Contacts of the strand formed by residues 746 - 751 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741D THR 4.0 0.3 - - - +
742D THR* 3.6 2.3 - - - -
743D SER* 2.8 48.0 + - - +
745D MET* 1.4 90.4 - - - +
747D PHE* 1.3 60.5 + - - +
748D CYS* 4.0 17.2 - - - -
757D GLN* 3.4 30.2 + - + +
758D PHE 3.3 4.3 - - - +
759D ASN* 3.3 22.0 + - - +
760D ARG* 3.8 8.4 - - - -
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Residues in contact with PHE 747 (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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740D LEU* 4.0 11.2 - - + -
741D THR 3.6 1.6 - - - -
742D THR* 3.8 24.0 - - + -
746D ASP* 1.3 76.5 - - - +
748D CYS* 1.3 61.1 + - - +
749D ILE* 3.6 5.1 - - + +
757D GLN* 3.6 1.9 - - - -
758D PHE* 2.8 38.8 + - + +
760D ARG* 3.3 49.6 - - + -
825D CYS* 3.8 26.0 - - - -
826D THR* 3.7 18.8 - - - -
827D ALA* 3.8 29.8 - - + -
836D ILE* 4.1 18.6 - - + -
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Residues in contact with CYS 748 (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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739D HIS 3.5 0.9 - - - +
740D LEU* 3.4 5.4 - - - +
741D THR* 2.8 54.5 + - - +
746D ASP* 4.0 10.1 - - - -
747D PHE* 1.3 77.4 - - - +
749D ILE* 1.3 63.7 + - - +
750D GLU 4.2 0.2 - - - -
755D ARG* 5.4 13.5 - - + +
756D TRP 3.5 4.0 - - - +
757D GLN* 3.6 35.9 - - - -
769D TRP* 5.8 1.1 - - + -
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Residues in contact with ILE 749 (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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738D PRO* 3.7 26.9 - - + -
739D HIS 3.2 5.2 - - - +
740D LEU* 4.3 7.0 - - + -
747D PHE* 3.6 17.0 - - + +
748D CYS* 1.3 84.4 - - - +
750D GLU* 1.3 62.7 + - - +
755D ARG* 3.1 5.3 - - - +
756D TRP* 2.8 56.1 + - + +
758D PHE* 3.8 20.6 - - + -
834D VAL* 3.9 27.1 - - + -
836D ILE* 4.5 4.3 - - + -
858D ILE* 4.2 15.7 - - + -
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Residues in contact with GLU 750 (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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738D PRO* 3.4 5.5 - - - +
739D HIS* 2.9 43.5 + - + +
748D CYS 4.2 0.2 - - - -
749D ILE* 1.3 75.2 - - - +
751D LEU* 1.3 63.3 - - - +
752D GLY 4.2 12.7 - - - +
754D LYS 3.2 9.2 - - - +
755D ARG* 4.1 22.8 - - + +
756D TRP* 4.6 0.2 - - - -
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Residues in contact with LEU 751 (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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736D ALA* 3.9 20.9 - - + -
737D ILE 3.7 9.0 - - - +
738D PRO* 3.5 35.4 - - + -
750D GLU* 1.3 75.0 - - - +
752D GLY* 1.3 58.5 + - - +
753D ASN 3.1 0.3 + - - -
754D LYS* 2.5 50.6 + - + +
756D TRP* 4.1 11.6 - - + -
859D ASP 3.5 8.7 - - - +
860D GLY* 3.5 11.7 - - - +
861D SER 4.2 0.4 - - - -
862D GLY* 3.4 37.5 - - - +
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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