Contacts of the strand formed by residues 747 - 751 (chain A) in PDB entry 4Z4H
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 747 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ARG* 2.7 54.5 + - - +
207A ARG* 5.9 0.3 + - - -
737A ASP* 4.2 0.2 - - - +
741A THR* 3.8 11.4 - - - +
742A HIS* 3.0 33.0 + - - +
745A GLU 3.4 1.4 + - - -
746A PHE* 1.3 76.4 - - - +
748A PHE* 1.3 67.2 + - - +
764A HIS* 2.8 29.4 + - + +
765A TYR 3.1 14.1 - - - +
766A HIS* 3.8 13.3 + - + +
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Residues in contact with PHE 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A ILE* 6.0 1.1 - - + -
735A THR* 4.5 1.8 - - + -
736A VAL 3.6 13.0 - - - +
737A ASP* 3.7 14.8 - - + -
741A THR* 4.3 3.1 - - - -
746A PHE* 4.6 11.0 - + - -
747A ASP* 1.3 80.9 - - - +
749A TYR* 1.3 75.1 + - - +
750A LEU* 4.0 14.4 - - + -
764A HIS* 3.6 3.2 - - - -
765A TYR* 2.8 71.3 + + + +
767A VAL* 5.2 3.4 - - + -
779A LEU* 4.4 19.3 - - + -
780A GLN* 3.7 42.0 - - + +
783A THR* 4.0 16.2 - - - -
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Residues in contact with TYR 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.9 8.1 - - - -
207A ARG* 4.7 10.0 + - - -
711A HIS* 3.7 12.2 - + - -
713A THR* 2.7 42.4 + - + +
715A LEU* 4.5 6.7 - - + -
734A THR 4.6 0.2 - - - -
735A THR* 3.4 8.2 - - - +
736A VAL* 2.9 48.0 + - + +
740A ILE* 3.9 34.3 + - + -
741A THR* 4.3 11.4 - - + -
748A PHE* 1.3 73.9 - - - +
750A LEU* 1.3 60.7 + - - +
751A CYS 4.3 0.2 - - - -
762A PRO* 3.9 24.7 - - + -
763A SER 3.4 2.2 - - - +
764A HIS* 3.4 36.6 + + + -
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Residues in contact with LEU 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 4.2 7.0 - - + -
733A GLY* 3.7 17.9 - - - +
734A THR 3.5 9.6 - - - +
735A THR* 3.4 23.1 - - + +
748A PHE* 4.0 12.5 + - + -
749A TYR* 1.3 74.7 - - - +
751A CYS* 1.3 59.6 + - - +
752A SER* 3.5 14.5 + - - -
762A PRO* 4.6 1.1 - - - -
763A SER* 2.9 35.8 + - - +
765A TYR* 3.8 13.0 - - + +
780A GLN 4.1 6.5 - - - +
783A THR* 4.0 16.6 - - + -
784A TYR* 3.8 39.3 - - + +
787A CYS* 5.1 0.2 - - - -
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Residues in contact with CYS 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715A LEU* 5.8 0.6 - - + +
730A ILE* 3.7 36.6 - - + -
731A PRO 4.9 1.6 - - - -
732A ALA* 3.7 2.1 - - - -
733A GLY 2.8 23.0 + - - -
734A THR* 3.0 16.8 + - - +
749A TYR 4.3 0.4 - - - -
750A LEU* 1.3 69.2 - - - +
752A SER* 1.3 58.2 + - - +
753A HIS* 3.6 35.8 + - - -
760A SER* 4.0 16.4 - - - -
762A PRO* 4.0 17.4 - - + +
763A SER 4.6 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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