Contacts of the helix formed by residues 1765 - 1773 (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 THR1765 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1512A ARG* 6.4 1.1 - - - +
1550A ALA 5.8 0.2 - - - -
1553A LEU* 3.9 8.7 - - - -
1557A GLN* 5.5 2.9 - - - +
1763A THR 4.4 7.2 - - - +
1764A LEU* 1.3 80.8 - - - +
1766A GLY* 1.3 65.4 + - - +
1767A GLU* 3.7 7.5 + - - +
1768A ARG* 3.0 27.7 + - + +
1769A ILE* 3.0 23.0 + - - +
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Residues in contact with GLY1766 (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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1544A LEU 4.0 6.2 - - - +
1545A ALA* 6.1 1.6 - - - -
1549A LEU* 4.4 9.0 - - - -
1550A ALA* 3.7 36.7 + - - +
1553A LEU* 3.8 10.1 - - - +
1765A THR* 1.3 73.5 - - - +
1767A GLU* 1.3 56.4 + - - +
1769A ILE* 3.4 2.4 + - - +
1770A GLU* 3.0 30.2 + - - +
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Residues in contact with GLU1767 (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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1550A ALA* 4.8 2.8 - - - +
1765A THR* 3.2 8.2 + - - +
1766A GLY* 1.3 76.5 - - - +
1768A ARG* 1.3 62.9 + - - +
1770A GLU* 3.4 5.6 + - - +
1771A ARG* 3.0 50.8 + - + +
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Residues in contact with ARG1768 (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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1757A ASP* 4.7 19.5 + - - +
1758A ASP* 5.9 0.2 + - - -
1759A GLY* 5.1 11.1 - - - +
1763A THR* 3.6 25.4 + - - +
1764A LEU* 4.5 16.3 - - + +
1765A THR* 3.0 32.8 + - + +
1767A GLU* 1.3 79.0 - - - +
1769A ILE* 1.3 63.9 + - - +
1771A ARG* 3.4 5.2 + - - +
1772A ALA* 3.1 30.0 + - + +
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Residues in contact with ILE1769 (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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1544A LEU* 4.1 10.1 - - + -
1549A LEU* 4.4 13.7 - - + -
1553A LEU* 3.8 28.7 - - + -
1595A VAL* 4.9 2.7 - - + -
1764A LEU* 4.1 27.1 - - + -
1765A THR 3.0 13.7 + - - +
1766A GLY 3.8 3.4 - - - +
1768A ARG* 1.3 76.7 - - - +
1770A GLU* 1.3 65.3 + - - +
1772A ALA* 3.4 3.5 + - - +
1773A SER* 3.0 27.7 + - - +
1811A GLY 4.3 6.5 - - - +
1812A GLY* 4.2 12.7 - - - +
1815A PRO* 3.6 42.0 - - + -
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Residues in contact with GLU1770 (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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1542A ALA* 3.4 24.3 - - + +
1543A PRO* 5.6 0.3 - - - +
1544A LEU* 3.5 42.2 + - + +
1545A ALA* 3.6 13.5 - - + +
1766A GLY 3.0 18.2 + - - +
1767A GLU* 3.6 6.7 - - - +
1769A ILE* 1.3 79.2 - - - +
1771A ARG* 1.3 81.7 + - - +
1773A SER* 3.5 10.2 + - - -
1774A ARG* 3.7 23.5 + - - +
1777A VAL* 6.1 0.9 - - - +
1778A LEU* 5.0 5.0 - - - +
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Residues in contact with ARG1771 (chain A).
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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1767A GLU* 3.0 37.5 + - + +
1768A ARG* 3.8 6.1 - - - +
1770A GLU* 1.3 85.4 - - - +
1772A ALA* 1.3 60.5 + - - +
1774A ARG* 3.0 65.9 + - - +
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Residues in contact with ALA1772 (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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1755A THR* 2.7 33.2 + - - +
1757A ASP* 4.8 15.0 - - + +
1768A ARG* 3.1 24.7 + - - +
1769A ILE* 4.2 3.1 - - - +
1771A ARG* 1.3 79.1 - - - +
1773A SER* 1.3 57.5 + - - +
1774A ARG 3.4 1.9 + - - -
1775A ALA 5.1 0.9 + - - -
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Residues in contact with SER1773 (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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1544A LEU* 2.9 33.5 - - - +
1755A THR* 4.8 0.2 - - - -
1769A ILE* 3.0 15.8 + - - -
1770A GLU 3.6 3.7 + - - -
1771A ARG 3.4 0.6 - - - -
1772A ALA* 1.3 77.3 - - - +
1774A ARG* 1.3 58.6 + - - +
1775A ALA 3.4 2.5 - - - -
1776A LYS* 3.4 8.8 + - - +
1777A VAL* 2.9 33.1 + - - +
1816A GLY* 4.4 10.8 - - - -
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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