Contacts of the helix formed by residues 925 - 930 (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 GLN 925 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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902A GLN* 5.5 4.9 + - - -
916A GLU* 3.3 25.6 - - + +
923A ARG 5.6 1.6 - - - +
924A LEU* 1.3 77.2 - - - +
926A LEU* 1.3 58.7 + - - +
927A LYS* 3.1 35.3 - - + +
928A ASP* 2.7 38.8 + - - +
929A ILE* 3.1 12.1 + - - +
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Residues in contact with LEU 926 (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* 3.7 24.0 - - + -
813A PHE* 3.5 48.7 - - + -
831A ILE* 4.6 9.0 - - + -
832A PHE* 4.5 8.7 - - + -
898A ILE* 3.7 33.0 - - + -
908A PHE* 4.9 3.1 - - + -
912A VAL* 4.6 14.1 - - + -
916A GLU* 2.9 19.1 + - - +
925A GLN* 1.3 68.0 - - - +
927A LYS* 1.3 63.6 - - - +
929A ILE* 3.0 16.2 + - - +
930A ILE* 3.2 27.0 + - + +
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Residues in contact with LYS 927 (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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895A LEU* 3.7 36.1 - - + +
898A ILE* 4.9 8.8 - - + +
899A LYS* 6.3 3.6 - - + -
925A GLN* 3.1 34.0 - - + +
926A LEU* 1.3 79.4 - - - +
928A ASP* 1.3 83.6 + - - +
931A PRO* 3.0 24.1 - - - +
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Residues in contact with ASP 928 (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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924A LEU* 3.8 31.5 - - + +
925A GLN* 2.7 40.5 + - - +
927A LYS* 1.3 96.2 + - - +
929A ILE* 1.3 60.6 + - - +
931A PRO* 3.5 11.9 - - - +
932A THR* 4.4 6.6 - - - +
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Residues in contact with ILE 929 (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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805A THR* 4.5 18.6 - - + +
808A VAL* 4.4 10.3 - - + -
809A LEU* 3.7 28.8 - - + +
813A PHE* 4.1 25.4 - - + -
921A CYS* 4.1 22.0 - - + +
924A LEU* 4.2 20.2 - - + +
925A GLN 3.4 15.0 - - - +
926A LEU 3.0 5.7 + - - +
928A ASP* 1.3 75.8 - - - +
930A ILE* 1.3 64.0 + - - +
931A PRO* 3.2 2.9 - - - -
932A THR* 2.7 38.5 + - + +
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Residues in contact with ILE 930 (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* 4.0 25.0 - - + +
831A ILE* 4.6 14.1 - - + +
832A PHE* 5.4 4.9 - - + -
887A PHE* 3.5 35.9 - - + -
891A GLN* 4.1 27.2 - - + +
894A ALA* 5.2 4.3 - - + -
895A LEU* 4.2 9.2 - - + -
898A ILE* 3.9 26.2 - - + -
926A LEU* 3.2 25.8 + - + +
927A LYS 4.5 0.9 - - - +
929A ILE* 1.3 74.3 - - - +
931A PRO* 1.3 68.4 - - + +
932A THR* 2.9 7.8 + - - -
933A GLN* 3.5 4.3 + - - +
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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