Contacts of the strand formed by residues 225 - 233 (chain A) in PDB entry 2JFS
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 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA 4.2 0.3 - - - +
11A THR* 3.5 1.6 - - - -
12A ASP* 2.8 41.0 + - - +
184A SER* 3.6 2.9 - - - -
186A GLY* 3.3 22.1 + - - -
187A LEU* 3.9 29.2 - - + +
213A VAL* 4.2 16.9 - - + +
216A ALA* 3.5 19.8 - - + +
217A ASN* 5.1 4.4 + - - -
221A GLY* 6.1 0.2 - - - -
223A ASP 3.6 6.2 + - - -
224A ASN* 1.3 71.9 - - - +
226A THR* 1.3 65.0 + - - +
227A VAL* 4.2 12.3 - - + -
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Residues in contact with THR 226 (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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10A ALA 3.3 11.7 - - - +
11A THR* 2.6 27.9 + - - +
22A ASP* 2.6 28.6 + - - +
23A ALA 4.1 9.9 - - - +
24A CYS* 3.6 30.5 - - + -
33A VAL* 4.4 7.6 - - + -
182A ILE 4.6 0.2 - - - -
183A SER* 3.2 5.2 - - - +
184A SER* 2.9 33.6 + - - +
225A THR* 1.3 71.9 - - - +
227A VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 227 (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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9A THR* 3.2 4.0 - - - -
10A ALA* 2.9 41.6 + - + +
181A LEU* 4.0 11.7 - - + -
182A ILE 3.3 4.5 - - - -
183A SER* 3.8 16.2 - - - -
187A LEU* 4.0 17.3 - - + -
209A VAL* 3.8 38.6 - - + +
212A LEU* 4.2 13.0 - - + -
213A VAL* 4.4 4.7 - - + -
225A THR* 4.2 10.1 - - + -
226A THR* 1.3 82.9 - - - +
228A VAL* 1.3 66.7 + - - +
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Residues in contact with VAL 228 (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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8A ALA 3.4 9.2 - - - +
9A THR* 3.9 12.8 - - + -
24A CYS* 3.9 19.1 - - + -
25A LEU 4.4 2.0 - - - +
31A TYR* 3.9 37.9 - - + -
32A ALA 3.9 7.2 - - - +
33A VAL* 3.7 21.5 - - + -
180A LEU 3.7 0.7 - - - +
181A LEU* 3.3 5.5 - - - +
182A ILE* 2.9 40.7 + - + +
227A VAL* 1.3 80.5 - - - +
229A VAL* 1.3 63.2 + - - +
230A ILE* 4.1 8.6 - - + +
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Residues in contact with VAL 229 (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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7A ALA* 3.1 6.8 - - - +
8A ALA 2.9 33.0 + - - +
179A ARG* 3.4 44.2 - - + +
180A LEU 3.4 2.9 - - - +
181A LEU* 3.8 21.3 - - + -
200A ALA* 5.4 1.6 - - + +
205A PRO* 3.8 16.8 - - + +
208A ALA* 4.3 7.0 - - + -
209A VAL* 3.6 24.0 - - + +
212A LEU* 4.2 11.4 - - + -
228A VAL* 1.3 75.7 - - - +
230A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 230 (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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4A VAL* 3.9 34.8 - - + -
6A SER 3.7 2.7 - - - -
7A ALA* 4.3 0.2 - - - -
31A TYR* 3.6 48.7 - - + -
94A VAL* 4.7 5.4 - - + -
96A VAL* 4.6 2.7 - - + -
179A ARG* 3.3 4.7 - - - -
180A LEU* 2.8 63.6 + - + +
182A ILE* 4.4 11.0 - - + -
228A VAL* 4.1 7.2 - - + -
229A VAL* 1.3 79.6 - - - +
231A ASP* 1.3 63.7 + - - +
232A LEU* 3.9 17.7 + - + +
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Residues in contact with ASP 231 (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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4A VAL* 3.6 4.9 - - - +
5A LEU* 2.8 36.9 + - + -
6A SER* 2.9 25.4 + - - +
178A ASP 3.9 2.6 - - - +
179A ARG* 2.7 55.6 + - - +
203A PRO 4.0 2.1 - - - +
205A PRO* 3.2 18.9 - - - +
229A VAL 4.2 0.4 - - - -
230A ILE* 1.3 72.1 - - - +
232A LEU* 1.3 58.5 + - - +
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Residues in contact with LEU 232 (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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2A ALA* 4.2 12.1 - - + -
3A SER 3.2 13.0 - - - +
5A LEU* 3.9 9.0 - - - +
96A VAL* 4.1 24.5 - - + -
174A CYS* 3.6 37.9 - - + -
175A GLY 3.8 16.4 - - - +
176A PRO* 4.3 0.2 - - - -
177A GLY* 2.9 24.2 + - - -
178A ASP* 3.0 22.7 + - + +
180A LEU* 4.2 15.0 - - + -
230A ILE* 3.9 26.5 - - + +
231A ASP* 1.3 75.7 - - - +
233A GLY* 1.3 58.2 + - - +
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Residues in contact with GLY 233 (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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2A ALA* 3.6 7.6 + - - -
3A SER* 2.8 39.6 + - - -
5A LEU* 3.5 27.4 - - - +
176A PRO* 3.6 28.6 - - - +
177A GLY 4.4 0.7 - - - -
232A LEU* 1.3 74.6 - - - +
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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