Contacts of the strand formed by residues 287 - 294 (chain C) in PDB entry 2P80
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 ALA 287 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A GLU* 3.5 18.4 - - + +
280A THR* 4.0 13.0 - - - +
133C VAL* 4.0 6.3 - - - +
247C GLN 3.3 16.6 + - - +
266C ALA 5.9 0.2 - - - +
267C THR* 5.2 6.5 - - - +
283C ILE* 2.8 20.7 - - + +
284C PRO* 3.1 28.6 + - + +
286C GLY* 1.3 82.2 - - - +
288C ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLU* 3.2 7.1 + - - -
131C VAL* 2.7 31.9 - - + +
132C PHE 4.1 11.9 - - - -
133C VAL* 3.6 9.3 - - + +
153C ALA* 4.2 6.1 - - + -
244C VAL* 4.8 1.1 - - + -
245C HIS 3.2 7.9 - - - +
246C SER* 3.3 26.7 - - - +
266C ALA 4.9 0.4 - - - -
267C THR 4.0 0.5 - - - +
268C GLY* 3.1 11.1 + - - -
269C LYS* 3.9 1.7 + - - -
283C ILE* 4.3 1.3 - - - -
287C ALA* 1.3 73.5 - - - +
289C GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C VAL* 3.4 12.1 - - - +
244C VAL* 3.5 4.0 - - - +
245C HIS* 2.9 27.6 + - - -
265C TRP 3.5 13.7 - - - -
266C ALA* 3.8 8.7 - - - -
268C GLY* 3.7 1.8 - - - -
283C ILE* 3.7 15.5 - - - +
288C ALA* 1.3 74.5 - - - +
290C ALA* 1.3 64.6 + - - +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C VAL* 4.4 10.8 - - + -
242C LEU* 4.1 15.7 - - + -
243C ILE 3.8 7.9 - - - -
244C VAL* 4.1 17.0 - - + -
264C VAL* 3.3 6.0 - - - +
265C TRP* 2.9 47.8 + - + +
268C GLY* 5.7 0.2 - - - -
270C PHE* 5.4 4.9 - - + -
281C TRP* 6.2 0.2 - - - -
283C ILE* 5.2 0.4 - - - +
289C GLY* 1.3 76.9 - - - +
291C ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241C VAL 3.6 1.6 - - - +
242C LEU* 3.4 4.0 - - - -
243C ILE* 2.9 43.5 + - + +
261C GLY* 4.5 7.0 - - - -
263C TYR 3.4 5.6 - - - -
264C VAL* 3.4 26.0 - - + -
281C TRP* 4.2 16.8 - - + +
290C ALA* 1.3 76.2 - - - +
292C PHE* 1.3 60.0 + - - +
293C TYR* 5.5 0.4 - - + -
303C TYR* 6.2 1.6 - - + -
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Residues in contact with PHE 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C LEU* 6.4 0.9 - - + -
170C LEU* 4.8 18.2 - - + -
171C THR 3.5 22.2 - - - -
172C TYR* 3.9 18.6 - + + -
240C LYS* 2.8 38.6 - - + -
241C VAL 3.4 7.2 - - - -
242C LEU* 3.7 15.7 - - + +
262C ASP* 3.1 26.8 + - + +
263C TYR* 2.9 33.7 + + + +
265C TRP* 4.3 10.5 - + + -
291C ALA* 1.3 74.5 - - - +
293C TYR* 1.3 70.2 + - - +
294C THR* 3.3 20.2 - - - -
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Residues in contact with TYR 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B THR* 3.4 29.3 + - - +
128B LYS* 5.2 5.4 - - - -
239C GLU 3.8 0.3 - - - +
240C LYS* 3.7 0.2 - - - -
241C VAL* 3.1 29.1 + - - +
243C ILE* 6.2 4.5 - - + -
256C LEU* 4.2 14.8 - - + -
259C GLY* 4.4 9.7 - - - -
260C HIS* 2.9 42.0 - - + +
261C GLY* 4.5 1.3 - - - -
262C ASP* 3.0 33.0 - - - -
291C ALA 4.2 0.9 + - - -
292C PHE* 1.3 85.5 - - - +
294C THR* 1.3 84.7 + - - +
295C PHE* 3.4 31.0 + + + -
296C GLN* 3.8 13.9 + - - +
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Residues in contact with THR 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C GLY* 4.0 18.2 - - - +
239C GLU 3.3 12.8 - - - +
240C LYS* 3.9 5.0 - - + +
262C ASP* 3.1 10.9 + - - -
292C PHE* 3.3 22.9 - - - -
293C TYR* 1.3 92.8 + - - +
295C PHE* 1.3 72.2 + - - +
296C GLN* 3.4 10.2 + - + +
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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