Contacts of the helix formed by residues 1948 - 1970 (chain A) in PDB entry 5PBK
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 SER1948 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1944A ASN* 4.0 5.4 + - - +
1945A GLU* 2.5 36.8 + - - -
1946A ASP 3.2 0.8 + - - -
1947A ASP* 1.3 76.9 - - - +
1949A ASP* 1.3 67.2 + - - +
1950A ILE* 3.8 4.5 + - - +
1951A GLY* 3.0 16.1 + - - -
1952A ARG* 3.0 32.2 + - - +
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Residues in contact with ASP1949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1887A TRP* 4.4 21.1 - - + -
1948A SER* 1.3 73.8 - - - +
1950A ILE* 1.3 59.7 + - + +
1952A ARG* 3.4 21.0 + - - +
1953A ALA* 2.9 28.4 + - - +
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Residues in contact with ILE1950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1887A TRP* 3.6 30.7 - - + -
1888A PRO* 4.0 19.5 - - + -
1889A PHE* 4.2 0.4 - - + -
1940A CYS* 3.5 12.2 - - - -
1944A ASN* 3.4 37.2 - - - +
1948A SER* 3.2 3.4 + - - +
1949A ASP* 1.3 75.6 - - + +
1951A GLY* 1.4 58.2 + - - +
1953A ALA* 3.2 7.3 + - - +
1954A GLY 2.9 25.5 + - - -
2001A EDO 4.0 21.5 - - - +
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Residues in contact with GLY1951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940A CYS* 4.4 5.5 - - - -
1941A GLU* 6.0 1.0 - - - +
1944A ASN* 4.1 10.9 - - - +
1945A GLU 3.3 23.6 - - - -
1946A ASP* 4.0 6.3 - - - -
1948A SER* 3.0 10.0 + - - -
1950A ILE* 1.4 77.1 - - - +
1952A ARG* 1.3 59.7 + - - +
1954A GLY* 3.4 2.4 + - - -
1955A HIS* 3.1 30.8 + - - -
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Residues in contact with ARG1952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1946A ASP 3.6 9.8 + - - +
1947A ASP* 2.9 30.5 + - - +
1948A SER* 3.0 37.6 + - - +
1949A ASP* 3.8 22.3 + - - +
1951A GLY* 1.3 75.1 - - - +
1953A ALA* 1.3 64.8 + - - +
1955A HIS* 3.3 8.1 + - + +
1956A ASN* 2.9 34.9 + - - +
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Residues in contact with ALA1953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1885A ASP* 3.6 35.2 - - + +
1887A TRP* 5.2 4.0 - - + +
1888A PRO* 4.0 17.7 - - + -
1889A PHE* 4.0 2.5 - - + -
1949A ASP 2.9 16.1 + - - +
1950A ILE 3.2 8.7 + - - +
1952A ARG* 1.3 74.4 - - - +
1954A GLY* 1.3 59.1 + - - +
1956A ASN* 3.4 3.6 + - - +
1957A MET* 2.9 33.6 + - - +
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Residues in contact with GLY1954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1889A PHE* 3.6 20.8 - - - -
1937A PHE* 3.9 14.1 - - - +
1940A CYS* 4.0 8.7 - - - -
1941A GLU* 6.2 2.2 - - - -
1950A ILE 2.9 12.1 + - - -
1951A GLY 3.4 3.3 + - - -
1952A ARG 3.2 0.2 - - - -
1953A ALA* 1.3 74.3 - - - +
1955A HIS* 1.3 65.7 + - - +
1957A MET 3.4 0.3 + - - -
1958A ARG* 3.0 26.1 + - - +
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Residues in contact with HIS1955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941A GLU* 3.5 37.8 + - + +
1946A ASP* 3.1 34.6 + - + -
1951A GLY* 3.1 27.3 + - - -
1952A ARG* 3.3 8.7 + - + +
1954A GLY* 1.3 78.0 - - - +
1956A ASN* 1.4 63.5 + - - +
1958A ARG* 3.7 9.0 + - - +
1959A LYS* 3.1 23.9 + - - +
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Residues in contact with ASN1956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1883A HIS* 4.9 8.1 + - + +
1885A ASP* 3.1 26.0 + - - +
1952A ARG* 2.9 27.0 + - - +
1953A ALA 3.6 4.3 - - - +
1955A HIS* 1.4 77.2 - - - +
1957A MET* 1.3 59.6 + - - +
1959A LYS* 3.4 7.5 + - - +
1960A TYR* 3.0 28.3 + - - +
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Residues in contact with MET1957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1880A MET* 3.6 48.0 - - + +
1883A HIS* 3.4 43.7 - - + -
1885A ASP* 3.7 22.9 - - + +
1889A PHE* 4.0 11.2 - - + -
1911A PHE* 4.3 8.5 - - + -
1937A PHE* 3.4 22.7 - - + -
1953A ALA 2.9 19.9 + - - +
1954A GLY 4.0 0.4 - - - +
1956A ASN* 1.3 74.1 - - - +
1958A ARG* 1.3 61.3 + - - +
1960A TYR* 3.4 4.3 + - + +
1961A PHE* 2.9 30.3 + - - +
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Residues in contact with ARG1958 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934A ARG* 4.2 16.5 + - + +
1937A PHE* 3.4 49.9 + - + +
1938A ASP* 2.7 33.5 + - - +
1941A GLU* 3.0 27.8 + - - +
1954A GLY 3.0 18.2 + - - +
1955A HIS* 3.7 10.3 + - - +
1957A MET* 1.3 75.2 - - - +
1959A LYS* 1.3 60.1 + - - +
1961A PHE* 3.2 3.0 + - + +
1962A GLU* 2.9 52.3 + - + +
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Residues in contact with LYS1959 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1955A HIS 3.1 11.4 + - - +
1956A ASN* 3.6 10.8 - - - +
1958A ARG* 1.3 80.9 - - - +
1960A TYR* 1.3 60.5 + - - +
1962A GLU* 3.3 4.8 + - + +
1963A LYS* 3.2 26.3 + - + +
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Residues in contact with TYR1960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1879A GLU* 3.7 35.5 + - + +
1880A MET* 4.0 17.9 - - + -
1883A HIS* 3.6 34.9 - + + +
1956A ASN 3.0 19.4 + - - +
1957A MET* 3.6 6.1 - - + +
1959A LYS* 1.3 73.1 - - - +
1961A PHE* 1.3 63.7 + - - +
1963A LYS* 3.6 5.1 + - - +
1964A LYS* 3.3 58.7 + - + +
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Residues in contact with PHE1961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1876A ILE* 3.9 15.9 - - + -
1880A MET* 3.6 25.6 - - + -
1929A PHE* 4.3 3.6 - + - -
1930A ALA* 4.1 13.0 - - + -
1933A VAL* 3.7 37.9 - - + -
1934A ARG* 4.1 16.4 - - + -
1937A PHE* 4.3 6.7 - + + -
1957A MET 2.9 18.4 + - - +
1958A ARG 3.2 3.3 + - - +
1960A TYR* 1.3 77.0 - - - +
1962A GLU* 1.3 87.7 + - + +
1964A LYS* 3.1 5.7 + - - +
1965A TRP* 2.8 61.4 + + + +
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Residues in contact with GLU1962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934A ARG* 2.8 54.6 + - - +
1958A ARG* 2.9 36.6 + - + +
1959A LYS* 3.3 5.6 + - + +
1961A PHE* 1.3 87.9 - - + +
1963A LYS* 1.3 57.4 + - - +
1965A TRP* 3.4 6.0 + - - +
1966A THR* 3.0 34.7 + - - -
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Residues in contact with LYS1963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1959A LYS* 3.2 19.0 + - + +
1960A TYR* 3.9 5.8 - - - +
1962A GLU* 1.3 74.8 - - - +
1964A LYS* 1.3 62.0 + - + +
1966A THR* 3.5 4.0 + - - -
1967A ASP* 2.6 68.4 + - - +
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Residues in contact with LYS1964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1876A ILE* 4.1 25.0 - - + +
1879A GLU* 3.0 34.5 + - + +
1880A MET* 5.8 0.4 - - + -
1960A TYR* 3.3 56.7 + - + +
1961A PHE* 3.1 8.3 + - - +
1963A LYS* 1.3 80.0 - - + +
1965A TRP* 1.3 57.6 + - - +
1967A ASP* 3.9 4.8 - - - +
1968A THR* 2.5 37.7 + - - +
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Residues in contact with TRP1965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1873A CYS* 4.0 1.6 - - - -
1876A ILE* 4.0 7.6 - - + +
1926A LEU* 3.3 49.4 - - + -
1927A GLU* 4.3 15.2 + - - -
1929A PHE* 3.7 23.8 - + - -
1930A ALA* 3.6 17.9 - - + +
1934A ARG* 3.7 20.3 - - - +
1961A PHE* 2.8 42.2 + + + +
1962A GLU* 3.6 10.3 - - - +
1963A LYS 3.1 0.2 - - - -
1964A LYS* 1.3 73.8 - - - +
1966A THR* 1.3 62.6 + - - +
1968A THR 3.4 0.7 + - - -
1969A PHE* 3.0 67.6 + + + +
1970A LYS* 4.1 1.5 + - + -
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Residues in contact with THR1966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962A GLU 3.0 17.6 + - - -
1963A LYS* 3.8 5.4 - - - -
1965A TRP* 1.3 79.8 - - - +
1967A ASP* 1.3 67.1 + - - +
1970A LYS* 2.9 49.4 + - + +
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Residues in contact with ASP1967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1963A LYS* 2.6 61.4 + - - +
1964A LYS* 4.2 5.0 - - - +
1966A THR* 1.3 81.6 - - - +
1968A THR* 1.3 61.8 + - - +
1970A LYS 4.9 2.3 - - - +
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Residues in contact with THR1968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1872A LEU* 3.8 32.8 - - + +
1876A ILE* 3.9 13.5 - - + +
1964A LYS* 2.5 25.6 + - - +
1965A TRP 3.9 2.5 - - - -
1966A THR 3.3 0.2 - - - -
1967A ASP* 1.3 78.8 - - - +
1969A PHE* 1.3 88.4 + - + +
1970A LYS 4.0 0.4 - - - -
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Residues in contact with PHE1969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1864A ARG* 3.6 17.0 + - - +
1869A ASP* 3.6 22.2 - - - -
1872A LEU* 3.7 36.3 - - + -
1873A CYS* 4.1 5.4 - - - -
1876A ILE* 3.9 7.2 - - + -
1926A LEU* 3.4 31.9 - - + -
1965A TRP* 3.0 61.3 + + + +
1968A THR* 1.3 92.6 - - + +
1970A LYS* 1.3 61.4 + - + +
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Residues in contact with LYS1970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965A TRP* 4.1 1.5 + - + +
1966A THR* 2.9 44.4 + - + +
1967A ASP 5.3 1.7 - - - +
1969A PHE* 1.3 74.9 + - - +
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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