Contacts of the helix formed by residues 1933 - 1953 (chain F) in PDB entry 5G1N
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 THR1933 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1931F GLN 3.3 8.7 + - - +
1932F PHE* 1.3 77.0 - - - +
1934F LYS* 1.3 65.2 + - - +
1935F ASP* 4.0 11.9 - - - +
1936F GLN* 3.1 35.5 + - - +
1937F MET* 3.2 22.8 + - - +
2096F GLN* 5.2 3.1 - - - +
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Residues in contact with LYS1934 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1932F PHE 3.9 0.6 + - - -
1933F THR* 1.3 72.9 - - - +
1935F ASP* 1.3 63.8 + - - +
1937F MET* 3.5 9.5 + - - +
1938F SER* 3.1 24.7 + - - -
2071F ASN* 4.0 16.0 + - - +
2096F GLN* 3.0 48.2 + - + +
2097F TYR* 3.3 45.6 + - + +
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Residues in contact with ASP1935 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1933F THR* 3.2 9.9 - - - +
1934F LYS* 1.3 77.1 + - - +
1936F GLN* 1.3 60.0 + - - +
1938F SER* 3.3 5.3 + - - -
1939F HIS* 3.0 29.5 + - - +
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Residues in contact with GLN1936 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1920F SER* 3.5 37.5 + - - +
1921F LEU* 4.1 35.3 - - + +
1931F GLN* 3.5 19.2 + - - +
1932F PHE* 3.9 10.0 - - + -
1933F THR* 3.1 30.6 + - - +
1935F ASP* 1.3 75.0 - - + +
1937F MET* 1.3 66.4 + - + +
1939F HIS* 3.5 8.6 + - + +
1940F LEU* 3.1 23.7 + - - +
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Residues in contact with MET1937 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1932F PHE* 4.0 14.6 - - + +
1933F THR 3.2 15.4 + - - +
1934F LYS* 3.8 12.8 - - - +
1935F ASP 3.3 0.2 - - - -
1936F GLN* 1.3 77.1 - - - +
1938F SER* 1.3 52.3 + - - +
1940F LEU* 3.2 6.0 + - - +
1941F PHE* 2.7 46.5 + - + -
2057F LEU* 4.0 24.0 - - + -
2060F ILE* 3.4 37.2 - - + -
2093F LEU* 3.8 26.9 - - + -
2096F GLN* 5.1 4.5 - - - -
2097F TYR* 3.7 28.3 - - + +
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Residues in contact with SER1938 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934F LYS* 3.1 18.1 + - - -
1935F ASP* 3.3 5.6 + - - -
1937F MET* 1.3 74.1 - - - +
1939F HIS* 1.3 59.4 + - - +
1940F LEU 3.1 1.3 - - - -
1941F PHE* 3.4 9.8 + - - +
1942F ASN* 2.7 42.6 + - - +
2064F ARG* 3.7 17.2 + - - -
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Residues in contact with HIS1939 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920F SER* 5.8 5.0 + - - -
1921F LEU* 4.1 14.1 - - + -
1935F ASP 3.0 14.8 + - - +
1936F GLN* 3.5 12.1 - - - +
1938F SER* 1.3 73.9 - - - +
1940F LEU* 1.3 56.3 + - - +
1942F ASN* 3.3 11.6 + - - +
1943F VAL* 3.1 40.9 + - + +
2220F THR* 4.0 22.0 - - + +
2225F PHE 3.4 25.5 + - - -
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Residues in contact with LEU1940 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1921F LEU* 4.7 9.0 - - + -
1936F GLN 3.1 16.0 + - - +
1937F MET* 3.4 5.2 - - - +
1939F HIS* 1.3 78.4 - - - +
1941F PHE* 1.3 66.7 + - + +
1942F ASN 3.2 0.9 - - - -
1943F VAL* 4.5 3.4 - - - +
1944F ALA* 3.1 23.9 + - - +
2057F LEU* 3.4 35.7 - - + -
2213F ILE* 3.7 24.7 - - + +
2216F ALA* 3.4 39.8 - - + +
2217F LEU* 3.5 15.7 - - + +
2220F THR* 3.9 10.5 - - + +
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Residues in contact with PHE1941 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937F MET* 2.7 34.1 + - + +
1938F SER* 3.4 6.5 + - - +
1940F LEU* 1.3 74.5 - - + +
1942F ASN* 1.3 57.9 + - - +
1944F ALA* 3.4 3.3 + - - +
1945F HIS* 3.0 26.2 + - - -
2057F LEU* 3.5 33.4 - - + -
2060F ILE* 4.0 15.3 - - + -
2061F PHE* 3.3 53.8 - + + -
2064F ARG* 3.3 48.5 - - + +
2070F VAL* 6.0 0.2 - - + -
2097F TYR* 4.2 15.7 - + - -
2213F ILE* 4.0 5.6 - - + -
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Residues in contact with ASN1942 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1938F SER* 2.7 31.2 + - - +
1939F HIS* 3.4 11.1 - - - +
1940F LEU 3.2 0.2 - - - -
1941F PHE* 1.3 76.0 - - - +
1943F VAL* 1.3 60.0 + - + +
1945F HIS* 3.1 9.6 + - - +
1946F THR* 3.0 31.6 + - - +
2064F ARG* 4.3 13.9 + - - -
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Residues in contact with VAL1943 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1939F HIS* 3.1 37.5 + - + +
1940F LEU* 3.7 1.8 + - - +
1942F ASN* 1.3 74.3 - - + +
1944F ALA* 1.3 58.1 - - - +
1946F THR* 3.3 6.9 + - - -
1947F LEU* 2.8 45.5 + - + +
2216F ALA* 3.9 19.3 - - + +
2220F THR* 4.3 4.7 - - + -
2225F PHE* 3.5 46.7 - - + -
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Residues in contact with ALA1944 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940F LEU 3.1 19.6 + - - +
1941F PHE 3.4 6.5 - - - +
1943F VAL* 1.3 78.8 - - - +
1945F HIS* 1.3 57.1 + - - +
1947F LEU* 4.2 1.1 - - - -
1948F ARG* 3.1 28.2 + - - +
2061F PHE* 4.2 7.3 - - + -
2212F TYR* 3.8 23.8 - - + +
2213F ILE* 3.5 25.8 - - + -
2216F ALA* 3.6 8.2 - - + +
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Residues in contact with HIS1945 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1941F PHE 3.0 15.8 + - - +
1942F ASN* 3.1 11.7 + - - +
1944F ALA* 1.3 73.8 - - - +
1946F THR* 1.3 63.5 + - - +
1948F ARG* 4.0 13.9 - - + +
1949F MET* 3.2 21.3 + - - +
2061F PHE* 3.5 16.7 - + - -
2064F ARG* 3.8 19.3 + - - -
2065F GLU* 2.8 39.5 + - - -
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Residues in contact with THR1946 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1942F ASN 3.0 14.5 + - - -
1943F VAL* 3.5 11.1 - - - -
1945F HIS* 1.3 76.7 - - - +
1947F LEU* 1.3 58.7 + - - +
1949F MET* 2.8 36.6 + - + +
1950F MET* 3.2 20.2 + - + +
2225F PHE* 3.8 30.2 - - + -
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Residues in contact with LEU1947 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1943F VAL* 2.8 40.0 + - + +
1944F ALA* 4.3 3.8 - - - +
1946F THR* 1.3 71.2 - - - +
1948F ARG* 1.3 61.2 + - - +
1950F MET* 3.4 8.6 + - - +
1951F VAL* 3.2 29.4 + - - +
1957F LEU* 4.0 13.4 - - + +
1959F ILE* 3.8 16.6 - - + -
1987F LEU* 4.0 15.3 - - + -
2212F TYR* 4.5 2.0 - - + +
2215F MET* 3.7 46.2 - - + +
2216F ALA 4.0 0.9 - - - +
2219F ALA* 4.1 6.1 - - + -
2225F PHE* 3.7 24.5 - - + -
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Residues in contact with ARG1948 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1944F ALA 3.1 20.3 + - - +
1945F HIS* 4.0 17.3 - - + +
1947F LEU* 1.3 74.6 - - - +
1949F MET* 1.3 61.4 + - - +
1951F VAL* 4.1 1.2 - - - +
1952F GLN* 2.9 44.0 + - - +
2061F PHE* 4.6 9.6 - - - -
2065F GLU* 4.8 8.2 + - - +
2205F ARG* 5.2 0.8 + - - +
2208F GLU* 3.8 24.0 + - - +
2209F ASN* 2.7 30.7 + - - +
2212F TYR* 3.1 56.3 + - + +
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Residues in contact with MET1949 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1945F HIS 3.2 13.4 + - - +
1946F THR* 2.8 23.9 + - + +
1948F ARG* 1.3 73.7 - - - +
1950F MET* 1.3 60.5 + - + +
1952F GLN* 3.3 10.7 + - - +
1953F LYS* 2.8 70.6 + - + +
1955F ARG* 3.9 20.9 - - - +
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Residues in contact with MET1950 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1946F THR* 3.2 32.1 + - + +
1947F LEU* 3.8 14.6 - - - +
1949F MET* 1.3 81.4 - - + +
1951F VAL* 1.3 60.5 + - - +
1953F LYS* 4.3 4.0 - - - -
1954F GLU 3.0 5.9 + - - -
1955F ARG* 2.7 84.2 + - + +
1957F LEU* 3.8 29.2 - - + -
1959F ILE* 5.8 0.9 - - + -
2225F PHE* 4.5 10.1 - - + -
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Residues in contact with VAL1951 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1947F LEU 3.2 17.6 + - - +
1948F ARG 4.1 4.0 - - - +
1950F MET* 1.3 75.4 - - - +
1952F GLN* 1.3 61.6 + - + +
1954F GLU* 3.2 15.2 + - - +
1955F ARG 5.8 0.2 - - - -
1957F LEU* 3.9 20.6 - - + -
1986F ARG* 4.1 30.7 - - + +
2212F TYR* 3.9 28.9 - - + +
2215F MET* 4.0 14.1 - - + -
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Residues in contact with GLN1952 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1948F ARG* 2.9 37.2 + - + +
1949F MET* 3.5 13.2 - - - +
1951F VAL* 1.3 79.1 - - + +
1953F LYS* 1.3 68.8 + - + +
1954F GLU* 3.2 12.5 + - - +
2212F TYR* 5.6 3.6 - - - +
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Residues in contact with LYS1953 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1949F MET* 2.8 51.6 + - - +
1950F MET* 4.0 8.1 - - - +
1951F VAL 3.4 0.2 - - - -
1952F GLN* 1.3 81.5 + - + +
1954F GLU* 1.3 69.2 + - - +
1955F ARG* 3.2 13.7 + - - +
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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
------------------------------------------------------------
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