Contacts of the helix formed by residues 1596 - 1603 (chain D) in PDB entry 5EK0
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 THR1596 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1694A TYR* 4.3 6.2 - - - -
1801A PX4 3.9 26.8 + - - +
1595D PRO* 1.3 80.6 - - + +
1597D LEU* 1.4 68.5 + - + +
1598D PHE 3.3 1.8 - - - -
1599D ARG* 3.1 40.1 + - - +
1600D VAL* 3.3 23.7 + - - +
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Residues in contact with LEU1597 (chain D).
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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1801A PX4 4.8 23.6 - - - -
1588D ILE* 3.9 30.1 - - + -
1595D PRO* 3.5 10.2 - - + +
1596D THR* 1.4 81.6 - - + +
1598D PHE* 1.3 57.2 + - - +
1600D VAL* 3.3 8.6 + - + -
1601D ILE* 2.9 49.5 + - + +
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Residues in contact with PHE1598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537D TYR* 3.5 24.2 - + - -
1585D ALA* 3.4 27.4 - - + -
1588D ILE* 4.4 11.8 - - + +
1589D GLU* 3.4 42.2 - - + +
1595D PRO* 3.9 24.6 + - + +
1596D THR 3.3 0.2 - - - -
1597D LEU* 1.3 78.2 - - - +
1599D ARG* 1.4 60.5 + - + +
1601D ILE* 4.2 4.0 - - - +
1602D ARG* 3.2 44.3 + - + +
1806D 5P2 3.3 28.5 - - - -
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Residues in contact with ARG1599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1653A GLN* 2.9 36.1 + - - +
1654A LEU* 3.2 63.1 + - + +
1657A GLU* 4.0 21.5 - - - +
1694A TYR* 3.3 22.3 - - - -
1801A PX4 3.2 32.7 + - - +
1595D PRO 3.8 16.2 - - - +
1596D THR* 3.1 35.3 + - - +
1597D LEU 3.3 0.4 - - - -
1598D PHE* 1.4 77.8 - - + +
1600D VAL* 1.4 69.0 + - - +
1602D ARG* 3.4 6.2 + - - +
1603D LEU* 3.7 1.6 + - - +
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Residues in contact with VAL1600 (chain D).
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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1654A LEU* 4.5 7.4 - - + -
1801A PX4 4.2 45.8 - - - +
1596D THR 3.3 15.9 - - - +
1597D LEU* 3.3 14.9 + - + +
1599D ARG* 1.4 91.2 - - - +
1601D ILE* 1.4 60.6 + - + +
1603D LEU* 3.1 31.6 - - + +
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Residues in contact with ILE1601 (chain D).
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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1581D GLY* 4.3 8.3 - - - +
1584D LEU* 3.8 32.1 - - + -
1585D ALA* 4.1 24.2 - - + +
1588D ILE* 4.1 12.3 - - + -
1597D LEU* 2.9 45.3 + - + +
1598D PHE 4.3 2.5 - - - +
1600D VAL* 1.4 78.5 - - + +
1602D ARG* 1.4 53.8 + - - +
1603D LEU* 2.8 18.2 + - - +
1604D ALA* 3.1 18.2 + - + +
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Residues in contact with ARG1602 (chain D).
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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1653A GLN* 3.5 22.5 - - - +
1524D GLU* 2.8 40.2 + - - -
1537D TYR* 3.4 30.9 + - - -
1540D ASN* 5.2 1.6 - - - +
1585D ALA* 4.3 12.3 - - + -
1598D PHE* 3.2 50.6 + - + +
1599D ARG* 3.4 2.0 + - - +
1601D ILE* 1.4 74.3 - - - +
1603D LEU* 1.4 55.8 + - - +
1604D ALA* 3.0 7.5 + - - -
1605D ARG* 3.2 50.8 + - - +
1806D 5P2 2.8 37.8 + - + +
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Residues in contact with LEU1603 (chain D).
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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1650A MET* 5.2 12.1 - - + -
1653A GLN* 3.5 11.5 - - - +
1654A LEU* 4.2 31.6 - - + -
1700A PHE* 6.5 0.2 - - + -
1599D ARG 3.7 0.9 + - - +
1600D VAL* 3.1 31.6 - - + +
1601D ILE 2.8 8.1 + - - +
1602D ARG* 1.4 67.8 - - - +
1604D ALA* 1.3 59.6 + - - +
1605D ARG 3.1 4.9 - - - -
1606D ILE* 3.3 38.4 - - + +
1607D GLY 4.5 0.7 + - - -
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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