Contacts of the strand formed by residues 243 - 249 (chain A) in PDB entry 3O9Z
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 THR 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A VAL 3.3 8.3 - - - -
158A THR* 3.8 20.0 - - - +
159A GLY 4.5 1.8 - - - +
232A VAL* 3.8 10.8 - - - +
236A LEU* 4.9 3.3 - - - +
241A LYS* 3.7 8.0 - - - +
242A ARG* 1.3 88.0 - - + +
244A TYR* 1.3 66.0 + - - +
245A ARG* 3.8 22.9 + - - +
255A GLU* 4.4 2.3 - - - +
257A SER* 3.6 15.3 + - - -
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR* 3.4 32.0 - - + +
157A VAL* 2.8 41.8 + - + -
232A VAL* 4.3 4.0 - - + -
233A PRO* 3.4 37.6 - - + +
236A LEU* 3.6 25.6 - - + -
243A THR* 1.3 76.8 - - - +
245A ARG* 1.3 59.4 + - - +
246A SER* 3.4 20.2 + - - -
253A GLU* 2.8 26.4 + - - -
255A GLU* 3.5 22.4 - - + -
308A PHE* 4.9 2.2 - + - -
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Residues in contact with ARG 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A THR 3.5 3.8 - - - -
156A TYR* 3.6 27.5 + - + +
157A VAL 4.3 6.7 - - - +
158A THR* 3.5 10.1 + - - -
243A THR* 3.8 18.8 + - - +
244A TYR* 1.3 76.2 - - - +
246A SER* 1.3 59.7 + - - +
255A GLU* 2.9 13.6 + - - -
256A PHE* 2.9 57.7 + - + -
257A SER* 2.9 39.5 + - - +
260A PHE* 3.7 28.5 - - - +
261A THR* 5.6 2.2 - - - +
312A AKG 2.9 40.4 + - - -
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Residues in contact with SER 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A VAL 3.8 1.2 + - - +
154A LEU* 3.4 8.0 - - - +
155A THR* 2.8 39.4 + - - +
244A TYR* 3.4 36.7 + - - -
245A ARG* 1.3 73.8 - - - +
247A ILE* 1.3 61.6 + - - +
248A ALA* 4.1 4.2 + - - +
253A GLU* 2.6 30.0 + - - -
254A VAL 3.4 4.9 - - - -
255A GLU* 4.3 0.7 - - - +
256A PHE* 3.8 4.9 - - - -
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Residues in contact with ILE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 4.1 7.0 - - + -
139A LEU* 3.7 20.9 - - + -
152A VAL* 3.7 19.3 - - + -
153A VAL 3.7 2.0 - - - -
154A LEU* 3.7 13.2 - - + -
189A LEU* 4.3 5.2 - - + -
190A LEU* 4.0 22.0 - - + -
193A LEU* 3.8 28.3 - - + -
194A PHE* 4.3 2.0 - - + -
246A SER* 1.3 73.9 - - - +
248A ALA* 1.3 62.3 + - - +
249A VAL* 3.9 14.2 + - + +
252A GLU 3.6 2.3 - - - +
254A VAL* 2.9 46.0 + - + +
256A PHE* 3.8 11.4 - - + -
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASP 3.8 0.9 - - - +
152A VAL* 3.2 6.8 - - - +
153A VAL* 2.9 51.8 + - + +
246A SER* 4.1 2.2 - - - +
247A ILE* 1.3 73.4 - - - +
249A VAL* 1.3 62.3 + - - +
250A ASP 4.0 0.2 + - - -
251A GLY* 4.6 7.6 + - - -
252A GLU 3.2 15.7 - - - +
253A GLU* 4.2 11.7 - - + +
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Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LEU* 4.4 22.7 - - + -
143A LEU* 3.9 14.6 - - + -
146A GLU* 5.0 2.0 - - - +
150A LYS* 3.8 33.7 - - + -
151A ASP 3.7 2.7 - - - -
152A VAL* 4.2 10.5 - - + -
194A PHE* 4.4 6.5 - - + -
247A ILE* 3.9 25.1 - - + +
248A ALA* 1.3 75.3 - - - +
250A ASP* 1.3 75.8 + - + +
251A GLY 3.1 0.2 - - - -
252A GLU* 2.9 29.0 + - + +
254A VAL* 6.5 0.2 - - + -
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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