Contacts of the strand formed by residues 226 - 229 (chain E) in PDB entry 1PPF
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 ASP 226 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160E VAL* 5.8 1.6 - - - +
181E VAL 3.7 0.3 - - - +
182E CYS* 3.1 7.0 - - - -
183E THR* 2.7 47.5 + - - +
184E LEU* 6.0 0.2 - - - -
188E ALA 5.3 1.0 - - - +
189E GLY* 3.3 11.7 - - - -
190E VAL* 2.9 52.2 + - + +
215E PHE 4.0 4.3 - - - +
216E VAL* 3.6 16.2 - - - +
220E ALA* 5.1 5.4 + - - -
224E TYR 4.5 4.5 - - - +
225E PRO* 1.4 74.8 - - - +
227E ALA* 1.3 60.8 + - - +
228E PHE* 3.8 7.3 - - + -
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Residues in contact with ALA 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E ASN* 4.1 10.5 - - + -
181E VAL 3.6 4.3 - - - -
182E CYS* 4.3 7.9 - - - -
190E VAL* 5.6 0.2 - - - +
213E ALA* 4.1 0.9 - - - +
214E SER* 3.0 20.9 + - - -
215E PHE* 3.0 61.6 + - + +
217E ARG* 4.7 3.1 - - - +
225E PRO 3.7 0.8 + - - -
226E ASP* 1.3 73.6 - - - +
228E PHE* 1.3 63.8 + - - +
18I LEU* 5.2 1.2 - - - +
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Residues in contact with PHE 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E ALA* 4.4 7.4 - - + -
180E ASN* 2.9 19.6 + - - -
181E VAL* 2.8 39.4 + - + +
183E THR* 3.3 34.5 - - + -
190E VAL* 3.9 22.0 - - + -
197E SER 4.3 4.3 - - - -
198E PRO 4.7 2.7 - - - -
199E LEU* 3.6 37.0 - - + -
211E GLY* 3.7 15.3 - - - -
212E ILE 3.1 7.9 - - - +
213E ALA* 3.2 36.3 - - + -
214E SER* 4.0 1.3 - - - +
226E ASP* 3.8 15.7 - - + -
227E ALA* 1.3 76.8 - - - +
229E ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E ASP* 3.5 38.6 - - + +
103E ILE* 5.0 2.7 - - + -
180E ASN* 4.1 3.8 - - - +
211E GLY* 3.0 9.2 - - - -
212E ILE* 2.7 47.6 + - + +
214E SER* 3.9 4.3 - - - -
228E PHE* 1.3 72.0 - - - +
230E PRO* 1.4 66.9 - - + +
231E VAL* 3.3 4.4 + - - +
234E PHE* 5.2 3.1 - - + -
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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