Contacts of the helix formed by residues 726 - 740 (chain A) in PDB entry 5WRZ
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 726 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725A SER* 1.3 74.0 - - - +
727A SER* 1.3 57.5 + - - +
729A ILE* 4.2 4.5 - - - +
730A LEU* 3.3 26.5 + - - +
751A LEU* 3.5 29.0 - - + +
753A ASN* 3.6 22.1 + - - +
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Residues in contact with SER 727 (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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725A SER* 3.2 11.5 + - - -
726A ASP* 1.3 74.0 - - - +
728A GLN* 1.3 63.5 + - - +
729A ILE 3.2 1.6 - - - -
730A LEU* 3.4 14.6 + - - +
731A ASP* 3.0 16.3 - - - +
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Residues in contact with GLN 728 (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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719A ALA* 5.3 7.1 - - + +
725A SER* 3.7 11.4 + - - +
727A SER* 1.3 76.0 - - - +
729A ILE* 1.3 65.4 + - + +
731A ASP* 3.6 15.2 - - - +
732A LEU* 3.7 29.7 - - + +
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Residues in contact with ILE 729 (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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716A VAL* 4.6 4.5 - - + +
719A ALA* 3.4 31.9 - - + +
720A VAL* 3.7 27.1 - - + +
723A GLY 4.6 1.3 - - - +
725A SER 2.9 31.1 + - - +
726A ASP* 4.2 4.7 - - - +
727A SER 3.2 0.6 - - - -
728A GLN* 1.3 74.7 - - - +
730A LEU* 1.3 67.8 + - - +
731A ASP 3.1 2.2 - - - -
732A LEU* 2.8 20.2 + - + +
733A SER* 3.0 10.5 + - - +
751A LEU* 4.0 14.1 - - + -
752A LEU 3.4 23.8 - - - +
753A ASN* 4.1 11.9 - - + +
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Residues in contact with LEU 730 (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 ASP 3.3 18.0 + - - +
727A SER* 3.4 9.4 + - - +
729A ILE* 1.3 77.3 - - - +
731A ASP* 1.3 60.5 + - - +
733A SER* 3.3 1.6 + - - -
734A ASN* 3.0 60.0 + - - +
751A LEU* 3.7 21.3 - - + -
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Residues in contact with ASP 731 (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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727A SER 3.0 20.1 - - - +
728A GLN* 3.6 16.3 - - + +
729A ILE 3.0 0.2 + - - -
730A LEU* 1.3 80.2 - - - +
732A LEU* 1.3 63.3 + - + +
734A ASN* 3.8 6.8 + - - +
735A ARG* 3.2 47.6 + - - +
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Residues in contact with LEU 732 (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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712A ILE* 3.5 13.1 - - + +
715A GLU* 3.6 42.8 - - + +
716A VAL* 3.7 19.9 - - + +
719A ALA* 3.5 31.4 - - + -
728A GLN* 3.7 25.1 - - + +
729A ILE* 2.8 11.8 + - + +
731A ASP* 1.3 78.1 - - + +
733A SER* 1.3 62.3 + - - +
735A ARG* 3.2 39.0 + - - +
736A PHE* 3.3 9.9 + - - +
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Residues in contact with SER 733 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716A VAL* 4.1 3.7 - - - +
729A ILE* 3.0 9.3 + - - -
730A LEU 3.5 8.7 - - - -
732A LEU* 1.3 75.6 - - - +
734A ASN* 1.3 65.7 + - - +
736A PHE* 3.2 13.7 + - - +
737A TYR* 3.1 27.1 + - - -
751A LEU* 3.9 13.9 - - - +
752A LEU* 2.9 51.6 + - - +
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Residues in contact with ASN 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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730A LEU* 3.0 46.7 + - - +
731A ASP* 3.9 7.0 - - - +
733A SER* 1.3 76.6 - - - +
735A ARG* 1.3 59.7 + - + +
737A TYR* 3.2 8.2 + - - +
738A THR* 2.9 32.3 + - - +
749A PRO* 4.1 22.5 - - - +
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Residues in contact with ARG 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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712A ILE* 3.9 19.5 - - + -
715A GLU* 3.8 15.3 + - - -
731A ASP* 3.2 31.4 + - - +
732A LEU* 3.4 33.5 - - - +
733A SER 3.2 1.2 - - - -
734A ASN* 1.3 72.8 - - + +
736A PHE* 1.3 68.5 + - - +
738A THR* 3.3 17.0 + - - +
739A LEU* 3.3 18.0 + - - +
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Residues in contact with PHE 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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709A ALA* 3.8 35.9 - - + -
712A ILE* 3.5 13.3 - - + +
713A LEU* 3.8 24.0 - - + -
716A VAL* 5.3 1.1 - - + -
732A LEU 3.3 5.3 + - - +
733A SER 3.2 11.3 + - - +
735A ARG* 1.3 78.2 - - - +
737A TYR* 1.3 68.2 + + - +
739A LEU* 3.1 7.8 + - - +
740A ILE* 3.1 29.0 + - + -
742A HIS* 3.9 16.8 - + - -
752A LEU* 3.8 23.3 - - + -
761A LYS* 3.9 29.2 - - + -
764A MET* 3.6 23.6 - - + -
765A LEU* 4.0 6.5 - - + -
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Residues in contact with TYR 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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733A SER* 3.1 34.0 + - - -
734A ASN* 3.2 9.5 + - - +
736A PHE* 1.3 77.8 - + - +
738A THR* 1.3 64.9 + - - +
740A ILE 3.3 17.6 - - - +
741A PRO* 3.8 7.4 - - - +
742A HIS* 3.8 49.7 + + + +
744A PHE* 4.4 1.8 - + - -
747A LYS* 5.3 11.5 + - - +
749A PRO* 3.6 33.2 - - + -
750A PRO* 2.8 39.1 + - - +
752A LEU* 3.2 23.3 - - + +
761A LYS* 4.2 6.1 + - - -
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Residues in contact with THR 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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734A ASN* 2.9 15.5 + - - +
735A ARG* 3.4 13.9 - - - +
736A PHE 3.2 0.2 - - - -
737A TYR* 1.3 80.5 - - - +
739A LEU* 1.3 65.2 + - + +
741A PRO* 4.5 7.4 - - - +
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Residues in contact with LEU 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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696A MET* 3.8 9.2 - - - +
705A GLN* 4.7 20.5 + - - +
708A ALA* 3.6 34.1 - - + +
709A ALA* 3.9 12.3 - - + +
712A ILE* 3.5 33.2 - - + -
735A ARG* 3.3 8.2 + - + +
736A PHE 3.1 7.4 + - - +
738A THR* 1.3 84.6 - - + +
740A ILE* 1.3 67.9 + - + +
741A PRO* 3.4 8.5 - - - +
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Residues in contact with ILE 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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691A ILE* 4.1 26.0 - - + -
696A MET* 4.4 15.5 - - + -
701A LEU* 5.6 1.3 - - + -
705A GLN* 4.3 12.8 - - + +
706A ILE* 4.8 5.4 - - + -
709A ALA* 3.6 30.3 - - + -
736A PHE* 3.1 14.6 + - + +
737A TYR* 3.3 14.1 - - - +
739A LEU* 1.3 86.9 - - - +
741A PRO* 1.3 59.5 - - + +
742A HIS* 2.8 41.3 + - + -
764A MET* 4.3 6.3 - - + -
765A LEU* 4.1 13.9 - - + -
768A LEU* 4.5 8.3 - - + -
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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