Contacts of the strand formed by residues 1644 - 1652 (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 GLY1644 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1624A HIS* 5.2 8.4 - - - -
1640A LEU* 4.0 0.3 - - - -
1641A ARG* 2.9 32.9 + - - +
1642A ALA 3.5 2.4 + - - -
1643A ASP* 1.3 77.1 - - - +
1645A VAL* 1.3 65.8 + - - -
1646A TYR* 3.6 9.3 - - - -
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Residues in contact with VAL1645 (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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1461A PRO* 3.3 8.1 - - - +
1462A THR* 3.1 39.0 + - + +
1463A GLY* 5.5 4.9 - - - +
1624A HIS* 3.5 33.0 - - + +
1628A VAL* 5.5 2.0 - - + -
1638A LEU* 4.0 28.7 - - + -
1639A ALA 3.7 3.1 - - - -
1640A LEU* 3.5 31.6 - - + -
1644A GLY* 1.3 76.4 - - - -
1646A TYR* 1.3 65.0 + - - +
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Residues in contact with TYR1646 (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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1459A TRP* 3.5 41.3 - - + -
1460A ARG 3.3 4.7 - - - +
1461A PRO* 3.6 32.3 - - + +
1462A THR* 4.1 0.7 - - - -
1578A THR* 4.5 12.3 - - + -
1638A LEU* 3.2 13.0 - - - +
1639A ALA* 2.8 44.5 + - + +
1641A ARG* 4.0 14.8 - - + -
1643A ASP* 3.1 45.0 + - - -
1644A GLY* 3.6 17.5 - - - -
1645A VAL* 1.3 76.8 - - - +
1647A GLY* 1.3 59.8 + - - +
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Residues in contact with GLY1647 (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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1459A TRP* 3.5 5.4 - - - -
1460A ARG 2.8 32.8 + - - +
1462A THR* 3.8 4.0 - - - +
1635A GLU* 4.0 2.0 - - - -
1637A GLN 3.6 7.0 - - - -
1638A LEU* 3.7 9.9 - - - -
1646A TYR* 1.3 75.3 - - - +
1648A ARG* 1.3 66.3 + - - -
1649A ARG* 3.5 18.7 + - - +
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Residues in contact with ARG1648 (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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1457A ILE* 3.5 39.6 - - + +
1458A GLU 3.8 4.0 - - - -
1459A TRP* 3.6 32.9 - - + -
1593A TRP* 4.8 2.2 - - - -
1597A ARG* 3.5 21.0 - - - +
1637A GLN* 3.1 47.6 + - + +
1647A GLY* 1.3 71.0 - - - -
1649A ARG* 1.3 78.7 + - - +
1803A SER 3.7 8.5 + - - -
1804A ALA* 2.9 35.4 + - - +
1906A LEU* 3.4 37.2 - - + +
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Residues in contact with ARG1649 (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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1457A ILE* 3.5 5.5 - - - -
1458A GLU 2.9 36.4 + - - +
1460A ARG* 4.3 21.3 - - + +
1462A THR* 4.0 11.9 + - - -
1635A GLU* 2.6 43.0 + - - -
1647A GLY* 3.5 17.1 - - - +
1648A ARG* 1.3 91.9 + - - +
1650A TRP* 1.3 66.1 + - - +
1651A VAL* 3.8 10.0 + - + +
1905A ARG* 3.2 42.0 + - - +
1906A LEU* 3.3 9.9 - - - +
1908A ASP* 3.9 17.1 + - - +
1909A GLU* 4.4 12.2 + - + +
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Residues in contact with TRP1650 (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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1455A TYR* 4.0 24.5 - + + -
1456A ARG 3.7 4.0 - - - -
1457A ILE* 3.5 13.5 - - + +
1649A ARG* 1.3 72.1 - - - +
1651A VAL* 1.3 64.2 + - - +
1801A PHE* 5.6 0.4 - - + -
1804A ALA* 3.2 35.7 + - + -
1805A PHE* 3.2 39.9 - + - +
1885A ILE* 3.7 32.3 - - + -
1887A ILE* 4.2 12.3 - - + -
1889A VAL* 5.7 0.9 - - + -
1891A TRP* 3.8 25.6 - + - -
1906A LEU* 2.8 39.5 + - + +
1907A PHE* 3.8 22.1 - + + -
1909A GLU* 4.0 10.0 - - - +
1910A ILE* 3.5 18.3 + - + +
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Residues in contact with VAL1651 (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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1455A TYR* 3.2 3.1 - - - +
1456A ARG* 2.8 60.1 + - + +
1458A GLU* 3.0 29.8 - - + +
1460A ARG* 3.5 5.8 - - - +
1649A ARG 4.2 8.3 - - - +
1650A TRP* 1.3 82.8 - - - +
1652A ARG* 1.3 66.6 + - - +
1909A GLU* 3.3 33.0 - - + +
1910A ILE* 3.9 8.3 - - - -
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Residues in contact with ARG1652 (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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1451A SER 5.1 3.6 + - - +
1452A ALA* 3.3 27.6 + - - +
1454A ARG 3.5 8.4 + - - +
1455A TYR* 3.0 42.8 + - + -
1456A ARG* 4.9 1.6 + - - +
1651A VAL* 1.3 84.5 - - - +
1653A ALA* 1.3 65.0 + - - +
1654A ALA 4.1 0.5 + - - -
1891A TRP* 3.6 10.3 - - - +
1909A GLU 5.6 1.2 + - - -
1910A ILE* 4.1 7.2 - - + +
1911A ASP* 2.6 33.0 + - - +
1912A ASP* 3.2 28.7 + - - +
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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