Contacts of the strand formed by residues 226 - 230 (chain S) in PDB entry 5JBA
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 GLY 226 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182S CYS* 3.3 5.9 - - - -
183S ALA 3.0 37.1 + - - -
189S ASP* 3.4 24.0 + - - -
215S TRP 4.1 0.9 - - - -
225S TYR* 1.3 73.1 - - - +
227S ILE* 1.3 61.2 + - - -
228S TYR* 3.3 11.6 - - - -
302S 0G6 3.6 12.3 - - - -
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Residues in contact with ILE 227 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171S SER* 5.5 2.9 - - - +
172S THR* 5.5 2.2 - - + -
176S ILE* 4.0 13.7 - - + -
180S MET* 3.9 20.0 - - + -
181S PHE 3.5 8.3 - - - +
182S CYS* 3.5 30.7 - - - -
213S ILE* 5.4 0.2 - - - +
214S SER* 3.2 8.6 + - - -
215S TRP* 2.9 90.5 + - + +
216S GLY* 4.5 1.1 - - - -
225S TYR* 3.6 11.4 - - + +
226S GLY* 1.3 75.6 - - - -
228S TYR* 1.3 69.4 + - - +
302S 0G6 4.5 1.1 + - - -
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Residues in contact with TYR 228 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138S VAL* 3.5 32.2 - - + +
160S VAL* 4.4 7.0 - - + +
180S MET* 3.1 8.5 - - - -
181S PHE* 2.8 69.4 + + + +
183S ALA* 3.8 20.5 + - + -
189S ASP* 4.2 2.9 + - - -
190S SER* 2.8 30.0 + - - -
199S HIS* 4.1 11.0 - + + -
212S VAL 3.4 7.9 - - - +
213S ILE* 3.6 31.6 - - + -
214S SER* 4.2 2.9 - - - -
226S GLY* 3.3 28.9 - - - -
227S ILE* 1.3 74.9 - - - +
229S THR* 1.3 62.6 + - - +
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Residues in contact with THR 229 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99S TYR 5.3 0.3 + - - -
102S ASP* 2.8 41.1 + - - +
103S ILE* 4.1 12.3 - - + -
179S ASN 3.6 7.2 - - - +
180S MET* 5.2 1.8 - - - -
181S PHE* 3.8 1.0 - - - -
211S GLY* 3.1 10.4 - - - -
212S VAL* 2.9 36.5 + - - -
214S SER* 3.6 14.7 - - - -
228S TYR* 1.3 70.7 - - - +
230S LYS* 1.3 61.0 + - - +
231S VAL* 3.2 3.0 + - - +
234S TYR* 3.7 31.2 - - + -
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Residues in contact with LYS 230 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129S ASN* 5.0 8.7 - - + -
131S LEU* 4.4 14.4 - - + -
165S ARG* 4.3 7.4 - - - +
178S ASN* 2.9 42.5 + - - +
179S ASN* 2.8 23.4 + - - +
180S MET 3.5 16.0 + - - +
181S PHE* 3.9 25.1 - - + -
210S THR 5.2 0.2 - - - +
228S TYR 3.4 1.6 + - - -
229S THR* 1.3 68.2 - - - +
231S VAL* 1.3 64.5 + - - +
232S SER* 3.5 21.5 - - - +
233S ARG* 3.2 19.6 + - + +
234S TYR* 3.3 15.3 - - - -
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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
------------------------------------------------------------
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