Contacts of the helix formed by residues 262 - 271 (chain J) in PDB entry 2AAZ
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 HIS 262 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219J ASP* 3.6 28.9 + - - -
221J GLY* 4.1 3.6 - - - -
222J LEU* 3.8 21.3 - - + -
258J VAL* 4.1 3.3 - - + +
259J TYR* 2.8 27.5 + + + +
261J ASP* 1.3 94.3 + - - +
263J VAL* 1.3 66.2 + - - +
265J PRO* 3.2 9.3 - - - +
266J LEU* 2.9 37.8 + - + +
313J MET* 3.7 32.6 - - + +
314J LYS 2.7 28.8 + - - -
315J MET* 5.2 0.4 - - - -
316J SER 5.9 0.4 - - - -
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Residues in contact with VAL 263 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J ILE* 4.2 24.9 - - + +
46J VAL* 4.9 8.5 - - + -
258J VAL* 4.2 15.0 - - + +
259J TYR 3.5 9.2 + - - +
260J ARG* 3.5 22.2 + - - +
262J HIS* 1.3 78.8 - - - +
264J GLU* 1.3 70.7 + - + +
266J LEU* 3.4 2.4 + - - +
267J LYS* 3.1 50.0 + - - +
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Residues in contact with GLU 264 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260J ARG 5.0 0.4 + - - -
261J ASP 5.2 0.2 - - - -
263J VAL* 1.3 81.2 - - + +
265J PRO* 1.3 73.2 - - + +
267J LYS* 3.0 54.5 + - - +
268J THR* 3.5 8.5 + - - -
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Residues in contact with PRO 265 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261J ASP 3.7 17.5 - - - +
262J HIS* 3.2 16.2 - - - +
264J GLU* 1.3 93.7 - - + +
266J LEU* 1.3 60.3 + - - +
268J THR* 3.3 21.7 + - - +
269J GLN 3.5 3.5 + - - -
311J ILE* 3.6 19.3 - - + +
312J ASP 3.8 23.3 - - - +
313J MET* 3.9 12.6 - - + -
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Residues in contact with LEU 266 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J TYR* 4.4 0.7 - - - +
27J ILE* 3.8 40.2 - - + -
31J ILE* 4.7 2.2 - - + -
221J GLY* 4.1 13.5 - - - +
258J VAL* 3.5 34.1 - - + -
262J HIS* 2.9 26.4 + - + +
263J VAL* 3.7 3.6 - - - +
265J PRO* 1.3 72.9 - - - +
267J LYS* 1.3 61.2 + - - +
268J THR 3.1 2.0 - - - -
269J GLN* 2.9 29.5 + - - +
270J LEU* 2.9 32.7 + - - +
313J MET* 3.8 22.0 - - + -
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Residues in contact with LYS 267 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31J ILE* 4.6 18.6 - - + +
263J VAL* 3.1 34.7 + - + +
264J GLU* 3.0 42.2 + - - +
266J LEU* 1.3 76.5 - - - +
268J THR* 1.3 62.3 + - - +
270J LEU* 3.4 21.3 + - + +
271J GLU* 3.4 20.3 + - - +
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Residues in contact with THR 268 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264J GLU 3.5 7.8 + - - -
265J PRO* 3.3 12.9 + - - +
266J LEU 3.1 0.4 - - - -
267J LYS* 1.3 79.9 - - - +
269J GLN* 1.3 60.9 + - - +
271J GLU* 3.3 30.4 + - - +
272J ARG* 3.9 28.5 - - - +
311J ILE* 5.0 5.2 - - + -
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Residues in contact with GLN 269 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J TYR* 3.8 20.8 + - - -
24J LEU* 4.3 7.1 - - + +
27J ILE* 5.7 0.4 - - - -
66J LEU* 4.8 2.1 - - - +
68J THR* 2.7 42.0 + - - +
69J LYS* 3.8 25.4 - - - +
265J PRO 3.5 1.4 + - - -
266J LEU* 2.9 34.0 + - + +
268J THR* 1.3 76.5 - - - +
270J LEU* 1.3 62.2 + - + +
271J GLU 3.0 4.9 - - - -
272J ARG* 3.0 26.4 + - - +
311J ILE* 3.2 25.5 - - + +
313J MET* 4.3 3.6 - - - +
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Residues in contact with LEU 270 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J LEU* 3.4 50.7 - - + +
27J ILE* 4.2 19.3 - - + -
28J ARG* 3.5 49.9 + - + +
31J ILE* 4.4 8.5 - - + -
266J LEU 2.9 18.6 + - - +
267J LYS* 3.6 20.2 - - + +
268J THR 3.3 0.4 - - - -
269J GLN* 1.3 76.4 - - + +
271J GLU* 1.3 59.8 + - + +
272J ARG 3.3 5.4 + - - +
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Residues in contact with GLU 271 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267J LYS* 3.4 20.1 - - - +
268J THR* 3.5 21.7 + - - +
269J GLN 3.0 1.0 - - - -
270J LEU* 1.3 77.3 - - + +
272J ARG* 1.3 61.5 + - + +
273J GLU 3.9 0.9 + - - -
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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