Contacts of the helix formed by residues 1974 - 1987 (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 THR1974 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1973E SER* 1.3 75.1 + - - +
1975E ARG* 1.3 86.9 + - - +
1976E THR 3.5 0.4 - - - -
1977E SER* 4.0 1.3 - - - -
1978E SER* 2.5 37.1 + - - -
3226E PAL 3.0 6.4 + - - -
1994F PHE* 3.5 20.6 - - + -
1999F SER* 3.6 0.2 - - - -
2000F SER* 2.9 25.1 + - - -
2001F VAL 4.6 0.2 + - - -
2005F GLU* 3.9 9.9 + - - +
2010F SER* 5.1 3.3 - - - +
2013F THR* 4.3 9.2 - - + -
2014F MET* 4.2 20.9 - - + -
2017F TYR* 5.0 0.2 - - - -
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Residues in contact with ARG1975 (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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1974E THR* 1.3 76.1 - - - +
1976E THR* 1.3 63.3 + - - +
1979E SER* 2.9 35.8 + - - -
2055E GLN* 5.7 2.7 - - - +
2184E PRO 3.5 9.4 - - - -
2185E MET* 3.3 37.7 - - - +
2186E PRO 3.6 10.3 - - - -
2207E ALA* 4.4 9.9 - - + -
2214E ARG* 4.8 6.1 - - - +
3226E PAL 2.9 38.7 + - + +
2000F SER* 3.5 13.9 - - - -
2005F GLU* 2.9 41.4 + - - -
2013F THR* 3.4 32.1 + - + +
2017F TYR* 3.2 23.8 - - - +
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Residues in contact with THR1976 (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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1969E PHE* 4.1 4.0 - - + -
1973E SER* 3.6 2.5 - - - -
1975E ARG* 1.3 78.2 - - - +
1977E SER* 1.3 63.9 + - - +
1979E SER* 4.0 0.5 + - - -
1980E PHE* 3.1 36.3 + - + +
2024E ARG* 3.5 4.2 + - - -
2045E ALA* 3.4 35.0 - - + +
2052E HIS* 3.5 16.4 + - + -
2055E GLN* 4.8 1.6 + - - -
2214E ARG* 4.3 14.8 + - - +
3226E PAL 2.7 39.7 + - - +
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Residues in contact with SER1977 (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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1965E MET* 5.3 0.3 - - - +
1967E SER* 4.7 5.6 + - - -
1969E PHE* 3.5 32.9 - - - -
1973E SER* 3.0 36.2 + - - -
1974E THR* 3.7 1.9 + - - -
1976E THR* 1.3 76.5 - - - +
1978E SER* 1.3 60.3 + - - +
1980E PHE* 3.6 2.5 + - - +
1981E ALA* 3.0 30.0 + - - +
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Residues in contact with SER1978 (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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1974E THR* 2.5 27.0 + - - -
1977E SER* 1.3 79.2 + - - +
1979E SER* 1.3 52.0 + - - +
1981E ALA* 3.2 0.4 + - - -
1982E ALA* 2.7 36.9 + - - +
1992F LEU* 3.4 15.7 - - - +
1993F SER 5.3 3.5 + - - -
1994F PHE* 5.1 2.3 - - - -
2014F MET* 3.5 26.8 - - - +
2017F TYR* 3.6 21.1 - - - -
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Residues in contact with SER1979 (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 2.9 22.3 + - - -
1978E SER* 1.3 71.2 - - - +
1980E PHE* 1.3 60.0 + - - +
1982E ALA* 4.0 3.1 - - - -
1983E ALA* 3.2 25.6 + - - +
2210E GLY 3.8 4.4 + - - -
2211E MET* 4.0 15.8 - - - +
2214E ARG* 2.9 32.7 + - - +
2017F TYR* 3.2 32.7 - - - -
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Residues in contact with PHE1980 (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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1965E MET* 3.8 16.8 - - + +
1967E SER* 6.1 0.7 - - - +
1969E PHE* 5.2 1.6 - + + -
1976E THR* 3.1 35.9 + - + +
1977E SER* 3.9 4.3 - - - +
1979E SER* 1.3 77.0 + - - +
1981E ALA* 1.3 59.1 + - - +
1983E ALA* 3.5 2.9 + - - +
1984E MET* 3.1 27.9 + - - +
2022E VAL* 3.6 39.7 - - + -
2043E ILE* 3.9 24.0 - - + -
2045E ALA* 4.3 3.4 - - + -
2054E THR* 4.1 11.0 - - - -
2214E ARG* 3.2 43.1 - - + -
2217E LEU* 4.2 9.4 - - + -
2218E LEU* 4.0 20.5 - - + +
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Residues in contact with ALA1981 (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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1965E MET* 4.0 9.4 - - + -
1967E SER* 6.1 0.9 - - - -
1977E SER 3.0 18.7 + - - +
1978E SER* 4.4 0.4 - - - -
1980E PHE* 1.3 75.6 - - - +
1982E ALA* 1.3 63.8 + - - +
1984E MET* 3.7 1.9 + - - +
1985E ALA* 3.2 24.3 + - - +
1991E VAL* 4.0 21.0 - - + +
1993E SER* 6.2 0.2 - - - +
1992F LEU* 3.5 20.8 - - + +
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Residues in contact with ALA1982 (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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1978E SER 2.7 21.8 + - - +
1979E SER* 4.3 0.9 - - - -
1981E ALA* 1.3 70.3 - - - +
1983E ALA* 1.3 59.4 + - - +
1985E ALA* 3.4 4.9 + - - +
1986E ARG* 2.9 37.5 + - - +
2211E MET* 3.7 26.2 - - + -
1964F VAL* 5.0 4.7 - - + -
1992F LEU* 3.6 12.0 - - + +
2017F TYR* 3.8 20.2 - - + +
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Residues in contact with ALA1983 (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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1979E SER 3.2 19.8 + - - +
1980E PHE* 3.6 6.3 - - - +
1981E ALA 3.4 0.2 - - - -
1982E ALA* 1.3 78.9 - - - +
1984E MET* 1.3 63.2 + - - +
1986E ARG* 3.2 2.8 + - - -
1987E LEU* 3.1 29.0 + - - +
2211E MET* 3.7 9.3 - - - +
2214E ARG 3.8 8.7 - - - +
2215E MET* 3.4 39.0 - - + +
2218E LEU* 4.0 2.5 - - + -
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Residues in contact with MET1984 (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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1960E LEU* 3.8 23.3 - - + -
1963E LYS* 4.2 6.1 - - - +
1964E VAL 4.9 0.9 - - - -
1965E MET* 3.6 24.5 - - + +
1980E PHE 3.1 11.9 + - - +
1983E ALA* 1.3 77.6 - - - +
1985E ALA* 1.3 62.9 + - - +
1987E LEU* 2.9 16.6 + - - +
1988E GLY 3.1 0.2 + - - -
1989E GLY* 3.0 40.7 + - - -
1990E ALA 3.0 25.4 - - - +
1991E VAL* 3.5 18.4 - - + -
2020E VAL* 4.2 7.2 - - + -
2218E LEU* 3.6 30.0 - - + +
2222E LEU* 4.8 3.8 - - + -
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Residues in contact with ALA1985 (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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1981E ALA 3.2 16.5 + - - +
1982E ALA* 3.7 6.1 - - - +
1984E MET* 1.3 78.8 - - - +
1986E ARG* 1.3 58.2 + - - +
1988E GLY* 3.1 16.1 + - - -
1989E GLY 3.7 12.8 - - - +
1991E VAL* 4.7 2.2 - - + +
1962F GLY* 5.9 1.4 - - - -
1964F VAL* 4.7 5.4 - - + -
1990F ALA* 3.5 32.0 - - + +
1991F VAL 6.1 0.2 - - - +
1992F LEU* 6.4 0.2 - - + -
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Residues in contact with ARG1986 (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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1951E VAL* 4.5 26.4 - - + +
1957E LEU* 3.6 23.7 - - - +
1982E ALA* 2.9 19.8 + - - +
1983E ALA 3.2 4.0 + - - +
1984E MET 3.1 0.2 - - - -
1985E ALA* 1.3 74.9 - - - +
1987E LEU* 1.3 61.3 + - - +
1988E GLY 3.6 0.2 + - - -
2211E MET* 3.4 35.2 - - - +
2212E TYR* 5.2 0.4 - - - -
2215E MET* 4.1 19.1 - - + -
1962F GLY* 2.9 40.4 + - - +
1963F LYS* 5.7 0.4 - - - +
1964F VAL* 3.9 14.7 - - + +
2017F TYR 2.5 28.7 + - - -
2018F ALA* 4.0 0.8 - - - +
2019F ASP* 3.1 28.9 + - - -
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Residues in contact with LEU1987 (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* 4.2 27.6 - - + -
1957E LEU* 3.7 9.0 - - + -
1958E ASP* 3.2 2.4 - - - -
1959E ILE* 2.9 49.3 + - + -
1960E LEU* 3.2 37.8 + - + +
1983E ALA 3.1 25.1 + - - +
1984E MET* 2.9 8.1 + - - +
1986E ARG* 1.3 76.1 - - - +
1988E GLY* 1.3 56.4 + - - +
1989E GLY 3.5 0.2 - - - -
2215E MET* 3.7 33.7 - - + +
2218E LEU* 4.0 7.4 - - + -
2219E ALA* 4.4 5.8 - - + +
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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