Contacts of the helix formed by residues 2052 - 2068 (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 HIS2052 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1976E THR* 3.5 17.8 + - + -
2024E ARG* 3.0 14.4 + - - -
2045E ALA* 3.8 20.4 - - - -
2046E GLY 4.6 3.6 - - - +
2051E GLU* 1.3 75.4 - - - +
2053E PRO* 1.3 66.5 - - - +
2054E THR* 3.1 3.8 + - - -
2055E GLN* 3.2 32.0 + - + +
2056E ALA 3.2 9.2 + - - -
2085E ARG* 3.2 19.0 + - + +
2086E THR* 3.5 31.1 - - + -
2089E SER* 2.7 14.4 + - - -
2214E ARG* 4.2 4.9 - - - -
3226E PAL 2.9 28.2 + - - -
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Residues in contact with PRO2053 (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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1926E ILE* 4.0 12.1 - - + +
1927E LEU 3.6 20.0 - - - +
1928E SER* 4.2 14.1 - - - +
1929E VAL* 3.7 26.3 - - + +
1932E PHE* 4.2 7.4 - - + -
2044E ASN* 3.3 44.4 - - + +
2051E GLU* 3.9 2.5 - - + -
2052E HIS* 1.3 84.5 - - - +
2054E THR* 1.3 55.9 + - + +
2055E GLN 3.4 0.2 - - - -
2056E ALA* 3.4 5.9 + - - +
2057E LEU* 3.3 28.3 + - - +
2089E SER* 4.2 0.7 - - - +
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Residues in contact with THR2054 (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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1926E ILE* 3.9 13.5 - - + -
1980E PHE* 4.1 6.3 - - + -
2043E ILE* 3.9 20.2 - - + -
2044E ASN 4.5 5.9 + - - +
2045E ALA* 5.1 0.3 - - - -
2052E HIS* 3.3 6.5 + - - -
2053E PRO* 1.3 75.2 - - - +
2055E GLN* 1.3 64.0 + - - +
2056E ALA 3.3 0.9 - - - -
2057E LEU* 3.7 11.1 + - + +
2058E LEU* 3.3 26.0 + - - +
2213E ILE* 4.5 3.4 - - - +
2214E ARG* 2.7 31.6 + - - -
2217E LEU* 3.3 34.8 - - + -
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Residues in contact with GLN2055 (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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1975E ARG* 5.7 2.3 - - - +
1976E THR* 4.8 1.4 + - - -
2052E HIS* 3.2 33.4 + - + +
2054E THR* 1.3 77.4 + - - +
2056E ALA* 1.3 54.6 + - - +
2057E LEU 3.4 0.2 - - - -
2058E LEU* 3.6 22.1 - - - +
2059E ASP* 2.7 64.5 + - - +
2086E THR* 3.6 22.7 - - + -
2184E PRO* 3.4 36.6 + - - +
2206E GLN* 3.8 4.8 - - - +
2214E ARG* 3.7 8.8 + - - +
3226E PAL 4.5 6.1 - - - +
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Residues in contact with ALA2056 (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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1929E VAL* 3.8 2.5 - - + -
2052E HIS 3.2 5.5 + - - -
2053E PRO 3.5 10.5 - - - +
2054E THR 3.3 0.4 - - - -
2055E GLN* 1.3 75.9 - - - +
2057E LEU* 1.3 63.9 + - - +
2059E ASP* 3.5 9.8 + - - +
2060E ILE* 3.1 27.7 + - - +
2086E THR* 5.3 1.5 + - - -
2089E SER* 3.6 27.6 - - - -
2090E LEU* 3.9 13.8 - - - +
2093E LEU* 3.7 19.0 - - + +
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Residues in contact with LEU2057 (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* 3.6 44.9 - - + -
1937E MET* 4.4 19.7 - - + -
1940E LEU* 5.2 12.3 - - + -
1941E PHE* 3.3 22.6 - - + -
2053E PRO 3.3 17.2 + - - +
2054E THR* 3.7 23.3 - - + +
2055E GLN 3.4 0.4 - - - -
2056E ALA* 1.3 77.2 - - - +
2058E LEU* 1.3 56.8 + - - +
2060E ILE* 3.4 1.5 + - - -
2061E PHE 2.9 22.9 + - - -
2093E LEU* 4.3 10.8 - - + -
2213E ILE* 4.4 10.5 - - + -
2217E LEU* 4.6 14.8 - - + -
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Residues in contact with LEU2058 (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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2054E THR 3.3 17.9 + - - +
2055E GLN* 3.6 22.4 - - - +
2057E LEU* 1.3 75.4 - - - +
2059E ASP* 1.3 70.9 + - - +
2061E PHE* 3.5 8.2 - - - +
2062E THR* 2.7 38.1 + - - -
2206E GLN* 3.5 30.3 - - + +
2207E ALA* 5.5 1.1 - - - -
2209E ASN 4.9 0.7 - - - -
2210E GLY* 3.6 23.3 - - - +
2213E ILE* 4.1 12.3 - - + +
2214E ARG* 3.1 35.4 - - - +
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Residues in contact with ASP2059 (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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2055E GLN* 2.7 44.7 + - - +
2056E ALA* 3.5 8.8 - - - +
2058E LEU* 1.3 77.8 - - - +
2060E ILE* 1.3 58.4 + - - +
2062E THR* 3.5 0.8 + - - -
2063E ILE* 3.0 33.4 + - - +
2086E THR 4.5 2.3 - - - +
2090E LEU* 4.1 21.8 - - + +
2143E TYR* 3.2 26.9 + - - -
2182E MET* 3.4 14.9 - - + +
2206E GLN* 2.9 26.2 + - - +
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Residues in contact with ILE2060 (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* 4.1 2.9 - - + -
1941E PHE* 3.6 14.1 - - + -
2056E ALA 3.1 11.6 + - - +
2057E LEU 4.0 2.9 - - - +
2059E ASP* 1.3 73.7 - - - +
2061E PHE* 1.3 65.4 + - - +
2063E ILE* 3.5 7.2 + - + +
2064E ARG* 3.1 21.1 + - - +
2070E VAL* 3.9 6.8 - - + +
2090E LEU* 3.9 11.9 - - + -
2093E LEU* 3.7 32.5 - - + -
2094E LEU* 3.6 40.6 - - + +
2097E TYR* 3.5 39.9 - - + +
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Residues in contact with PHE2061 (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* 3.7 24.6 - + + -
1944E ALA* 4.5 5.8 - - + -
1945E HIS* 3.2 44.9 - + - -
1948E ARG* 4.6 5.4 - - - -
2057E LEU 2.9 15.5 + - - +
2058E LEU 3.5 7.0 - - - +
2060E ILE* 1.3 73.0 - - - +
2062E THR* 1.3 63.0 + - - +
2064E ARG* 3.1 21.4 + - - +
2065E GLU* 2.9 45.0 + - + +
2209E ASN* 3.5 39.3 - - + -
2212E TYR* 6.1 3.6 - - + -
2213E ILE* 3.7 27.8 - - + -
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Residues in contact with THR2062 (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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2058E LEU 2.7 21.0 + - - -
2059E ASP 3.8 3.8 - - - -
2061E PHE* 1.3 71.5 - - - +
2063E ILE* 1.3 57.4 + - - +
2065E GLU* 3.8 1.7 - - - -
2066E GLU* 2.8 54.3 + - + +
2182E MET* 4.5 8.1 - - - -
2202E ALA* 4.5 7.4 - - + +
2205E ARG 4.7 0.2 - - - -
2206E GLN* 3.7 40.4 + - + +
2209E ASN* 3.1 29.9 + - - +
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Residues in contact with ILE2063 (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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2059E ASP 3.0 25.4 + - - +
2060E ILE* 3.8 7.9 - - + +
2061E PHE 3.3 0.2 - - - -
2062E THR* 1.3 75.2 - - - +
2064E ARG* 1.3 64.0 - - - +
2066E GLU* 4.6 3.4 - - - -
2067E LEU* 3.2 28.9 + - + +
2069E THR 4.0 8.3 - - - +
2070E VAL* 3.9 20.6 - - + -
2073E MET* 4.9 3.6 - - + -
2075E ILE* 4.0 16.2 - - + -
2090E LEU* 5.2 6.1 - - + -
2094E LEU* 4.7 15.0 - - + -
2141E VAL* 3.8 36.6 - - + -
2182E MET* 3.5 22.2 - - + -
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Residues in contact with ARG2064 (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* 6.0 0.6 - - - +
1941E PHE* 3.2 54.8 - - - +
1942E ASN* 4.4 8.7 + - - -
1945E HIS* 3.9 20.6 + - - -
2060E ILE 3.1 12.7 + - - +
2061E PHE* 3.1 26.1 + - - +
2063E ILE* 1.3 78.2 - - - +
2065E GLU* 1.3 59.5 + - - +
2068E GLY* 2.9 35.9 + - - +
2069E THR* 4.4 13.9 - - - +
2070E VAL* 4.0 18.4 - - + +
2097E TYR* 4.6 7.2 - - - -
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Residues in contact with GLU2065 (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* 3.4 24.4 + - + +
1948E ARG* 4.3 11.1 + - - -
2061E PHE* 2.9 45.6 + - + +
2062E THR* 3.9 4.9 - - - +
2064E ARG* 1.3 78.5 - - - +
2066E GLU* 1.3 63.2 + - + +
2067E LEU 3.6 0.3 + - - -
2068E GLY 4.3 2.3 + - - -
2209E ASN* 3.8 12.7 + - - +
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Residues in contact with GLU2066 (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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2062E THR* 2.8 38.1 + - + +
2063E ILE 4.0 2.9 - - - +
2065E GLU* 1.3 79.0 - - + +
2067E LEU* 1.3 66.2 + - - +
2178E LYS* 5.0 2.4 + - - -
2180E VAL* 3.2 38.1 - - + +
2202E ALA* 3.7 9.1 - - + +
2205E ARG* 2.7 47.1 + - - +
2209E ASN* 5.8 0.3 + - - -
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Residues in contact with LEU2067 (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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2063E ILE* 3.2 19.1 + - + +
2066E GLU* 1.3 89.2 - - + +
2068E GLY* 1.3 58.5 - - - +
2069E THR* 3.1 10.3 + - - +
2073E MET* 3.4 36.6 - - + +
2140E ASP* 3.4 20.9 - - + +
2141E VAL* 3.6 19.3 - - + -
2178E LYS* 3.5 35.4 + - + +
2179E MET* 3.9 28.9 - - - +
2180E VAL* 4.0 12.1 - - + -
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Residues in contact with GLY2068 (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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2064E ARG* 2.9 22.5 + - - +
2065E GLU 4.3 2.7 + - - -
2066E GLU 3.8 1.0 - - - -
2067E LEU* 1.3 74.7 - - - +
2069E THR* 1.3 59.9 + - - +
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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
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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