Contacts of the strand formed by residues 162 - 168 (chain D) in PDB entry 1Y8R
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 HIS 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D VAL* 3.3 5.5 - - - +
159D PHE* 2.6 46.3 + - + +
160D GLY 3.2 0.2 - - - -
161D TYR* 1.3 83.1 - - + +
163D GLY* 1.3 55.9 + - - +
239D ASP* 3.0 35.6 + - - +
242D LEU* 3.8 26.4 - - + +
291D PHE* 5.6 4.5 - - + -
294D TYR* 3.2 37.2 + + + -
295D CYS* 4.6 0.6 - - + +
302D VAL* 3.9 4.7 - - - -
331D PHE 3.4 4.0 - - - +
332D ASP* 2.9 33.9 + - + -
334D MET* 5.6 1.6 - - + -
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Residues in contact with GLY 163 (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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157D ASP 3.3 12.3 - - - -
158D VAL* 3.8 11.4 - - - -
159D PHE* 4.9 3.4 - - - -
162D HIS* 1.3 77.3 - - - +
164D TYR* 1.3 62.9 + - - +
239D ASP* 4.6 1.7 - - - +
302D VAL* 4.2 1.6 - - - +
306D VAL* 4.0 11.7 - - - -
329D PHE* 6.2 0.2 - - - -
330D PHE* 3.8 5.2 - - - +
331D PHE 3.2 29.3 + - - +
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Residues in contact with TYR 164 (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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139D ILE* 4.1 12.1 - - - +
155D THR* 3.2 27.4 + - + +
156D GLY* 3.2 32.1 - - - -
157D ASP* 3.0 52.9 + - + +
159D PHE* 3.6 24.7 - + + -
163D GLY* 1.3 74.2 - - - +
165D THR* 1.3 69.1 + - - +
166D PHE* 4.4 11.0 - - + -
243D LEU* 3.7 34.9 - - + +
247D LEU* 5.4 2.5 - - + +
306D VAL* 3.9 6.6 - - - +
328D PHE* 4.0 9.4 - + - -
329D PHE* 3.2 7.9 - - - -
330D PHE* 3.7 22.7 - - + -
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Residues in contact with THR 165 (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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154D PHE* 5.4 1.3 - - + -
155D THR 3.5 4.7 - - - -
164D TYR* 1.3 81.7 + - - +
166D PHE* 1.3 66.9 + - - +
167D ALA* 5.7 1.8 - - + -
306D VAL* 3.5 18.0 + - - +
309D ILE* 5.2 1.3 - - + -
310D LEU* 3.5 44.5 - - + +
313D GLU* 5.1 8.7 - - + -
327D ASN 3.8 0.3 - - - +
328D PHE* 3.4 5.5 - - - -
329D PHE* 2.7 56.1 + - + -
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Residues in contact with PHE 166 (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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153D PHE* 4.0 5.2 - + - -
154D PHE* 3.3 6.4 - - - +
155D THR* 2.9 55.0 + - + +
164D TYR* 4.3 4.4 - - + -
165D THR* 1.3 78.2 - - - +
167D ALA* 1.3 80.3 + - - +
168D ASN* 3.8 7.9 - - + -
214D CYS 3.7 17.7 - - - -
216D VAL* 3.4 38.6 - - + -
219D ALA* 3.9 11.7 - - + -
327D ASN* 3.0 39.9 - - - -
328D PHE* 3.6 30.5 - + + -
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Residues in contact with ALA 167 (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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153D PHE 3.4 5.6 - - - -
154D PHE* 3.4 28.9 - - + -
165D THR* 5.7 2.2 - - + -
166D PHE* 1.3 95.2 - - - +
168D ASN* 1.3 60.3 + - - +
169D LEU* 4.8 4.0 - - + -
213D PHE* 3.7 27.0 - - + +
313D GLU* 5.6 4.5 - - + +
324D PRO* 6.3 0.7 - - + -
325D HIS 4.6 5.6 - - - +
327D ASN* 3.1 12.2 + - - +
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Residues in contact with ASN 168 (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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143D ASP* 2.8 33.2 + - - +
147D HIS* 4.2 25.9 - - - +
151D ILE 4.4 2.4 + - - +
152D LYS* 4.1 1.4 - - - -
153D PHE* 2.8 32.1 + - + +
166D PHE* 3.8 12.1 - - + -
167D ALA* 1.3 76.2 - - - +
169D LEU* 1.3 59.9 + - - +
170D GLY* 3.2 5.7 + - - +
213D PHE* 3.6 15.1 - - - +
214D CYS 3.1 27.6 + - - +
215D PRO* 3.8 1.3 - - - +
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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