Contacts of the strand formed by residues 202 - 207 (chain D) in PDB entry 3UX9
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172D ARG* 3.9 10.5 - - - -
182D VAL* 3.9 16.8 - - + -
194D TYR* 3.1 20.5 - - + -
198D VAL* 3.1 41.4 + - + +
200D GLY* 4.3 5.2 + - - -
201D ARG* 1.3 109.5 + - + +
203D THR* 1.3 67.8 + - - +
215D LEU* 3.9 12.3 - - + -
216D GLN 3.1 5.4 - - - +
217D MET* 3.6 50.7 - - + -
218D ASN 4.1 2.5 - - - -
220D LEU* 4.0 4.9 - - + -
224D ASP* 3.7 24.9 - - - -
228D TYR* 4.0 2.2 - + - -
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Residues in contact with THR 203 (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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194D TYR* 3.4 11.1 + - - +
200D GLY 5.1 3.5 + - - -
201D ARG 4.6 3.1 + - - -
202D PHE* 1.3 78.1 + - - +
204D ILE* 1.3 68.6 + - - +
205D SER* 3.8 10.2 + - - +
215D LEU* 3.5 3.8 + - - -
216D GLN* 2.8 47.4 + - + +
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Residues in contact with ILE 204 (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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168D MET 4.4 2.0 - - - +
169D SER* 4.7 0.9 - - - -
170D TRP* 3.6 20.2 - - + -
183D SER* 3.0 33.4 - - - +
184D ALA* 3.6 27.8 - - - +
185D ILE* 3.5 37.1 - - + +
192D THR* 3.8 15.8 - - - +
194D TYR* 3.1 18.9 + - + +
203D THR* 1.3 77.5 - - - +
205D SER* 1.3 63.4 + - - +
213D LEU* 3.9 4.7 - - + -
214D TYR 3.6 14.6 - - - +
215D LEU* 4.1 2.9 - - + +
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Residues in contact with SER 205 (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 ARG* 5.6 1.6 + - - -
185D ILE* 3.8 4.7 - - - +
203D THR* 4.3 11.4 + - - +
204D ILE* 1.3 74.4 + - - +
206D ARG* 1.3 66.8 + - - +
213D LEU* 3.4 12.5 - - - +
214D TYR* 3.1 50.3 + - - +
216D GLN* 5.7 1.2 + - - +
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Residues in contact with ARG 206 (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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163D PHE* 3.3 38.3 + - + -
166D TYR 2.3 31.2 + - - -
167D ALA* 3.6 2.8 - - - +
168D MET* 3.3 29.4 - - - +
185D ILE* 3.5 19.6 + - + +
186D SER 3.0 17.4 + - - -
187D GLY 3.4 19.5 + - - -
188D SER 4.1 8.5 - - - +
189D GLY* 5.1 1.8 - - - -
205D SER* 1.3 82.6 - - - +
207D ASP* 1.3 62.7 + - - +
208D ASN* 3.0 38.0 + - - +
212D THR 3.6 5.8 - - - +
213D LEU* 5.2 2.5 - - + -
214D TYR* 4.4 2.7 - - - -
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Residues in contact with ASP 207 (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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206D ARG* 1.3 74.7 - - - +
208D ASN* 1.3 58.2 + - - +
209D SER* 2.4 32.7 + - - -
210D LYS* 3.1 21.0 + - + +
211D ASN 3.0 22.3 + - - -
212D THR* 2.9 17.2 + - - +
214D TYR* 4.0 23.3 + - + +
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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