Contacts of the strand formed by residues 287 - 293 (chain A) in PDB entry 3APO
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 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A VAL* 4.2 2.9 - - - +
258A GLY 3.6 10.1 - - - +
259A TRP 3.9 2.2 - - - -
260A LEU* 3.4 27.6 - - + +
280A SER 5.5 0.5 - - - +
283A LEU* 3.1 28.7 + - + +
284A ASP* 5.2 0.9 - - - -
285A GLY 3.9 2.3 + - - -
286A LEU* 1.3 86.5 + - + +
288A ASN* 1.3 81.1 + - - +
289A VAL* 3.8 8.1 + - + +
313A TYR* 4.0 10.1 - - + -
343A ILE* 3.7 27.8 - - + -
347A LEU* 4.0 12.3 - - + -
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Residues in contact with ASN 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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238A THR* 5.6 0.2 - - - +
255A ALA* 6.3 0.2 - - - +
257A VAL* 3.5 28.2 + - - +
258A GLY 2.9 9.6 + - - +
259A TRP* 3.4 54.4 - - + +
260A LEU 2.8 28.6 + - - +
287A VAL* 1.3 75.2 - - - +
289A VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 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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236A THR 3.9 14.5 + - - +
237A VAL* 3.6 7.7 - - + -
238A THR* 3.0 28.0 + - - -
259A TRP* 3.9 2.4 - - - -
260A LEU* 3.4 24.9 - - + +
271A LEU* 6.2 0.9 - - + -
276A ARG* 3.6 36.3 - - + +
279A LEU* 4.2 10.1 - - + +
280A SER* 3.6 28.3 - - - +
283A LEU* 5.2 2.2 - - + -
287A VAL* 3.8 9.2 + - + +
288A ASN* 1.3 77.0 - - - +
290A GLY* 1.3 65.1 + - - +
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Residues in contact with GLY 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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237A VAL* 4.6 1.1 - - - -
238A THR 3.0 16.8 - - - -
240A LEU* 4.4 3.6 - - - -
259A TRP* 4.2 10.4 - - - -
260A LEU 2.9 10.5 + - - +
261A ILE* 3.5 6.7 - - - -
262A THR* 3.2 18.9 + - - +
276A ARG* 4.8 1.0 - - - -
288A ASN 4.0 0.4 + - - -
289A VAL* 1.3 81.1 - - - +
291A TRP* 1.3 67.7 + - - +
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Residues in contact with TRP 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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237A VAL* 3.7 25.8 + - + +
238A THR 3.3 4.2 + - - -
239A GLU* 3.5 55.0 - - + +
240A LEU* 2.8 28.5 + - - +
261A ILE* 4.1 2.8 - - - +
262A THR* 3.3 25.8 - - + -
264A CYS* 4.2 15.7 - - + -
276A ARG* 3.8 30.7 - - - +
290A GLY* 1.3 74.6 - - - +
292A VAL* 1.3 68.3 + - - +
293A ASP* 4.0 27.9 + - + -
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Residues in contact with VAL 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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240A LEU* 3.8 22.4 - - + +
245A PHE* 4.2 11.2 - - + -
261A ILE* 3.8 17.3 - - + -
262A THR 2.9 5.9 + - - +
263A PHE* 3.7 22.9 - - + -
264A CYS* 2.9 28.1 + - - -
291A TRP* 1.3 80.9 - - - +
293A ASP* 1.3 60.0 + - - +
294A CYS 3.3 2.4 + - - -
297A GLN* 4.0 20.4 - - + -
300A LEU* 4.0 7.6 - - + -
301A CYS* 3.7 28.0 - - - -
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Residues in contact with ASP 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* 5.3 5.7 - - + +
240A LEU 4.7 3.4 + - - -
264A CYS* 3.7 8.5 - - - +
291A TRP* 4.0 25.2 + - + -
292A VAL* 1.3 69.8 - - - +
294A CYS* 1.3 56.5 + - - +
295A ASP* 3.0 24.7 + - - +
296A ALA* 3.0 26.2 + - + +
297A GLN* 2.8 28.5 + - + +
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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