Contacts of the strand formed by residues 226 - 233 (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 ALA 226 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLN* 4.0 6.7 + - - +
172D ARG* 3.9 15.0 - - + -
173D GLN 2.9 35.4 - - - +
174D ALA* 3.5 4.5 - - + +
223D GLU 5.6 0.2 - - - +
224D ASP 3.3 8.6 + - - +
225D THR* 1.3 78.8 - - - +
227D VAL* 1.3 57.5 + - - +
228D TYR* 3.1 11.4 - - + -
248D LEU* 3.9 6.7 - - - -
249D VAL 2.8 28.1 + - - -
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Residues in contact with VAL 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 4.1 21.7 - - + +
171D VAL 3.9 0.7 - - - +
172D ARG* 3.2 4.5 - - - -
173D GLN* 2.9 35.2 + - + +
226D ALA* 1.3 72.4 - - - +
228D TYR* 1.3 61.5 + - - +
229D TYR* 3.8 26.6 + - + +
245D GLN 4.5 2.2 - - - +
246D GLY* 3.7 27.4 - - - -
247D THR 3.5 11.0 - - - +
248D LEU* 4.3 8.5 - - + +
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Residues in contact with TYR 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D GLU* 3.5 8.0 - - - +
154D LEU* 3.6 28.7 - - + -
170D TRP* 4.2 9.2 - + + -
171D VAL 3.7 2.7 - - - -
172D ARG* 3.0 39.6 + - + -
182D VAL* 4.6 6.3 - - + -
202D PHE* 4.4 4.3 - + - -
215D LEU* 4.2 15.0 - - + -
217D MET* 3.2 24.2 - - + +
224D ASP* 2.6 30.7 + - - +
226D ALA* 3.1 22.7 - - + -
227D VAL* 1.3 73.4 - - - +
229D TYR* 1.3 61.2 + - - +
246D GLY* 3.3 2.6 - - - -
247D THR* 2.8 33.8 + - + +
249D VAL* 3.8 19.5 - - + -
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Residues in contact with TYR 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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41D GLN* 3.8 13.2 + - - -
44D GLY 5.2 1.9 + - - -
45D THR 4.1 6.6 + - - -
46D ALA* 3.7 17.9 - - + -
47D PRO* 4.3 11.4 - - + -
140D GLU* 3.6 2.7 - - - +
170D TRP* 3.3 7.4 - - - -
171D VAL* 2.7 50.2 + - - +
173D GLN* 4.2 19.9 + - + -
179D LEU* 4.7 4.7 - - + -
227D VAL* 3.8 28.8 - - + +
228D TYR* 1.3 73.2 - - - +
230D CYS* 1.3 63.6 + - - +
243D TRP* 3.8 28.5 - + + -
244D GLY 3.4 18.6 - - - +
245D GLN 3.4 21.2 + - - -
246D GLY* 3.8 7.6 - - - -
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Residues in contact with CYS 230 (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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138D LEU* 3.7 17.4 - - - +
140D GLU* 2.8 18.7 + - - -
156D CYS* 2.0 53.8 - - + -
168D MET* 4.2 1.8 - - + -
169D SER 3.2 4.7 - - - -
170D TRP* 3.8 10.2 - - + -
213D LEU* 3.7 15.9 - - + -
229D TYR* 1.3 76.2 - - - +
231D ALA* 1.3 62.9 + - - +
243D TRP* 3.6 1.6 - - - -
244D GLY 3.1 24.1 + - - -
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Residues in contact with ALA 231 (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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138D LEU* 4.0 1.1 - - - -
168D MET* 3.3 11.1 - - - +
169D SER* 2.9 45.7 + - - +
171D VAL* 5.2 1.6 - - + -
230D CYS* 1.3 77.6 - - - +
232D ARG* 1.3 60.5 + - - +
233D TYR 3.8 0.3 + - - -
240D MET* 3.9 20.9 - - + -
242D PHE 3.2 12.3 - - - +
243D TRP* 4.1 17.9 - - + -
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Residues in contact with ARG 232 (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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136D VAL* 4.5 20.3 - - - +
138D LEU* 4.0 6.4 - - + +
161D PHE* 3.4 39.0 - - + +
166D TYR* 3.2 62.8 + - + -
168D MET* 3.7 16.2 - - - -
231D ALA* 1.3 71.0 - - - +
233D TYR* 1.3 60.4 + - - +
234D ILE* 4.1 5.5 - - - +
240D MET* 3.0 22.6 - - - +
241D ASP* 2.7 55.7 + - - +
242D PHE* 3.0 21.4 + - + +
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Residues in contact with TYR 233 (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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30C LEU* 5.2 1.8 - - + -
92D GLN* 5.0 0.2 - - - -
101D TRP* 3.4 29.3 - + - -
166D TYR* 3.5 22.7 - - - +
167D ALA* 2.8 39.4 + - + +
168D MET 3.5 24.5 - - - -
169D SER* 3.2 24.6 + - - -
181D TRP* 3.2 27.9 + - - -
184D ALA* 3.7 11.0 - - + -
231D ALA 3.8 0.8 + - - -
232D ARG* 1.3 71.6 - - - +
234D ILE* 1.3 62.6 + - - +
235D ASP 3.6 1.4 + - - +
237D GLY* 3.5 37.2 - - - +
239D HIS 3.5 10.8 - - - -
240D MET* 3.9 20.0 - - + +
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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