Contacts of the helix formed by residues 733 - 740 (chain A) in PDB entry 4PE5
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 SER 733 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536A GLN* 4.7 3.1 - - - -
537A GLY 2.4 47.8 + - - +
539A THR* 3.5 19.2 - - - +
731A TRP 3.6 0.2 + - - -
732A ASP* 1.3 63.6 - - - +
734A ALA* 1.3 58.7 + - - +
735A VAL 3.0 4.7 - - - -
737A GLU* 2.9 52.7 + - - +
752A LEU* 3.3 22.7 - - - +
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Residues in contact with ALA 734 (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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407A PRO* 3.4 15.0 - - - +
408A PHE* 3.6 27.8 - - + -
534A LYS* 5.5 1.8 - - + -
536A GLN* 3.8 23.6 - - + +
732A ASP 3.2 0.6 - - - -
733A SER* 1.3 78.5 - - - +
735A VAL* 1.3 58.9 + - + +
737A GLU* 5.4 0.4 - - - -
738A PHE* 3.7 11.0 + - - +
758A PHE* 3.8 9.2 - - + -
793A VAL* 5.5 9.5 - - + +
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Residues in contact with VAL 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A GLN* 3.5 27.8 - - + +
406A GLU* 4.1 11.9 - - + -
407A PRO* 3.7 27.8 - - + -
408A PHE* 5.2 4.5 - - + -
516A PRO* 5.7 0.2 - - + -
714A ALA* 5.6 0.4 - - + -
718A ILE* 4.6 8.1 - - + -
731A TRP* 3.6 28.9 - - + +
732A ASP* 3.2 13.0 + - + +
733A SER 3.0 0.6 - - - -
734A ALA* 1.3 82.2 - - + +
736A LEU* 1.3 59.2 + - + +
737A GLU 3.3 1.6 - - - -
738A PHE* 3.0 5.7 + - - +
739A GLU* 2.9 38.0 + - + +
758A PHE* 5.5 0.7 - - + -
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Residues in contact with LEU 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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539A THR* 3.3 42.0 - - + +
541A LEU* 3.5 40.2 - - + +
718A ILE* 5.0 0.9 - - + -
729A PHE* 3.4 26.2 - - + +
731A TRP* 3.5 27.8 - - + +
732A ASP 2.9 17.0 + - - +
735A VAL* 1.3 79.7 - - + +
737A GLU* 1.3 61.0 + - - +
739A GLU* 3.3 9.2 + - + +
740A ALA* 3.2 17.2 + - - +
748A THR* 3.3 15.9 - - + +
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Residues in contact with GLU 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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539A THR* 5.0 2.9 - - + +
733A SER* 2.9 37.6 + - - +
734A ALA* 5.4 0.6 - - - -
736A LEU* 1.3 75.7 - - - +
738A PHE* 1.3 59.6 + - - +
740A ALA* 3.7 6.1 + - - +
741A SER* 2.8 24.9 + - - -
748A THR* 3.9 22.7 + - + +
752A LEU* 5.9 3.1 - - - +
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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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406A GLU* 4.1 3.4 - - + -
407A PRO* 3.5 27.6 - - + -
410A TYR* 3.2 28.0 - + - -
734A ALA 3.7 16.2 + - - +
735A VAL 3.0 10.1 + - - +
737A GLU* 1.3 78.3 - - - +
739A GLU* 1.3 73.9 + - - +
740A ALA 3.2 1.6 - - - -
741A SER* 3.1 21.0 + - - -
742A GLN* 3.1 26.5 + - + +
792A TRP 3.3 26.5 - - - -
793A VAL* 4.3 19.3 - - + -
795A TYR 4.8 9.4 - - - -
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Residues in contact with GLU 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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406A GLU* 3.3 24.7 - - - +
541A LEU* 4.4 15.0 - - + -
718A ILE* 3.6 42.1 - - + +
735A VAL 2.9 19.5 + - - +
736A LEU* 3.3 10.7 + - - +
738A PHE* 1.3 94.9 - - - +
740A ALA* 1.3 57.5 + - - +
741A SER 3.2 1.1 - - - -
742A GLN* 3.9 4.5 - - - +
743A LYS* 3.2 33.1 + - - +
746A LEU* 4.2 11.4 - - + +
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Residues in contact with ALA 740 (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 LEU 3.2 13.2 + - - +
737A GLU* 4.0 7.9 - - - +
738A PHE 3.2 0.8 - - - -
739A GLU* 1.3 76.9 - - - +
741A SER* 1.3 60.6 + - - +
743A LYS 3.4 9.9 - - - +
744A CYS* 5.2 0.2 - - - -
746A LEU 3.3 23.5 - - - +
747A VAL* 4.5 5.6 - - + -
748A THR* 4.4 14.1 - - + +
798A CYS* 4.3 10.0 - - - +
799A ASP 4.5 5.9 - - - +
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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