Contacts of the helix formed by residues 1972 - 1996 (chain A) in PDB entry 6FF7
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 THR1972 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1971A LEU* 1.3 79.3 - - - +
1973A ASP* 1.3 62.0 + - - +
1974A GLU* 3.3 5.4 - - - -
1975A GLU* 3.3 9.5 + - - +
1976A TRP* 2.8 25.2 + - - +
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Residues in contact with ASP1973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1972A THR* 1.3 72.6 - - - +
1974A GLU* 1.3 61.2 + - - +
1976A TRP* 3.2 10.3 + - - +
1977A ILE* 3.0 29.3 + - - +
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Residues in contact with GLU1974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1972A THR* 3.3 4.4 - - - -
1973A ASP* 1.3 79.6 - - - +
1975A GLU* 1.3 57.0 + - - +
1977A ILE* 3.4 4.2 + - - +
1978A LYS* 2.9 27.0 + - - +
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Residues in contact with GLU1975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1971A LEU* 5.1 9.4 - - + -
1972A THR* 3.3 14.8 + - - +
1974A GLU* 1.3 75.8 - - - +
1976A TRP* 1.3 61.2 + - - +
1978A LYS* 3.7 8.6 - - + +
1979A VAL* 2.9 29.1 + - - +
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Residues in contact with TRP1976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1971A LEU* 5.3 3.8 - - - +
1972A THR 2.8 15.6 + - - +
1973A ASP* 3.2 14.5 + - - +
1975A GLU* 1.3 76.0 - - - +
1977A ILE* 1.3 58.5 + - - +
1979A VAL* 3.3 7.0 + - - +
1980A GLU* 3.0 25.1 + - - +
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Residues in contact with ILE1977 (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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1973A ASP 3.0 15.2 + - - +
1974A GLU* 4.2 3.8 - - - +
1976A TRP* 1.3 76.1 - - - +
1978A LYS* 1.3 58.4 + - - +
1980A GLU* 3.5 9.6 - - + +
1981A VAL* 2.9 28.8 + - - +
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Residues in contact with LYS1978 (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 GLU 2.9 19.4 + - - +
1975A GLU* 3.7 12.1 - - + +
1977A ILE* 1.3 74.8 - - - +
1979A VAL* 1.3 59.7 + - - +
1981A VAL* 3.3 6.2 + - - +
1982A GLN* 3.0 30.7 + - - +
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Residues in contact with VAL1979 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1953A ILE* 5.0 19.6 - - + +
1954A LEU* 5.7 3.4 - - - -
1975A GLU 2.9 18.1 + - - +
1976A TRP* 3.7 5.6 - - - +
1978A LYS* 1.3 74.8 - - - +
1980A GLU* 1.3 56.4 + - - +
1982A GLN* 3.8 3.7 - - - +
1983A LEU* 2.9 32.6 + - - +
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Residues in contact with GLU1980 (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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1935A ARG* 6.0 8.7 - - + -
1938A LEU* 5.7 6.9 - - + +
1976A TRP 3.0 13.8 + - - +
1977A ILE* 3.5 13.9 - - + +
1979A VAL* 1.3 77.2 - - - +
1981A VAL* 1.3 57.0 + - - +
1983A LEU* 3.4 3.7 + - - +
1984A LYS* 3.0 30.1 + - - +
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Residues in contact with VAL1981 (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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1977A ILE 2.9 16.4 + - - +
1978A LYS* 3.3 6.5 + - - +
1980A GLU* 1.3 76.1 - - - +
1982A GLN* 1.3 58.4 + - - +
1984A LYS* 3.4 4.6 + - - +
1985A ASP* 2.9 28.1 + - - +
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Residues in contact with GLN1982 (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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1953A ILE* 5.7 8.1 - - + -
1978A LYS 3.0 16.9 + - - +
1979A VAL* 4.3 4.0 - - - +
1981A VAL* 1.3 77.4 - - - +
1983A LEU* 1.3 57.1 + - - +
1985A ASP* 3.5 7.9 + - - +
1986A LEU* 2.9 24.6 + - - +
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Residues in contact with LEU1983 (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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1938A LEU* 4.9 10.0 - - + +
1939A ILE* 5.2 7.0 - - + -
1942A ALA* 4.1 22.6 - - + +
1950A ALA* 6.0 2.5 - - + -
1953A ILE* 5.9 5.2 - - + -
1979A VAL 2.9 19.1 + - - +
1980A GLU* 4.1 4.0 - - - +
1982A GLN* 1.3 75.4 - - - +
1984A LYS* 1.3 60.1 + - - +
1986A LEU* 3.2 9.1 + - - +
1987A ILE* 3.0 26.0 + - - +
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Residues in contact with LYS1984 (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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1938A LEU* 5.7 9.5 - - + +
1980A GLU 3.0 17.3 + - - +
1981A VAL* 4.1 4.7 - - - +
1983A LEU* 1.3 76.3 - - - +
1985A ASP* 1.3 57.8 + - - +
1987A ILE* 3.3 7.3 + - - +
1988A LEU* 2.9 29.3 + - - +
2011A ILE* 5.7 9.4 - - + -
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Residues in contact with ASP1985 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1981A VAL 2.9 18.7 + - - +
1982A GLN* 3.6 10.1 - - - +
1984A LYS* 1.3 74.9 - - - +
1986A LEU* 1.3 58.7 + - - +
1988A LEU* 3.8 5.3 - - - +
1989A ALA* 2.9 31.6 + - - +
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Residues in contact with LEU1986 (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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1942A ALA* 5.0 9.0 - - + +
1946A ASN* 6.3 3.6 - - + -
1949A ARG* 5.9 8.3 - - + -
1950A ALA* 6.0 4.7 - - + +
1982A GLN 2.9 15.5 + - - +
1983A LEU* 3.3 12.6 - - - +
1985A ASP* 1.3 75.5 - - - +
1987A ILE* 1.3 57.3 + - - +
1989A ALA* 3.4 5.9 + - - +
1990A ASP* 2.9 29.8 + - - +
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Residues in contact with ILE1987 (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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1938A LEU 5.9 1.3 - - - +
1941A ARG* 5.7 6.7 - - + +
1942A ALA* 5.4 12.1 - - - +
1945A VAL* 5.7 5.8 - - + -
1983A LEU 3.0 15.6 + - - +
1984A LYS* 3.8 8.1 - - - +
1985A ASP 3.3 0.2 - - - -
1986A LEU* 1.3 75.3 - - - +
1988A LEU* 1.3 57.9 + - - +
1990A ASP* 3.3 6.8 + - - +
1991A TYR* 3.0 28.4 + - - +
2010A ILE* 6.0 2.5 - - - +
2011A ILE* 5.9 8.7 - - + -
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Residues in contact with LEU1988 (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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1984A LYS 2.9 18.0 + - - +
1985A ASP* 4.0 5.8 - - - +
1987A ILE* 1.3 77.0 - - - +
1989A ALA* 1.3 56.1 + - - +
1991A TYR* 3.4 7.6 + - - +
1992A GLY* 2.9 25.1 + - - -
1999A VAL* 4.8 18.5 - - + +
2010A ILE* 6.2 2.7 - - - -
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Residues in contact with ALA1989 (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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1985A ASP 2.9 20.5 + - - +
1986A LEU* 3.8 5.6 - - - +
1988A LEU* 1.3 73.0 - - - +
1990A ASP* 1.3 61.8 + - - +
1992A GLY* 3.4 2.2 + - - +
1993A LYS* 2.9 30.3 + - - +
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Residues in contact with ASP1990 (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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1945A VAL* 4.5 24.7 - - + +
1946A ASN* 5.8 4.5 - - + -
1986A LEU 2.9 17.9 + - - +
1987A ILE* 3.7 5.2 - - - +
1989A ALA* 1.3 74.8 - - - +
1991A TYR* 1.3 59.2 + - - +
1993A LYS* 3.8 5.5 - - - +
1994A LYS* 2.9 30.9 + - - +
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Residues in contact with TYR1991 (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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1987A ILE 3.0 17.3 + - - +
1988A LEU* 3.6 8.3 - - - +
1989A ALA 3.3 0.2 - - - -
1990A ASP* 1.3 77.2 - - - +
1992A GLY* 1.3 56.8 + - - +
1994A LYS* 3.9 3.5 - - - +
1995A ASN* 3.0 34.5 + - - +
1997A VAL* 4.9 2.3 - - - +
2010A ILE* 5.2 13.7 - - + -
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Residues in contact with GLY1992 (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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1988A LEU 2.9 16.2 + - - -
1989A ALA* 3.7 2.7 - - - -
1991A TYR* 1.3 77.6 - - - +
1993A LYS* 1.3 56.6 + - - +
1996A ASN* 3.3 24.8 + - - -
1997A VAL* 3.3 28.7 + - - +
1999A VAL* 5.7 2.7 - - - -
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Residues in contact with LYS1993 (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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1989A ALA 2.9 18.4 + - - +
1990A ASP* 3.9 5.8 - - - +
1991A TYR 3.2 0.2 - - - -
1992A GLY* 1.3 78.0 - - - +
1994A LYS* 1.3 63.6 + - - +
1996A ASN* 4.2 3.5 + - - +
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Residues in contact with LYS1994 (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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1990A ASP 2.9 19.8 + - - +
1991A TYR* 3.3 4.7 + - - +
1993A LYS* 1.3 79.2 - - - +
1995A ASN* 1.3 62.0 + - + +
1996A ASN* 5.3 0.3 - - - +
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Residues in contact with ASN1995 (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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1991A TYR 3.0 14.3 + - - +
1994A LYS* 1.3 77.8 - - + +
1996A ASN* 1.3 70.8 + - - +
1997A VAL* 3.4 10.4 + - + +
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Residues in contact with ASN1996 (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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1992A GLY 3.3 13.5 + - - -
1993A LYS 4.2 3.7 + - - +
1994A LYS 3.5 2.8 - - - +
1995A ASN* 1.3 79.2 - - - +
1997A VAL* 1.3 58.7 + - - +
1998A ASN 4.3 0.2 + - - -
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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
------------------------------------------------------------
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