Contacts of the strand formed by residues 734 - 739 (chain A) in PDB entry 5A7R
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 LEU 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733A MET* 1.3 68.1 - - - +
735A GLN* 1.3 58.9 + - - +
736A VAL 3.8 0.3 + - - -
820A GLU* 3.6 29.8 - - + +
822A VAL* 3.7 26.9 - - + +
851A GLY 3.8 11.9 - - - +
852A PHE* 4.2 16.2 - - + -
854A ARG* 3.5 32.3 - - - +
863A SER* 3.3 5.0 + - - +
864A ALA 3.1 10.9 + - - +
865A VAL* 3.6 8.7 - - + +
866A ALA 2.8 30.8 + - - +
895A ARG* 3.7 33.7 - - - +
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Residues in contact with GLN 735 (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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726A ILE* 3.6 27.1 + - + +
730A GLY 3.0 28.5 + - - +
731A GLN* 4.4 0.6 - - - +
732A GLY 4.8 1.6 - - - +
733A MET 3.5 11.3 + - - +
734A LEU* 1.3 71.7 - - - +
736A VAL* 1.3 62.9 + - - +
758A ARG* 2.8 38.7 + - - +
819A THR* 4.0 6.5 - - - +
820A GLU 2.9 16.0 + - - +
821A ILE* 3.2 10.9 - - + +
822A VAL* 2.9 25.8 + - - -
866A ALA* 3.7 6.5 - - + -
1974A GOL 3.0 25.5 + - - -
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Residues in contact with VAL 736 (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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726A ILE* 4.0 9.2 - - - +
734A LEU 4.6 0.7 - - - +
735A GLN* 1.3 72.8 - - - +
737A ASP* 1.3 62.2 + - - +
738A PHE* 3.7 24.4 - - + -
754A GLN* 3.0 20.3 + - - -
758A ARG* 5.5 2.0 + - - -
821A ILE* 4.9 0.9 - - - -
822A VAL* 3.7 10.3 - - + +
824A ILE* 3.8 27.8 - - + -
852A PHE* 4.0 15.3 - - + -
865A VAL* 3.8 15.5 - - + -
866A ALA 3.1 10.4 + - - +
867A THR* 3.7 30.3 - - - +
870A TRP* 4.8 2.2 - - + -
886A GLN* 5.1 0.2 - - - +
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Residues in contact with ASP 737 (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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735A GLN 3.7 0.4 + - - -
736A VAL* 1.3 74.7 - - - +
738A PHE* 1.3 58.6 + - - +
739A ALA* 2.9 10.0 + - - +
754A GLN* 3.8 3.9 - - - +
755A GLU* 2.6 56.5 - - - +
758A ARG* 4.7 6.7 - - + +
759A PHE* 3.8 14.4 - - - -
821A ILE* 3.9 18.8 - - + -
822A VAL 2.8 15.7 + - - +
823A ALA* 3.3 20.1 - - + +
824A ILE 3.2 20.1 + - - +
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Residues in contact with PHE 738 (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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726A ILE* 3.8 10.8 - - + -
736A VAL* 3.7 25.6 - - + -
737A ASP* 1.3 65.9 - - - +
739A ALA* 1.3 63.8 + - - +
754A GLN* 2.8 36.4 + - + +
755A GLU* 3.5 16.1 + - - +
824A ILE 4.0 4.3 - - - -
867A THR* 3.9 6.7 - - - -
868A GLY* 3.7 18.6 - - - -
869A ASN 3.9 1.8 - - - -
870A TRP* 3.6 44.4 - + + -
1964A AR6 3.4 78.9 - - - +
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Residues in contact with ALA 739 (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 ASP* 2.9 12.7 + - - +
738A PHE* 1.3 76.3 - - - +
740A ASN* 1.3 68.6 + - - +
743A VAL* 5.1 1.8 - - + -
755A GLU* 3.3 22.0 - - - +
775A LEU* 5.3 0.9 - - + -
823A ALA* 3.8 14.4 - - + -
824A ILE 3.0 22.0 + - - +
825A ASP* 3.2 18.4 - - + +
826A ALA 4.1 1.0 + - - -
875A PHE* 3.9 13.2 - - - -
1964A AR6 3.9 3.0 + - - +
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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