Contacts of the strand formed by residues 288 - 293 (chain B) in PDB entry 5XOC
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 288 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B ASP* 4.7 0.4 + - - -
238B PHE* 3.1 38.8 + - + -
283B ILE* 3.6 38.2 - - + +
285B GLY 2.3 31.3 + - - -
286B ILE* 3.8 0.4 - - - +
287B PRO* 1.3 76.0 + - - +
289B LEU* 1.3 72.8 - - - +
290B LEU* 4.5 4.5 - - + -
300B THR* 5.1 2.9 - - - +
301B LYS 3.7 5.8 - - - +
302B VAL* 3.5 21.2 - - + +
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Residues in contact with LEU 289 (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 LEU* 3.9 23.3 - - + -
236B VAL 3.5 2.5 - - - +
237B ASP* 3.3 42.2 - - + +
249B ILE* 4.5 10.8 - - + -
253B LEU* 4.8 7.6 - - + -
287B PRO* 5.7 1.1 - - + -
288B THR* 1.3 75.2 - - - +
290B LEU* 1.3 64.9 + - - +
291B LEU 4.1 0.2 + - - -
300B THR* 3.3 5.5 - - - -
301B LYS* 2.8 52.9 + - + +
303B GLY 6.1 0.7 - - - +
305B LEU* 4.5 15.3 - - + -
310B LEU* 3.7 33.2 - - + -
313B PHE* 4.8 2.9 - - + -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE 3.6 1.6 - - - +
235B LEU* 4.4 2.5 - - - -
236B VAL* 2.9 37.4 + - - +
238B PHE* 3.6 28.5 - - + -
281B TYR* 3.8 22.9 - - + +
283B ILE* 3.8 24.0 - - + -
288B THR* 4.1 3.1 + - + -
289B LEU* 1.3 73.4 - - - +
291B LEU* 1.3 61.4 + - - +
292B PHE* 3.6 29.5 + - + -
297B VAL* 4.3 15.5 - - + -
299B ALA 3.8 1.1 - - - +
300B THR* 3.7 25.8 - - + +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ALA* 4.0 10.8 - - + -
234B ILE 3.6 19.1 - - - +
235B LEU* 4.3 9.4 - - + +
264B LEU* 4.0 17.7 - - + -
289B LEU 4.1 1.0 + - - -
290B LEU* 1.3 70.2 - - - +
292B PHE* 1.3 61.1 + - - +
293B LYS* 4.6 6.7 - - + -
297B VAL* 3.7 2.2 - - - -
298B ALA* 2.8 33.8 + - + +
299B ALA* 2.8 25.2 + - + +
313B PHE* 4.5 14.1 - - + -
314B LEU* 5.1 7.6 - - + -
317B ASN* 3.7 42.2 - - + +
318B LEU* 4.7 8.3 - - + +
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Residues in contact with PHE 292 (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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223B PHE* 4.0 11.7 - + - -
227B VAL* 3.5 30.1 - - + +
228B LEU* 4.0 17.9 - - + -
232B GLY 4.1 0.6 - - - +
233B ALA* 3.2 6.4 - - - +
234B ILE* 2.8 43.2 + - + +
236B VAL* 3.6 21.3 - - + -
281B TYR* 3.4 35.4 - + - -
290B LEU* 3.6 29.4 - - + -
291B LEU* 1.3 72.0 - - - +
293B LYS* 1.3 62.0 + - - +
295B GLY 4.3 4.3 - - - +
296B GLU 3.3 21.1 - - - +
297B VAL* 3.5 22.0 - - + -
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Residues in contact with LYS 293 (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 GLY 4.3 3.4 - - - +
233B ALA* 3.6 23.8 - - + +
291B LEU* 4.0 5.5 + - + -
292B PHE* 1.3 76.8 - - - +
294B ASN* 1.3 75.5 + - + +
295B GLY 3.3 0.4 - - - -
296B GLU* 3.0 27.8 + - - +
298B ALA* 3.7 27.2 - - + +
317B ASN 3.0 27.0 + - - +
318B LEU* 5.2 1.6 - - - -
319B ALA* 3.7 6.8 - - - +
320B GLY* 3.3 19.0 - - - +
321B SER* 3.5 40.8 + - - +
322B GLY* 5.8 2.3 + - - +
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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