Contacts of the strand formed by residues 226 - 231 (chain E) in PDB entry 6XAV
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 GLU 226 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E ALA* 3.8 19.0 - - + +
72E TYR* 3.6 7.6 + - - -
203E VAL* 6.5 0.2 - - + -
204E LEU 3.7 10.7 + - - +
205E MET* 3.4 33.2 - - + +
206E VAL* 3.5 19.2 + - - +
225E GLY* 1.3 71.1 - - - -
227E VAL* 1.3 64.2 + - - +
228E VAL* 3.9 17.2 + - + -
249E LYS* 2.9 33.1 + - - -
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E SER* 4.7 2.4 + - - -
206E VAL* 3.6 20.9 - - + +
208E LEU* 4.9 2.9 - - + -
216E VAL 4.9 0.9 - - - +
219E MET* 4.1 20.6 - - + -
220E GLN* 3.7 49.1 + - + +
223E VAL* 3.7 30.1 - - + -
225E GLY 3.7 7.5 + - - +
226E GLU* 1.3 78.1 - - - +
228E VAL* 1.3 65.3 + - - +
229E ALA* 3.9 7.1 + - + -
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Residues in contact with VAL 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ALA 4.9 7.9 - - - +
71E SER* 3.8 20.0 - - - +
72E TYR* 3.6 42.6 - - + -
205E MET* 5.1 5.2 - - + -
206E VAL 3.2 10.1 + - - +
207E LEU* 3.2 15.3 - - + +
208E LEU 3.0 21.1 + - - -
226E GLU* 3.9 23.2 + - + +
227E VAL* 1.3 73.2 - - - +
229E ALA* 1.3 62.2 + - - +
242E VAL* 4.0 15.7 - - + -
246E VAL* 4.3 6.7 - - + -
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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
----------------------------------------------------------
71E SER* 3.0 28.8 + - - +
208E LEU* 3.4 21.1 - - + -
216E VAL* 3.7 41.3 - - + -
220E GLN* 4.8 5.1 - - - +
227E VAL* 3.9 4.5 + - + -
228E VAL* 1.3 76.5 - - - +
230E SER* 1.3 61.2 + - - +
231E THR* 4.1 1.3 + - - -
242E VAL* 5.3 0.4 - - - -
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Residues in contact with SER 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E SER* 5.7 0.2 - - - -
208E LEU 2.7 14.0 + - - -
209E ILE* 3.6 17.2 - - - -
210E ASP 2.8 28.4 + - - -
211E GLU* 3.8 1.9 + - - -
216E VAL* 5.8 0.2 - - - -
229E ALA* 1.3 75.3 - - - +
231E THR* 1.3 61.9 + - - +
234E GLU* 4.1 14.0 - - - +
238E ARG* 4.5 1.0 + - - +
239E HIS* 3.3 18.9 + - - -
242E VAL* 4.1 22.8 - - - +
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Residues in contact with THR 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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210E ASP* 4.3 0.7 - - - -
211E GLU 3.3 12.8 - - - +
213E PRO* 3.8 27.6 - - + -
216E VAL* 3.7 31.0 - - + -
229E ALA* 5.5 0.7 - - + -
230E SER* 1.3 73.5 - - - +
232E PHE* 1.3 59.3 + - - +
233E ASP* 3.0 32.1 + - - +
234E GLU* 3.3 12.2 + - - +
239E HIS* 3.0 18.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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