Contacts of the helix formed by residues 1675 - 1689 (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 GLY1675 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301A NDP 3.3 29.1 - - - -
1672A GLY* 3.0 14.3 + - - -
1674A THR* 1.3 84.1 + - - +
1676A GLY* 1.3 66.3 + - - -
1677A VAL 3.5 1.6 - - - -
1679A GLY* 3.0 19.0 + - - -
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Residues in contact with GLY1676 (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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301A NDP 3.4 18.5 + - - -
1675A GLY* 1.3 73.6 - - - +
1677A VAL* 1.3 61.9 + - - +
1679A GLY* 4.0 0.9 - - - -
1680A GLN* 3.4 25.3 + - - +
1683A ARG* 4.7 1.0 + - - -
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Residues in contact with VAL1677 (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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301A NDP 2.4 71.4 + - + +
1676A GLY* 1.3 68.8 - - - -
1678A GLY* 1.3 64.7 + - - +
1679A GLY 3.0 1.6 - - - -
1680A GLN* 3.0 8.1 + - - +
1681A ILE* 2.9 21.3 + - - +
1752A ALA* 4.9 0.2 - - + -
1798A PHE* 3.5 35.0 - - + -
1842A TRP* 3.9 37.9 - - + +
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Residues in contact with GLY1678 (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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301A NDP 4.1 1.4 + - - -
1670A VAL* 3.9 10.7 - - - +
1672A GLY 3.1 26.0 + - - -
1673A GLY* 3.6 8.8 - - - +
1675A GLY 4.2 0.2 - - - -
1676A GLY 3.5 0.2 - - - -
1677A VAL* 1.3 78.6 - - - +
1679A GLY* 1.3 56.3 + - - +
1681A ILE* 3.4 5.6 + - - +
1682A ALA* 2.9 28.1 + - - +
1752A ALA* 4.1 14.5 - - - +
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Residues in contact with GLY1679 (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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1673A GLY 3.3 14.5 + - - -
1675A GLY 3.0 17.8 + - - -
1676A GLY 4.0 0.2 - - - -
1678A GLY* 1.3 76.4 - - - +
1680A GLN* 1.3 59.8 + - - +
1682A ALA* 3.3 6.7 + - - +
1683A ARG* 2.9 45.6 + - - +
1709A LEU* 4.9 7.6 - - - +
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Residues in contact with GLN1680 (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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1676A GLY 3.4 15.8 + - - +
1677A VAL 3.0 7.5 + - - +
1679A GLY* 1.3 73.2 - - - +
1681A ILE* 1.3 66.1 + - - +
1683A ARG* 3.1 35.6 + - - +
1684A TRP* 3.0 23.9 + - - +
1687A ARG* 5.0 2.8 + - - +
1842A TRP* 3.9 21.1 - - + -
1866A PRO* 3.4 35.9 - - + +
1867A GLU* 4.1 8.5 + - - -
1870A CYS* 4.2 4.1 - - - -
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Residues in contact with ILE1681 (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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1670A VAL* 4.5 5.4 - - + -
1677A VAL* 2.9 19.8 + - + +
1678A GLY* 3.6 11.2 - - - +
1680A GLN* 1.3 75.8 - - - +
1682A ALA* 1.3 57.2 + - - +
1684A TRP* 3.2 15.1 + - + +
1685A LEU* 2.9 48.2 + - + +
1750A PHE* 4.1 25.6 - - + -
1798A PHE* 3.3 35.2 - - + -
1839A TRP* 4.6 1.3 - - + -
1842A TRP* 4.1 7.9 - - + -
1870A CYS* 3.8 21.3 - - - -
1873A LEU* 4.4 10.8 - - + -
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Residues in contact with ALA1682 (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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1670A VAL* 5.1 0.9 - - + -
1678A GLY 2.9 14.1 + - - +
1679A GLY* 3.5 11.9 - - - +
1681A ILE* 1.3 77.3 - - - +
1683A ARG* 1.3 62.6 + - - +
1685A LEU* 3.2 11.9 + - - +
1686A ALA* 3.0 19.8 + - - +
1693A LEU* 3.5 12.6 - - + +
1695A LEU* 3.8 28.0 - - + -
1709A LEU* 5.1 0.7 - - + -
1713A LEU* 3.6 19.3 - - + -
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Residues in contact with ARG1683 (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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1676A GLY 4.7 1.2 + - - -
1679A GLY* 2.9 45.3 + - - +
1680A GLN* 3.1 38.9 + - - +
1682A ALA* 1.3 75.0 - - - +
1684A TRP* 1.3 63.5 + - - +
1686A ALA* 3.3 3.1 + - - +
1687A ARG* 3.0 43.9 + - - +
1709A LEU* 4.7 17.8 - - + +
1712A GLU* 2.8 39.0 + - - +
1713A LEU* 3.7 18.2 - - + -
1716A LEU* 3.8 6.8 - - + +
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Residues in contact with TRP1684 (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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1662A TRP* 3.9 17.7 - + - -
1680A GLN 3.0 14.3 + - - +
1681A ILE* 3.4 28.9 - - + +
1683A ARG* 1.3 77.0 - - - +
1685A LEU* 1.3 73.5 + - + +
1687A ARG* 3.2 24.9 + - + +
1688A ARG* 2.8 48.0 + - + +
1750A PHE* 3.8 19.5 - + - -
1867A GLU 5.7 0.2 - - - -
1870A CYS* 3.4 45.7 + - + -
1871A ARG* 5.0 8.0 - - + +
1873A LEU* 4.1 20.0 - - + -
1874A GLN* 3.5 27.1 + - + +
1877A LEU* 4.3 7.0 - - + -
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Residues in contact with LEU1685 (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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1662A TRP* 3.9 26.7 - - + -
1664A PRO* 4.6 6.1 - - + -
1668A VAL* 3.7 25.6 - - + -
1670A VAL* 3.7 17.5 - - + -
1681A ILE* 2.9 25.7 + - + +
1682A ALA* 3.6 7.4 - - - +
1684A TRP* 1.3 102.0 - - + +
1686A ALA* 1.3 63.7 + - - +
1688A ARG* 3.1 14.1 + - + +
1689A GLY 3.1 0.5 + - - -
1690A ALA* 3.0 26.5 + - + +
1693A LEU* 3.7 21.5 - - + -
1750A PHE* 4.0 5.2 - - + -
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Residues in contact with ALA1686 (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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1682A ALA 3.0 12.6 + - - +
1683A ARG 3.5 8.3 - - - +
1685A LEU* 1.3 77.4 - - - +
1687A ARG* 1.3 62.2 + - - +
1689A GLY* 3.1 14.6 + - - -
1690A ALA* 4.0 3.5 + - - +
1693A LEU* 4.4 1.5 - - + +
1713A LEU* 4.1 9.2 - - + +
1716A LEU* 3.6 40.0 - - + +
1717A GLY 5.3 1.0 - - - +
1718A ALA* 4.0 25.5 - - + +
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Residues in contact with ARG1687 (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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1680A GLN* 5.0 2.8 + - - +
1683A ARG* 3.0 38.6 + - - +
1684A TRP* 3.2 36.3 + - + +
1686A ALA* 1.3 75.7 - - - +
1688A ARG* 1.3 61.2 - - - +
1689A GLY* 3.3 1.2 + - - -
1716A LEU* 4.1 25.4 - - + +
1866A PRO 5.4 0.4 - - - -
1867A GLU* 4.1 38.7 + - - +
1870A CYS* 5.2 1.2 - - - +
1871A ARG* 4.6 13.7 - - - +
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Residues in contact with ARG1688 (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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1661A GLU* 3.5 21.5 + - - -
1662A TRP* 2.6 27.9 + - + -
1663A LYS* 3.1 40.0 - - - +
1664A PRO* 3.9 18.1 - - + +
1684A TRP* 2.8 38.2 + - + +
1685A LEU* 3.1 14.3 + - - +
1687A ARG* 1.3 76.8 - - - +
1689A GLY* 1.3 57.8 + - - +
1874A GLN* 3.1 32.0 + - - +
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Residues in contact with GLY1689 (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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1663A LYS* 6.1 0.6 - - - +
1664A PRO* 4.4 5.7 - - - +
1686A ALA 3.1 12.0 + - - -
1687A ARG 3.1 1.9 - - - -
1688A ARG* 1.3 80.6 - - - +
1690A ALA* 1.3 67.2 + - - +
1691A PRO* 3.3 10.2 - - - +
1717A GLY 5.8 1.8 - - - -
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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