Contacts of the strand formed by residues 226 - 233 (chain B) 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 ALA 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ARG* 3.8 16.2 - - + -
173B GLN 2.9 35.2 - - - +
174B ALA* 3.5 4.0 - - + +
175B PRO* 4.1 4.0 - - - -
224B ASP 3.2 8.3 + - - +
225B THR* 1.3 79.5 - - - +
227B VAL* 1.3 58.0 + - - +
228B TYR* 3.1 11.3 - - + -
248B LEU* 3.9 7.9 - - - -
249B VAL 2.8 27.2 + - - -
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL 3.9 0.7 - - - +
172B ARG* 3.2 4.9 - - - -
173B GLN* 3.0 35.7 + - + +
226B ALA* 1.3 71.2 - - - +
228B TYR* 1.3 63.4 + - - +
229B TYR* 3.9 27.9 + - + +
245B GLN 4.4 2.5 - - - +
246B GLY* 3.7 27.4 - - - -
247B THR 3.5 10.3 - - - +
248B LEU* 4.2 16.6 - - + +
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Residues in contact with TYR 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLU* 3.5 8.3 - - - +
154B LEU* 3.6 28.9 - - + -
170B TRP* 4.3 8.9 - + + -
171B VAL 3.7 2.7 - - - -
172B ARG* 3.0 39.2 + - + -
182B VAL* 4.6 6.3 - - + -
202B PHE* 4.0 5.1 - + - -
215B LEU* 4.2 15.5 - - + -
217B MET* 3.2 29.8 - - + +
224B ASP* 2.7 28.5 + - - +
226B ALA* 3.1 32.3 - - + -
227B VAL* 1.3 73.2 - - - +
229B TYR* 1.3 62.5 + - - +
246B GLY* 3.2 2.6 - - - -
247B THR* 2.8 34.7 + - + +
249B VAL* 3.8 14.1 - - + -
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Residues in contact with TYR 229 (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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41B GLN* 3.7 14.1 + - - -
44B GLY 5.2 2.6 + - - -
45B THR 4.0 6.2 + - - -
46B ALA* 3.6 23.7 - - + -
47B PRO* 4.2 7.2 - - + -
140B GLU* 3.6 2.2 - - - -
170B TRP* 3.3 8.0 - - - -
171B VAL* 2.7 46.7 + - - +
173B GLN* 4.2 20.9 + - + -
179B LEU* 4.8 4.5 - - + -
227B VAL* 3.9 28.9 - - + +
228B TYR* 1.3 74.6 - - - +
230B CYS* 1.3 62.4 + - - +
243B TRP* 3.8 29.2 - + + -
244B GLY 3.4 18.4 - - - -
245B GLN 3.4 20.1 + - - -
246B GLY* 3.8 7.6 - - - -
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Residues in contact with CYS 230 (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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138B LEU* 3.6 17.4 - - - +
140B GLU* 2.8 18.5 + - - -
156B CYS* 2.0 53.6 - - + -
168B MET* 4.1 1.8 - - - -
169B SER 3.3 10.1 - - - +
170B TRP* 3.8 9.3 - - + -
213B LEU* 3.8 10.8 - - + -
229B TYR* 1.3 77.3 - - - +
231B ALA* 1.3 63.1 + - - +
243B TRP* 3.5 1.2 - - - -
244B GLY 3.1 24.4 + - - -
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Residues in contact with ALA 231 (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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138B LEU* 4.0 1.6 - - - -
168B MET* 3.3 11.5 - - - +
169B SER* 2.9 47.2 + - - +
171B VAL* 5.2 2.2 - - + -
230B CYS* 1.3 77.5 - - - +
232B ARG* 1.3 61.4 + - - +
233B TYR 3.8 0.3 + - - -
240B MET* 3.8 20.4 - - + -
242B PHE 3.3 12.6 - - - +
243B TRP* 4.2 16.6 - - + -
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Residues in contact with ARG 232 (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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136B VAL* 4.7 7.4 - - - +
138B LEU* 4.0 6.4 - - + +
161B PHE* 3.5 37.7 - - + +
166B TYR* 3.1 67.5 + - + -
168B MET* 3.8 15.0 - - - -
231B ALA* 1.3 71.6 - - - +
233B TYR* 1.3 60.1 + - - +
234B ILE* 4.0 5.1 - - - +
240B MET* 3.1 21.9 - - - +
241B ASP* 2.7 56.1 + - - +
242B PHE* 3.0 33.7 + - + +
223D GLU* 3.8 1.8 + - - -
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Residues in contact with TYR 233 (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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30A LEU* 5.0 1.6 - - + -
92B GLN* 5.0 0.2 - - - -
101B TRP* 3.5 39.2 - + - -
166B TYR* 3.4 21.7 - - - +
167B ALA* 2.8 40.7 + - + +
168B MET 3.4 24.7 - - - -
169B SER* 3.1 26.0 + - - -
181B TRP* 3.2 28.4 + - - -
184B ALA* 3.7 10.1 - - + -
231B ALA 3.8 0.2 + - - -
232B ARG* 1.3 70.5 - - - +
234B ILE* 1.3 62.6 + - - +
235B ASP 3.6 1.4 + - - +
237B GLY* 3.5 28.7 - - - +
239B HIS 3.6 11.0 - - - -
240B MET* 3.9 20.4 - - + +
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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