Contacts of the helix formed by residues 1967 - 1978 (chain r) 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 THR1967 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1961r LYS* 6.0 1.6 - - - +
1965r HIS 3.8 3.8 + - - -
1966r PHE* 1.3 78.3 - - - +
1968r SER* 1.3 64.2 + - - +
1969r GLU* 3.3 11.0 - - - -
1970r HIS* 3.3 24.6 - - - +
1971r ILE* 3.8 4.9 + - - +
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Residues in contact with SER1968 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1967r THR* 1.3 71.5 - - - +
1969r GLU* 1.3 58.8 + - - +
1970r HIS 3.1 4.7 - - - -
1971r ILE* 3.1 27.8 + - - +
1972r LYS* 3.7 3.6 + - - +
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Residues in contact with GLU1969 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967r THR* 3.3 6.5 - - - -
1968r SER* 1.3 76.8 - - - +
1970r HIS* 1.3 64.2 + - - +
1971r ILE 3.3 0.2 - - - -
1972r LYS* 3.7 19.2 - - + +
1973r ARG* 4.1 5.4 + - - +
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Residues in contact with HIS1970 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1966r PHE* 4.7 6.5 - - + -
1967r THR* 3.3 29.6 + - - +
1968r SER 3.1 0.4 - - - -
1969r GLU* 1.3 78.6 - - - +
1971r ILE* 1.3 59.1 + - - +
1973r ARG* 3.2 7.7 + - - +
1974r CYS* 2.9 28.4 + - + +
1997r LEU* 5.6 12.6 - - + -
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Residues in contact with ILE1971 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1958r SER* 4.8 18.2 - - - -
1960r LEU* 6.3 2.5 - - + -
1967r THR 3.8 4.0 + - - +
1968r SER* 3.1 17.3 + - - +
1970r HIS* 1.3 77.2 - - - +
1972r LYS* 1.3 63.9 + - - +
1974r CYS* 3.8 8.2 - - - +
1975r THR* 2.9 28.9 + - - -
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Residues in contact with LYS1972 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1968r SER 3.7 4.4 + - - +
1969r GLU* 3.7 16.6 - - + +
1970r HIS 3.2 0.4 - - - -
1971r ILE* 1.3 78.3 - - - +
1973r ARG* 1.3 57.4 - - + +
1975r THR* 4.0 1.5 - - - -
1976r ASP* 2.9 30.6 + - - +
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Residues in contact with ARG1973 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1969r GLU 4.1 4.7 + - - +
1970r HIS* 3.2 7.8 + - - +
1972r LYS* 1.3 77.7 - - + +
1974r CYS* 1.3 60.7 + - - +
1976r ASP* 3.9 6.9 - - - +
1977r LYS* 3.0 29.3 + - - +
1996r LEU 6.1 1.3 - - - +
1997r LEU* 5.8 8.3 - - + -
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Residues in contact with CYS1974 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1960r LEU* 5.8 9.2 - - + -
1970r HIS* 2.9 18.4 + - + +
1971r ILE* 3.9 8.5 - - - +
1973r ARG* 1.3 78.1 - - - +
1975r THR* 1.3 58.5 + - - +
1977r LYS* 3.5 6.2 - - - +
1978r GLY 3.3 3.8 + - - -
1979r VAL* 3.0 40.4 + - + +
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Residues in contact with THR1975 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1971r ILE* 2.9 18.4 + - - -
1972r LYS* 4.1 2.0 - - - -
1974r CYS* 1.3 74.8 - - - +
1976r ASP* 1.3 65.9 + - - +
1977r LYS 3.3 0.2 - - - -
1978r GLY* 3.2 12.6 + - - +
1979r VAL 4.0 8.9 + - - +
1980r GLU* 5.9 3.8 - - - -
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Residues in contact with ASP1976 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1972r LYS 2.9 18.9 + - - +
1973r ARG* 4.1 7.0 - - - +
1975r THR* 1.3 74.2 - - - +
1977r LYS* 1.3 64.4 + - - +
1978r GLY* 3.1 1.5 + - - -
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Residues in contact with LYS1977 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1973r ARG 3.0 20.4 + - - +
1974r CYS* 3.5 9.4 - - - +
1976r ASP* 1.3 78.1 - - - +
1978r GLY* 1.3 58.6 + - - +
1979r VAL* 4.3 5.4 - - + +
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Residues in contact with GLY1978 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1974r CYS 3.3 0.4 + - - -
1975r THR 3.2 12.8 + - - -
1976r ASP 3.1 4.8 - - - -
1977r LYS* 1.3 79.6 - - - +
1979r VAL* 1.3 61.5 + - - +
1980r GLU* 3.5 6.1 + - - +
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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