Contacts of the strand formed by residues 287 - 294 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A VAL* 4.1 6.8 - - - +
247A GLN 3.3 17.1 + - - +
267A THR* 5.1 7.0 - - - +
283A ILE* 2.8 25.0 - - + +
284A PRO* 3.1 22.8 + - + +
286A GLY* 1.3 81.1 - - - +
288A ALA* 1.3 61.5 + - - +
279B GLU* 3.4 21.5 - - + +
280B THR* 4.0 10.1 - - - +
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Residues in contact with ALA 288 (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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131A VAL* 2.7 33.7 - - + +
132A PHE 4.1 12.8 - - - -
133A VAL* 3.7 8.6 - - + +
153A ALA* 4.2 5.2 - - + -
244A VAL* 4.8 1.1 - - + -
245A HIS 3.1 15.3 - - - +
246A SER* 3.5 18.4 - - - -
266A ALA 4.9 0.4 - - - -
267A THR 3.9 2.6 - - - +
268A GLY* 3.1 10.6 - - - -
269A LYS* 3.9 0.2 + - - -
283A ILE* 4.3 1.6 - - - -
287A ALA* 1.3 74.6 - - - +
289A GLY* 1.3 58.6 + - - +
279B GLU* 3.2 7.3 + - - -
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Residues in contact with GLY 289 (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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131A VAL* 3.4 11.6 - - - +
244A VAL* 3.5 4.0 - - - +
245A HIS* 2.9 26.7 + - - -
265A TRP 3.5 13.9 - - - -
266A ALA* 3.8 9.4 - - - -
268A GLY* 3.7 2.0 - - - -
283A ILE* 3.7 16.4 - - - +
288A ALA* 1.3 73.7 - - - +
290A ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 290 (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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131A VAL* 4.3 11.0 - - + +
242A LEU* 4.1 18.6 - - + -
243A ILE 3.7 7.4 - - - -
244A VAL* 4.2 13.9 - - + -
264A VAL* 3.4 5.9 - - - +
265A TRP* 2.9 48.0 + - + +
270A PHE* 5.3 5.8 - - + -
283A ILE* 5.2 0.8 - - - +
289A GLY* 1.3 75.5 - - - +
291A ALA* 1.3 61.4 + - - +
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Residues in contact with ALA 291 (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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241A VAL 3.6 1.7 - - - +
242A LEU* 3.3 4.1 - - - -
243A ILE* 2.8 44.8 + - + +
261A GLY* 4.5 7.2 - - - -
263A TYR 3.4 4.9 - - - -
264A VAL* 3.4 24.7 - - + -
281A TRP* 4.3 17.0 - - + +
290A ALA* 1.3 75.2 - - - +
292A PHE* 1.3 60.5 + - - +
293A TYR* 4.2 1.1 - - + -
303A TYR* 6.3 1.3 - - + -
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Residues in contact with PHE 292 (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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162A LEU* 5.8 0.9 - - + -
170A LEU* 4.4 18.2 - - + -
171A THR 3.4 14.4 - - - -
172A TYR* 3.1 41.3 - + + -
240A LYS* 2.7 46.0 - - + -
241A VAL 3.5 3.8 - - - -
242A LEU* 3.8 18.4 - - + +
261A GLY 5.0 0.2 - - - -
262A ASP* 3.1 27.5 + - + +
263A TYR* 2.9 29.0 + + + +
265A TRP* 4.2 11.2 - + + -
291A ALA* 1.3 74.2 - - - +
293A TYR* 1.3 66.0 + - - +
294A THR* 3.8 12.1 - - - -
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Residues in contact with TYR 293 (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 GLU 3.7 0.7 - - - +
241A VAL* 3.1 27.6 + - - +
243A ILE* 6.1 4.0 - - + -
256A LEU* 4.2 20.6 - - + -
259A GLY* 4.3 3.7 - - - -
260A HIS* 2.7 41.7 - - + +
261A GLY* 4.5 1.8 - - - -
262A ASP* 3.0 32.5 - - - +
291A ALA* 4.2 1.1 - - + -
292A PHE* 1.3 81.6 - - - +
294A THR* 1.3 83.9 + - - +
295A PHE* 3.4 35.7 + + + -
296A GLN* 3.8 11.6 + - + +
103C THR* 3.5 29.3 + - - +
128C LYS* 5.2 4.7 - - - -
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Residues in contact with THR 294 (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 GLY* 4.1 16.8 - - - +
239A GLU 3.3 12.8 - - - +
240A LYS* 4.0 9.5 - - + +
262A ASP* 3.1 13.5 + - - -
292A PHE* 3.8 14.4 - - - -
293A TYR* 1.3 93.6 + - - +
295A PHE* 1.3 68.5 + - - +
296A GLN* 3.4 24.8 - - - +
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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