Contacts of the strand formed by residues 746 - 751 (chain A) in PDB entry 1JZ3
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 ASP 746 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741A THR 4.1 0.2 - - - +
742A THR* 3.6 3.3 - - - -
743A SER* 3.1 39.9 + - - +
745A MET* 1.3 90.9 - - - +
747A PHE* 1.3 59.8 + - - +
748A CYS* 4.0 17.3 - - - -
757A GLN* 3.7 25.0 - - - +
758A PHE 3.2 11.6 - - - +
759A ASN* 3.8 13.9 + - - -
760A ARG* 3.6 10.5 - - - +
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Residues in contact with PHE 747 (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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740A LEU* 4.1 6.3 - - + -
741A THR 3.8 2.0 - - - -
742A THR* 3.9 20.6 - - + -
746A ASP* 1.3 77.4 - - - +
748A CYS* 1.3 61.8 + - - +
749A ILE* 4.3 1.6 - - - -
756A TRP 3.8 1.0 - - - +
757A GLN* 3.4 1.6 - - - -
758A PHE* 2.7 44.7 + - + +
760A ARG* 3.2 50.0 - - + -
825A CYS* 3.8 25.4 - - - -
826A THR* 3.7 19.1 - - - -
827A ALA* 3.5 32.8 - - + -
836A ILE* 4.0 22.7 - - + -
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Residues in contact with CYS 748 (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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739A HIS 3.7 0.7 - - - +
740A LEU* 3.3 4.4 - - - +
741A THR* 2.8 50.2 + - + +
746A ASP* 4.0 12.8 - - - -
747A PHE* 1.3 77.0 - - - +
749A ILE* 1.3 64.5 + - - +
755A ARG* 6.5 0.9 - - + -
756A TRP 3.3 6.3 - - - +
757A GLN* 3.7 29.6 - - + -
769A TRP* 6.3 0.2 - - - -
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Residues in contact with ILE 749 (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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738A PRO* 3.7 26.9 - - + -
739A HIS 3.2 7.0 - - - +
740A LEU* 4.2 4.5 - - + -
747A PHE 4.1 5.2 - - - +
748A CYS* 1.3 81.4 - - - +
750A GLU* 1.4 64.1 - - - +
755A ARG* 3.2 6.4 - - - +
756A TRP* 2.7 55.7 + - + +
758A PHE* 3.6 37.7 - - + -
834A VAL* 3.9 23.8 - - + -
836A ILE* 4.2 13.2 - - + -
858A ILE* 4.1 14.8 - - + -
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Residues in contact with GLU 750 (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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737A ILE 4.6 0.2 - - - +
738A PRO* 3.2 4.3 - - - +
739A HIS* 2.7 45.6 + - + +
749A ILE* 1.4 76.9 - - - +
751A LEU* 1.3 65.1 + - - +
752A GLY 4.1 14.5 - - - +
754A LYS 3.5 9.4 - - - +
755A ARG* 3.7 26.1 + - + +
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Residues in contact with LEU 751 (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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736A ALA* 4.0 21.1 - - + -
737A ILE 3.8 7.4 - - - +
738A PRO* 3.6 34.1 - - + -
750A GLU* 1.3 76.6 - - - +
752A GLY* 1.3 64.2 + - - +
753A ASN* 3.1 0.5 + - - +
754A LYS* 2.7 41.2 + - - +
756A TRP* 3.9 14.8 - - + -
859A ASP 3.3 8.5 - - - +
860A GLY 3.4 9.2 - - - +
861A SER 3.8 1.1 - - - -
862A GLY* 3.1 41.1 - - - +
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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