Contacts of the strand formed by residues 225 - 230 (chain E) in PDB entry 5IJ7
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 225 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E ASN* 2.8 22.5 + - - -
195E VAL* 3.3 29.6 - - + +
196E SER 3.0 13.4 + - - +
199E HIS 3.3 34.5 - - - +
200E ALA 3.9 6.3 - - - +
201E LEU* 4.0 12.8 - - + -
221E HIS* 3.7 30.5 - - + +
224E GLU* 1.4 70.4 - - - +
226E LEU* 1.3 59.0 + - - +
227E SER 4.1 6.7 - - - +
239E SER* 4.1 2.7 - - - -
240E CYS 3.4 15.5 - - - +
241E GLY* 4.3 1.1 - - - -
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Residues in contact with LEU 226 (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* 3.6 16.0 - - - +
181E GLU* 4.1 1.4 - - - +
195E VAL* 4.0 3.6 - - - -
224E GLU* 3.8 25.6 - - + +
225E VAL* 1.3 75.5 - - - +
227E SER* 1.3 59.5 + - - +
240E CYS 2.9 6.7 + - - -
241E GLY* 4.1 2.7 - - - -
242E MET* 3.7 16.6 - - + -
294E TYR* 4.1 3.6 - - + -
295E VAL 3.3 28.5 - - - +
296E ASP* 3.8 19.2 - - + +
350E TRP* 3.5 44.2 - - + +
351E TYR* 4.6 7.2 - - + -
353E ARG* 2.8 29.0 + - - +
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Residues in contact with SER 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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181E GLU* 2.7 26.4 + - - -
195E VAL* 3.8 4.4 - - - +
225E VAL* 3.7 2.5 - - - +
226E LEU* 1.3 80.0 - - - +
228E ALA* 1.4 61.8 + - - +
239E SER* 3.4 2.4 - - - -
240E CYS* 3.0 45.6 + - - +
296E ASP 3.6 12.8 - - - -
297E CYS* 3.6 5.8 - - - -
298E VAL* 3.3 15.6 + - - -
299E ARG* 3.6 8.3 + - - -
353E ARG* 4.7 0.8 + - - -
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Residues in contact with ALA 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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181E GLU* 3.8 3.1 + - - +
183E LYS* 3.5 17.9 - - + +
193E LEU* 3.9 13.5 - - + -
195E VAL* 3.4 25.3 - - + +
201E LEU* 3.8 14.8 - - + -
227E SER* 1.4 77.6 + - - +
229E ASP* 1.3 61.1 + - - +
237E ILE* 4.2 2.0 - - + -
238E MET 3.2 12.8 - - - +
239E SER* 4.2 1.8 - - - -
298E VAL* 3.8 1.6 - - - -
299E ARG* 3.1 16.4 + - - -
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Residues in contact with ASP 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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183E LYS* 4.0 19.1 + - - +
193E LEU* 5.3 0.7 - - - -
228E ALA* 1.3 76.6 - - - +
230E TYR* 1.3 73.4 + - - +
237E ILE* 3.4 5.0 - - - -
238E MET* 3.0 32.0 + - + +
298E VAL 3.5 14.6 - - - +
299E ARG* 3.4 23.9 - - - +
300E TRP* 2.9 38.8 + - + +
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Residues in contact with TYR 230 (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 LYS* 3.6 20.6 - - + +
184E PHE 3.5 17.9 - - - -
185E HIS* 3.4 29.5 - + - +
186E PRO* 3.6 16.2 - - + -
191E LEU 3.6 9.0 + - - -
193E LEU* 3.4 20.1 - - + +
203E LEU* 3.2 26.5 - - + +
229E ASP* 1.3 87.9 + - - +
231E ASP* 1.3 70.1 + - - +
234E GLY* 4.4 4.7 - - - -
236E LYS 3.4 5.4 - - - +
237E ILE* 3.7 20.6 - - + +
251E ILE* 3.6 30.1 - - + -
300E TRP* 3.2 10.4 - - - +
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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