Contacts of the strand formed by residues 222 - 229 (chain D) in PDB entry 5Y7K
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 PHE 222 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216D TRP* 3.6 8.2 - - - -
217D SER* 2.7 39.2 + - - -
219D ASN* 5.6 0.2 - - - -
221D THR* 1.3 91.5 - - + +
223D LEU* 1.3 58.9 + - - +
224D ALA 4.0 0.4 - - - -
270D VAL* 3.8 11.4 - - + -
271D VAL 3.3 7.0 - - - -
272D ASN* 3.9 26.2 - - + -
305D TRP* 3.5 26.0 - + + -
308D GLN 3.3 26.9 - - - -
309D GLU* 4.4 8.1 - - + -
330D TYR* 3.7 39.7 - + - -
337D TRP* 3.6 24.5 - + - -
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Residues in contact with LEU 223 (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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165D ALA* 4.0 10.5 - - + -
172D ILE* 4.1 8.3 - - + -
174D VAL* 3.7 30.1 - - + -
185D ILE* 5.3 0.2 - - + -
214D LEU* 4.0 29.4 - - + -
215D TRP 4.1 3.4 - - - +
216D TRP* 3.8 41.7 - - + +
221D THR 4.2 0.4 + - - -
222D PHE* 1.3 71.4 - - - +
224D ALA* 1.3 62.3 + - - +
225D TYR* 3.9 6.1 + - + -
270D VAL* 3.5 2.6 - - - -
271D VAL* 2.7 50.8 + - + +
273D THR* 3.9 11.9 - - + +
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Residues in contact with ALA 224 (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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214D LEU* 3.5 1.4 - - - -
215D TRP* 2.6 54.5 + - + +
222D PHE 4.0 1.2 - - - -
223D LEU* 1.3 72.8 - - - +
225D TYR* 1.3 57.8 + - - +
268D PHE* 3.4 26.2 - - + -
269D PHE 3.3 4.9 - - - -
270D VAL* 3.8 7.0 - - + +
305D TRP* 3.7 10.3 - - + +
311D ILE* 3.7 15.9 - - + -
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Residues in contact with TYR 225 (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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172D ILE* 3.3 18.6 - - + -
185D ILE* 4.0 17.6 + - + -
186D THR* 3.8 26.1 - - + +
196D ASN* 4.4 6.5 - - - -
197D GLY 4.5 0.7 - - - -
213D ALA 3.2 13.7 - - - +
214D LEU* 3.5 19.1 - - + -
215D TRP* 4.0 5.2 - - - -
223D LEU* 3.9 13.5 - - + -
224D ALA* 1.3 74.2 - - - +
226D ALA* 1.3 70.4 + - - +
227D GLN* 5.7 0.2 - - - -
268D PHE* 3.5 4.4 - - - -
269D PHE* 2.9 72.1 + + + +
271D VAL* 4.4 8.1 - - + -
284D SER* 3.1 28.8 + - - -
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Residues in contact with ALA 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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195D TYR 3.8 1.2 - - - +
197D GLY* 3.3 23.9 + - - -
213D ALA* 3.2 10.2 + - + +
215D TRP* 3.9 17.5 - - + -
225D TYR* 1.3 80.4 - - - +
227D GLN* 1.3 60.9 + - - +
228D PHE* 3.9 27.7 - - + -
266D VAL* 4.5 1.6 - - + -
267D LYS 3.3 9.0 - - - +
268D PHE* 4.3 0.4 - - + -
300D LEU* 4.0 17.9 - - + -
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Residues in contact with GLN 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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186D THR* 5.8 0.4 - - - +
188D THR* 3.1 24.2 + - - +
194D ILE* 4.1 17.7 - - + +
195D TYR 3.1 6.7 - - - +
196D ASN* 2.9 27.8 + - - +
225D TYR* 5.1 0.6 - - + -
226D ALA* 1.3 73.4 - - - +
228D PHE* 1.3 66.7 - - - +
229D ASN* 5.4 4.2 - - + +
265D THR 3.7 0.5 - - - +
266D VAL* 3.2 6.8 - - - +
267D LYS* 2.7 60.9 + - + +
269D PHE* 4.0 25.6 - - + -
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Residues in contact with PHE 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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193D ILE 3.6 0.5 - - - +
194D ILE* 3.4 5.9 - - - +
195D TYR* 2.8 46.7 + - + +
198D ILE 3.2 27.6 - - - -
199D THR* 3.6 29.6 - - + -
200D ASP* 4.5 5.6 - - + +
203D TYR* 3.4 53.6 - + - -
208D PHE* 4.0 8.1 - + - -
213D ALA* 3.8 12.1 - - + -
226D ALA* 3.9 18.2 - - + -
227D GLN* 1.3 75.3 - - - +
229D ASN* 1.3 60.3 + - - +
230D ASP* 4.0 11.0 - - - +
264D PRO* 5.0 1.3 - - + -
265D THR 3.3 6.3 - - - +
266D VAL* 3.7 18.8 - - + -
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Residues in contact with ASN 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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193D ILE 3.3 2.8 - - - +
194D ILE* 3.2 21.9 - - + +
227D GLN* 4.3 6.0 + - - +
228D PHE* 1.3 72.6 - - - +
230D ASP* 1.3 60.4 + - - +
231D THR* 2.4 37.2 + - - -
233D VAL* 4.5 0.2 - - - +
264D PRO* 3.2 4.5 - - - +
265D THR* 2.9 51.0 + - - +
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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