Contacts of the strand formed by residues 293 - 298 (chain B) in PDB entry 1OX4
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 GLU 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B TYR* 4.7 5.4 + - - -
239B ARG* 3.1 29.1 + - - -
240B ILE 3.8 1.0 + - - -
241B ILE* 3.7 31.4 - - + +
242B ALA 3.1 24.3 + - - -
291B ALA* 3.2 5.5 + - - +
292B ASP* 1.3 85.5 - - + +
294B VAL* 1.3 69.7 + - - +
295B THR* 4.3 3.7 + - - +
325B VAL* 4.3 3.4 - - - -
326B PRO* 3.6 24.5 - - + +
328B THR* 3.4 14.3 + - - +
360B LYS* 2.9 29.3 + - - -
465B GLU* 4.7 0.3 - - - +
497B ILE* 5.1 1.6 - - - +
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Residues in contact with VAL 294 (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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242B ALA 3.3 5.6 - - - +
244B LEU* 3.5 29.2 - - + -
283B ALA* 4.1 30.5 - - + +
286B TYR* 4.3 13.9 - - + -
287B TYR 4.7 2.0 - - - +
291B ALA* 4.5 4.9 - - + -
293B GLU* 1.3 79.2 - - - +
295B THR* 1.3 64.7 + - - +
296B PHE* 4.1 12.5 + - + -
323B VAL* 4.6 6.5 - - + -
325B VAL* 4.4 15.0 - - + -
326B PRO 3.1 9.0 + - - +
327B LEU* 3.4 9.3 - - + +
328B THR 2.9 24.6 + - - +
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Residues in contact with THR 295 (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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241B ILE* 3.7 15.8 - - - +
242B ALA 2.9 14.2 + - - -
243B CYS* 3.3 21.3 - - - -
244B LEU* 2.9 30.0 + - - +
293B GLU* 4.3 3.8 + - - -
294B VAL* 1.3 73.8 - - - +
296B PHE* 1.3 70.0 + - - +
297B LEU* 4.1 10.3 - - + -
328B THR* 3.3 31.3 + - + +
330B GLY 5.4 1.1 - - - +
362B SER* 6.2 2.0 - - - -
467B LEU* 5.3 7.6 - - + -
521B LEU* 4.5 8.3 - - + +
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Residues in contact with PHE 296 (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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244B LEU* 3.5 28.7 - - + -
246B VAL* 4.0 14.8 - - + -
279B PRO 4.2 1.1 - - - -
283B ALA* 3.7 31.0 - - + -
294B VAL* 4.2 12.3 - - + -
295B THR* 1.3 74.9 - - - +
297B LEU* 1.3 62.3 + - - +
298B ASN 3.5 1.6 + - - -
312B MET* 3.8 21.1 - - + -
315B VAL* 3.9 16.4 - - + -
316B LEU* 3.7 27.6 - - + -
319B ALA* 4.2 14.8 - - + -
327B LEU* 4.1 15.7 - - + -
328B THR 2.7 20.7 + - - +
329B VAL* 3.4 3.3 - - - +
330B GLY* 3.0 26.2 + - - -
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Residues in contact with LEU 297 (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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243B CYS* 3.5 29.4 - - - -
244B LEU 2.9 10.0 + - - +
245B ASP* 3.3 25.4 - - - +
246B VAL* 3.0 25.7 + - - +
295B THR* 4.1 9.2 - - + -
296B PHE* 1.3 74.1 - - - +
298B ASN* 1.3 63.7 + - - +
299B ILE* 3.2 9.8 + - + +
330B GLY* 3.7 11.4 - - - +
362B SER* 6.1 1.8 - - - +
467B LEU* 5.2 11.2 - - + -
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Residues in contact with ASN 298 (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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246B VAL* 4.1 5.1 + - - -
296B PHE 3.5 2.6 + - - -
297B LEU* 1.3 69.1 - - - +
299B ILE* 1.3 66.3 + - - +
300B THR* 2.9 38.9 + - - +
310B THR* 4.9 1.7 - - - +
312B MET* 3.5 39.6 - - + +
329B VAL* 4.5 4.0 - - + -
330B GLY 2.9 22.2 + - - +
331B GLY* 3.6 27.8 - - - +
332B GLY* 5.4 0.5 - - - -
353B TYR* 3.7 8.7 + - - -
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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