Contacts of the helix formed by residues 1933 - 1953 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1919E HIS 4.4 8.5 + - - +
1931E GLN 4.7 3.1 - - - +
1932E PHE* 1.3 76.6 - - - +
1934E LYS* 1.3 61.4 + - - +
1935E ASP* 3.6 7.6 + - - +
1936E GLN* 3.1 38.4 + - - +
1937E MET* 3.1 28.5 + - - +
2096E GLN* 3.9 8.1 - - - +
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Residues in contact with LYS1934 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1933E THR* 1.3 74.9 - - - +
1935E ASP* 1.3 67.1 + - - +
1937E MET* 3.2 15.3 + - + +
1938E SER* 2.9 36.5 + - - +
2071E ASN* 4.4 9.1 + - - +
2096E GLN* 2.6 41.7 + - + +
2097E TYR* 3.5 37.9 - - + +
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Residues in contact with ASP1935 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1919E HIS* 5.0 16.8 - - + +
1933E THR* 3.4 6.6 + - - +
1934E LYS* 1.3 81.4 - - - +
1936E GLN* 1.3 60.3 + - - +
1938E SER* 3.9 9.8 + - - -
1939E HIS* 3.2 28.1 + - - +
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Residues in contact with GLN1936 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1919E HIS* 3.6 23.9 - - - +
1920E SER 3.5 22.4 + - - +
1921E LEU* 3.4 38.2 - - + +
1924E GLN* 6.1 0.6 - - - +
1931E GLN 3.2 16.8 + - - +
1932E PHE* 3.4 8.6 - - + -
1933E THR* 3.1 42.2 + - - +
1934E LYS 3.3 0.2 - - - -
1935E ASP* 1.3 74.8 - - - +
1937E MET* 1.3 60.8 + - - +
1939E HIS* 4.2 5.1 - - - +
1940E LEU* 3.1 28.6 + - - +
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Residues in contact with MET1937 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1932E PHE* 4.5 6.3 - - + -
1933E THR 3.1 19.3 - - - +
1934E LYS* 3.2 13.4 + - - +
1936E GLN* 1.3 76.4 - - - +
1938E SER* 1.3 55.7 + - - +
1940E LEU* 3.1 5.2 + - - +
1941E PHE* 2.6 60.3 + - + -
2057E LEU* 4.4 17.5 - - + -
2060E ILE* 4.1 26.2 - - + -
2093E LEU* 3.7 45.1 - - + +
2096E GLN* 4.9 8.3 - - - -
2097E TYR* 4.3 15.5 - - + +
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Residues in contact with SER1938 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934E LYS* 2.9 25.3 + - - +
1935E ASP* 3.9 9.4 + - - -
1937E MET* 1.3 76.5 - - - +
1939E HIS* 1.3 57.6 + - - -
1941E PHE* 3.2 8.7 + - - +
1942E ASN* 2.8 41.7 + - - +
2064E ARG* 6.0 0.7 - - - +
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Residues in contact with HIS1939 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1919E HIS* 6.4 1.3 - - + -
1920E SER* 6.0 6.3 - - - -
1921E LEU* 6.3 2.7 - - + -
1935E ASP 3.2 17.5 + - - +
1936E GLN* 4.2 5.6 - - - +
1938E SER* 1.3 78.1 - - - +
1940E LEU* 1.3 59.4 + - + +
1942E ASN* 3.2 14.0 + - - +
1943E VAL* 2.9 55.6 + - + +
2220E THR* 4.1 12.3 - - + +
2225E PHE* 3.4 33.7 + - + -
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Residues in contact with LEU1940 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1921E LEU* 4.7 9.2 - - + -
1936E GLN 3.1 18.7 + - - +
1937E MET* 3.1 6.6 + - - +
1939E HIS* 1.3 79.4 - - + +
1941E PHE* 1.3 65.7 + - + +
1943E VAL* 3.6 2.0 + - - +
1944E ALA* 3.0 27.7 + - - +
2057E LEU* 5.2 11.9 - - + -
2213E ILE* 4.0 36.3 - - + +
2216E ALA* 3.4 37.9 - - + +
2217E LEU* 3.7 16.8 - - + +
2220E THR* 3.6 18.8 - - + +
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Residues in contact with PHE1941 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937E MET* 2.6 44.7 + - + +
1938E SER* 3.5 8.1 - - - +
1940E LEU* 1.3 74.1 - - + +
1942E ASN* 1.3 64.2 + - - +
1944E ALA* 3.1 7.5 + - - +
1945E HIS* 3.1 27.4 + - - -
2057E LEU* 3.3 35.0 - - + -
2060E ILE* 3.6 19.7 - - + -
2061E PHE* 3.7 15.8 - + + -
2064E ARG* 3.2 42.4 - - - +
2097E TYR* 3.8 22.2 - - - -
2213E ILE* 3.6 18.2 - - + -
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Residues in contact with ASN1942 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1938E SER* 2.8 30.2 + - - +
1939E HIS* 3.3 13.2 + - - +
1941E PHE* 1.3 75.5 - - - +
1943E VAL* 1.3 58.2 + - + +
1945E HIS* 3.1 26.0 + - - +
1946E THR* 3.1 16.2 + - - -
2064E ARG* 4.4 10.2 + - - -
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Residues in contact with VAL1943 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1939E HIS* 2.9 47.9 + - + +
1940E LEU* 4.1 5.2 - - - +
1942E ASN* 1.3 73.0 - - + +
1944E ALA* 1.3 64.2 + - - +
1946E THR* 3.7 8.0 - - - +
1947E LEU* 3.1 35.3 + - + +
2216E ALA* 4.0 17.7 - - + -
2219E ALA* 5.0 0.4 - - + -
2220E THR* 4.8 4.5 - - + -
2225E PHE* 3.8 39.5 - - + -
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Residues in contact with ALA1944 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1940E LEU 3.0 15.3 + - - +
1941E PHE 3.1 9.4 + - - +
1943E VAL* 1.3 77.5 - - - +
1945E HIS* 1.3 58.7 + - - +
1947E LEU* 3.6 1.5 + - - +
1948E ARG* 3.0 27.7 + - - +
2061E PHE* 4.5 7.0 - - + -
2212E TYR* 3.5 34.9 - - + +
2213E ILE* 3.9 22.9 - - + -
2216E ALA* 3.7 2.9 - - + +
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Residues in contact with HIS1945 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941E PHE 3.1 12.5 + - - -
1942E ASN* 3.1 12.9 + - - +
1944E ALA* 1.3 75.1 - - - +
1946E THR* 1.3 63.9 + - - +
1948E ARG* 3.4 14.8 + - - +
1949E MET* 3.1 23.7 + - - +
2061E PHE* 3.2 38.7 - + - -
2064E ARG* 3.9 22.5 + - - -
2065E GLU* 3.4 20.3 + - + +
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Residues in contact with THR1946 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1942E ASN 3.1 13.4 + - - -
1943E VAL* 3.3 15.1 + - - +
1945E HIS* 1.3 74.5 - - - +
1947E LEU* 1.3 62.7 + - + +
1949E MET* 3.3 15.4 - - + +
1950E MET* 3.2 46.9 + - + +
2225E PHE* 4.6 16.6 - - + -
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Residues in contact with LEU1947 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1943E VAL* 3.1 25.0 + - + +
1944E ALA 4.1 2.5 - - - +
1946E THR* 1.3 74.8 - - + +
1948E ARG* 1.3 67.4 + - - +
1950E MET* 3.2 10.2 + - - +
1951E VAL* 2.7 28.5 + - - +
1957E LEU* 4.5 11.4 - - + -
1959E ILE* 4.7 6.1 - - + -
1987E LEU* 4.2 19.1 - - + -
2212E TYR* 4.6 1.6 - - + +
2215E MET* 3.6 46.9 - - + +
2216E ALA* 3.6 17.7 - - + +
2219E ALA* 4.5 2.9 - - + -
2225E PHE* 4.6 20.4 - - + -
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Residues in contact with ARG1948 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1944E ALA 3.0 18.7 + - - +
1945E HIS* 3.6 17.1 - - - +
1947E LEU* 1.3 74.5 - - - +
1949E MET* 1.3 51.9 + - - +
1951E VAL* 2.9 7.3 + - - +
1952E GLN* 2.6 63.3 + - - +
2061E PHE* 4.6 5.1 - - - -
2065E GLU* 4.3 17.6 + - - -
2208E GLU* 3.7 17.6 + - - +
2209E ASN* 2.7 32.3 + - - +
2212E TYR* 3.4 49.7 - - + +
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Residues in contact with MET1949 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1945E HIS 3.1 11.9 + - - +
1946E THR* 3.3 18.2 - - + +
1947E LEU 3.2 0.2 - - - -
1948E ARG* 1.3 79.4 - - - +
1950E MET* 1.3 82.9 + - + +
1952E GLN* 3.0 12.4 + - - +
1953E LYS* 2.9 56.7 + - + +
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Residues in contact with MET1950 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1946E THR* 3.2 34.7 + - + +
1947E LEU* 3.2 17.9 + - - +
1949E MET* 1.3 101.3 - - + +
1951E VAL* 1.3 59.6 + - - +
1953E LYS* 3.4 3.7 + - - +
1954E GLU 3.5 0.3 + - - -
1955E ARG* 3.1 40.8 + - + +
1957E LEU* 3.8 35.7 - - + -
1959E ILE* 5.1 7.6 - - + -
2225E PHE* 5.3 7.6 - - + -
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Residues in contact with VAL1951 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1947E LEU 2.7 16.6 + - - +
1948E ARG 3.1 9.4 - - - +
1950E MET* 1.3 77.2 - - - +
1952E GLN* 1.3 61.3 + - - +
1953E LYS 3.3 1.0 + - - -
1954E GLU* 3.3 14.7 + - - +
1955E ARG 5.5 0.4 - - - -
1957E LEU* 4.2 10.1 - - + -
1986E ARG* 4.5 26.7 - - + +
2212E TYR* 3.0 31.4 - - + +
2215E MET* 3.6 28.0 - - + -
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Residues in contact with GLN1952 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1948E ARG* 2.6 63.0 + - - +
1949E MET* 3.0 14.6 + - - +
1951E VAL* 1.3 74.4 - - - +
1953E LYS* 1.3 65.0 + - + +
1954E GLU* 3.4 5.4 + - - +
2208E GLU* 5.6 1.0 + - - -
2212E TYR* 4.1 10.5 + - - -
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Residues in contact with LYS1953 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1949E MET* 2.9 41.7 + - - +
1950E MET* 3.4 6.0 + - - +
1951E VAL 3.2 0.6 - - - -
1952E GLN* 1.3 85.9 - - + +
1954E GLU* 1.3 68.1 + - - +
1955E ARG* 2.9 12.3 + - + +
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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
------------------------------------------------------------
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