Contacts of the helix formed by residues 813 - 821 (chain A) in PDB entry 1TXD
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 PHE 813 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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808A VAL* 4.0 5.2 - - + -
809A LEU* 3.2 18.1 + - - +
812A VAL* 1.4 84.3 - - + +
814A TYR* 1.3 64.7 + - - +
815A GLN 3.5 1.1 - - - -
816A ARG 4.2 0.4 - - - -
817A VAL* 3.0 24.3 + - - +
832A PHE* 4.0 18.8 - - + -
911A PHE* 3.4 17.2 - + + -
912A VAL* 4.5 4.9 - - + -
915A ALA* 3.6 24.5 - - + -
916A GLU* 3.9 22.4 - - + -
921A CYS* 3.7 31.9 - - - -
926A LEU* 3.5 44.4 - - + -
929A ILE* 4.1 12.3 - - + -
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Residues in contact with TYR 814 (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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809A LEU 3.0 15.4 + - - +
810A ASP* 3.7 9.0 - - - +
813A PHE* 1.3 72.4 - - - +
815A GLN* 1.3 96.0 + - - +
817A VAL* 3.4 1.6 - - - +
818A SER* 3.0 40.0 + - - -
828A LEU* 4.1 26.0 - - + +
832A PHE* 3.4 43.1 - + + -
833A SER 6.0 0.9 - - - -
835A LEU* 4.0 18.4 - - + -
836A GLU* 5.0 11.8 + - + -
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Residues in contact with GLN 815 (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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810A ASP* 2.8 41.0 + - - +
811A GLN* 3.4 31.0 - - - +
814A TYR* 1.3 100.2 - - - +
816A ARG* 1.3 63.2 + - - +
818A SER* 3.4 4.3 + - - -
819A ARG* 3.0 44.2 + - - +
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Residues in contact with ARG 816 (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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811A GLN 3.5 20.0 + - - +
812A VAL* 3.5 15.1 + - - +
813A PHE 3.7 0.4 + - - -
814A TYR 3.4 0.4 - - - -
815A GLN* 1.3 77.3 - - - +
817A VAL* 1.3 56.7 + - - +
819A ARG* 3.1 35.1 + - - +
820A GLU* 3.0 41.7 + - - +
911A PHE* 3.5 20.6 - - + -
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Residues in contact with VAL 817 (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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813A PHE 3.0 16.8 + - - +
814A TYR 3.4 10.5 - - - +
816A ARG* 1.3 72.9 - - - +
818A SER* 1.3 68.0 + - - +
820A GLU* 3.2 2.9 + - - +
821A GLY* 3.1 18.2 + - - -
822A ILE* 3.8 19.5 + - + -
823A LEU* 4.0 24.7 + - + -
828A LEU* 4.0 13.4 - - + +
832A PHE* 3.9 24.2 - - + -
908A PHE* 4.3 6.1 - - + -
911A PHE* 3.5 31.8 - - + -
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Residues in contact with SER 818 (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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814A TYR* 3.0 37.3 + - - -
815A GLN* 3.6 4.9 - - - -
817A VAL* 1.3 82.6 - - - +
819A ARG* 1.3 65.4 + - - +
821A GLY* 3.2 14.3 + - - -
828A LEU* 4.5 18.9 - - - +
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Residues in contact with ARG 819 (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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811A GLN* 5.6 2.2 + - - -
815A GLN* 3.0 37.9 + - - +
816A ARG* 3.1 49.7 + - - +
818A SER* 1.3 78.6 - - - +
820A GLU* 1.3 60.6 + - + +
821A GLY* 3.4 0.7 + - - -
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Residues in contact with GLU 820 (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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816A ARG* 3.0 27.5 + - - +
817A VAL* 3.2 5.3 + - - +
819A ARG* 1.3 78.0 - - + +
821A GLY* 1.3 63.8 + - - +
822A ILE* 3.4 24.7 + - + +
907A ARG* 4.4 7.9 + - - +
911A PHE* 3.3 35.5 - - - +
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Residues in contact with GLY 821 (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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817A VAL 3.1 6.4 + - - -
818A SER* 3.2 12.8 + - - -
819A ARG 3.2 0.8 - - - -
820A GLU* 1.3 79.5 - - - +
822A ILE* 1.3 62.7 + - - +
823A LEU 3.4 11.6 + - - +
907A ARG* 4.9 3.1 + - - -
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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