Contacts of the helix formed by residues 3347 - 3354 (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 ASP3347 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3343D ILE* 3.0 17.4 + - - +
3346D GLU* 1.3 82.8 - - - +
3348D TYR* 1.3 74.8 + - - +
3349D VAL 3.4 0.7 - - - -
3350D GLN* 2.4 24.1 + - - +
3351D HIS* 3.0 4.5 + - - -
3563D SER* 3.4 13.6 - - - -
3564D ILE* 2.7 41.8 + - - +
3580D PHE* 3.6 16.6 - - + -
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Residues in contact with TYR3348 (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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3198D PHE* 4.1 19.1 - + - -
3201D PHE* 3.2 28.7 - + + -
3202D ALA* 2.9 49.4 - - + +
3205D PHE* 4.8 4.9 - + - -
3206D THR* 4.1 5.7 - - - +
3343D ILE 3.9 0.2 - - - +
3344D VAL* 3.3 22.2 + - + +
3347D ASP* 1.3 86.2 - - - +
3349D VAL* 1.3 78.8 + - + +
3350D GLN 2.9 0.2 + - - -
3351D HIS* 3.0 3.8 + - - +
3352D LEU* 3.0 36.1 + - + +
3387D TRP* 3.5 12.0 - - - -
3580D PHE* 3.3 22.9 - + + -
3701D PGX 2.8 40.0 - - - +
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Residues in contact with VAL3349 (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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3344D VAL* 2.9 27.2 + - + +
3345D ILE* 3.4 15.0 - - + +
3348D TYR* 1.3 82.0 - - - +
3350D GLN* 1.3 65.8 + - - +
3352D LEU* 3.3 6.8 + - - +
3353D SER* 3.1 18.2 + - - -
3359D LEU* 3.7 19.7 - - + -
3530D SER* 4.8 6.3 - - - +
3531D LEU* 5.3 10.3 - - + -
3534D LEU* 4.8 1.6 - - + -
3701D PGX 3.3 43.7 - - + +
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Residues in contact with GLN3350 (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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3345D ILE 3.3 6.3 + - - +
3346D GLU* 2.9 29.8 + - - +
3347D ASP* 2.4 17.7 + - - +
3349D VAL* 1.3 70.8 - - - +
3351D HIS* 1.3 67.0 + - + +
3353D SER* 2.8 32.1 + - - -
3354D GLY* 3.1 3.3 + - - -
3355D TYR 3.7 11.5 - - - +
3356D HIS 5.5 0.2 - - - -
3357D PHE 3.2 12.4 + - - +
3358D LYS* 3.0 27.3 - - + +
3359D LEU* 2.9 38.8 + - + +
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Residues in contact with HIS3351 (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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3192D GLN* 3.6 36.4 + - + +
3194D SER* 3.0 27.5 + - - -
3198D PHE* 3.6 24.5 - + - -
3347D ASP 3.0 5.1 + - - +
3348D TYR 3.0 6.4 + - - +
3350D GLN* 1.3 80.5 - - + +
3352D LEU* 1.3 75.2 + - + +
3353D SER 2.6 12.6 + - - -
3354D GLY* 2.6 18.3 + - - +
3580D PHE* 3.4 34.0 + - + -
3581D ASN* 3.7 18.1 + - + +
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Residues in contact with LEU3352 (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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3192D GLN* 4.0 14.8 - - - +
3194D SER* 5.1 1.3 - - - +
3198D PHE* 3.2 26.0 - - + -
3348D TYR* 3.0 34.2 + - + +
3349D VAL* 3.5 11.0 - - - +
3351D HIS* 1.3 83.7 - - + +
3353D SER* 1.3 57.1 + - - +
3387D TRP* 3.4 28.3 - - + -
3517D ILE* 4.3 11.0 - - + -
3518D PHE* 3.4 32.8 - - + -
3523D VAL* 5.5 1.6 - - - +
3701D PGX 3.5 28.5 - - + +
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Residues in contact with SER3353 (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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3090D HIS* 4.1 6.4 - - - -
3094D THR* 3.9 4.5 - - - +
3192D GLN* 4.6 2.9 - - - +
3349D VAL 3.1 7.1 + - - -
3350D GLN* 2.8 15.2 + - - -
3351D HIS 2.6 5.7 + - - -
3352D LEU* 1.3 75.8 - - - +
3354D GLY* 1.3 61.1 + - - +
3355D TYR* 2.8 56.2 + - - +
3359D LEU* 5.0 3.9 - - - +
3523D VAL* 6.3 0.7 - - - -
3701D PGX 2.9 26.2 - - - -
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Residues in contact with GLY3354 (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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3094D THR* 3.1 17.7 - - - +
3192D GLN* 4.2 10.1 - - - -
3350D GLN 3.1 3.1 + - - -
3351D HIS* 2.6 22.0 + - - -
3353D SER* 1.3 71.5 + - - +
3355D TYR* 1.3 65.8 + - - +
3356D HIS* 3.8 4.9 + - - -
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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