Contacts of the strand formed by residues 271 - 278 (chain A) in PDB entry 2ODP
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 VAL 271 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A HIS* 3.8 3.4 - - - -
233A LEU* 3.2 30.7 - - + +
235A LEU* 4.7 3.4 - - + -
264A ILE* 4.3 17.7 - - + +
265A PHE* 3.7 35.6 - - + -
269A ILE* 3.3 27.7 + - + +
270A ASN* 1.3 75.0 - - - +
272A SER* 1.3 74.5 + - - +
273A VAL* 4.3 9.6 - - + -
293A SER 3.9 0.9 - - - +
294A ARG* 3.6 24.7 + - - +
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Residues in contact with SER 272 (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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232A HIS* 2.6 26.2 + - - -
233A LEU 2.9 6.7 + - - +
234A ASN* 3.4 14.0 + - - -
235A LEU 2.9 25.6 + - - +
271A VAL* 1.3 74.4 - - - +
273A VAL* 1.3 64.6 + - - +
274A ALA 4.2 0.2 - - - -
288A VAL* 4.0 14.9 + - - +
293A SER* 3.3 20.4 + - - -
294A ARG* 3.2 14.6 - - - +
333A GLN* 5.8 0.2 + - - -
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Residues in contact with VAL 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 3.3 22.9 - - + +
237A LEU* 4.1 15.0 - - + -
261A VAL* 4.2 3.4 - - + -
264A ILE* 4.6 3.4 - - + -
265A PHE* 3.8 28.5 - - + -
271A VAL* 4.3 7.0 - - + -
272A SER* 1.3 78.5 - - - +
274A ALA* 1.3 73.1 + - - +
275A ILE* 3.7 18.7 - - + +
286A MET* 3.2 24.3 - - - +
288A VAL* 4.3 1.3 - - - -
293A SER* 2.9 18.1 + - - -
299A VAL* 3.7 17.6 - - + +
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Residues in contact with ALA 274 (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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235A LEU 2.8 9.5 + - - +
236A TYR* 3.8 20.2 - - + -
237A LEU 2.8 26.3 + - - -
273A VAL* 1.3 75.6 - - - +
275A ILE* 1.3 69.4 + - - +
276A ILE* 5.0 3.8 - - + -
286A MET 3.2 15.0 - - - +
288A VAL* 3.9 7.8 - - + +
329A MET* 3.8 27.8 - - + -
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Residues in contact with ILE 275 (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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237A LEU* 3.6 20.0 - - + +
239A LEU* 5.1 3.4 - - + -
273A VAL* 3.7 19.3 - - + -
274A ALA* 1.3 81.8 - - - +
276A ILE* 1.3 64.0 + - - +
277A THR* 5.0 3.6 - - + -
285A LEU* 2.7 53.7 + - + -
286A MET* 3.0 21.5 + - + +
299A VAL* 4.2 6.7 - - + -
302A SER* 3.7 18.2 - - - +
303A LEU* 3.7 43.7 - - + -
306A ALA* 5.4 0.2 - - + -
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Residues in contact with ILE 276 (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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237A LEU 3.0 10.7 + - - +
238A LEU* 3.3 18.7 - - + -
239A LEU* 2.9 24.9 + - - +
274A ALA* 5.0 4.3 - - + -
275A ILE* 1.3 82.9 - - - +
277A THR* 1.3 77.2 + - - +
278A PHE* 5.0 2.0 - - + -
282A PRO* 3.8 20.6 - - + -
283A LYS 3.2 13.2 - - - +
284A VAL* 4.0 15.0 - - + -
322A ALA* 4.5 1.3 - - - +
325A SER* 3.8 20.2 - - - +
326A VAL* 3.9 29.6 - - + +
329A MET* 4.4 12.6 - - + -
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Residues in contact with THR 277 (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 LEU* 3.3 16.4 - - + -
241A ALA* 4.7 0.2 - - - -
250A PHE* 3.8 28.7 - - + -
275A ILE* 5.0 1.8 - - + -
276A ILE* 1.3 77.3 - - - +
278A PHE* 1.3 61.6 + - - +
282A PRO* 3.2 1.9 - - - +
283A LYS* 2.6 48.0 + - - +
285A LEU* 3.7 25.9 - - + +
306A ALA* 4.1 6.7 - - + -
307A ASN 5.3 3.6 + - - +
310A ASP* 5.9 0.2 - - - +
311A HIS* 2.9 29.5 + - - -
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Residues in contact with PHE 278 (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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238A LEU* 4.0 20.9 - - + -
239A LEU 2.9 22.0 + - - -
240A ASP* 3.5 34.0 - - + +
241A ALA 2.7 30.1 + - - +
242A SER 3.6 0.7 + - - -
276A ILE* 5.0 1.1 - - + -
277A THR* 1.3 77.1 - - - +
279A ALA* 1.3 67.1 + - - +
281A GLU 3.6 4.9 - - - +
282A PRO* 3.9 11.0 - - + -
311A HIS* 3.7 4.6 - - - -
317A THR* 4.0 14.8 - - + -
318A ASN 4.0 10.1 - - - +
319A THR* 3.7 25.8 - - - -
322A ALA* 3.5 28.7 - - + +
353A LEU* 4.4 12.1 - - + -
354A LEU 4.5 0.7 - - - -
355A THR* 4.1 13.2 - - - -
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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