Contacts of the strand formed by residues 236 - 241 (chain A) in PDB entry 7UUT
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 VAL 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A THR* 3.6 28.9 - - + +
171A ALA* 3.9 21.3 - - + +
195A ILE* 4.5 3.8 - - + -
227A ILE* 3.9 24.5 - - + -
231A THR* 4.2 3.1 - - + -
235A GLY* 1.3 78.2 - - - -
237A ASP* 1.3 61.6 + - - +
238A ALA 3.4 24.5 - - - +
239A ALA 4.3 0.2 - - - +
255A ILE* 2.9 21.4 + - + +
256A VAL* 3.5 10.6 - - + -
257A LYS* 2.9 29.8 + - - +
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Residues in contact with ASP 237 (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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162A ALA 5.3 0.2 - - - +
165A GLU* 5.3 5.3 - - - +
168A ALA* 3.4 22.7 - - + -
169A THR* 2.7 39.8 + - - +
236A VAL* 1.3 73.9 - - - +
238A ALA* 1.3 61.9 + - + +
256A VAL* 4.6 0.9 - - - -
257A LYS* 2.8 37.8 + - - +
260A GLY* 3.2 25.8 - - - -
261A THR* 3.4 0.9 + - - -
97B ARG* 4.2 10.6 + - - -
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Residues in contact with ALA 238 (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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162A ALA* 3.7 36.1 - - + +
163A ASP 5.5 0.9 - - - +
164A ILE* 4.6 3.1 - - + -
168A ALA* 6.4 0.2 - - + -
169A THR 3.4 2.0 + - - -
170A VAL* 3.3 18.0 - - + +
171A ALA 2.9 23.4 + - - +
236A VAL* 3.3 8.7 - - - +
237A ASP* 1.3 81.1 - - + +
239A ALA* 1.3 61.2 + - - +
256A VAL* 4.5 1.1 - - - -
261A THR 3.3 13.5 - - - +
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Residues in contact with ALA 239 (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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171A ALA* 3.2 8.3 - - + +
173A LEU* 4.6 4.5 - - + -
236A VAL* 4.4 0.9 - - + -
238A ALA* 1.3 75.1 - - - +
240A ILE* 1.3 62.3 + - - +
241A ILE 4.0 0.7 + - - -
252A ALA* 4.3 15.3 - - + -
255A ILE* 4.1 22.0 - - + -
256A VAL* 3.5 21.4 - - + +
261A THR 3.1 6.3 + - - +
262A ILE* 3.5 4.2 - - + +
263A ALA* 2.9 26.5 + - - +
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Residues in contact with ILE 240 (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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158A GLY* 3.8 22.4 - - - +
159A ALA* 3.6 32.1 - - + +
162A ALA* 4.1 12.3 - - + -
164A ILE* 4.8 0.4 - - + -
170A VAL* 4.1 22.2 - - + -
171A ALA 2.8 11.6 + - - +
172A VAL* 3.5 9.0 - - + +
173A LEU* 2.8 32.6 + - - -
182A ALA* 3.8 34.5 - - + +
186A ALA* 4.7 1.8 - - + -
239A ALA* 1.3 74.5 - - - +
241A ILE* 1.3 66.8 + - - +
242A ALA* 3.6 1.5 + - + +
263A ALA* 3.2 9.2 - - + +
265A VAL* 4.5 3.6 - - + -
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Residues in contact with ILE 241 (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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173A LEU* 4.0 12.1 - - + -
239A ALA 4.9 0.4 - - - +
240A ILE* 1.3 72.4 - - - +
242A ALA* 1.3 60.5 + - - +
243A GLY 3.8 7.9 - - - +
248A ILE* 3.6 25.1 - - + +
249A MET* 4.0 30.7 - - + -
252A ALA* 3.7 31.4 - - + -
262A ILE* 3.7 18.8 - - + -
263A ALA 2.8 9.6 + - - +
264A ASN* 3.2 24.5 - - + +
265A VAL* 2.9 32.1 + - - +
266A ASN* 3.4 8.0 + - + -
268A PHE* 4.3 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