Contacts of the helix formed by residues 1729 - 1739 (chain A) in PDB entry 2FR1
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 ASP1729 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1726A ASP* 2.9 18.4 + - + +
1728A THR* 1.3 78.2 + - - +
1730A ARG* 1.3 64.3 + - - +
1731A GLU* 3.2 20.8 + - - +
1732A SER* 3.0 34.0 + - - +
1733A VAL* 3.2 14.4 + - - +
1782A ASN* 4.1 1.8 - - - -
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Residues in contact with ARG1730 (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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1728A THR 3.5 5.6 + - - +
1729A ASP* 1.3 71.5 + - - +
1731A GLU* 1.3 59.7 + - + +
1733A VAL* 3.3 5.4 + - - +
1734A ARG* 2.9 46.0 + - - +
1782A ASN* 3.6 27.7 + - - +
1785A GLU* 2.7 49.5 + - - +
1786A LEU* 3.6 32.7 - - + +
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Residues in contact with GLU1731 (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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1729A ASP* 3.2 10.3 + - - +
1730A ARG* 1.3 76.4 - - + +
1732A SER* 1.3 67.4 + - - +
1734A ARG* 3.3 42.3 + - - +
1735A GLU* 3.0 40.4 + - - +
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Residues in contact with SER1732 (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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1725A CYS* 3.8 19.0 - - - -
1726A ASP* 4.1 8.3 + - - +
1729A ASP* 3.0 31.8 + - - +
1731A GLU* 1.3 78.4 - - - +
1733A VAL* 1.3 57.6 + - - +
1735A GLU* 3.4 11.2 + - - +
1736A LEU* 2.9 27.9 + - - +
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Residues in contact with VAL1733 (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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1725A CYS* 4.0 10.8 - - - -
1726A ASP 4.1 1.3 - - - +
1727A VAL* 3.8 36.3 - - + +
1729A ASP 3.2 13.4 + - - +
1730A ARG* 3.6 7.4 - - - +
1732A SER* 1.3 74.9 - - - +
1734A ARG* 1.3 66.4 + - - +
1736A LEU* 3.0 9.6 + - + +
1737A LEU* 2.8 35.9 + - + +
1782A ASN* 4.6 4.0 - - + -
1783A LEU* 4.0 23.3 - - + -
1786A LEU* 3.4 20.2 - - + -
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Residues in contact with ARG1734 (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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1730A ARG* 2.9 42.1 + - - +
1731A GLU* 3.4 35.4 + - - +
1733A VAL* 1.3 77.6 - - - +
1735A GLU* 1.3 57.2 + - + +
1737A LEU* 3.4 7.1 + - - +
1738A GLY* 2.9 26.2 + - - -
1786A LEU* 3.7 24.7 - - + +
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Residues in contact with GLU1735 (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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1731A GLU* 3.0 34.4 + - + +
1732A SER* 3.7 8.3 - - - +
1734A ARG* 1.3 74.3 - - + +
1736A LEU* 1.3 66.1 + - - +
1738A GLY* 3.3 2.9 + - - -
1739A GLY* 3.1 18.5 + - - -
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Residues in contact with LEU1736 (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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1669A LEU* 4.2 20.6 - - + -
1694A LEU* 3.9 17.9 - - + +
1696A VAL* 3.5 36.6 - - + -
1723A ALA* 4.1 15.7 - - + -
1724A ALA 5.8 0.4 - - - +
1725A CYS* 3.8 20.6 - - + -
1727A VAL* 6.2 1.1 - - + -
1732A SER 2.9 15.6 + - - +
1733A VAL* 3.0 14.6 + - + +
1735A GLU* 1.3 74.6 - - - +
1737A LEU* 1.3 66.2 + - + +
1739A GLY* 3.0 15.1 + - - -
1740A ILE* 3.7 7.1 + - - +
1783A LEU* 6.2 0.4 - - + -
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Residues in contact with LEU1737 (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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1669A LEU* 4.2 19.5 - - + -
1733A VAL* 2.8 32.9 + - + +
1734A ARG* 3.7 5.2 - - - +
1736A LEU* 1.3 74.8 - - + +
1738A GLY* 1.3 63.7 + - - +
1740A ILE* 3.0 33.2 + - + +
1746A LEU* 3.6 30.7 - - + -
1783A LEU* 5.4 0.9 - - + -
1786A LEU* 3.6 42.8 - - + +
1787A THR* 4.1 9.6 - - + -
1790A LEU* 4.9 6.5 - - + -
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Residues in contact with GLY1738 (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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1734A ARG 2.9 17.1 + - - -
1735A GLU* 3.3 4.0 + - - -
1736A LEU 3.2 0.2 - - - -
1737A LEU* 1.3 75.3 - - - +
1739A GLY* 1.3 57.6 + - - +
1740A ILE 3.2 6.3 + - - +
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Residues in contact with GLY1739 (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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1735A GLU 3.1 7.9 + - - -
1736A LEU 3.0 12.0 + - - -
1738A GLY* 1.3 76.6 - - - +
1740A ILE* 1.3 62.5 + - - +
1741A GLY* 3.4 2.8 + - - -
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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