Contacts of the strand formed by residues 227 - 232 (chain E) in PDB entry 2BQZ
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 GLY 227 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222E LEU* 3.4 12.1 - - - +
223E ILE* 2.8 30.0 + - - +
225E GLY 3.9 0.8 - - - +
226E LYS* 1.3 76.0 - - - +
228E ARG* 1.3 61.9 + - - -
1354E SAH 3.9 4.3 - - - -
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Residues in contact with ARG 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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220E ILE* 4.2 22.9 - - + -
221E ASP 3.4 7.2 - - - +
222E LEU* 4.2 14.8 - - + -
223E ILE* 4.4 0.4 - - - -
227E GLY* 1.3 74.8 - - - -
229E GLY* 1.3 58.9 + - - +
271E TYR* 3.3 18.8 + - - -
289E GLU* 3.0 40.8 + - - -
296E LEU* 3.5 30.7 - - + +
298E ASN* 3.0 9.0 + - - +
1354E SAH 2.7 51.1 + - - +
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Residues in contact with GLY 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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220E ILE* 3.3 8.4 - - - +
221E ASP 2.9 31.1 + - - -
223E ILE* 3.2 23.2 - - - +
228E ARG* 1.3 75.8 - - - +
230E VAL* 1.3 64.3 - - - +
231E ILE* 5.3 0.2 - - - -
296E LEU* 3.6 7.2 - - - -
298E ASN* 3.4 8.1 - - - -
331E GLU* 4.1 0.2 - - - -
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Residues in contact with VAL 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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218E MET* 3.7 31.0 - - + -
219E LYS 3.4 11.2 - - - +
220E ILE* 4.8 5.6 - - + -
223E ILE* 4.2 1.0 - - - +
229E GLY* 1.3 77.9 - - - +
231E ILE* 1.3 60.5 + - - +
293E LEU* 3.6 31.6 - - + +
296E LEU* 3.8 15.8 + - + -
297E ILE* 3.7 21.4 - - + +
331E GLU* 3.5 6.2 - - - +
332E LEU* 2.8 45.2 + - + +
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Residues in contact with ILE 231 (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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218E MET* 3.3 4.1 - - - -
219E LYS* 2.8 42.7 + - + +
221E ASP* 3.4 38.4 - - + +
223E ILE* 4.9 9.9 - - + -
230E VAL* 1.3 80.1 - - - +
232E ALA* 1.3 77.6 + - - +
233E THR* 3.5 3.5 + - + +
329E GLY* 3.4 28.0 - - - +
330E GLU 3.5 2.0 - - - -
331E GLU* 4.1 17.7 - - + +
332E LEU* 4.9 0.7 - - - -
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Residues in contact with ALA 232 (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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217E GLY 3.5 6.1 - - - -
218E MET* 4.7 0.7 - - - +
230E VAL 4.3 0.4 + - - -
231E ILE* 1.3 77.0 - - - +
233E THR* 1.3 57.4 + - - +
234E LYS 3.5 17.9 - - - +
236E PHE* 4.0 13.0 - - + -
326E ILE* 4.0 12.1 - - + -
327E ALA 3.7 16.8 - - - +
329E GLY* 2.6 28.6 + - - -
330E GLU 2.9 13.1 + - - +
332E LEU* 4.4 7.6 - - + +
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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