Contacts of the helix formed by residues 1974 - 1987 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1973A SER* 1.3 71.3 - - - +
1975A ARG* 1.3 68.0 + - - +
1976A THR 3.6 0.2 - - - -
1977A SER* 3.5 1.5 + - - -
1978A SER* 2.8 34.2 + - - -
3226A PAL 2.8 13.9 + - - -
1994B PHE* 3.7 23.7 - - + -
1999B SER* 3.5 9.6 + - - -
2000B SER* 3.0 24.5 + - - -
2001B VAL 4.3 0.2 + - - -
2005B GLU* 3.8 9.6 + - - +
2010B SER* 4.8 2.2 - - - +
2013B THR* 3.8 26.0 - - + -
2014B MET* 3.9 9.2 - - - -
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Residues in contact with ARG1975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974A THR* 1.3 78.1 - - - +
1976A THR* 1.3 60.4 + - - +
1979A SER* 2.8 35.0 + - - -
2055A GLN* 6.0 1.1 - - - +
2184A PRO 3.7 9.6 - - - -
2185A MET* 3.3 38.2 - - - +
2186A PRO* 3.6 7.9 - - - +
2207A ALA* 4.3 13.5 - - + -
2214A ARG* 4.4 5.2 - - - +
3226A PAL 2.6 44.8 + - + +
2000B SER* 3.5 11.9 - - - -
2005B GLU* 2.6 45.8 + - - -
2013B THR* 3.3 27.7 + - + -
2017B TYR* 3.2 23.0 + - - +
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Residues in contact with THR1976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1969A PHE* 3.9 3.1 - - + -
1973A SER* 3.9 1.6 - - - -
1975A ARG* 1.3 72.4 - - - +
1977A SER* 1.3 65.9 + - - +
1979A SER* 3.5 4.4 + - - -
1980A PHE* 3.2 37.0 + - + -
2024A ARG* 3.1 6.1 + - - +
2045A ALA* 3.9 22.7 - - + -
2052A HIS* 3.8 22.4 + - + -
2055A GLN* 4.4 3.1 + - - -
2214A ARG* 3.9 17.2 + - - +
3226A PAL 2.5 41.3 + - - +
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Residues in contact with SER1977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967A SER* 4.9 5.2 + - - -
1969A PHE* 3.4 28.1 - - - -
1973A SER* 2.7 46.4 + - - -
1974A THR 3.5 3.5 + - - -
1976A THR* 1.3 74.9 - - - +
1978A SER* 1.3 67.8 + - - -
1980A PHE* 3.8 2.8 - - - +
1981A ALA* 3.2 22.1 + - - +
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Residues in contact with SER1978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1974A THR* 2.8 23.5 + - - -
1977A SER* 1.3 79.3 + - - +
1979A SER* 1.3 58.1 + - - +
1981A ALA* 4.5 1.1 - - - +
1982A ALA* 2.8 34.3 + - - +
1992B LEU* 3.8 13.0 - - - +
1993B SER 5.3 5.0 + - - -
1994B PHE* 5.4 2.3 - - - +
2014B MET* 3.5 22.2 - - - +
2017B TYR* 3.6 21.3 - - - -
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Residues in contact with SER1979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975A ARG 2.8 22.8 + - - -
1976A THR 3.5 3.3 + - - -
1978A SER* 1.3 70.9 - - - +
1980A PHE* 1.3 59.6 + - - +
1982A ALA* 3.9 1.1 - - - +
1983A ALA* 2.8 32.2 + - - +
2210A GLY 4.3 0.2 - - - -
2211A MET* 4.0 15.0 - - - +
2214A ARG* 2.7 44.0 + - - -
2017B TYR* 4.0 25.2 - - - -
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Residues in contact with PHE1980 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965A MET* 4.0 18.2 - - + +
1969A PHE* 5.1 1.8 - + + -
1976A THR* 3.2 37.1 + - + +
1977A SER* 3.8 3.4 - - - +
1978A SER 3.3 0.4 - - - -
1979A SER* 1.3 80.5 + - - +
1981A ALA* 1.3 60.5 + - - +
1983A ALA* 3.5 3.5 - - - +
1984A MET* 2.9 31.4 + - - +
2022A VAL* 3.7 37.9 - - + -
2043A ILE* 3.7 33.7 - - + -
2045A ALA* 4.5 2.0 - - + -
2054A THR* 4.2 10.8 - - + -
2214A ARG* 3.1 39.3 - - + -
2217A LEU* 5.0 3.8 - - + -
2218A LEU* 4.2 18.9 - - + +
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Residues in contact with ALA1981 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965A MET* 4.9 0.8 - - + +
1967A SER* 6.2 0.9 - - - -
1977A SER 3.2 14.5 + - - +
1978A SER* 4.6 0.9 - - - -
1980A PHE* 1.3 78.4 - - - +
1982A ALA* 1.3 59.0 + - - +
1984A MET* 3.5 2.4 + - - +
1985A ALA* 2.9 29.6 + - - +
1991A VAL* 3.9 34.1 - - + +
1991B VAL 5.8 0.2 - - - +
1992B LEU* 3.4 21.5 - - + -
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Residues in contact with ALA1982 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1978A SER 2.8 21.1 + - - +
1979A SER 3.9 2.0 - - - +
1981A ALA* 1.3 70.0 - - - +
1983A ALA* 1.3 65.9 + - - +
1985A ALA* 3.2 5.4 + - - +
1986A ARG* 2.9 33.0 + - - +
2211A MET* 3.8 23.6 - - + -
1964B VAL* 5.0 2.0 - - + -
1992B LEU* 3.5 24.3 - - + +
2017B TYR* 3.9 9.4 - - + +
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Residues in contact with ALA1983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1979A SER 2.8 23.0 + - - +
1980A PHE 3.5 5.4 - - - +
1982A ALA* 1.3 76.2 - - - +
1984A MET* 1.3 64.0 + - - +
1986A ARG* 3.2 6.9 + - - -
1987A LEU* 3.3 12.3 + - - +
2211A MET* 3.7 8.2 - - - +
2214A ARG* 4.0 7.0 - - + -
2215A MET* 3.5 50.5 - - + +
2218A LEU* 4.0 7.0 - - + -
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Residues in contact with MET1984 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1960A LEU* 3.5 26.7 - - + -
1963A LYS* 3.4 45.3 - - + +
1964A VAL 3.7 17.9 - - - +
1965A MET* 3.7 14.8 - - + +
1980A PHE 2.9 19.0 + - - +
1981A ALA 3.8 3.4 - - - +
1983A ALA* 1.3 72.5 - - - +
1985A ALA* 1.3 61.6 + - - +
1987A LEU* 3.3 6.2 + - - +
1988A GLY 3.2 4.2 + - - -
1989A GLY* 2.8 43.4 + - - -
1990A ALA 3.8 8.1 - - - +
1991A VAL* 4.0 9.2 - - + -
2020A VAL* 5.0 0.4 - - + -
2218A LEU* 3.8 15.8 - - + +
2222A LEU* 4.6 7.4 - - + -
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Residues in contact with ALA1985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1981A ALA 2.9 18.3 + - - +
1982A ALA* 3.5 8.3 - - - +
1983A ALA 3.2 0.2 - - - -
1984A MET* 1.3 76.3 - - - +
1986A ARG* 1.3 58.7 + - - +
1988A GLY* 2.9 20.3 + - - -
1989A GLY 4.1 9.4 - - - +
1991A VAL* 4.9 2.9 - - + +
1961B LYS* 4.9 3.5 + - - -
1962B GLY* 5.6 1.7 - - - -
1964B VAL* 4.5 7.6 - - + -
1990B ALA* 3.7 30.4 - - + +
1992B LEU* 5.8 1.3 - - + -
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Residues in contact with ARG1986 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1951A VAL* 4.1 26.1 - - + +
1957A LEU* 3.8 24.1 + - - +
1982A ALA* 2.9 21.8 + - - +
1983A ALA 3.9 3.4 - - - +
1985A ALA* 1.3 73.9 - - - +
1987A LEU* 1.3 60.7 + - - +
1988A GLY 3.5 0.4 - - - -
2211A MET* 3.6 29.8 - - - +
2212A TYR* 5.7 0.7 - - - -
2215A MET* 4.2 15.3 - - + -
1961B LYS* 4.4 4.9 + - - +
1962B GLY* 3.2 30.3 + - - +
1963B LYS* 4.6 0.2 - - - +
1964B VAL* 3.9 19.6 - - + +
2017B TYR 3.0 30.1 + - - -
2018B ALA* 4.3 1.0 - - - +
2019B ASP* 3.1 30.7 + - - +
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Residues in contact with LEU1987 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1947A LEU* 4.2 13.2 - - + -
1957A LEU* 3.7 23.8 - - + -
1958A ASP 3.5 0.2 - - - -
1959A ILE* 3.2 18.7 + - + -
1960A LEU* 2.8 59.3 + - + +
1983A ALA 3.3 10.0 + - - +
1984A MET 3.3 8.4 + - - +
1985A ALA 3.1 1.0 - - - -
1986A ARG* 1.3 77.8 - - - +
1988A GLY* 1.3 57.1 + - - +
1989A GLY 3.4 0.7 - - - -
2215A MET* 3.2 58.8 - - + +
2218A LEU* 5.0 1.3 - - + -
2219A ALA* 4.3 9.6 - - + +
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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