Contacts of the strand formed by residues 233 - 239 (chain B) in PDB entry 2Y7Q
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 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B PRO 4.5 3.3 + - - -
232B PRO* 1.3 74.1 - - - +
234B VAL* 1.3 65.9 + - - +
235B LYS* 4.1 4.2 + - + -
255B LEU 3.1 6.6 - - - +
256B VAL* 3.5 1.6 - - - -
257B SER* 3.0 39.4 + - - -
258B GLY* 5.2 1.2 + - - -
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Residues in contact with VAL 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B PRO* 4.0 6.3 + - + +
233B THR* 1.3 82.3 - - - +
235B LYS* 1.3 65.0 + - - +
254B CYS* 3.7 28.5 - - - -
255B LEU 3.4 2.7 - - - +
256B VAL* 4.4 6.3 - - + -
312B CYS* 4.0 8.5 - - - +
314B VAL* 3.5 27.6 - - + -
321B PHE* 3.9 22.4 - - + -
322B GLU 4.6 5.7 - - - +
323B ASP* 3.8 31.2 - - + +
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Residues in contact with LYS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B THR* 4.1 3.6 + - + -
234B VAL* 1.3 76.7 - - - +
236B ILE* 1.3 64.3 + - - +
237B LEU* 4.4 13.2 - - + -
253B LEU 3.5 0.3 - - - +
254B CYS* 3.6 1.2 - - - -
255B LEU* 2.7 68.0 + - + +
323B ASP* 4.0 6.7 - - - +
252D GLN* 5.2 12.3 - - - -
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LYS* 1.3 76.8 - - - +
237B LEU* 1.3 73.4 + - - +
253B LEU* 3.0 39.3 - - + +
254B CYS* 4.9 1.1 - - - -
268B TRP* 4.3 10.5 - - + -
310B TYR 4.5 1.1 - - - +
312B CYS* 4.1 17.9 - - + -
323B ASP* 3.5 41.5 + - + +
324B SER* 4.2 0.9 - - - -
325B THR* 3.5 23.3 - - + -
239D SER* 4.2 0.2 - - - -
240D SER* 2.9 42.6 + - - +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B LYS* 4.1 13.7 + - + -
236B ILE* 1.3 82.6 - - - +
238B GLN* 1.3 59.7 + - - +
253B LEU* 2.7 45.6 + - + +
255B LEU* 3.5 26.7 - - + -
237D LEU* 3.8 26.2 - - + +
238D GLN 3.1 13.9 - - - +
239D SER* 4.0 13.0 - - - +
252D GLN* 5.4 9.4 - - + -
253D LEU* 3.6 36.8 - - + -
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Residues in contact with GLN 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ILE 4.3 0.4 + - - -
237B LEU* 1.3 75.5 - - - +
239B SER* 1.3 74.2 + - - +
247B PHE* 5.8 1.4 - - - -
251B ILE* 4.7 5.2 - - + +
252B GLN 3.3 11.2 - - - +
253B LEU* 3.9 13.1 - - + +
304B TRP* 3.7 35.4 - - - +
325B THR* 4.1 1.7 + - - -
326B LYS 5.0 0.5 - - - +
328B CYS* 5.5 8.7 - - - +
237D LEU* 3.3 12.7 - - - -
238D GLN* 2.7 65.8 + - + +
239D SER 4.2 4.9 - - - +
240D SER* 3.6 18.8 - - - -
241D CYS* 4.2 2.3 + - - +
328D CYS* 5.1 7.5 - - - -
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238B GLN* 1.3 91.5 + - - +
240B SER* 1.3 63.9 + - - +
241B CYS* 5.5 1.4 - - - -
248B PRO* 3.9 24.0 - - - +
250B THR 3.9 3.8 + - - -
251B ILE* 3.7 10.0 - - - +
252B GLN* 2.8 40.7 + - - +
236D ILE 4.6 0.2 - - - -
237D LEU* 4.3 9.0 - - - +
238D GLN* 3.9 3.1 + - - -
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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