Contacts of the helix formed by residues 741 - 748 (chain A) in PDB entry 2RD0
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 ARG 741 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.6 25.3 - - - +
16A MET 4.6 2.0 + - - -
18A PRO* 4.0 23.4 - - - +
38A ARG* 3.1 27.1 - - - +
39A GLU* 3.0 27.1 + - - -
737A GLU 3.6 10.7 + - - +
738A GLN* 2.8 41.9 + - - +
740A ARG* 1.3 80.1 - - - +
742A PRO* 1.3 72.9 - - + +
743A ASP* 3.1 17.7 + - - +
744A PHE* 3.2 3.8 + - - +
745A MET* 3.0 18.0 + - - +
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Residues in contact with PRO 742 (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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39A GLU* 4.1 25.6 - - + +
88A ARG* 3.3 24.0 - - - +
740A ARG 3.5 3.3 - - - +
741A ARG* 1.3 85.8 - - + +
743A ASP* 1.3 61.3 + - - +
745A MET* 3.7 9.4 - - + -
746A ASP* 3.1 33.2 + - - +
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Residues in contact with ASP 743 (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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38A ARG* 2.9 38.6 + - - -
39A GLU* 3.9 5.8 - - + +
88A ARG* 3.7 21.6 - - - +
90A CYS* 3.6 23.5 - - - -
91A ASP* 4.1 9.5 - - - +
711A LYS* 3.5 19.7 + - - -
741A ARG* 3.1 14.9 - - - +
742A PRO* 1.3 77.3 - - - +
744A PHE* 1.3 68.1 + - - -
746A ASP* 3.8 2.3 - - - +
747A ALA* 3.1 29.1 + - - +
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Residues in contact with PHE 744 (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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8A GLY 5.3 5.4 - - - -
15A LEU* 5.7 2.5 - - + -
38A ARG* 4.5 2.7 - - - -
711A LYS* 3.9 31.9 - - + -
712A LEU* 4.9 0.4 - - + -
715A LEU* 3.6 45.5 - - + -
738A GLN* 3.4 37.7 - - + +
739A MET* 3.8 20.4 - - + -
741A ARG 3.2 7.8 + - - +
743A ASP* 1.3 97.4 - - - +
745A MET* 1.3 68.0 + - - +
746A ASP 3.1 0.2 - - - -
747A ALA* 4.5 0.2 - - - -
748A LEU* 2.9 60.9 + - + +
764A LEU* 5.7 0.2 - - - -
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Residues in contact with MET 745 (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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739A MET 3.0 27.6 - - - +
740A ARG* 3.5 15.5 - - - +
741A ARG 3.0 13.2 + - - +
742A PRO* 3.8 9.4 - - + +
743A ASP 3.3 0.2 - - - -
744A PHE* 1.3 80.6 - - - +
746A ASP* 1.3 64.1 + - - +
749A GLN* 2.7 64.8 + - - +
764A LEU* 3.5 26.9 - - + +
766A LEU* 4.4 12.6 - - + -
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Residues in contact with ASP 746 (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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88A ARG* 2.8 26.7 + - - +
742A PRO* 3.1 20.8 + - - +
743A ASP* 3.8 3.8 - - - +
745A MET* 1.3 83.0 - - - +
747A ALA* 1.3 64.1 + - - +
748A LEU 3.5 0.3 + - - -
749A GLN* 3.9 6.5 + - - +
750A GLY 4.5 6.2 + - - -
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Residues in contact with ALA 747 (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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91A ASP* 5.8 1.3 - - - +
704A ARG* 4.3 5.0 - - - +
707A GLU* 4.8 15.4 - - + +
708A ALA* 3.6 25.0 + - - +
711A LYS* 3.8 30.5 - - + -
743A ASP 3.1 17.7 + - - +
744A PHE* 3.2 3.5 + - - +
746A ASP* 1.3 75.9 - - - +
748A LEU* 1.3 62.0 + - + +
749A GLN 3.5 2.5 + - - -
750A GLY 5.2 0.3 + - - -
751A PHE* 4.0 5.2 - - - +
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Residues in contact with LEU 748 (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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708A ALA* 3.8 24.9 - - + +
711A LYS* 4.3 5.8 - - + -
712A LEU* 3.7 34.3 - - + -
739A MET* 5.1 6.3 - - + -
744A PHE* 2.9 50.5 + - + +
747A ALA* 1.3 80.7 - - + +
749A GLN* 1.3 60.6 + - - +
751A PHE* 3.6 5.8 - - + -
764A LEU* 3.7 13.9 - - + +
781A LEU* 5.3 0.9 - - + -
783A TRP* 2.4 57.4 - - + -
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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