 + - + +
1994B ILE* 4.5 21.4 - - + +
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Residues in contact with GLN1959 (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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1924B VAL* 6.1 0.9 - - - +
1927B VAL* 4.7 7.1 - - - +
1955B ARG 3.1 17.7 + - - +
1956B LEU* 3.6 24.8 - - + +
1958B HIS* 1.3 78.0 - - - +
1960B LEU* 1.3 56.3 + - - +
1962B THR* 3.6 5.7 + - - -
1963B ASP* 2.9 62.2 + - - +
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Residues in contact with LEU1960 (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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1910B TRP* 3.6 29.4 - - + -
1927B VAL* 3.9 18.6 - - + -
1932B ILE* 4.8 7.4 - - + -
1935B TRP* 3.7 52.3 - - + +
1942B LEU* 4.2 11.7 - - + -
1956B LEU* 2.8 21.8 + - + +
1957B ILE 3.8 3.8 - - - +
1959B GLN* 1.3 76.3 + - - +
1961B LEU* 1.3 62.0 + - + +
1963B ASP* 3.0 9.5 + - + +
1964B ILE* 2.8 43.2 + - + +
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Residues in contact with LEU1961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1939B ILE* 5.2 3.4 - - + +
1942B LEU* 4.2 29.4 - - + +
1943B ILE* 4.3 9.4 - - + -
1946B ILE* 3.7 37.5 - - + -
1957B ILE* 3.0 32.3 + - + +
1958B HIS 4.1 2.9 - - - +
1960B LEU* 1.3 75.8 - - + +
1962B THR* 1.3 56.7 + - - +
1964B ILE* 4.2 8.5 - - + -
1965B GLY* 2.8 23.0 + - - -
1972B LEU* 3.1 37.2 - - + +
1976B LEU* 5.2 0.7 - - + -
1994B ILE* 3.9 21.3 - - + +
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Residues in contact with THR1962 (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 HIS* 2.6 24.9 + - - +
1959B GLN* 3.6 7.4 - - - -
1960B LEU 3.2 0.2 - - - -
1961B LEU* 1.3 76.2 - - - +
1963B ASP* 1.3 58.8 + - - +
1965B GLY* 3.1 4.0 + - - +
1966B ARG* 3.1 23.2 + - - +
1994B ILE* 4.2 19.1 - - + +
1997B ASN* 3.8 38.4 + - + +
1998B MET* 5.3 2.7 - - + +
2000B GLU* 5.8 1.6 - - - +
2001B HIS* 5.2 1.7 - - - -
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Residues in contact with ASP1963 (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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1927B VAL* 5.4 3.3 - - - +
1932B ILE* 3.5 22.9 - - + +
1959B GLN* 2.9 47.2 + - - +
1960B LEU* 3.0 13.6 + - + +
1962B THR* 1.3 74.9 - - - +
1964B ILE* 1.3 63.8 + - - +
1966B ARG* 3.2 33.0 + - - +
1967B TYR* 3.3 15.6 + - + -
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Residues in contact with ILE1964 (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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1932B ILE* 3.8 24.2 - - + +
1935B TRP* 3.5 28.3 - - + +
1936B LEU* 3.7 28.3 - - + -
1939B ILE* 4.4 5.4 - - + -
1942B LEU* 4.5 9.0 - - + -
1960B LEU* 2.8 40.7 + - + +
1961B LEU* 4.2 8.3 - - + -
1963B ASP* 1.3 68.0 - - - +
1965B GLY* 1.3 59.6 + - - +
1967B TYR 2.3 27.0 - - - +
1968B HIS* 3.0 16.4 - - + +
1972B LEU* 3.6 23.3 - - + -
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Residues in contact with GLY1965 (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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1961B LEU 2.8 15.4 + - - -
1962B THR 3.1 6.9 + - - -
1964B ILE* 1.3 75.6 - - - +
1966B ARG* 1.3 62.6 + - - +
1969B PRO* 3.4 19.0 - - - +
1972B LEU* 3.5 7.2 - - - +
1998B MET* 3.9 22.7 - - - -
2001B HIS* 2.9 19.5 + - - -
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Residues in contact with ARG1966 (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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1962B THR 3.1 10.7 + - - +
1963B ASP* 3.2 25.0 + - - +
1965B GLY* 1.3 76.9 - - - +
1967B TYR* 1.3 104.2 + - + +
1968B HIS 4.1 0.7 + - - -
1969B PRO* 4.2 4.9 - - - +
2001B HIS* 3.4 32.8 + - + +
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Residues in contact with TYR1967 (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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1932B ILE* 4.2 23.6 - - + -
1963B ASP* 3.3 16.6 + - + +
1964B ILE* 2.3 29.5 - - - +
1966B ARG* 1.3 124.4 + - + +
1968B HIS* 1.3 82.3 + - + +
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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
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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