Contacts of the strand formed by residues 278 - 281 (chain E) in PDB entry 5ITX
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 THR 278 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ASN* 3.0 32.2 + - - +
179E ARG* 3.5 0.9 - - - -
270E SER* 3.7 17.0 - - - +
271E LEU 3.2 10.3 - - - +
272E GLN* 3.6 13.6 + - - +
276E GLY 3.8 1.5 + - - -
277E ARG* 1.3 70.2 - - - +
279E ILE* 1.3 69.1 + - - +
280E TRP* 3.4 30.7 - - + +
296F A 3.5 28.6 + - - +
297F CTG 5.4 0.2 - - - -
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Residues in contact with ILE 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E CYS* 3.8 16.6 - - + -
176E ASN 5.9 0.2 - - - -
179E ARG* 3.4 44.6 - - + +
180E ALA* 4.4 3.1 - - + -
183E LEU* 4.3 6.7 - - + -
190E PRO* 4.0 17.5 - - + -
191E PHE* 4.3 17.3 - - + -
270E SER* 3.1 29.6 - - - -
271E LEU* 3.0 31.6 + - + +
272E GLN 5.5 0.4 - - - -
273E ASP* 5.8 0.9 - - + +
277E ARG 3.4 2.3 + - - +
278E THR* 1.3 70.5 - - - +
280E TRP* 1.3 88.0 + - - +
281E PHE* 4.0 14.1 - - + -
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Residues in contact with TRP 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E ASN 5.7 0.2 - - - -
180E ALA* 3.5 26.1 - - + +
183E LEU* 5.4 1.4 - - - +
262E CYS* 3.7 11.9 - - - -
263E TYR* 2.9 53.1 - + - -
264E GLY* 3.6 27.8 - - - -
265E MET 4.5 3.6 - - - -
266E PRO 5.9 0.2 - - - -
268E MET* 3.7 26.0 - - + -
269E SER 2.9 26.2 - - - -
270E SER* 3.8 15.9 - - - -
278E THR* 3.4 23.4 - - + +
279E ILE* 1.3 84.8 - - - +
281E PHE* 1.3 65.3 + - - +
296F A 5.1 5.6 + - - -
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Residues in contact with PHE 281 (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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183E LEU* 5.9 4.0 - - + -
184E TYR* 5.2 5.4 - - - +
188E ILE 5.4 1.8 - - - +
190E PRO* 3.6 28.3 - - + -
262E CYS* 3.8 6.8 - - - -
268E MET* 3.5 10.3 - - - +
269E SER* 3.3 56.5 + - - -
270E SER* 3.8 14.4 - - - -
271E LEU* 3.6 25.6 - - + -
279E ILE* 4.0 18.4 - - + -
280E TRP* 1.3 83.1 - - - +
282E GLN* 1.3 64.4 + - - +
283E GLY 4.0 6.5 - - - -
284E ASP 3.5 17.3 - - - -
285E PRO* 3.6 27.1 - - + -
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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