Contacts of the helix formed by residues 3237 - 3244 (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 THR3237 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2671C NAG 5.6 2.7 - - - -
3235D GLY 4.2 0.7 - - - -
3236D GLU* 1.3 86.0 - - + +
3238D LEU* 1.3 59.1 + - - +
3239D ASP* 3.9 10.1 + - - +
3240D ARG* 3.3 23.8 + - - +
3241D GLN* 2.9 26.9 + - - +
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Residues in contact with LEU3238 (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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2134C TYR* 5.9 0.2 - - - +
2140C GLU* 3.5 39.0 - - + +
2671C NAG 4.0 49.9 + - - +
3236D GLU 4.0 1.2 + - - -
3237D THR* 1.3 69.2 - - - +
3239D ASP* 1.3 69.0 + - - +
3241D GLN* 2.9 20.9 + - + +
3242D HIS* 2.7 67.4 + - + +
3326D GLU* 5.4 2.7 - - - +
3330D GLN* 5.9 0.7 - - - +
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Residues in contact with ASP3239 (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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3237D THR* 3.9 10.5 - - - +
3238D LEU* 1.3 79.9 - - - +
3240D ARG* 1.3 66.3 + - - +
3242D HIS* 3.3 9.5 + - - +
3243D LYS* 3.1 40.9 + - + +
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Residues in contact with ARG3240 (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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3235D GLY* 3.3 22.4 - - - -
3236D GLU 4.2 4.0 - - - +
3237D THR* 3.2 21.0 + - - +
3238D LEU 3.1 0.2 - - - -
3239D ASP* 1.3 79.2 - - - +
3241D GLN* 1.3 54.9 + - - +
3243D LYS* 2.7 37.9 + - - +
3244D LEU* 3.1 18.6 + - + +
3271D VAL* 3.2 17.7 - - + +
3272D GLU* 2.7 53.7 + - - +
3273D MET* 3.5 7.5 - - - -
3287D VAL 2.8 24.0 + - - -
3288D GLY* 3.0 16.8 + - - -
3290D GLU* 3.6 18.4 + - - +
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Residues in contact with GLN3241 (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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2140C GLU* 5.5 2.6 + - - +
3234D TYR* 3.1 23.8 + - + +
3235D GLY 5.1 0.4 - - - +
3237D THR 2.9 9.4 + - - +
3238D LEU* 2.9 27.1 + - + +
3240D ARG* 1.3 79.9 - - - +
3242D HIS* 1.3 73.3 + - - +
3244D LEU* 3.0 7.7 + - - +
3245D ARG* 2.9 47.3 + - - +
3252D LEU* 5.2 0.3 - - - +
3329D PHE* 2.7 45.4 - - - -
3330D GLN* 4.7 4.0 + - - +
3333D ARG* 3.7 17.4 - - - +
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Residues in contact with HIS3242 (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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3238D LEU* 2.7 57.8 + - + +
3239D ASP* 3.7 7.6 - - - +
3241D GLN* 1.3 78.1 + - - +
3243D LYS* 1.3 59.0 + - + +
3245D ARG* 3.1 44.7 + - - +
3247D PHE* 3.1 38.1 - + + -
3253D LYS* 5.0 0.3 - - - -
3326D GLU* 4.3 6.5 - - + -
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Residues in contact with LYS3243 (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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3239D ASP* 3.1 33.9 + - - +
3240D ARG* 2.7 19.2 + - - +
3242D HIS* 1.3 69.6 - - + +
3244D LEU* 1.3 58.7 + - - +
3245D ARG 3.1 4.9 - - - -
3253D LYS* 2.9 31.0 - - - +
3269D THR* 3.3 39.1 - - - +
3270D GLN* 4.0 23.7 + - - +
3271D VAL* 3.6 14.7 - - + +
3272D GLU* 5.7 3.0 - - - +
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Residues in contact with LEU3244 (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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3233D ILE 3.6 6.1 - - - +
3234D TYR 3.6 21.5 - - - +
3235D GLY 3.8 0.7 - - - +
3240D ARG* 3.1 19.0 + - + +
3241D GLN 3.0 8.1 + - - +
3243D LYS* 1.3 74.7 - - - +
3245D ARG* 1.3 58.4 + - - +
3252D LEU* 2.9 27.9 - - + +
3253D LYS* 2.9 26.0 + - - +
3264D PRO* 5.8 3.8 - - + -
3269D THR* 5.0 2.2 - - + +
3271D VAL* 3.3 34.8 - - + -
3286D ALA* 4.2 7.4 - - + +
3287D VAL* 3.9 16.2 - - - +
3288D GLY* 3.5 32.8 - - - +
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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