Contacts of the strand formed by residues 1473 - 1478 (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 THR1473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1472A GLY* 1.3 73.6 - - - -
1474A TRP* 1.3 69.1 + - - +
1475A LEU* 4.1 8.4 - - + +
1500A ARG* 3.0 24.1 + - - +
1502A ARG* 4.6 8.5 - - - +
1522A VAL* 5.2 7.1 - - + +
1524A GLU* 2.8 30.3 - - + +
1525A VAL* 3.7 7.8 - - + +
1526A ALA* 2.8 30.0 + - - +
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Residues in contact with TRP1474 (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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1470A LEU* 4.2 21.1 - - + +
1471A ASP 4.8 1.2 + - - -
1473A THR* 1.3 75.7 + - - +
1475A LEU* 1.3 63.4 + - - +
1494A LEU* 4.2 26.9 - - + -
1499A ALA* 4.0 20.2 - - + -
1500A ARG 2.7 11.6 + - - +
1501A VAL* 3.4 8.2 - - + +
1502A ARG 3.0 24.6 + - - -
1526A ALA* 3.7 26.0 - - + +
1527A GLY* 3.3 30.3 - - - -
1528A VAL 3.6 22.2 - - - -
1529A LEU* 4.2 10.5 - - + -
1567A PRO* 5.2 3.8 - - + -
1569A TRP* 3.8 21.5 - + - -
1629A VAL* 3.5 45.3 - - + -
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Residues in contact with LEU1475 (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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1473A THR* 4.1 9.9 - - - +
1474A TRP* 1.3 79.7 - - - +
1476A VAL* 1.3 58.6 + - - +
1477A ALA 4.0 0.4 - - - -
1502A ARG* 3.2 15.9 - - + +
1503A GLU 5.5 0.2 - - - +
1504A LEU* 4.3 24.9 - - + -
1519A LEU* 3.8 29.4 - - + -
1522A VAL* 3.8 33.4 - - + -
1525A VAL* 3.7 23.3 - - + -
1527A GLY 3.0 10.5 + - - +
1528A VAL* 3.4 14.0 - - + +
1529A LEU* 2.8 31.7 + - - +
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Residues in contact with VAL1476 (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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1474A TRP 5.0 0.2 - - - +
1475A LEU* 1.3 77.4 - - - +
1477A ALA* 1.3 62.6 + - - +
1478A LYS* 3.6 9.6 + - + +
1487A SER* 3.9 18.6 - - - +
1490A ALA* 5.0 4.3 - - + -
1494A LEU* 4.5 11.9 - - + -
1501A VAL* 3.7 26.5 - - + -
1502A ARG 2.9 11.9 + - - +
1503A GLU* 3.6 7.6 - - + +
1504A LEU* 2.8 24.5 + - - +
1529A LEU* 3.3 17.9 - - + +
1531A LEU* 3.6 34.5 - - + -
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Residues in contact with ALA1477 (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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1475A LEU 4.0 1.2 - - - -
1476A VAL* 1.3 70.0 - - - +
1478A LYS* 1.3 62.7 + - - +
1504A LEU* 3.4 19.7 - - + +
1506A VAL* 4.1 12.1 - - + -
1528A VAL* 4.7 3.5 - - + +
1529A LEU 2.9 13.4 + - - +
1530A SER* 4.3 4.5 - - - -
1531A LEU* 2.7 32.9 + - - +
1532A LEU* 3.6 8.6 + - + -
1555A LEU* 3.9 27.6 - - + -
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Residues in contact with LYS1478 (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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1476A VAL* 3.9 11.4 - - + +
1477A ALA* 1.3 77.4 - - - +
1479A TYR* 1.3 85.0 + - - +
1480A ALA* 4.6 1.2 - - - +
1481A GLY 4.3 4.2 - - - +
1482A THR 3.0 27.3 + - - +
1483A ALA* 4.0 1.1 - - + -
1484A ASP* 3.4 20.7 + - - -
1487A SER* 3.6 22.7 - - - +
1503A GLU* 3.4 34.0 + - + +
1504A LEU 3.3 4.8 + - - +
1505A VAL* 3.4 14.4 - - + +
1506A VAL* 3.0 22.6 + - - +
1531A LEU* 4.4 16.4 - - + +
1532A LEU* 3.8 12.7 - - - +
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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