Contacts of the strand formed by residues 167 - 173 (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 167 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C SER* 3.8 16.5 - - - +
30C LEU* 3.7 30.7 - - + -
166D TYR* 1.3 77.3 - - - +
168D MET* 1.3 63.6 + - - +
185D ILE 3.4 15.9 - - - +
187D GLY 4.0 2.5 - - - +
206D ARG* 3.6 0.7 - - - +
232D ARG 3.8 0.2 - - - -
233D TYR* 2.8 45.8 + - + +
235D ASP 5.1 0.9 + - - +
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Residues in contact with MET 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LEU* 3.8 24.0 - - + -
156D CYS* 4.5 2.2 - - - -
161D PHE* 4.6 4.3 - - - -
163D PHE* 3.8 27.8 - - + -
166D TYR* 4.7 1.6 - - - +
167D ALA* 1.3 75.6 - - - +
169D SER* 1.3 61.5 + - - +
184D ALA* 3.4 3.1 - - - -
185D ILE* 3.0 33.4 + - + +
206D ARG* 3.3 21.1 - - - +
213D LEU* 3.8 34.5 - - + -
230D CYS* 4.2 4.0 - - - -
231D ALA 3.3 28.3 - - - +
232D ARG* 3.7 23.1 - - - -
233D TYR* 3.5 6.4 - - - -
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Residues in contact with SER 169 (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* 1.3 72.2 - - - +
170D TRP* 1.3 65.5 + - - +
171D VAL* 3.9 5.0 - - - +
181D TRP* 3.9 4.9 - - - -
183D SER 3.4 14.1 - - - -
184D ALA* 4.2 0.4 - - - +
204D ILE* 4.7 1.1 - - - -
213D LEU* 3.9 2.2 - - - +
230D CYS* 3.2 8.7 - - - +
231D ALA* 2.9 47.8 + - - +
233D TYR* 3.2 30.3 - - - -
240D MET* 3.6 11.3 - - - -
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Residues in contact with TRP 170 (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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140D GLU* 4.1 11.4 - - + -
154D LEU* 3.7 30.1 - - + -
155D SER 3.6 22.0 - - - -
156D CYS* 3.8 8.1 - - + -
169D SER* 1.3 73.3 - - - +
171D VAL* 1.3 65.8 + - - +
181D TRP* 3.8 0.2 - - - -
182D VAL* 3.2 33.8 + - + +
183D SER* 3.1 10.6 + - - +
204D ILE* 3.6 21.3 - - + -
213D LEU* 3.3 41.8 - - + +
214D TYR 2.9 22.0 + - - -
215D LEU* 3.5 33.1 - - + +
228D TYR* 4.2 16.4 - - + -
229D TYR 3.3 20.4 - - - -
230D CYS* 3.8 12.8 - - + -
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Residues in contact with VAL 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PHE* 4.0 24.9 - - + -
169D SER* 3.9 15.9 - - - +
170D TRP* 1.3 81.8 - - - +
172D ARG* 1.3 62.2 - - - +
179D LEU* 4.2 9.9 - - + -
180D GLU 3.5 24.2 - - - +
181D TRP* 4.2 9.2 - - + -
182D VAL* 4.3 1.3 - - - -
228D TYR* 4.6 1.3 - - - -
229D TYR* 2.7 45.5 + - - +
231D ALA* 5.2 0.9 - - + -
240D MET* 4.5 2.9 - - - -
243D TRP* 3.9 32.1 - - + -
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Residues in contact with ARG 172 (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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162B THR* 5.6 2.6 + - - -
171D VAL* 1.3 77.4 - - - +
173D GLN* 1.3 61.0 + - - +
174D ALA* 5.1 1.6 - - + +
178D GLY 4.2 0.2 - - - +
179D LEU* 3.7 3.8 - - - -
180D GLU* 2.9 70.4 + - + +
182D VAL* 3.5 18.0 - - + +
197D SER* 4.0 17.8 - - - -
198D VAL* 4.1 7.2 - - - +
201D ARG* 5.3 0.2 - - - +
202D PHE* 3.9 11.5 - - - -
223D GLU* 4.1 11.7 + - - +
224D ASP* 3.1 35.8 + - - +
226D ALA* 3.9 12.3 - - + -
227D VAL 3.2 10.5 - - - +
228D TYR* 3.0 39.9 + - + -
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Residues in contact with GLN 173 (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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20A GLN* 3.8 2.9 + - - -
41D GLN* 3.2 39.9 + - - -
88D ASP* 5.0 2.6 + - - -
90D TYR* 3.3 15.2 + - - -
172D ARG* 1.3 74.4 - - - +
174D ALA* 1.3 67.4 + - - +
177D LYS 2.7 31.6 + - - +
178D GLY* 3.8 6.9 - - - -
179D LEU* 3.7 14.7 - - + +
226D ALA* 2.9 15.7 - - - +
227D VAL* 2.9 24.9 + - + +
229D TYR* 4.2 11.3 + - + -
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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