Contacts of the strand formed by residues 1637 - 1641 (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 GLN1637 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1459A TRP* 3.8 0.6 - - - -
1593A TRP* 3.9 20.4 - - + -
1597A ARG* 3.1 40.1 + - + +
1610A LEU* 3.6 9.2 - - + -
1635A GLU* 3.6 3.1 + - - +
1636A ASP* 1.3 102.2 + - - +
1638A LEU* 1.3 59.4 + - - +
1647A GLY* 3.6 4.2 - - - -
1648A ARG* 3.1 49.7 + - + +
1898A TYR* 4.8 3.6 + - - -
1904A THR* 4.7 4.2 + - - -
1906A LEU* 3.7 27.7 - - - +
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Residues in contact with LEU1638 (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* 3.9 4.5 - - - -
1462A THR* 3.9 11.0 - - + -
1463A GLY 5.6 2.0 - - - +
1464A ALA* 6.1 3.6 - - - -
1569A TRP* 5.5 1.1 - - + -
1593A TRP* 3.5 6.3 - - - -
1610A LEU 3.0 11.1 + - - +
1611A VAL* 3.3 11.9 - - + -
1612A ASP 2.9 23.7 + - - -
1628A VAL* 4.1 34.8 - - + -
1635A GLU* 3.7 40.6 - - + +
1637A GLN* 1.3 77.3 - - - +
1639A ALA* 1.3 59.9 + - - +
1640A LEU* 4.2 0.9 - - + -
1645A VAL* 4.0 14.8 - - + -
1646A TYR 3.2 22.9 - - - +
1647A GLY* 3.7 13.5 - - - -
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Residues in contact with ALA1639 (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* 3.7 18.1 - - + -
1576A VAL* 4.3 7.4 - - + -
1578A THR* 3.7 28.9 - - + -
1612A ASP 3.4 5.8 - - - +
1638A LEU* 1.3 74.1 - - - +
1640A LEU* 1.3 63.3 + - - +
1641A ARG* 4.1 13.0 - - - +
1645A VAL* 3.6 0.9 - - - -
1646A TYR* 2.8 41.0 + - + +
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Residues in contact with LEU1640 (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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1611A VAL* 3.7 28.9 - - + -
1612A ASP 2.8 11.8 + - - +
1613A VAL* 3.9 9.2 - - + -
1614A PRO* 3.0 24.2 - - - +
1620A GLU* 3.6 38.8 - - + +
1621A LEU* 4.0 9.0 - - + +
1624A HIS* 4.1 16.2 - - + +
1625A LEU* 4.8 2.9 - - - +
1628A VAL* 4.6 8.5 - - + -
1638A LEU* 5.0 2.2 - - + -
1639A ALA* 1.3 72.4 - - - +
1641A ARG* 1.3 67.5 + - - +
1644A GLY 4.0 2.2 - - - -
1645A VAL* 3.5 39.5 - - + -
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Residues in contact with ARG1641 (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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1574A SER* 4.8 3.3 - - - +
1576A VAL* 3.0 32.7 + - - +
1578A THR* 3.6 22.9 - - + +
1582A GLU* 2.9 37.4 + - - +
1612A ASP* 3.0 33.3 + - - -
1613A VAL 3.6 12.3 - - - -
1614A PRO* 3.7 14.0 - - - +
1620A GLU* 3.6 11.5 - - - +
1623A ARG* 4.6 2.1 + - - -
1624A HIS* 5.1 3.8 - - - -
1639A ALA* 4.1 3.4 - - - +
1640A LEU* 1.3 88.9 + - - +
1642A ALA* 1.3 65.8 + - - +
1643A ASP* 2.9 21.8 + - - +
1644A GLY 2.9 21.6 + - - +
1646A TYR* 4.0 10.3 - - + -
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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