Contacts of the helix formed by residues 287 - 296 (chain A) in PDB entry 2ARR
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 THR 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.6 11.0 - - - -
17A LYS* 4.6 5.8 - - - +
285A GLU 3.3 10.9 + - - +
286A ILE* 1.3 81.1 - - - +
288A TYR* 1.3 65.7 + - - +
289A ASP* 3.5 8.0 + - - +
290A LYS* 3.2 34.2 + - + +
291A LEU* 2.9 24.1 + - - +
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Residues in contact with TYR 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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3A ASP* 2.5 35.8 + - - +
6A VAL* 3.3 31.2 - - + +
9A THR* 3.5 30.7 - - + -
10A LEU* 3.5 28.6 - - + +
13A LEU* 3.3 15.2 - - + +
287A THR* 1.3 73.1 - - - +
289A ASP* 1.3 75.1 + - - +
291A LEU* 4.8 2.0 - - + -
292A ASN* 2.8 67.7 + - + +
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Residues in contact with ASP 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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287A THR* 3.3 8.1 + - - +
288A TYR* 1.3 99.5 - - - +
290A LYS* 1.3 63.3 + - + +
292A ASN* 4.4 1.0 - - - +
293A LYS* 3.3 24.6 + - - +
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Residues in contact with LYS 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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246A ILE* 4.5 7.5 - - + +
248A ASP* 3.9 33.2 + - + +
249A LEU* 4.1 23.6 - - + +
285A GLU* 2.7 52.2 + - - +
287A THR* 3.2 24.3 + - - +
289A ASP* 1.3 80.3 - - + +
291A LEU* 1.3 59.5 + - - +
293A LYS* 3.9 6.0 - - - +
294A TRP* 3.3 25.1 - - - -
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Residues in contact with LEU 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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9A THR* 5.1 4.9 - - + -
13A LEU* 4.7 14.1 - - + -
246A ILE* 5.2 4.3 - - + -
249A LEU* 5.6 0.7 - - + -
253A ILE* 4.8 2.0 - - + -
265A PHE* 6.1 0.4 - - + -
267A LEU* 4.1 34.3 - - + -
286A ILE* 4.5 18.5 - - + +
287A THR 2.9 16.0 + - - +
288A TYR* 4.0 2.7 - - + +
290A LYS* 1.3 77.7 - - - +
292A ASN* 1.3 60.8 + - - +
294A TRP* 2.9 20.8 + - - +
295A THR* 3.0 33.4 + - + +
397A LEU* 4.1 20.9 - - + -
399A MET* 6.0 2.5 - - + -
406A ILE* 4.5 16.2 - - + -
409A PHE* 5.1 0.2 - - + -
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Residues in contact with ASN 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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3A ASP* 4.0 3.5 - - - +
288A TYR* 2.8 59.1 + - + +
289A ASP* 4.4 1.8 - - - +
291A LEU* 1.3 72.2 - - + +
293A LYS* 1.3 66.6 + - - +
295A THR* 3.6 6.0 + - - -
296A SER* 3.0 38.8 + - - -
399A MET* 5.5 0.5 - - - +
404A ASN* 3.0 24.6 + - - +
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Residues in contact with LYS 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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248A ASP* 5.7 2.6 + - - -
289A ASP 3.3 17.3 + - - +
290A LYS* 3.9 8.3 - - - +
292A ASN* 1.3 78.3 - - - +
294A TRP* 1.3 79.2 + - + +
296A SER 4.3 7.0 + - - -
299A LYS* 3.2 64.4 + - + +
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Residues in contact with TRP 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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244A GLY* 3.9 18.8 - - - -
245A TYR 3.3 26.5 - - - -
246A ILE* 3.6 28.0 - - + +
247A GLU 5.5 0.4 - - - -
253A ILE* 3.9 23.8 - - + -
290A LYS 3.3 19.1 - - - -
291A LEU 2.9 7.8 + - - +
293A LYS* 1.3 101.2 - - + +
295A THR* 1.3 61.6 + - - +
296A SER 3.4 0.8 + - - -
299A LYS* 3.5 58.0 + - + +
300A MET* 3.0 45.6 + - + +
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Residues in contact with THR 295 (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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253A ILE* 4.1 4.0 - - + -
265A PHE* 3.5 51.1 - - + -
291A LEU* 3.0 40.4 + - + +
292A ASN* 3.6 9.4 + - - -
294A TRP* 1.3 78.4 - - - +
296A SER* 1.3 79.0 + - - +
397A LEU* 5.0 2.2 - - + -
399A MET* 3.9 16.5 - - + +
401A LYS* 4.2 9.7 + - - -
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Residues in contact with SER 296 (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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292A ASN* 3.0 33.5 + - - -
293A LYS* 4.5 7.2 - - - -
294A TRP 3.4 2.0 - - - -
295A THR* 1.3 97.7 + - - +
299A LYS 6.0 2.7 - - - -
399A MET* 4.1 0.2 - - - +
404A ASN* 2.6 34.0 + - - -
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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