Contacts of the strand formed by residues 225 - 232 (chain D) in PDB entry 5E5R
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 TYR 225 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225C VAL* 5.7 0.7 - - + -
226C HIS* 3.6 19.1 - + + -
288C PHE* 3.4 36.6 - + + -
299C VAL* 4.3 15.0 - - + +
137D GLY 3.9 8.6 + - - -
138D GLN 3.8 0.7 - - - -
139D GLY* 3.0 32.6 + - - -
184D ALA 3.8 1.4 + - - -
222D MET* 4.3 13.7 - - + -
223D GLY 3.7 9.2 - - - -
224D GLU* 1.3 78.3 - - - +
226D GLU* 1.3 83.4 + - + +
228D LYS* 5.5 0.2 - - + -
252D LEU* 4.2 3.7 - - - +
253D GLY* 3.5 27.1 + - - -
254D ASN* 3.0 24.5 + - + +
301D ASN* 2.9 21.1 + - - -
303D ARG* 3.6 10.9 - - - +
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Residues in contact with GLU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C LYS 4.8 4.6 - - - +
225C VAL* 3.5 45.6 - - + +
226C HIS* 2.8 24.8 + - - +
229C LYS* 4.0 10.2 + - - +
225D TYR* 1.3 83.4 - - - +
227D PRO* 1.3 72.3 - - + +
301D ASN* 3.9 4.3 - - - -
303D ARG* 3.6 22.7 - - - +
304D GLY* 4.1 6.8 - - - +
305D LYS 4.1 4.3 - - - +
306D ASN* 3.3 23.6 + - - +
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Residues in contact with PRO 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C HIS* 3.5 1.0 - - - -
226D GLU* 1.3 90.2 - - + +
228D LYS* 1.3 55.9 + - - +
229D ILE 4.1 0.2 - - - -
251D ALA* 4.1 0.9 - - + -
252D LEU 3.4 8.3 - - - +
253D GLY* 4.4 0.4 - - - -
257D PRO* 3.9 16.8 - - + -
299D ALA* 3.4 36.3 - - + +
300D GLU* 3.5 15.9 - - - +
301D ASN* 3.4 23.3 - - - +
304D GLY 3.4 11.0 - - - +
305D LYS* 4.5 1.6 - - - +
306D ASN* 2.4 38.4 + - + -
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C HIS* 3.3 45.8 - - + +
227C HIS* 3.6 22.2 + - - +
228C GLU* 4.8 6.3 + - - +
290C THR* 3.6 29.8 - - + +
297C LYS* 4.6 4.2 - - - +
299C VAL* 4.5 11.4 - - + -
225D TYR* 5.5 0.2 - - + -
226D GLU 3.6 0.4 + - - -
227D PRO* 1.3 72.0 - - - +
229D ILE* 1.3 69.2 + - - +
230D GLU* 3.1 29.2 + - - +
251D ALA* 3.8 2.5 - - - -
252D LEU* 2.7 44.3 + - + +
306D ASN* 4.5 1.1 - - - +
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Residues in contact with ILE 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D PRO 4.1 0.2 - - - -
228D LYS* 1.3 78.9 + - - +
230D GLU* 1.3 59.5 + - - +
231D VAL 3.3 23.3 - - - +
232D GLN* 3.9 26.4 + - + +
249D CYS* 3.9 19.7 - - - -
250D PHE 3.6 6.7 - - - +
251D ALA* 3.9 2.7 - - + +
297D CYS 4.2 2.0 - - - +
299D ALA* 4.0 21.5 - - + -
306D ASN* 3.6 30.5 - - + +
307D VAL* 3.7 4.0 - - - +
308D ALA* 3.6 28.3 - - + +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297C LYS* 2.5 38.9 + - - +
141D VAL* 3.6 26.9 - - + +
182D TYR* 3.8 14.0 - - + -
228D LYS* 3.1 40.7 + - - +
229D ILE* 1.3 73.9 - - - +
231D VAL* 1.3 66.1 + - - +
232D GLN* 5.7 1.3 - - - -
250D PHE 2.9 8.7 + - - +
252D LEU* 4.0 19.5 - - + +
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D PHE* 4.3 8.5 - - + -
175D SER* 4.2 8.5 - - - +
177D GLU* 6.0 0.7 - - + -
178D THR* 3.9 19.1 - - + -
182D TYR* 3.1 50.3 - - + +
229D ILE* 3.3 6.4 - - - +
230D GLU* 1.3 78.0 - - - +
232D GLN* 1.3 69.1 + - - +
248D GLU* 4.5 8.1 - - + +
249D CYS* 3.4 1.6 - - - -
250D PHE* 3.1 45.3 + - + +
401D MLI 5.8 1.6 - - - +
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Residues in contact with GLN 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ILE* 3.9 27.2 + - + +
230D GLU 5.7 0.6 - - - -
231D VAL* 1.3 82.1 - - - +
233D PHE* 1.3 76.3 + - + +
234D PRO* 3.7 2.1 - - - +
248D GLU* 3.2 12.5 - - - +
249D CYS* 4.6 2.0 - - - -
308D ALA* 3.2 35.7 - - + +
309D ARG 4.6 5.9 + - - +
401D MLI 4.0 9.7 - - - +
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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