Contacts of the helix formed by residues 239 - 247 (chain D) in PDB entry 5U07
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 LEU 239 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D THR* 3.0 25.6 + - + +
4D VAL* 3.6 31.2 - - + +
237D VAL* 3.3 22.2 - - + +
238D ASN* 1.3 70.8 - - - +
240D ASP* 1.3 59.9 + - - +
242D LEU* 2.9 10.8 + - + +
243D VAL* 2.8 35.2 + - + +
252D ALA* 6.4 0.4 - - + -
256D VAL* 4.4 19.5 - - + -
367D ALA* 3.4 34.1 - - + +
368D PHE* 4.0 22.2 - - + -
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Residues in contact with ASP 240 (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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2D THR* 2.7 41.5 + - - -
3D PHE* 4.9 2.1 - - - -
238D ASN* 3.2 7.5 + - - +
239D LEU* 1.3 75.4 - - - +
241D ARG* 1.3 83.3 + - - +
243D VAL* 3.2 7.6 + - - +
244D GLU* 2.9 28.4 + - + +
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Residues in contact with ARG 241 (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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3D PHE* 6.2 0.4 - - - -
185D ALA* 3.9 18.2 - - + -
238D ASN* 3.2 24.3 + - + +
239D LEU 3.4 0.2 - - - -
240D ASP* 1.3 93.5 + - - +
242D LEU* 1.3 57.4 + - - +
244D GLU* 3.5 30.7 + - - -
245D ASN* 2.9 46.5 + - - +
132N PRO 5.1 0.4 + - - -
133N TYR* 2.9 75.4 + - - +
134N TRP* 3.4 21.4 - - + +
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Residues in contact with LEU 242 (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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165D VAL* 5.3 1.1 - - + -
168D ASN* 3.7 20.6 - - - +
169D LEU* 3.8 42.2 - - + +
184D GLY 5.1 2.2 - - - +
185D ALA* 4.9 3.3 - - + +
237D VAL* 4.5 6.3 - - + -
238D ASN 3.3 10.5 + - - +
239D LEU* 2.9 13.3 + - + +
241D ARG* 1.3 80.5 - - - +
243D VAL* 1.3 54.0 + - + +
246D THR* 2.4 54.2 + - + +
252D ALA* 4.9 10.1 - - + -
255D ALA* 4.5 9.9 - - + -
256D VAL* 3.7 29.6 - - + -
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Residues in contact with VAL 243 (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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239D LEU* 2.8 19.2 + - + +
240D ASP* 3.7 8.3 - - - +
242D LEU* 1.3 74.0 - - + +
244D GLU* 1.3 66.0 + - + +
246D THR* 3.8 4.7 - - - -
247D GLY* 3.0 33.1 + - - +
248D ASP 5.8 0.4 - - - -
249D ALA* 5.5 7.9 - - + -
252D ALA* 4.4 9.4 - - + -
368D PHE* 3.9 34.1 - - + -
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Residues in contact with GLU 244 (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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240D ASP* 2.9 16.4 + - + +
241D ARG* 3.5 39.0 + - - +
243D VAL* 1.3 78.8 - - + +
245D ASN* 1.3 67.3 + - - +
247D GLY* 4.5 2.6 + - - -
46N ARG* 5.3 4.0 + - - -
133N TYR* 4.2 11.8 + - - -
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Residues in contact with ASN 245 (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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168D ASN* 3.0 35.0 + - - +
181D GLU* 4.1 25.0 + - + +
185D ALA* 5.8 2.0 - - - +
241D ARG* 2.9 31.2 + - - +
244D GLU* 1.3 88.1 - - - +
246D THR* 1.3 63.3 + - - +
247D GLY 3.6 0.2 + - - -
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Residues in contact with THR 246 (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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164D ASN 6.0 0.2 - - - -
165D VAL* 4.1 20.9 - - + -
168D ASN* 3.2 27.8 - - + +
242D LEU* 2.4 42.9 + - + +
243D VAL* 3.8 4.3 - - - -
245D ASN* 1.3 73.8 - - - +
247D GLY* 1.3 60.8 + - - +
248D ASP* 3.3 10.3 + - - +
251D THR* 3.7 21.6 + - - +
252D ALA* 4.5 6.2 - - - +
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Residues in contact with GLY 247 (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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243D VAL* 3.0 28.1 + - - +
244D GLU 4.5 2.2 - - - -
245D ASN 3.4 2.0 - - - -
246D THR* 1.3 76.1 + - - +
248D ASP* 1.3 63.8 + - - -
249D ALA* 3.4 3.3 + - - +
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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