Contacts of the strand formed by residues 202 - 208 (chain B) in PDB entry 1YXJ
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 202 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B PHE* 4.2 21.5 - + + -
159B SER 5.0 2.7 - - - -
195B ILE* 3.7 33.7 - - + -
198B SER* 3.9 10.5 - - - -
200B PHE* 3.4 40.8 - + + -
201B PRO* 1.3 72.0 - - - +
203B TRP* 1.3 64.2 + - - +
204B MSE 3.7 0.2 + - - -
245B TYR* 3.6 3.8 - - - -
246B ILE* 2.8 43.9 + - + +
261B PHE* 3.4 28.5 - + + +
262B SER* 4.0 13.5 - - - -
263B ILE* 3.9 27.6 - - + -
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Residues in contact with TRP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B PHE 2.9 20.9 + - - -
165B TRP* 3.4 35.1 - + + +
168B SER* 3.4 24.7 - - - -
179B LEU* 4.2 5.6 - - + +
201B PRO 4.3 0.2 - - - -
202B PHE* 1.3 73.9 - - - +
204B MSE 1.3 59.9 + - - +
243B CYS* 3.4 35.2 - - + -
244B ALA 3.4 17.7 - - - -
245B TYR* 3.8 10.0 - + + +
254B GLU* 3.2 34.3 - - + -
255B ASN 3.8 8.7 - - - -
256B CYS* 3.9 3.6 - - - -
258B LEU 3.2 22.4 - - - -
260B ALA* 3.6 11.2 - - + +
261B PHE 2.8 23.9 + - - +
262B SER* 3.7 7.9 - - - +
263B ILE* 3.3 26.9 + - - +
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Residues in contact with MSE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TRP* 2.9 22.2 + - - -
179B LEU* 3.9 4.7 - - - -
180B LEU* 3.7 26.0 - - + +
182B ILE* 3.9 16.2 - - + -
202B PHE 3.7 0.2 + - - -
203B TRP* 1.3 74.1 - - - +
205B GLY* 1.3 60.2 + - - +
206B LEU* 3.1 17.6 + - + +
217B TRP* 3.7 24.0 - - + -
228B PHE* 3.9 14.4 - - - -
244B ALA 3.1 21.7 + - - +
245B TYR 4.2 0.2 - - - -
246B ILE* 3.7 35.7 - - + +
251B VAL* 3.7 27.8 - - + -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TRP* 4.0 7.8 - - - -
179B LEU* 3.5 22.0 - - - +
180B LEU 2.7 20.3 + - - -
204B MSE 1.3 69.4 - - - +
206B LEU* 1.3 57.8 + - - +
207B SER* 3.9 0.7 + - - -
216B LEU 3.6 0.7 - - - +
217B TRP* 3.3 10.3 - - - -
218B GLU* 3.0 39.2 + - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TRP* 4.1 1.2 + - - -
204B MSE 3.1 8.2 + - + +
205B GLY* 1.3 76.4 - - - +
207B SER* 1.3 66.0 + - - +
215B TRP* 3.9 27.8 - - + +
216B LEU* 3.5 27.8 - - - +
217B TRP* 3.7 32.7 - - + +
223B LEU* 4.3 8.5 - - + -
228B PHE* 4.1 29.4 - - + -
230B VAL* 4.1 13.0 - - + -
243B CYS* 3.7 0.5 - - - -
244B ALA* 3.0 42.9 + - + -
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B TRP* 4.0 20.0 - - - -
205B GLY 4.9 0.2 + - - -
206B LEU* 1.3 78.7 - - - +
208B ARG* 1.3 67.0 + - - +
214B PRO 4.0 0.7 - - - +
215B TRP* 3.8 7.9 - - - -
216B LEU* 3.1 31.4 + - - +
242B THR 3.4 14.8 - - - -
243B CYS* 3.8 17.3 - - - -
256B CYS* 4.9 0.4 - - - -
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B SER* 1.3 81.7 - - - +
209B ARG* 1.3 60.8 + - - +
210B ASN* 3.4 14.6 + - - +
211B PRO* 3.8 20.1 + - - +
213B TYR* 2.9 31.2 + - + +
214B PRO* 3.4 16.8 - - - +
215B TRP* 3.4 57.1 - - + +
234B VAL* 3.1 31.5 + - - +
241B GLY* 3.7 1.4 - - - -
242B THR* 2.9 32.3 + - - -
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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