Contacts of the strand formed by residues 239 - 247 (chain A) in PDB entry 5ON2
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 TYR 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A VAL* 3.3 38.8 + - + +
237A ASN 3.4 3.7 + - - +
238A ASP* 1.3 77.9 - - - +
240A ASP* 1.3 66.5 + - - +
241A ASN* 3.2 52.9 + - + +
243A LEU* 4.5 3.4 - - + -
266A PRO* 3.2 31.1 + - - +
267A LEU* 3.4 37.1 + - + -
270A LYS* 3.8 39.5 - - + +
307A PHE* 4.6 6.5 - + + -
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Residues in contact with ASP 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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239A TYR* 1.3 78.9 - - - +
241A ASN* 1.3 72.5 + - - +
242A THR* 3.6 8.1 + - - +
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Residues in contact with ASN 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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236A VAL* 4.4 4.3 + - - +
239A TYR* 3.2 48.9 + - + +
240A ASP* 1.3 85.3 - - - +
242A THR* 1.3 65.6 + - - +
243A LEU* 4.1 1.9 + - - +
266A PRO* 5.5 8.2 - - + +
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Residues in contact with THR 242 (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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233A THR* 4.0 17.2 - - + +
234A PHE 3.3 11.7 - - - +
235A ASN* 3.4 28.0 - - - +
236A VAL* 5.5 0.4 - - - -
240A ASP 3.6 6.7 + - - +
241A ASN* 1.3 80.3 - - - +
243A LEU* 1.3 65.3 + - - +
244A THR* 4.1 4.4 + - - -
265A HIS* 5.9 0.2 - - - -
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Residues in contact with LEU 243 (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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233A THR* 3.5 0.8 - - - -
234A PHE* 2.7 53.2 + - + +
236A VAL* 4.7 7.7 - - + +
239A TYR* 4.5 2.5 - - + -
241A ASN 4.1 7.2 + - - +
242A THR* 1.3 78.3 - - - +
244A THR* 1.3 61.4 + - - +
245A VAL* 5.2 2.7 - - + -
259A LEU* 4.7 9.4 - - + -
261A VAL* 4.2 24.5 - - + -
265A HIS* 3.9 25.1 - - + -
267A LEU* 3.4 38.1 - - + -
309A ALA* 5.5 0.4 - - + -
320A VAL* 4.5 13.0 - - + -
334A ALA* 4.5 8.5 - - + -
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Residues in contact with THR 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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231A GLU* 3.8 35.2 - - + +
232A ILE 3.4 9.9 - - - +
233A THR* 3.8 24.3 + - - +
242A THR* 4.1 5.7 + - - -
243A LEU* 1.3 73.3 - - - +
245A VAL* 1.3 60.1 + - - +
265A HIS* 5.5 2.3 + - - -
332A THR* 2.6 35.0 + - + -
334A ALA* 4.3 5.2 + - - +
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Residues in contact with VAL 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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230A VAL 3.7 0.2 - - - +
231A GLU* 3.2 3.8 - - - -
232A ILE* 2.7 52.3 + - + +
234A PHE* 3.7 26.2 - - + -
243A LEU* 4.8 3.1 - - + +
244A THR* 1.3 78.6 - - - +
246A TYR* 1.3 59.4 + - - +
259A LEU* 5.1 4.7 - - + -
332A THR* 3.5 8.1 - - - -
334A ALA* 3.4 34.1 - - + +
335A VAL* 3.7 14.1 - - - +
336A MET* 4.0 26.5 - - + +
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Residues in contact with TYR 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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227A SER* 2.9 32.7 + - - -
228A GLU 3.5 1.2 - - - -
229A GLY* 3.0 31.7 + - - -
230A VAL 3.6 7.9 - - - -
231A GLU* 3.7 21.3 - - + +
245A VAL* 1.3 80.2 - - - +
247A THR* 1.3 71.8 + - - +
248A THR* 4.1 17.2 - - + +
330A TYR* 4.7 3.4 - + - -
331A GLY* 4.5 17.5 - - - -
332A THR* 4.0 5.0 + - - +
334A ALA 4.0 5.1 + - - -
335A VAL* 4.7 4.2 - - - +
336A MET* 4.7 0.9 - - - +
412A LYS* 3.4 18.9 + - + -
414A ASN* 3.3 32.8 - - + -
902A VRT 3.7 41.6 + + + +
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Residues in contact with THR 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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229A GLY* 3.3 2.1 - - - -
230A VAL* 2.9 40.1 + - - +
232A ILE* 3.8 15.0 - - + -
246A TYR* 1.3 81.2 - - - +
248A THR* 1.3 63.0 + - - +
249A ARG* 3.1 17.5 + - - +
250A PRO* 4.1 17.2 - - + +
336A MET* 3.6 27.1 - - + +
902A VRT 3.1 26.6 + - - -
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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