Contacts of the helix formed by residues 733 - 741 (chain A) in PDB entry 7ACN
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 GLU 733 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705A PHE 4.7 4.5 - - - +
707A PRO* 3.8 19.5 - - + +
732A ASN* 1.3 70.6 - - - +
734A THR* 1.3 64.8 + - - +
736A ILE* 3.3 15.2 + - - +
737A GLU* 3.2 20.5 + - - +
740A ARG* 2.7 38.9 + - - -
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Residues in contact with THR 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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63A ARG* 3.9 15.2 + - - +
196A GLU* 3.2 34.4 + - - +
732A ASN* 3.2 10.5 + - - -
733A GLU* 1.3 76.2 - - - +
735A GLN* 1.3 63.2 + - - +
737A GLU* 3.2 20.5 + - - +
738A TRP* 3.5 33.6 + - + +
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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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61A TYR* 3.7 26.7 - - - -
196A GLU* 3.7 17.2 + - - +
670A THR* 6.2 1.8 - - - +
673A LYS* 2.8 33.4 + - + +
730A THR 3.4 2.4 - - - +
731A PHE* 3.4 32.7 - - + -
732A ASN* 2.9 17.4 + - - +
734A THR* 1.3 73.4 - - - +
736A ILE* 1.3 64.2 + - - +
738A TRP* 3.0 51.2 + - + +
739A PHE 3.2 9.2 + - - -
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Residues in contact with ILE 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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705A PHE* 3.8 48.2 - - + +
706A ALA* 3.8 7.4 - - - +
707A PRO* 3.8 27.6 - - + -
731A PHE* 3.8 18.8 - - + -
732A ASN 3.1 12.7 + - - +
733A GLU* 3.3 15.0 + - - +
735A GLN* 1.3 74.7 - - - +
737A GLU* 1.3 62.3 + - - +
739A PHE* 3.2 5.5 + - - +
740A ARG* 2.9 56.7 + - + +
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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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733A GLU* 3.2 15.2 + - - +
734A THR* 3.2 14.6 + - - +
736A ILE* 1.3 76.3 - - - +
738A TRP* 1.3 58.4 + - - +
740A ARG* 2.6 41.4 + - - +
741A ALA* 3.0 26.5 + - - +
747A ARG* 3.5 50.2 + - + +
750A GLU* 4.8 1.2 - - - +
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Residues in contact with TRP 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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188A ASP* 5.0 1.6 - - - -
196A GLU* 5.1 6.5 - - + -
670A THR* 4.6 8.1 - - + -
673A LYS* 3.6 36.1 - - + +
674A LYS* 3.6 46.2 - - + +
676A GLY* 4.5 0.2 - - - -
734A THR* 3.5 33.8 + - + +
735A GLN* 3.0 38.4 + - + +
737A GLU* 1.3 72.7 - - - +
739A PHE* 1.3 63.6 + - - +
741A ALA 3.4 0.2 + - - -
742A GLY 3.1 4.0 + - - -
743A SER* 3.1 33.8 + - - +
744A ALA* 3.8 29.2 + - + +
747A ARG* 4.1 14.3 - - + +
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Residues in contact with PHE 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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547A TRP* 3.6 55.3 - + + +
552A LEU* 5.8 4.3 - - + -
657A ARG 5.8 1.1 - - - -
673A LYS 4.8 1.4 + - - -
676A GLY* 3.8 29.7 - - - +
677A LEU 4.7 1.1 - - - +
678A LEU* 3.8 28.7 - - + -
702A LEU* 4.2 24.7 - - + -
705A PHE* 3.8 21.3 - + + -
731A PHE* 4.2 14.4 - - + -
735A GLN 3.2 7.7 + - - +
736A ILE 3.2 7.6 + - - +
738A TRP* 1.3 79.1 - - - +
740A ARG* 1.3 69.9 + - + +
742A GLY* 3.2 12.3 + - - -
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Residues in contact with ARG 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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546A LYS* 3.9 4.0 - - - +
547A TRP* 3.0 59.3 + - + +
703A LYS 5.5 4.2 + - - -
705A PHE* 4.8 8.5 + - + +
733A GLU* 2.7 31.7 + - - -
736A ILE* 2.9 41.3 + - + +
737A GLU* 2.6 38.9 + - - +
739A PHE* 1.3 78.9 - - + +
741A ALA* 1.3 57.1 + - - +
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Residues in contact with ALA 741 (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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546A LYS* 2.9 25.8 - - - +
737A GLU* 3.0 17.7 + - - +
740A ARG* 1.3 76.5 - - - +
742A GLY* 1.3 54.8 + - - +
743A SER 3.4 17.5 - - - +
746A ASN* 2.9 17.7 + - - +
747A ARG* 3.8 18.8 - - + +
750A GLU* 3.6 20.9 - - - +
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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