Contacts of the helix formed by residues 3265 - 3270 (chain D) in PDB entry 1DDX
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 THR3265 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A PHE* 4.0 21.0 - - + -
3255D GLN* 4.1 21.3 - - + +
3264D PRO* 1.3 75.4 - - + +
3266D VAL* 1.3 61.9 + - - +
3267D LYS* 2.7 19.8 + - - +
3268D ASP* 2.7 41.9 + - - +
3269D THR* 3.3 20.1 + - - +
3281D GLU 4.1 12.6 - - - +
3282D ASN* 5.5 2.7 - - - +
3284D GLN 3.3 10.8 - - - -
3285D PHE* 5.9 0.2 - - - -
3286D ALA* 4.0 1.1 - - - -
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Residues in contact with VAL3266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3265D THR* 1.3 73.8 + - - +
3267D LYS* 1.3 56.4 + - - +
3268D ASP 3.1 0.7 - - - -
3269D THR* 4.1 6.1 - - - -
3270D GLN* 2.7 33.1 + - - -
3271D VAL 3.3 19.3 - - - +
3273D MET* 3.6 38.1 - - + +
3275D TYR* 4.4 0.2 - - + -
3284D GLN* 3.0 44.7 + - + +
3285D PHE 3.7 3.6 - - - +
3286D ALA* 4.2 1.8 - - + -
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Residues in contact with LYS3267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A ASP* 6.1 1.8 - - - -
563A SER* 6.2 0.7 - - - -
564A ILE* 5.2 5.0 - - - +
565A GLN* 4.2 15.8 - - - +
577A PHE* 3.6 16.2 - - + -
578A THR 2.7 26.6 + - - -
579A SER* 2.8 29.9 + - - +
3265D THR* 2.7 7.7 + - - +
3266D VAL* 1.3 80.0 - - - +
3268D ASP* 1.3 69.8 + - - +
3270D GLN* 3.3 19.4 + - - +
3281D GLU* 3.7 32.4 + - + +
3284D GLN* 5.6 0.4 - - - +
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Residues in contact with ASP3268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565A GLN* 3.1 45.1 + - + +
569A CYS* 5.1 8.8 - - - -
575A CYS 5.5 1.6 - - - +
577A PHE* 5.0 1.0 - - - -
3253D LYS* 3.6 15.9 + - + +
3264D PRO* 5.6 2.3 - - + +
3265D THR* 2.7 40.1 + - - +
3266D VAL 3.1 0.2 - - - -
3267D LYS* 1.3 90.8 - - - +
3269D THR* 1.3 62.3 + - + +
3270D GLN* 3.2 8.8 - - - +
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Residues in contact with THR3269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3243D LYS* 3.3 37.3 - - - +
3244D LEU* 5.5 1.1 - - - -
3253D LYS* 4.0 14.6 - - + +
3264D PRO* 4.2 24.2 - - + -
3265D THR 3.3 18.2 + - - +
3266D VAL* 4.1 0.3 - - - -
3268D ASP* 1.3 83.0 - - + +
3270D GLN* 1.3 65.4 + - - +
3271D VAL* 2.7 43.7 + - + +
3286D ALA* 3.5 5.0 - - + +
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Residues in contact with GLN3270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A LYS* 5.0 12.4 - - - +
3243D LYS* 4.0 20.3 + - - +
3266D VAL* 2.7 16.8 + - - -
3267D LYS* 3.3 22.6 + - - +
3268D ASP 3.2 6.8 - - - +
3269D THR* 1.3 87.2 + - - +
3271D VAL* 1.3 67.6 + - - +
3272D GLU* 3.6 8.3 + - - +
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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