Contacts of the helix formed by residues 737 - 742 (chain A) in PDB entry 1D0N
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 737 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A GLN* 2.9 17.1 + - - +
735A GLY 4.8 2.5 - - - +
736A TRP* 1.3 78.3 - - - +
738A ASP* 1.3 62.9 + - - +
739A SER* 3.6 16.6 + - - -
740A TYR* 2.9 49.8 + - + +
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Residues in contact with ASP 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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457A SER 5.3 1.7 - - - +
458A ARG* 2.5 44.2 + - - +
663A GLN* 5.0 0.4 - - - +
736A TRP* 4.0 7.7 + - - +
737A ASP* 1.3 75.3 + - - +
739A SER* 1.3 58.9 + - - +
740A TYR 3.0 4.6 + - - -
741A TRP* 4.0 15.2 + - - +
742A SER 5.0 0.7 + - - -
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Residues in contact with SER 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* 3.2 16.5 + - - -
738A ASP* 1.3 76.9 - - - +
740A TYR* 1.3 64.6 + - - +
741A TRP 3.1 2.5 - - - -
742A SER* 2.7 38.7 + - - -
743A VAL* 4.2 3.5 + - - +
748A ARG* 5.0 0.5 + - - -
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Residues in contact with TYR 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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211A LEU* 4.6 6.4 - - - +
663A GLN* 3.5 34.1 - - + +
664A GLU* 3.7 39.0 + - + +
666A LEU 5.9 0.4 - - - -
737A ASP* 2.9 30.3 + - + +
738A ASP 3.0 0.8 - - - -
739A SER* 1.3 77.9 - - - +
741A TRP* 1.3 89.6 + + + +
743A VAL 3.3 5.5 - - - +
745A PRO* 3.5 22.8 - - + +
748A ARG* 2.5 56.7 + - - +
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Residues in contact with TRP 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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663A GLN* 3.7 21.1 - - + -
666A LEU* 4.3 14.5 + - + -
668A THR* 3.7 25.7 - - + +
683A TRP* 3.8 20.0 - + - -
686A LYS* 5.9 1.0 + - - -
722A GLN* 4.0 24.9 - - + +
723A GLY* 4.0 14.6 - - - -
725A GLU* 3.2 28.9 - - - -
736A TRP* 3.6 27.8 - + - -
738A ASP* 4.0 13.2 + - - +
739A SER 3.1 0.6 - - - -
740A TYR* 1.3 99.7 - + - +
742A SER* 1.3 64.1 + - - +
743A VAL 3.0 9.1 + - - +
744A ASP* 5.4 0.2 - - - -
745A PRO* 4.9 10.3 - - + +
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Residues in contact with SER 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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738A ASP 5.0 0.6 + - - -
739A SER* 2.7 34.2 + - - +
741A TRP* 1.3 79.3 - - - +
743A VAL* 1.3 63.9 + - - +
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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