Contacts of the helix formed by residues 262 - 271 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C ASP* 3.6 29.9 + - - -
221C GLY* 4.1 4.0 + - - -
222C LEU* 3.7 20.4 - - + -
258C VAL* 4.2 2.7 - - + -
259C TYR* 2.8 27.5 + + + +
261C ASP* 1.3 93.6 + - - +
263C VAL* 1.3 66.0 + - - +
265C PRO* 3.2 10.1 - - - +
266C LEU* 2.9 36.8 + - + +
313C MET* 3.7 32.2 - - + +
314C LYS 2.7 28.9 + - - -
315C MET* 5.3 0.2 - - - -
316C SER 5.9 0.4 - - - -
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Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ILE* 4.2 25.4 - - + +
46C VAL* 4.9 8.3 - - + -
258C VAL* 4.1 15.0 - - + -
259C TYR 3.5 8.9 + - - +
260C ARG* 3.5 22.4 + - - +
262C HIS* 1.3 77.8 - - - +
264C GLU* 1.3 70.2 + - + +
266C LEU* 3.4 2.3 + - - +
267C LYS* 3.1 50.1 + - - +
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Residues in contact with GLU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C ARG 5.0 1.0 + - - -
261C ASP 5.2 0.2 - - - -
263C VAL* 1.3 84.7 - - + +
265C PRO* 1.3 72.5 - - + +
267C LYS* 2.9 53.6 + - - +
268C THR* 3.5 8.8 + - - -
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Residues in contact with PRO 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C ASP 3.7 18.6 - - - +
262C HIS* 3.2 15.7 - - - +
264C GLU* 1.3 95.0 - - + +
266C LEU* 1.3 61.2 + - - +
268C THR* 3.3 21.3 + - - +
269C GLN 3.5 3.8 + - - -
311C ILE* 3.7 18.7 - - + +
312C ASP 3.8 23.8 - - - +
313C MET* 3.9 12.3 - - + -
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Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 4.3 0.4 - - - +
27C ILE* 3.9 39.7 - - + -
31C ILE* 4.8 2.0 - - + -
221C GLY* 4.1 15.3 - - - -
258C VAL* 3.6 33.7 - - + -
262C HIS* 2.9 25.6 + - + +
263C VAL* 3.8 4.5 - - - +
265C PRO* 1.3 72.0 - - - +
267C LYS* 1.3 60.4 + - - +
268C THR 3.1 2.2 - - - -
269C GLN* 3.0 30.3 + - + +
270C LEU* 2.8 33.8 + - + +
313C MET* 3.8 22.0 - - + -
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Residues in contact with LYS 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 4.7 17.7 - - + -
263C VAL* 3.1 32.6 + - + +
264C GLU* 2.9 43.2 + - - +
266C LEU* 1.3 76.8 - - - +
268C THR* 1.3 62.5 + - - +
270C LEU* 3.3 21.9 + - + +
271C GLU* 3.4 20.4 + - - +
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Residues in contact with THR 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264C GLU 3.5 8.2 + - - -
265C PRO* 3.3 12.7 + - - +
266C LEU 3.1 0.2 - - - -
267C LYS* 1.3 80.0 - - - +
269C GLN* 1.3 62.1 + - - +
271C GLU* 3.3 29.8 + - - +
272C ARG* 3.9 28.8 - - - +
311C ILE* 5.0 6.3 - - + -
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Residues in contact with GLN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR* 3.9 21.2 + - - -
24C LEU* 4.3 6.6 - - + +
27C ILE* 5.8 0.2 - - - -
66C LEU* 4.8 2.8 - - - +
68C THR* 2.7 40.7 + - - +
69C LYS* 3.7 27.3 - - - +
265C PRO 3.5 1.6 + - - -
266C LEU* 3.0 34.6 + - + +
268C THR* 1.3 81.6 - - - +
270C LEU* 1.3 63.1 + - + +
271C GLU 3.1 0.2 - - - -
272C ARG* 3.0 26.1 + - - +
311C ILE* 3.1 26.7 - - + +
313C MET* 4.3 2.6 - - - +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 3.4 51.9 - - + +
27C ILE* 4.2 23.1 - - + -
28C ARG* 3.6 43.9 + - + +
31C ILE* 4.4 11.2 - - + -
266C LEU 2.8 18.8 + - - +
267C LYS* 3.6 19.7 - - + +
268C THR 3.3 0.4 - - - -
269C GLN* 1.3 76.4 - - + +
271C GLU* 1.3 60.2 + - + +
272C ARG 3.2 5.2 + - - +
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Residues in contact with GLU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C LYS* 3.4 20.0 - - - +
268C THR* 3.5 21.9 + - - +
269C GLN 3.1 0.4 - - - -
270C LEU* 1.3 78.1 - - + +
272C ARG* 1.3 61.6 + - + +
273C 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