Contacts of the strand formed by residues 245 - 251 (chain A) in PDB entry 2AQ5
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 ARG 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A GLY 3.5 8.3 - - - +
239A PHE* 3.6 20.6 - - + -
244A GLU* 1.3 75.3 - - - +
246A GLN* 1.3 57.5 + - - +
264A LEU* 2.8 33.4 + - + -
265A ASP* 2.6 52.8 + - - +
267A SER* 3.6 24.2 + - - +
269A GLY* 2.8 44.0 + - - -
270A VAL 4.7 0.4 - - - -
271A LEU* 3.4 31.7 - - + +
289A ASP* 2.9 41.2 + - - -
291A SER* 5.7 0.2 + - - -
293A ARG* 3.8 9.9 - - - +
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Residues in contact with GLN 246 (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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218A HIS* 2.9 33.7 + - + +
219A GLU 4.9 0.7 + - - -
237A THR* 3.4 7.3 - - - -
238A GLY 2.8 28.5 + - - +
239A PHE 3.6 10.0 - - - +
240A SER* 3.6 23.0 - - - +
244A GLU 3.6 7.0 - - - +
245A ARG* 1.3 80.9 - - - +
247A VAL* 1.3 60.9 + - - +
261A LEU* 3.9 19.2 - - + +
262A GLN 3.3 7.6 - - - +
263A GLU* 2.9 36.6 + - - +
264A LEU* 4.3 6.3 - - - +
271A LEU* 4.8 1.6 - - - +
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Residues in contact with VAL 247 (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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218A HIS* 4.7 0.2 - - - -
235A LEU* 3.7 31.2 - - + -
236A THR 3.4 11.4 - - - +
237A THR* 4.7 1.6 - - + -
246A GLN* 1.3 74.4 - - - +
248A ALA* 1.3 63.5 + - - +
260A SER 4.1 0.2 - - - +
261A LEU* 3.5 2.6 - - - +
262A GLN* 2.8 52.7 + - + +
264A LEU* 4.2 7.4 - - + -
284A LEU* 4.0 20.9 - - + -
295A PHE* 3.9 24.5 - - + -
304A LEU* 4.0 13.6 - - + +
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Residues in contact with ALA 248 (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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218A HIS* 4.1 2.7 - - + -
235A LEU* 3.2 8.3 - - - +
236A THR* 2.9 38.3 + - - +
247A VAL* 1.3 76.5 - - - +
249A LEU* 1.3 60.4 + - - +
250A TRP* 3.4 29.8 - - + +
258A PRO* 4.1 2.9 - - + -
260A SER 3.2 10.8 - - - +
261A LEU* 3.8 19.3 - - + -
304A LEU* 4.8 1.1 - - - -
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Residues in contact with LEU 249 (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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229A VAL* 3.6 31.2 - - + -
233A LYS* 4.2 10.1 - - + -
234A ILE 3.6 9.0 - - - +
235A LEU* 4.6 4.7 - - + -
248A ALA* 1.3 72.8 - - - +
250A TRP* 1.3 56.0 + - - +
258A PRO* 3.4 4.3 - - - +
259A LEU* 2.7 48.7 + - + -
260A SER 2.9 11.4 + - - +
297A ILE* 4.1 21.1 - - + -
302A PRO 5.2 0.2 - - - +
303A PHE* 3.6 43.3 - - + +
304A LEU* 4.1 18.5 - - + +
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Residues in contact with TRP 250 (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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214A LYS* 3.6 33.9 - - + -
217A PRO* 3.5 35.7 - - + -
233A LYS* 3.2 9.9 - - - +
234A ILE* 2.8 54.1 + - + +
236A THR* 2.9 34.8 + - + +
248A ALA* 3.4 30.7 - - + +
249A LEU* 1.3 73.6 - - - +
251A ASP* 1.3 60.7 + - - +
255A LEU* 3.7 26.0 - - + -
257A GLU 3.7 7.2 - - - -
258A PRO* 3.3 44.4 - - + -
259A LEU* 4.2 6.7 - - - +
261A LEU* 5.7 0.4 - - + -
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Residues in contact with ASP 251 (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 GLY 3.7 9.8 - - - +
233A LYS* 4.4 4.0 - - - -
250A TRP* 1.3 71.8 - - - +
252A THR* 1.3 58.6 + - - +
253A LYS* 2.9 21.1 + - - +
254A HIS* 2.9 59.2 + - + +
255A LEU* 3.4 5.2 - - - +
257A GLU 5.4 1.0 + - - +
259A LEU* 4.0 30.2 - - + +
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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