Contacts of the helix formed by residues 1933 - 1953 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1931C GLN 4.6 4.5 - - - +
1932C PHE* 1.3 76.8 - - - +
1934C LYS* 1.3 64.3 + - - +
1935C ASP* 3.9 6.5 + - - +
1936C GLN* 3.0 36.2 + - - +
1937C MET* 3.1 25.6 + - - +
2096C GLN* 3.6 9.0 - - - +
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Residues in contact with LYS1934 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1933C THR* 1.3 75.6 - - - +
1935C ASP* 1.3 66.2 + - - +
1937C MET* 3.6 5.8 + - - +
1938C SER* 3.0 31.0 + - - -
2071C ASN* 3.9 16.7 - - - +
2096C GLN* 3.1 37.7 + - - +
2097C TYR* 3.9 39.2 + - + +
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Residues in contact with ASP1935 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1933C THR* 3.4 5.9 + - - +
1934C LYS* 1.3 83.7 - - - +
1936C GLN* 1.3 59.8 + - - +
1938C SER* 3.9 6.1 - - - -
1939C HIS* 3.1 27.9 + - - +
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Residues in contact with GLN1936 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920C SER* 4.4 19.0 + - - -
1921C LEU* 3.0 43.4 - - + +
1931C GLN 3.2 8.7 + - - +
1932C PHE* 3.1 20.2 - - + -
1933C THR* 3.0 44.2 + - - +
1935C ASP* 1.3 73.6 - - - +
1937C MET* 1.3 65.8 + - - +
1939C HIS* 3.1 9.9 + - - +
1940C LEU* 2.9 26.9 + - - +
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Residues in contact with MET1937 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1932C PHE* 4.5 7.8 - - + -
1933C THR 3.1 16.5 + - - +
1934C LYS* 3.8 6.3 - - - +
1936C GLN* 1.3 76.2 - - - +
1938C SER* 1.3 64.1 + - - +
1940C LEU* 2.9 11.5 + - - +
1941C PHE* 2.9 59.0 + - + -
2057C LEU* 3.4 19.3 - - + -
2060C ILE* 3.4 33.7 - - + -
2093C LEU* 3.6 31.6 - - - +
2096C GLN* 5.3 3.1 - - - +
2097C TYR* 3.5 20.6 - - + +
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Residues in contact with SER1938 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934C LYS* 3.0 18.6 + - - -
1935C ASP* 3.9 7.6 - - - -
1937C MET* 1.3 75.0 - - - +
1939C HIS* 1.3 64.1 + - - +
1941C PHE* 3.3 12.5 + - - +
1942C ASN* 3.0 34.6 + - - +
2064C ARG* 4.5 14.7 + - - +
2097C TYR* 5.6 1.3 + - - -
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Residues in contact with HIS1939 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1920C SER* 5.7 8.7 - - - -
1921C LEU* 6.4 2.0 - - + -
1935C ASP 3.1 16.4 + - - +
1936C GLN* 3.3 12.1 - - - +
1938C SER* 1.3 76.1 - - - +
1940C LEU* 1.3 64.5 + - + +
1942C ASN* 3.0 15.8 + - - +
1943C VAL* 3.0 42.3 + - + +
2220C THR* 4.0 12.1 - - + +
2225C PHE* 3.9 24.2 + + - -
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Residues in contact with LEU1940 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1921C LEU* 4.4 15.5 - - + -
1932C PHE* 5.0 3.1 - - + -
1936C GLN 2.9 14.5 + - - +
1937C MET* 3.4 10.1 - - - +
1939C HIS* 1.3 78.5 - - + +
1941C PHE* 1.3 63.1 + - + +
1943C VAL* 3.4 3.0 + - - -
1944C ALA* 3.1 25.1 + - - +
2057C LEU* 3.7 27.4 - - + -
2213C ILE* 5.0 5.7 - - + +
2216C ALA* 3.4 16.6 - - + +
2217C LEU* 3.5 41.7 - - + +
2220C THR* 3.3 33.0 - - + +
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Residues in contact with PHE1941 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937C MET* 2.9 56.1 + - + -
1938C SER* 3.5 8.3 - - - +
1940C LEU* 1.3 75.9 - - + +
1942C ASN* 1.3 64.6 + - - +
1944C ALA* 3.7 1.0 + - - -
1945C HIS* 3.0 31.9 + - - -
2057C LEU* 3.6 35.9 - - + -
2060C ILE* 4.0 7.0 - - + -
2061C PHE* 3.6 37.0 - + + -
2064C ARG* 3.4 37.0 - - - +
2097C TYR* 4.0 10.1 - - - -
2213C ILE* 3.8 14.1 - - + -
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Residues in contact with ASN1942 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938C SER* 3.0 29.9 + - - +
1939C HIS* 3.0 16.3 + - - +
1941C PHE* 1.3 76.9 - - - +
1943C VAL* 1.3 65.8 + - + +
1945C HIS* 3.2 12.4 + - - +
1946C THR* 3.1 24.6 + - - +
2064C ARG* 5.1 6.4 + - - -
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Residues in contact with VAL1943 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1939C HIS* 3.0 41.3 + - + +
1940C LEU* 3.4 5.4 + - - +
1942C ASN* 1.3 76.5 - - + +
1944C ALA* 1.3 52.2 + - - +
1946C THR* 3.2 7.8 + - - -
1947C LEU* 2.7 53.3 + - + +
2216C ALA* 4.2 12.1 - - + +
2220C THR* 4.2 8.3 - - + -
2225C PHE* 3.7 41.3 - - + -
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Residues in contact with ALA1944 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940C LEU 3.1 17.4 + - - +
1941C PHE 4.0 4.7 - - - +
1942C ASN 3.3 0.2 - - - -
1943C VAL* 1.3 74.6 - - - +
1945C HIS* 1.3 53.6 + - - +
1947C LEU* 3.9 4.0 - - - +
1948C ARG* 2.6 38.3 + - - +
2061C PHE* 4.5 9.0 - - + -
2212C TYR* 3.5 36.5 - - + +
2213C ILE* 4.1 13.0 - - + +
2216C ALA* 3.8 6.0 - - + +
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Residues in contact with HIS1945 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1941C PHE 3.0 15.1 + - - -
1942C ASN* 3.2 14.6 + - - +
1944C ALA* 1.3 74.5 - - - +
1946C THR* 1.3 65.5 + - - +
1948C ARG* 3.4 9.8 + - - +
1949C MET* 3.0 30.8 + - + +
2061C PHE* 3.5 24.4 - + - -
2064C ARG* 4.8 11.4 - - - -
2065C GLU* 2.6 33.6 + - - -
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Residues in contact with THR1946 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1942C ASN* 3.1 14.0 + - - +
1943C VAL* 3.3 10.5 - - - -
1945C HIS* 1.3 77.2 - - - +
1947C LEU* 1.3 64.6 + - - +
1949C MET* 3.3 2.7 + - - +
1950C MET* 3.2 51.8 + - + +
1953C LYS* 5.0 1.7 + - - +
2225C PHE* 3.8 23.2 - - + -
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Residues in contact with LEU1947 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1943C VAL* 2.7 35.1 + - + +
1944C ALA* 3.9 4.7 - - - +
1946C THR* 1.3 74.1 - - - +
1948C ARG* 1.3 62.1 + - - +
1950C MET* 3.6 15.2 + - - +
1951C VAL* 3.4 27.7 + - - +
1957C LEU* 4.8 8.4 - - + +
1959C ILE* 5.2 1.6 - - + -
1987C LEU* 4.0 22.4 - - + -
2212C TYR* 4.4 2.5 - - + -
2215C MET* 3.6 50.2 - - + +
2216C ALA* 3.7 4.5 - - - +
2219C ALA* 4.2 6.3 - - + -
2225C PHE* 4.0 24.7 - - + -
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Residues in contact with ARG1948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1944C ALA 2.6 23.8 + - - +
1945C HIS* 3.9 12.1 - - - +
1946C THR 3.3 0.2 - - - -
1947C LEU* 1.3 74.7 - - - +
1949C MET* 1.3 53.7 + - + +
1951C VAL* 3.3 3.8 + - - +
1952C GLN* 2.7 64.2 + - - +
2061C PHE* 4.1 13.3 - - - -
2065C GLU* 5.3 3.6 + - - -
2205C ARG 4.9 0.4 + - - -
2208C GLU* 3.6 38.4 + - - +
2209C ASN* 2.6 39.0 + - - +
2212C TYR* 3.4 45.8 - - + +
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Residues in contact with MET1949 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1945C HIS* 3.0 19.8 + - + +
1946C THR* 3.3 2.4 + - - +
1948C ARG* 1.3 75.8 - - + +
1950C MET* 1.3 55.8 + - - +
1952C GLN* 3.3 28.0 - - + +
1953C LYS* 2.6 62.8 + - + +
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Residues in contact with MET1950 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1946C THR* 3.2 42.3 + - + +
1947C LEU* 3.9 14.4 - - - +
1948C ARG 3.4 0.2 - - - -
1949C MET* 1.3 76.3 - - - +
1951C VAL* 1.3 52.7 + - - +
1953C LYS* 3.2 16.9 - - - +
1954C GLU 2.7 12.5 + - - -
1955C ARG* 2.7 49.1 + - + +
1957C LEU* 4.1 27.4 - - + -
2225C PHE* 4.6 11.0 - - + -
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Residues in contact with VAL1951 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962A GLY 5.5 2.0 - - - +
1947C LEU 3.4 13.4 + - - +
1948C ARG 3.3 7.5 + - - +
1949C MET 3.3 0.2 - - - -
1950C MET* 1.3 76.0 - - - +
1952C GLN* 1.3 60.6 + - - +
1954C GLU* 3.4 13.3 + - - +
1955C ARG 5.2 1.8 - - - -
1957C LEU* 4.2 13.2 - - + -
1986C ARG* 4.1 28.9 - - + +
2212C TYR* 3.6 25.6 - - + +
2215C MET* 4.0 23.1 - - + -
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Residues in contact with GLN1952 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1948C ARG* 2.7 52.4 + - + +
1949C MET* 3.2 40.5 + - + +
1951C VAL* 1.3 76.0 - - - +
1953C LYS* 1.3 57.0 + - - +
1954C GLU* 3.3 7.9 + - - +
2212C TYR* 5.3 4.0 - - - +
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Residues in contact with LYS1953 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1946C THR* 5.0 1.4 + - - +
1949C MET* 2.6 53.9 + - + +
1950C MET* 3.2 17.6 - - - +
1952C GLN* 1.3 71.7 - - - +
1954C GLU* 1.3 63.3 + - - +
1955C ARG* 3.0 13.5 + - + +
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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