Contacts of the strand formed by residues 152 - 159 (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 LEU 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142D GLY 3.4 21.3 - - - +
143D GLY 4.8 2.7 - - - +
144D GLY* 4.0 15.9 - - - +
145D LEU 5.8 0.2 - - - +
146D VAL* 4.1 29.2 - - + -
151D SER* 1.3 80.9 - - - +
153D ARG* 1.3 61.6 + - - +
154D LEU* 4.2 1.1 - - + -
215D LEU 3.7 0.6 - - - +
216D GLN* 3.4 6.6 - - - +
217D MET* 2.7 45.9 + - - +
220D LEU* 3.9 8.0 - - + +
249D VAL* 3.8 32.5 - - + -
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Residues in contact with ARG 153 (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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142D GLY* 3.7 19.1 - - - +
152D LEU* 1.3 78.1 - - - +
154D LEU* 1.3 74.2 + - - +
155D SER* 5.0 4.0 + - - +
205D SER* 5.6 1.6 + - - -
214D TYR* 3.4 47.2 - - + +
215D LEU 3.5 6.7 - - - +
216D GLN* 3.3 31.6 - - - +
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Residues in contact with LEU 154 (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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141D SER 3.6 13.2 - - - +
142D GLY 3.7 20.2 - - - +
143D GLY* 3.8 3.8 - - - +
152D LEU* 5.1 1.8 - - + -
153D ARG* 1.3 75.1 - - - +
155D SER* 1.3 61.4 + - - +
170D TRP* 3.7 22.4 - - + -
214D TYR* 3.0 30.5 - - - +
215D LEU* 2.9 21.1 + - + +
217D MET* 3.8 20.6 - - - -
228D TYR* 3.6 44.9 - - + -
247D THR* 3.8 11.0 - - + -
249D VAL* 4.1 8.3 - - + -
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Residues in contact with SER 155 (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* 3.1 8.0 - - - +
141D SER* 2.9 46.4 + - - +
142D GLY* 5.9 0.4 - - - -
153D ARG* 3.9 5.1 + - - -
154D LEU* 1.3 74.2 - - - +
156D CYS* 1.3 61.8 + - - +
157D ALA* 5.2 0.7 - - - -
170D TRP* 3.6 4.1 - - - -
212D THR* 3.9 10.4 - - - +
213D LEU 3.3 5.2 - - - -
214D TYR* 3.6 21.8 - - - -
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Residues in contact with CYS 156 (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* 3.9 21.8 - - - -
139D VAL 3.4 8.1 - - - -
140D GLU* 4.0 0.7 - - - +
155D SER* 1.3 76.3 - - - +
157D ALA* 1.3 60.8 + - - +
158D ALA* 3.7 1.9 + - - +
168D MET* 4.5 4.7 - - - -
170D TRP* 3.8 8.1 - - + -
211D ASN 3.6 1.0 - - - +
212D THR* 3.2 11.1 - - - +
213D LEU* 2.8 35.9 + - + +
230D CYS* 2.0 52.7 - - + -
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Residues in contact with ALA 157 (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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137D GLN 3.3 5.2 - - - +
138D LEU* 3.4 0.5 - - - -
139D VAL* 2.8 49.5 + - + +
141D SER* 5.2 2.6 + - - +
155D SER* 5.2 1.1 - - - -
156D CYS* 1.3 71.2 - - - +
158D ALA* 1.3 60.8 + - - +
159D SER* 5.4 0.7 - - - -
211D ASN 3.9 4.3 - - - -
212D THR* 4.9 5.6 - - + +
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Residues in contact with ALA 158 (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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137D GLN 3.2 4.3 - - - -
138D LEU* 3.8 10.3 - - + -
156D CYS* 4.8 2.2 - - - +
157D ALA* 1.3 75.5 - - - +
159D SER* 1.3 65.3 + - - +
161D PHE* 3.8 26.2 - - + -
163D PHE* 3.8 19.7 - - + -
211D ASN* 3.0 37.5 + - - +
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Residues in contact with SER 159 (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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135D GLU 4.3 3.1 + - - -
136D VAL* 3.2 2.6 - - - -
137D GLN* 2.6 51.7 + - - +
157D ALA 5.4 0.4 - - - -
158D ALA* 1.3 77.7 - - - +
160D GLY* 1.3 62.9 + - - +
161D PHE* 3.3 12.3 - - - +
211D ASN* 5.6 1.3 - - - +
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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