Contacts of the strand formed by residues 1607 - 1613 (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 TRP1607 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1552A THR* 4.5 8.7 - - + -
1556A VAL* 4.1 16.4 - - + -
1567A PRO* 4.1 3.9 - - - +
1568A LEU* 4.1 16.4 - - + +
1570A THR* 4.2 14.1 - - + -
1592A LEU 4.8 2.0 - - - -
1596A GLY* 3.4 36.8 + - - -
1597A ARG* 5.5 0.2 - - - +
1599A ILE* 3.5 35.0 - - + -
1600A ALA* 3.5 37.1 - - + +
1603A ASN 3.5 7.2 + - - +
1604A PRO 3.1 7.2 + - - +
1606A VAL* 1.3 79.9 - - - +
1608A GLY* 1.3 59.8 + - - +
1609A GLY* 3.6 21.9 - - - -
1610A LEU* 3.7 26.4 - - + +
1636A ASP* 5.1 2.4 + - - -
1902A ARG* 2.9 37.0 + - - +
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Residues in contact with GLY1608 (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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1567A PRO* 3.7 17.3 - - - -
1568A LEU 2.7 22.2 + - - +
1569A TRP* 3.7 25.6 - - - -
1607A TRP* 1.3 71.0 - - - +
1609A GLY* 1.3 56.9 + - - +
1636A ASP* 3.4 7.1 - - - +
1902A ARG* 2.9 20.4 + - - -
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Residues in contact with GLY1609 (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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1568A LEU 3.2 4.6 + - - +
1569A TRP* 3.5 18.0 - - - -
1570A THR* 3.0 24.8 + - - -
1607A TRP* 3.6 15.3 - - - +
1608A GLY* 1.3 79.0 - - - +
1610A LEU* 1.3 65.4 + - - +
1636A ASP* 3.2 13.2 - - - -
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Residues in contact with LEU1610 (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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1569A TRP* 4.3 0.7 - - - -
1570A THR* 3.5 28.7 - - + +
1572A THR* 4.9 0.4 - - + -
1592A LEU* 4.1 14.1 - - + +
1593A TRP* 3.7 68.2 - - + +
1596A GLY* 4.4 4.3 - - - -
1597A ARG* 4.7 3.4 - - + +
1607A TRP* 3.7 25.1 - - + +
1609A GLY* 1.3 75.6 - - - -
1611A VAL* 1.3 65.8 + - - +
1636A ASP 2.7 15.5 + - - +
1637A GLN* 4.7 6.5 - - + -
1638A LEU* 3.0 24.8 + - - +
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Residues in contact with VAL1611 (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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1529A LEU* 6.4 0.2 - - + -
1569A TRP* 3.9 15.5 - - + -
1570A THR 2.9 12.7 + - - +
1571A VAL* 3.1 17.1 - - + +
1572A THR 2.9 23.9 + - - -
1593A TRP* 4.1 2.7 - - - -
1610A LEU* 1.3 78.8 - - - +
1612A ASP* 1.3 61.5 + - - +
1613A VAL* 4.4 5.6 - - + -
1621A LEU* 4.6 6.3 - - + -
1625A LEU* 5.9 4.0 - - + -
1628A VAL* 3.8 30.1 - - + -
1638A LEU* 3.3 11.2 - - + +
1640A LEU* 3.7 37.0 - - + -
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Residues in contact with ASP1612 (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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1572A THR* 2.7 25.3 + - - +
1574A SER* 3.2 17.4 + - - -
1575A ALA* 2.7 26.2 + - - +
1576A VAL* 3.7 16.9 - - + +
1593A TRP* 3.7 13.6 - - + -
1611A VAL* 1.3 73.4 - - - +
1613A VAL* 1.3 64.3 + - - +
1638A LEU 2.9 10.2 + - - +
1639A ALA* 3.4 2.6 - - - -
1640A LEU* 2.8 28.8 + - - +
1641A ARG* 3.0 31.9 + - - -
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Residues in contact with VAL1613 (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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1486A THR* 5.9 2.0 - - + -
1534A VAL* 5.9 0.2 - - + -
1571A VAL* 3.9 13.5 - - + -
1572A THR 2.9 16.1 + - - +
1573A GLU* 3.3 14.4 - - + +
1574A SER 2.9 20.6 + - - -
1611A VAL* 4.4 2.9 - - + -
1612A ASP* 1.3 78.8 - - - +
1614A PRO* 1.3 83.6 - - + +
1617A SER 4.2 13.2 - - - +
1620A GLU* 5.0 1.6 - - + -
1621A LEU* 3.8 38.6 - - + +
1640A LEU* 3.8 21.1 - - + -
1641A ARG* 3.6 4.5 - - - +
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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