Contacts of the strand formed by residues 251 - 254 (chain E) in PDB entry 4O9U
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 VAL 251 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147E ALA* 3.9 11.2 - - + +
151E SER* 4.4 4.0 - - - +
155E PHE* 3.7 27.4 - - + -
168E ALA* 5.4 1.1 - - + -
169E LYS 3.3 3.1 + - - +
170E VAL* 3.3 18.2 - - + +
171E MET* 2.7 31.9 + - - -
249E MET* 4.5 0.5 - - - +
250E ASP* 1.3 88.5 - - + +
252E LEU* 1.3 62.2 + - - +
253E ILE* 3.7 24.9 - - + -
280E VAL* 3.0 25.4 - - + +
282E VAL* 3.9 11.2 - - + -
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Residues in contact with LEU 252 (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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171E MET* 3.3 45.5 - - + -
173E MET* 3.7 16.2 - - - -
246E VAL* 3.8 13.7 - - + -
249E MET* 3.7 20.9 - - + -
251E VAL* 1.3 73.6 - - - +
253E ILE* 1.3 58.7 + - - +
254E THR* 3.9 1.3 + - - +
267E LEU* 4.2 14.6 - - + -
275E LEU* 3.7 14.6 - - + -
279E THR* 3.5 29.2 - - + -
280E VAL 2.6 10.3 + - - +
281E VAL* 3.5 5.9 - - + +
282E VAL 2.7 33.0 + - - +
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Residues in contact with ILE 253 (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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143E ALA* 4.1 21.8 - - + +
144E ALA* 4.5 7.6 - - + -
147E ALA* 4.3 5.6 - - + -
155E PHE* 5.9 0.9 - - + -
170E VAL* 3.7 21.8 - - + -
171E MET 2.8 8.5 + - - +
172E VAL* 3.1 15.3 - - + +
173E MET 2.7 31.7 + - - -
182E ALA* 4.1 31.9 - - + +
186E ALA* 5.5 1.6 - - + -
251E VAL* 3.7 20.6 - - + -
252E LEU* 1.3 72.7 - - - +
254E THR* 1.3 56.0 + - - +
255E THR* 4.7 10.8 - - + -
282E VAL* 3.5 26.0 - - + -
284E LEU* 6.1 1.6 - - + +
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Residues in contact with THR 254 (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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173E MET* 3.5 36.3 - - + -
252E LEU 4.3 2.7 - - - +
253E ILE* 1.3 79.4 - - - +
255E THR* 1.3 62.7 + - - +
266E LEU* 5.1 1.3 - - + -
267E LEU* 4.3 17.3 - - + -
281E VAL* 5.3 1.6 - - + +
282E VAL 2.8 25.2 + - - +
283E ASP* 3.5 9.5 - - - +
284E LEU 3.2 22.2 + - - -
285E ALA 3.9 0.5 + - - -
291E ASN* 3.3 37.5 + - + +
292E CYS 4.9 0.5 + - - -
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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