Contacts of the strand formed by residues 233 - 237 (chain D) in PDB entry 5DO7
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 ILE 233 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASN* 3.7 27.5 - - + +
35D SER 4.6 3.1 - - - +
36D LEU* 5.4 5.8 - - + -
134D ILE* 3.8 20.2 - - + -
135D ASN* 4.5 0.7 - - - +
147D CYS* 4.3 5.9 + - + +
148D VAL* 3.6 46.2 - - + -
149D ALA 3.9 5.6 + - - -
231D PRO* 3.5 24.7 - - - +
232D GLY* 1.3 82.7 - - - +
234D LEU* 1.3 76.6 + - - +
235D ILE* 4.3 9.9 - - + -
264D LEU* 3.4 31.2 - - + -
266D LEU* 5.5 0.9 - - + -
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D ALA* 3.5 31.4 - - + +
151D VAL* 4.9 4.9 - - + -
223D ILE* 5.0 3.1 - - + -
226D GLN* 4.8 6.1 - - + -
227D LEU* 3.9 22.7 - - + -
231D PRO* 4.2 2.5 - - + +
233D ILE* 1.3 81.0 - - - +
235D ILE* 1.3 65.5 + - - +
236D LEU* 4.2 26.9 - - + -
255D LEU* 5.0 0.2 - - + -
258D LEU* 3.8 31.4 - - + -
263D ARG* 5.2 6.7 - - + -
264D LEU 2.8 14.4 + - - +
265D VAL* 3.4 12.9 - - + +
266D LEU 2.8 26.2 + - - +
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Residues in contact with ILE 235 (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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36D LEU* 5.9 2.2 - - + -
115D LEU* 3.8 34.3 - - + +
118D ILE* 4.7 20.4 - - + -
119D THR* 5.4 4.9 - - - -
148D VAL* 3.7 24.9 - - + -
149D ALA 2.8 12.7 + - - +
150D HIS* 3.5 28.5 + - + +
151D VAL* 2.8 28.9 + - - +
233D ILE* 4.3 6.7 - - + -
234D LEU* 1.3 79.3 - - - +
236D LEU* 1.3 64.2 + - - +
266D LEU* 3.6 22.0 - - + -
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Residues in contact with LEU 236 (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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115D LEU* 3.6 6.0 - - - +
151D VAL* 3.3 39.9 - - + +
223D ILE* 4.5 11.0 - - + -
234D LEU* 4.2 17.3 - - + -
235D ILE* 1.3 75.9 - - - +
237D ASP* 1.3 61.1 + - - +
238D GLU 3.4 5.6 + - - -
239D PRO* 3.8 17.1 - - + +
255D LEU* 3.2 45.1 - - + -
265D VAL* 4.2 17.3 - - + -
266D LEU 2.8 13.2 + - - +
267D ILE* 3.6 7.0 - - + -
268D SER 3.5 17.5 + - - -
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Residues in contact with ASP 237 (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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112D ALA* 3.4 26.2 - - - +
115D LEU* 3.6 17.6 - - + +
116D ASP* 3.2 23.2 - - - +
150D HIS* 4.2 6.3 + - - +
151D VAL* 2.8 17.9 + - - +
152D ARG* 3.9 19.6 + - - +
153D GLN* 3.1 30.7 + - + +
235D ILE 4.2 0.2 - - - -
236D LEU* 1.3 70.1 - - - +
238D GLU* 1.3 72.0 + - - +
239D PRO* 3.3 3.3 - - - +
268D SER* 3.4 12.1 + - - -
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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