Contacts of the helix formed by residues 1935 - 1952 (chain r) in PDB entry 6FF7
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 TRP1935 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1837r ASN 5.0 1.6 - - - +
1838r ALA* 4.3 31.6 - - + +
1930r LEU* 3.2 14.5 + - + +
1933r ASN* 5.2 3.8 - - + +
1934r GLY* 1.3 76.2 - - - +
1936r LEU* 1.3 64.1 + - - +
1937r SER 3.7 0.4 - - - +
1938r PRO* 4.7 10.3 - - + -
1939r ALA* 3.3 23.4 + - - +
2074r ASN* 3.7 6.7 - - + +
2076r LEU* 4.0 6.0 - - - +
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Residues in contact with LEU1936 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1935r TRP* 1.3 70.0 - - - +
1937r SER* 1.3 67.1 + - - +
1939r ALA* 3.2 4.2 + - - +
1940r LEU* 3.0 26.5 + - - +
2069r GLY* 5.9 2.7 - - - -
2070r ASP 5.1 2.5 - - - +
2071r ALA* 5.3 7.0 - - + -
2074r ASN* 3.3 28.1 + - - +
2075r SER 4.1 12.1 - - - +
2076r LEU* 4.0 9.9 - - - +
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Residues in contact with SER1937 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1838r ALA 5.1 6.2 + - - -
1839r LYS 6.6 0.4 - - - -
1840r THR 4.9 2.0 - - - -
1935r TRP* 3.7 0.6 - - - +
1936r LEU* 1.3 78.8 - - - +
1938r PRO* 1.4 64.4 - - - +
1940r LEU* 3.5 4.1 + - - +
1941r ALA* 2.9 26.0 + - - +
2074r ASN* 5.2 10.2 + - - +
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Residues in contact with PRO1938 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1836r LEU* 6.4 1.6 - - + -
1837r ASN 4.3 15.9 - - - +
1838r ALA 4.5 7.1 - - - +
1840r THR* 3.4 28.4 - - - +
1930r LEU* 4.6 13.7 - - + -
1935r TRP* 4.2 8.1 - - + +
1936r LEU 3.4 0.6 - - - -
1937r SER* 1.4 77.0 - - - +
1939r ALA* 1.3 58.1 + - - +
1941r ALA* 3.3 5.8 + - + +
1942r ALA* 2.9 29.5 + - - +
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Residues in contact with ALA1939 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927r VAL* 4.7 9.7 - - + +
1930r LEU* 4.2 17.0 - - + +
1931r SER* 4.5 13.2 - - - +
1935r TRP 3.3 19.8 + - - +
1936r LEU* 3.2 4.7 + - - +
1937r SER 3.2 0.6 - - - -
1938r PRO* 1.3 78.7 - - - +
1940r LEU* 1.3 64.4 + - - +
1942r ALA* 2.9 18.3 + - - +
1943r MET* 3.0 12.8 + - - +
2076r LEU* 5.7 2.0 - - + -
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Residues in contact with LEU1940 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1936r LEU 3.0 14.4 + - - +
1937r SER* 4.1 3.6 - - - +
1939r ALA* 1.3 77.9 - - - +
1941r ALA* 1.3 57.3 + - - +
1943r MET* 3.2 9.3 + - - +
1944r GLU* 2.9 27.3 + - - +
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Residues in contact with ALA1941 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1841r LYS* 5.0 7.2 - - + -
1842r VAL* 4.9 20.7 - - + +
1937r SER 2.9 19.8 + - - +
1938r PRO* 3.6 7.4 - - + +
1940r LEU* 1.3 79.1 - - - +
1942r ALA* 1.3 56.5 + - - +
1944r GLU* 3.3 9.8 - - - +
1945r LEU* 2.9 25.6 + - - +
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Residues in contact with ALA1942 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1845r LEU* 5.9 7.9 - - + -
1923r ILE* 4.6 12.4 - - - +
1926r CYS* 4.7 8.3 - - + -
1927r VAL* 4.4 22.9 - - + +
1930r LEU* 6.0 0.9 - - + -
1938r PRO 2.9 12.7 + - - +
1939r ALA* 2.9 12.2 + - - +
1941r ALA* 1.3 73.0 - - - +
1943r MET* 1.3 67.9 + - - +
1945r LEU* 3.0 9.5 + - - +
1946r ALA* 2.9 20.3 + - - +
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Residues in contact with MET1943 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1927r VAL* 5.3 6.6 - - + +
1939r ALA 3.0 10.9 + - - +
1940r LEU* 3.5 10.8 - - - +
1942r ALA* 1.3 75.1 - - - +
1944r GLU* 1.3 64.2 + - - +
1946r ALA* 3.0 20.2 + - - +
1947r GLN* 3.0 10.0 + - - +
2065r TRP* 5.6 6.5 - - + -
2109r MET* 4.4 17.0 - - + -
2110r SER 3.7 19.2 - - - +
2111r ASP* 6.0 0.2 - - - -
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Residues in contact with GLU1944 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940r LEU 2.9 14.7 + - - +
1941r ALA* 3.3 14.6 - - - +
1943r MET* 1.3 77.3 - - - +
1945r LEU* 1.3 55.9 + - - +
1947r GLN* 3.1 10.8 + - - +
1948r MET* 2.9 26.8 + - - +
1955r SER* 6.0 5.6 - - - -
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Residues in contact with LEU1945 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1842r VAL* 5.5 9.9 - - + -
1845r LEU* 5.6 8.5 - - + -
1923r ILE* 5.6 4.9 - - + -
1941r ALA 2.9 13.7 + - - +
1942r ALA* 3.3 13.2 - - - +
1944r GLU* 1.3 72.7 - - - +
1946r ALA* 1.3 67.8 + - - +
1948r MET* 3.2 9.2 + - - +
1949r VAL* 2.9 25.1 + - - +
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Residues in contact with ALA1946 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920r ILE* 6.0 5.2 - - + +
1923r ILE* 4.8 16.9 - - + +
1924r GLN* 6.0 0.7 - - - +
1942r ALA 2.9 11.8 + - - +
1943r MET* 3.0 14.6 + - - +
1945r LEU* 1.3 75.9 - - - +
1947r GLN* 1.3 62.9 + - - +
1949r VAL* 3.2 5.3 + - - +
1950r THR* 3.0 19.1 + - - -
2111r ASP* 3.2 32.1 - - + +
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Residues in contact with GLN1947 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1943r MET 3.0 8.2 + - - +
1944r GLU* 3.3 12.1 - - - +
1946r ALA* 1.3 79.7 - - - +
1948r MET* 1.3 57.0 + - - +
1950r THR 3.2 1.4 + - - -
1951r GLN* 3.0 29.5 + - - +
2110r SER 4.6 3.4 - - - +
2111r ASP 3.4 4.8 + - - -
2112r ALA 3.3 26.4 - - - +
2113r TYR 3.8 18.8 - - - +
2114r MET* 4.6 9.2 - - + +
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Residues in contact with MET1948 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1899r LEU* 5.4 2.9 - - + +
1944r GLU 2.9 12.7 + - - +
1945r LEU* 3.2 13.0 + - - +
1947r GLN* 1.3 76.0 - - - +
1949r VAL* 1.3 56.8 + - - +
1951r GLN* 5.4 0.9 - - - -
1952r ALA* 2.9 23.8 + - - +
1953r MET* 3.1 34.7 + - - +
1954r TRP 5.1 5.2 - - - -
1955r SER* 5.1 4.9 - - - +
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Residues in contact with VAL1949 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1919r ALA* 5.5 11.9 - - + -
1920r ILE* 6.2 2.2 - - - +
1945r LEU 2.9 15.9 + - - +
1946r ALA* 3.7 5.2 - - - +
1948r MET* 1.3 75.2 - - - +
1950r THR* 1.3 66.8 + - - +
1951r GLN 3.4 0.2 + - - -
1952r ALA* 3.4 11.2 + - - +
2055r LEU 6.1 0.3 - - - -
2056r PHE* 5.2 3.5 - - - +
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Residues in contact with THR1950 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1946r ALA 3.0 11.5 + - - -
1947r GLN 3.2 2.4 + - - -
1949r VAL* 1.3 78.2 - - - +
1951r GLN* 1.3 59.5 + - - +
1952r ALA* 3.7 1.0 + - - +
2053r ALA* 3.6 25.9 - - - +
2055r LEU* 5.1 2.3 - - - +
2056r PHE* 4.1 15.7 + - - +
2111r ASP 4.0 2.0 - - - -
2112r ALA* 3.3 39.5 - - - -
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Residues in contact with GLN1951 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1947r GLN 3.0 14.1 + - - +
1948r MET* 4.9 1.3 - - - +
1950r THR* 1.3 75.7 - - - +
1952r ALA* 1.3 72.7 + - - +
1953r MET* 3.7 7.0 - - + +
1962r GLN* 5.0 20.6 - - + -
2053r ALA* 5.0 5.6 - - + -
2055r LEU* 5.2 3.4 - - - +
2112r ALA 4.3 8.1 - - - +
2113r TYR* 5.7 0.9 - - - -
2114r MET* 5.4 11.2 - - + +
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Residues in contact with ALA1952 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1898r HIS* 3.7 21.6 - - + +
1899r LEU* 3.8 10.7 - - - +
1901r ARG* 4.7 11.7 - - + +
1948r MET 2.9 12.1 + - - -
1949r VAL* 3.4 10.5 + - - +
1950r THR 5.1 0.2 - - - +
1951r GLN* 1.3 82.3 - - - +
1953r MET* 1.3 59.3 + - - +
2055r LEU* 4.1 23.1 - - + +
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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