Contacts of the strand formed by residues 137 - 141 (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 GLN 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D GLU 4.5 4.5 - - - +
136D VAL* 1.3 82.9 + - - +
138D LEU* 1.3 67.1 + - - +
139D VAL* 4.8 14.9 - - + +
157D ALA 3.3 2.4 - - - +
158D ALA* 3.2 8.0 - - - -
159D SER* 2.6 49.3 + - - +
161D PHE* 4.5 0.2 - - - -
242D PHE* 4.8 2.7 - - + -
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Residues in contact with LEU 138 (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* 5.1 2.0 - - + -
137D GLN* 1.3 84.5 - - - +
139D VAL* 1.3 66.7 + - - +
140D GLU* 3.8 0.9 - - - +
156D CYS* 4.0 4.0 - - - -
157D ALA 3.4 1.6 - - - -
158D ALA* 3.8 20.2 - - + -
161D PHE* 4.2 10.8 - - + -
168D MET* 3.8 17.3 - - + -
230D CYS* 3.7 20.2 - - - +
231D ALA* 4.0 2.0 - - - -
232D ARG* 4.0 11.7 - - + +
242D PHE* 3.4 42.6 - - + +
243D TRP 3.9 1.8 + - - -
244D GLY* 3.4 35.3 - - - +
245D GLN 4.2 2.1 + - - -
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Residues in contact with VAL 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLN* 4.8 15.9 - - + +
138D LEU* 1.3 83.8 - - - +
140D GLU* 1.3 69.3 + - - +
141D SER* 3.8 7.7 + - - +
156D CYS* 3.4 2.6 - - - -
157D ALA* 2.8 45.9 + - + +
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Residues in contact with GLU 140 (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 1.9 - - - +
139D VAL* 1.3 81.9 - - - +
141D SER* 1.3 61.5 + - - +
155D SER 3.1 12.1 - - - +
156D CYS* 4.0 2.2 - - + +
170D TRP* 4.1 16.6 - - + -
228D TYR 3.5 3.4 - - - +
229D TYR* 3.6 2.9 - - - -
230D CYS* 2.8 33.3 + - - -
244D GLY* 3.2 12.4 - - - -
245D GLN* 2.8 24.2 + - - +
246D GLY* 2.9 40.7 + - - +
247D THR* 3.4 14.9 - - + +
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Residues in contact with SER 141 (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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139D VAL* 3.8 8.9 + - - +
140D GLU* 1.3 75.3 - - - +
142D GLY* 1.3 61.6 + - - +
143D GLY 3.3 6.0 + - - -
154D LEU* 3.6 8.8 - - - +
155D SER* 2.9 39.9 + - - +
157D ALA* 5.2 2.1 + - - +
247D THR* 4.0 7.3 - - - +
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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