Contacts of the strand formed by residues 1746 - 1751 (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 LEU1746 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1667A THR* 3.3 21.8 - - + +
1669A LEU* 3.7 21.3 - - + +
1737A LEU* 3.6 27.4 - - + -
1740A ILE* 3.7 26.1 - - + +
1744A VAL 3.7 1.8 + - - -
1745A PRO* 1.3 76.8 - - - +
1747A SER* 1.3 58.3 + - - +
1748A ALA 3.6 20.4 - - - +
1749A VAL* 4.0 16.6 - - + -
1787A THR* 4.2 2.7 - - + -
1790A LEU* 3.8 28.7 - - + +
1791A ASP 4.5 5.5 + - - +
1792A LEU* 4.0 15.2 - - + +
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Residues in contact with SER1747 (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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1662A TRP* 5.6 0.2 - - - -
1664A PRO* 4.9 0.5 - - - +
1665A THR* 2.6 50.2 + - - -
1667A THR 2.9 7.3 + - - -
1668A VAL* 4.2 1.2 - - - +
1745A PRO* 3.3 2.9 + - - -
1746A LEU* 1.3 74.9 - - - +
1748A ALA* 1.3 66.8 + - - +
1791A ASP 4.5 2.5 - - - -
1792A LEU* 3.1 12.4 - - - +
1793A THR* 2.6 44.4 + - - -
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Residues in contact with ALA1748 (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* 3.7 29.8 - - + -
1667A THR 3.8 1.4 + - - -
1668A VAL* 3.5 9.6 - - + -
1669A LEU 3.0 24.6 + - - -
1746A LEU* 3.6 3.7 - - - +
1747A SER* 1.3 87.2 + - - +
1749A VAL* 1.3 66.3 + - - +
1750A PHE* 4.0 11.0 - - + -
1792A LEU* 4.3 2.2 - - - +
1793A THR* 4.4 0.4 - - - +
1794A ALA* 3.2 15.0 - - + +
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Residues in contact with VAL1749 (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* 3.4 23.8 - - + +
1671A THR* 5.1 0.7 - - + -
1746A LEU* 4.0 18.2 - - + -
1748A ALA* 1.3 79.0 - - - +
1750A PHE* 1.3 70.2 + - - +
1751A HIS* 4.0 3.4 - - + +
1783A LEU* 4.0 27.6 - - + -
1787A THR* 4.5 7.0 - - + -
1792A LEU* 4.0 19.1 - - + -
1794A ALA 3.0 6.9 + - - +
1795A PHE* 3.5 22.1 - - + -
1796A VAL* 2.7 32.6 + - - +
1797A LEU* 6.4 0.2 - - + -
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Residues in contact with PHE1750 (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* 3.6 32.3 - + - -
1668A VAL* 3.5 31.0 - - + -
1669A LEU 2.8 11.4 + - - +
1670A VAL* 3.2 13.6 - - + +
1671A THR* 2.9 25.5 + - - +
1681A ILE* 4.1 19.7 - - + -
1684A TRP* 3.8 22.9 - + - -
1685A LEU* 4.0 7.0 - - + -
1748A ALA* 4.0 9.6 - - + -
1749A VAL* 1.3 76.5 - - - +
1751A HIS* 1.3 60.3 + - - +
1752A ALA* 3.5 2.8 + - + -
1794A ALA* 5.0 0.9 - - + -
1796A VAL* 3.5 34.8 - - + -
1798A PHE* 4.1 14.1 - + + -
1873A LEU* 4.1 8.1 - - + -
1877A LEU* 4.6 3.4 - - + -
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Residues in contact with HIS1751 (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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1671A THR* 2.7 28.1 + - - -
1727A VAL* 4.3 3.1 - - + -
1749A VAL* 4.0 3.1 - - + -
1750A PHE* 1.3 68.1 - - - +
1752A ALA* 1.3 58.7 + - - +
1753A ALA* 3.7 18.9 + - + +
1775A ALA 3.3 19.7 + - - -
1776A LYS* 3.0 34.2 + - + -
1779A GLY* 4.0 6.3 - - - -
1780A ALA* 3.4 24.4 + - + -
1783A LEU* 3.7 19.4 - - + +
1796A VAL 2.9 16.5 + - - +
1797A LEU* 3.8 15.3 - - + -
1798A PHE* 3.2 27.4 + - - +
1820A LEU* 4.8 4.9 - - + -
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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