Contacts of the helix formed by residues 1974 - 1987 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1994D PHE* 3.7 19.3 - - + -
1999D SER* 3.5 11.3 - - - -
2000D SER* 2.9 32.7 + - - -
2005D GLU* 4.2 5.7 + - - +
2010D SER* 5.2 4.8 + - - +
2013D THR* 4.6 8.5 - - + -
2014D MET* 4.4 14.4 - - + -
1973F SER* 1.3 72.6 + - - +
1975F ARG* 1.3 79.9 + - - +
1976F THR 3.5 0.2 - - - -
1977F SER 3.7 0.2 + - - -
1978F SER* 2.6 37.3 + - - -
3226F PAL 3.1 11.2 + - - -
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Residues in contact with ARG1975 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2000D SER* 3.7 4.2 - - - -
2005D GLU* 2.6 43.2 + - - -
2013D THR* 3.3 38.0 + - + +
2017D TYR* 3.1 21.4 + - - +
1974F THR* 1.3 79.2 - - - +
1976F THR* 1.3 52.9 + - - +
1979F SER* 2.7 42.3 + - - -
2055F GLN* 5.9 2.7 - - - +
2184F PRO 4.0 4.7 - - - +
2185F MET* 3.4 31.6 - - - +
2186F PRO* 3.3 23.6 - - - +
2207F ALA* 4.5 11.9 - - + +
2214F ARG* 4.7 4.3 - - - +
3226F PAL 2.6 42.4 + - + +
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Residues in contact with THR1976 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1969F PHE* 4.1 4.0 - - + -
1973F SER* 3.4 3.8 - - - -
1975F ARG* 1.3 72.6 - - - +
1977F SER* 1.3 60.2 + - - +
1979F SER* 2.9 16.2 + - - -
1980F PHE* 3.3 21.2 + - + -
2024F ARG* 3.1 13.9 + - - +
2045F ALA* 3.7 31.6 - - + +
2052F HIS* 3.1 16.7 + - + -
2055F GLN* 4.6 1.4 + - - -
2214F ARG* 3.7 19.9 + - - +
3226F PAL 2.7 32.7 + - - +
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Residues in contact with SER1977 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965F MET* 5.2 0.5 - - - +
1967F SER* 3.4 19.6 + - - -
1969F PHE* 3.7 22.2 - - - -
1973F SER* 2.9 28.4 + - - -
1974F THR 3.7 0.4 + - - -
1976F THR* 1.3 75.7 - - - +
1978F SER* 1.3 64.2 + - - +
1980F PHE* 3.7 3.0 + - - +
1981F ALA* 3.2 24.4 + - - +
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Residues in contact with SER1978 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1992D LEU* 4.0 7.6 - - - +
1994D PHE* 5.2 2.1 - - - -
2014D MET* 3.4 26.5 - - - +
2017D TYR* 3.8 23.8 - - - -
1974F THR* 2.6 25.9 + - - -
1977F SER* 1.3 76.7 - - - +
1979F SER* 1.3 60.0 + - - +
1981F ALA* 3.7 4.8 - - - +
1982F ALA* 2.8 33.5 + - - +
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Residues in contact with SER1979 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2017D TYR* 3.4 26.2 - - - -
1975F ARG 2.7 23.6 + - - -
1976F THR 2.9 8.0 + - - -
1978F SER* 1.3 76.2 - - - +
1980F PHE* 1.3 60.7 + - - +
1983F ALA* 3.1 29.1 + - - +
2211F MET* 4.0 12.7 - - - +
2214F ARG* 2.9 37.8 + - - +
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Residues in contact with PHE1980 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965F MET* 3.4 24.6 - - + +
1967F SER* 6.1 0.4 - - - -
1969F PHE* 5.1 0.7 - + + -
1976F THR* 3.3 30.8 + - + +
1977F SER* 4.1 3.8 - - - +
1978F SER 3.4 0.2 - - - -
1979F SER* 1.3 80.6 + - - +
1981F ALA* 1.3 59.1 + - - +
1983F ALA* 3.8 2.6 - - - +
1984F MET* 3.1 22.9 + - - +
2022F VAL* 3.7 33.2 - - + -
2043F ILE* 3.6 40.2 - - + -
2045F ALA* 4.5 2.7 - - + -
2054F THR* 3.9 13.9 - - + -
2214F ARG* 3.5 36.8 - - + -
2217F LEU* 4.5 4.5 - - + -
2218F LEU* 3.9 22.0 - - + +
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Residues in contact with ALA1981 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1991D VAL 6.1 0.2 - - - +
1992D LEU* 4.3 15.7 - - + +
1965F MET* 4.0 2.2 - - + -
1967F SER* 6.2 0.4 - - - -
1977F SER* 3.2 17.8 + - - +
1978F SER* 3.7 5.6 - - - +
1979F SER 3.3 0.2 - - - -
1980F PHE* 1.3 78.1 - - - +
1982F ALA* 1.3 59.5 + - - +
1984F MET 3.5 1.0 + - - -
1985F ALA* 2.9 29.8 + - - +
1991F VAL* 3.9 31.8 - - + +
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Residues in contact with ALA1982 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1964D VAL* 4.9 2.5 - - + -
1992D LEU* 3.8 16.3 - - + +
2017D TYR* 3.8 19.5 - - + +
1978F SER 2.8 18.0 + - - +
1979F SER 4.1 2.0 - - - +
1981F ALA* 1.3 76.4 - - - +
1983F ALA* 1.3 57.7 + - - +
1985F ALA* 3.6 3.6 + - - +
1986F ARG* 2.9 37.7 + - - +
2211F MET* 3.6 24.7 - - + -
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Residues in contact with ALA1983 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1979F SER 3.1 20.7 + - - +
1980F PHE* 3.8 5.6 - - - +
1982F ALA* 1.3 78.3 - - - +
1984F MET* 1.3 57.8 + - - +
1986F ARG* 3.2 2.1 + - - -
1987F LEU* 2.9 35.3 + - - +
2211F MET* 3.5 13.7 - - - +
2214F ARG 4.1 4.3 - - - -
2215F MET* 3.5 36.5 - - + +
2218F LEU* 4.1 4.0 - - + -
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Residues in contact with MET1984 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1960F LEU* 3.8 20.4 - - + -
1963F LYS* 3.2 42.8 - - + +
1964F VAL 3.6 2.7 - - - +
1965F MET* 3.4 35.4 - - + +
1980F PHE 3.1 16.4 + - - +
1983F ALA* 1.3 74.8 - - - +
1985F ALA* 1.3 58.7 + - - +
1987F LEU* 3.5 5.4 + - - +
1988F GLY 3.5 2.4 + - - -
1989F GLY* 2.7 40.0 + - - -
1990F ALA 3.6 16.2 - - - +
1991F VAL* 4.0 11.0 - - + -
2020F VAL* 4.8 0.7 - - + -
2218F LEU* 4.1 19.0 - - + +
2222F LEU* 4.4 5.8 - - + -
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Residues in contact with ALA1985 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962D GLY* 5.3 4.5 - - - +
1964D VAL* 4.5 7.4 - - + -
1990D ALA* 3.8 29.4 - - + -
1992D LEU* 5.3 3.1 - - + -
1981F ALA 2.9 18.7 + - - +
1982F ALA* 3.6 8.5 - - - +
1984F MET* 1.3 75.9 - - - +
1986F ARG* 1.3 54.6 + - - +
1988F GLY* 2.7 28.1 + - - -
1989F GLY 3.9 9.1 + - - +
1991F VAL* 4.9 2.8 - - + +
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Residues in contact with ARG1986 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1962D GLY* 3.6 34.4 + - - +
1963D LYS* 4.5 1.0 - - - +
1964D VAL* 3.9 11.3 - - + +
2016D CYS 5.3 0.4 + - - -
2017D TYR 2.7 27.1 + - - -
2018D ALA* 4.2 1.0 - - - +
2019D ASP* 3.5 31.9 + - - -
1951F VAL* 4.1 31.3 - - + +
1957F LEU* 3.2 28.1 - - - +
1982F ALA 2.9 21.6 + - - +
1983F ALA 3.2 4.0 + - - +
1985F ALA* 1.3 75.3 - - - +
1987F LEU* 1.3 57.7 + - - +
1988F GLY 3.2 1.1 - - - -
2211F MET* 3.3 33.8 - - - +
2215F MET* 4.1 13.2 - - + -
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Residues in contact with LEU1987 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1947F LEU* 4.0 24.5 - - + -
1957F LEU* 3.3 15.2 - - + +
1959F ILE* 3.4 20.5 + - + -
1960F LEU* 2.9 62.0 + - + +
1983F ALA 2.9 21.3 + - - +
1984F MET* 4.0 2.9 - - - +
1985F ALA 3.2 0.4 - - - -
1986F ARG* 1.3 75.4 - - - +
1988F GLY* 1.3 58.9 + - - +
1989F GLY 3.3 0.2 - - - -
2215F MET* 3.4 49.1 - - + +
2218F LEU* 4.1 7.9 - - + -
2219F ALA* 4.3 2.9 - - + +
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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