Contacts of the helix formed by residues 1974 - 1987 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1973D SER* 1.3 70.9 - - - +
1975D ARG* 1.3 69.9 + - - +
1977D SER* 3.1 3.3 + - - -
1978D SER* 3.0 28.4 + - - -
3226D PAL 2.9 13.9 + - - -
1994E PHE* 3.5 22.4 - - + -
1999E SER* 3.4 10.9 - - - -
2000E SER* 2.8 31.1 + - - -
2001E VAL 4.3 0.2 + - - -
2005E GLU* 4.2 10.7 + - - +
2010E SER* 5.1 3.7 + - - +
2013E THR* 4.3 17.5 - - + -
2014E MET* 4.0 16.2 - - + -
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Residues in contact with ARG1975 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974D THR* 1.3 76.9 - - - +
1976D THR* 1.3 51.7 + - - +
1978D SER 3.9 0.2 - - - -
1979D SER* 2.5 42.0 + - - -
2055D GLN* 5.7 3.6 - - - +
2184D PRO 3.4 21.5 - - - -
2185D MET* 3.4 24.4 - - - +
2186D PRO* 3.4 19.2 - - - +
2207D ALA* 4.3 9.4 - - + +
2214D ARG* 5.2 3.6 - - - +
3226D PAL 2.8 39.1 + - + +
2000E SER* 3.7 5.3 - - - -
2005E GLU* 2.8 41.8 + - - -
2013E THR* 3.3 31.7 + - + +
2017E TYR* 3.4 23.9 + - - +
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Residues in contact with THR1976 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1969D PHE* 4.0 4.3 - - + -
1973D SER* 3.5 3.6 - - - -
1975D ARG* 1.3 73.2 - - - +
1977D SER* 1.3 60.2 + - - +
1979D SER* 3.4 4.4 + - - -
1980D PHE* 3.0 45.9 + - + -
2024D ARG* 2.9 14.6 + - - -
2045D ALA* 3.7 30.7 - - + +
2052D HIS* 3.3 18.5 + - + -
2055D GLN* 5.0 1.0 + - - -
2214D ARG* 4.2 10.1 + - - +
3226D PAL 2.5 34.3 + - - +
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Residues in contact with SER1977 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967D SER* 4.9 5.2 + - - -
1969D PHE* 3.7 30.3 - - - -
1973D SER* 3.2 27.3 + - - -
1974D THR* 3.1 9.9 + - - -
1976D THR* 1.3 76.1 - - - +
1978D SER* 1.3 67.1 + - - +
1980D PHE* 3.7 2.7 + - - +
1981D ALA* 3.2 24.5 + - - +
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Residues in contact with SER1978 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974D THR* 3.0 20.6 + - - -
1977D SER* 1.3 79.7 + - - +
1979D SER* 1.3 51.7 + - - +
1981D ALA* 4.6 0.2 - - - -
1982D ALA* 2.7 38.0 + - - +
1992E LEU* 3.5 11.8 - - - +
1993E SER 5.5 2.3 + - - -
1994E PHE* 5.2 1.9 - - - -
2014E MET* 3.3 28.2 - - - +
2017E TYR* 3.6 26.5 - - - -
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Residues in contact with SER1979 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1975D ARG 2.5 24.5 + - - -
1976D THR 3.4 3.6 + - - -
1978D SER* 1.3 73.6 - - - +
1980D PHE* 1.3 62.1 + - - +
1982D ALA 4.6 0.2 - - - +
1983D ALA* 2.8 33.4 + - - +
2211D MET* 4.0 12.4 - - - +
2214D ARG* 2.8 37.5 + - - -
2017E TYR* 3.5 26.9 - - - -
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Residues in contact with PHE1980 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1965D MET* 3.5 21.4 - - + +
1967D SER* 5.4 0.2 - - - +
1976D THR* 3.0 42.6 + - + +
1977D SER* 4.1 3.1 - - - +
1979D SER* 1.3 79.2 + - - +
1981D ALA* 1.3 57.4 + - - +
1983D ALA* 3.5 3.9 - - - +
1984D MET* 2.9 29.6 + - - +
2022D VAL* 3.6 37.7 - - + -
2043D ILE* 3.8 36.3 - - + -
2045D ALA* 4.4 3.6 - - + -
2054D THR* 4.0 12.3 - - + -
2214D ARG* 3.6 33.6 - - + +
2217D LEU* 4.2 4.3 - - + -
2218D LEU* 4.0 17.5 - - + +
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Residues in contact with ALA1981 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1965D MET* 4.1 1.8 - - + +
1967D SER* 5.9 0.2 - - - +
1977D SER 3.2 18.7 + - - +
1978D SER* 4.6 0.2 - - - -
1979D SER 3.2 0.2 - - - -
1980D PHE* 1.3 74.7 - - - +
1982D ALA* 1.3 66.5 + - - +
1983D ALA 3.1 1.1 - - - -
1984D MET* 3.4 2.4 + - - +
1985D ALA* 3.0 24.6 + - - +
1991D VAL* 4.0 30.4 - - + +
1992E LEU* 3.6 18.2 - - + -
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Residues in contact with ALA1982 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1978D SER 2.7 21.8 + - - +
1981D ALA* 1.3 73.2 - - - +
1983D ALA* 1.3 56.9 + - - +
1985D ALA* 3.3 5.9 + - - +
1986D ARG* 3.0 36.9 + - - +
2211D MET* 3.4 28.5 - - + -
1964E VAL* 4.7 5.4 - - + -
1992E LEU* 3.4 14.6 - - + +
2017E TYR* 4.1 15.9 - - + +
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Residues in contact with ALA1983 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1979D SER 2.8 20.9 + - - +
1980D PHE 3.5 5.2 - - - +
1982D ALA* 1.3 74.4 - - - +
1984D MET* 1.3 66.3 + - - +
1986D ARG 3.4 1.0 + - - -
1987D LEU* 3.2 27.1 + - - +
2211D MET* 3.7 8.9 - - - +
2214D ARG* 3.9 8.3 - - + -
2215D MET* 3.5 41.2 - - + +
2218D LEU* 4.2 5.4 - - + -
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Residues in contact with MET1984 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1960D LEU* 3.6 21.1 - - + -
1963D LYS* 3.6 41.5 - - + +
1964D VAL 3.7 3.6 - - - +
1965D MET* 3.6 24.0 - - + +
1980D PHE 2.9 20.1 + - - +
1981D ALA 3.7 0.4 - - - +
1983D ALA* 1.3 72.0 - - - +
1985D ALA* 1.3 56.8 + - - +
1987D LEU* 3.2 11.6 + - - +
1989D GLY* 2.8 35.2 + - - -
1990D ALA 3.5 22.4 - - - +
1991D VAL* 3.7 18.2 - - + -
2020D VAL* 5.1 0.2 - - + -
2218D LEU* 3.8 16.4 - - + +
2222D LEU* 4.6 7.2 - - + -
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Residues in contact with ALA1985 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1981D ALA 3.0 17.8 + - - +
1982D ALA* 3.6 7.4 - - - +
1984D MET* 1.3 78.9 - - - +
1986D ARG* 1.3 60.7 + - - +
1987D LEU 3.2 0.2 - - - -
1988D GLY* 3.4 11.8 + - - -
1989D GLY 4.0 10.7 - - - +
1990D ALA* 6.0 0.2 - - - +
1991D VAL* 5.5 0.4 - - + +
1962E GLY* 4.9 7.8 + - - +
1964E VAL* 4.7 4.7 - - + -
1990E ALA* 3.5 32.3 - - + +
1992E LEU* 6.1 0.4 - - + -
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Residues in contact with ARG1986 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1951D VAL* 4.2 32.7 - - + +
1957D LEU* 3.0 30.7 - - + +
1982D ALA 3.0 20.5 + - - +
1983D ALA 4.1 2.5 - - - +
1985D ALA* 1.3 74.2 - - - +
1987D LEU* 1.3 59.5 + - - +
1988D GLY 3.2 3.0 + - - -
2211D MET* 3.6 31.6 - - - +
2212D TYR* 5.5 0.2 - - - -
2215D MET* 4.1 16.6 - - + -
1962E GLY* 3.5 30.8 + - - +
1963E LYS* 4.7 1.0 - - - +
1964E VAL* 3.6 14.3 - - + +
2016E CYS 5.5 0.2 + - - -
2017E TYR 2.8 25.1 + - - -
2018E ALA* 4.1 0.8 - - - +
2019E ASP* 3.2 33.1 + - - -
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Residues in contact with LEU1987 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1947D LEU* 4.1 15.3 - - + -
1957D LEU* 3.5 10.5 - - + -
1959D ILE* 3.2 30.3 + - + -
1960D LEU* 2.6 64.1 + - + +
1983D ALA 3.2 12.9 + - - +
1984D MET 3.2 10.1 + - - +
1986D ARG* 1.3 76.6 - - - +
1988D GLY* 1.3 56.3 + - - +
1989D GLY 3.3 0.7 - - - -
2215D MET* 3.6 50.0 - - + +
2218D LEU* 4.2 4.0 - - + -
2219D ALA* 4.2 8.3 - - + +
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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
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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