Contacts of the helix formed by residues 262 - 271 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219O ASP* 3.7 29.0 + - - -
221O GLY* 4.1 4.2 + - - -
222O LEU* 3.8 20.6 - - + -
258O VAL* 4.1 3.4 - - + -
259O TYR* 2.9 26.2 + + + +
261O ASP* 1.3 95.4 + - - +
263O VAL* 1.3 66.1 + - - +
265O PRO* 3.2 8.6 - - - +
266O LEU* 2.9 36.9 + - + +
313O MET* 3.7 30.0 - - + +
314O LYS 2.7 29.8 + - - -
315O MET* 5.2 0.4 - - - -
316O SER 5.9 0.2 - - - -
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Residues in contact with VAL 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O ILE* 4.2 24.4 - - + +
46O VAL* 5.0 8.5 - - + -
258O VAL* 4.2 14.6 - - + +
259O TYR 3.8 8.3 - - - +
260O ARG* 3.5 22.1 + - - +
262O HIS* 1.3 78.8 - - - +
264O GLU* 1.3 71.0 + - + +
266O LEU* 3.3 2.8 + - - +
267O LYS* 3.1 49.7 + - - +
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Residues in contact with GLU 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260O ARG 5.0 0.6 + - - -
261O ASP 5.2 0.2 - - - -
263O VAL* 1.3 80.7 - - + +
265O PRO* 1.3 73.8 - - + +
267O LYS* 3.0 53.5 + - - +
268O THR* 3.5 8.7 + - - -
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Residues in contact with PRO 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261O ASP 3.7 18.2 - - - +
262O HIS* 3.2 15.5 - - - +
264O GLU* 1.3 95.7 - - + +
266O LEU* 1.3 60.6 + - - +
268O THR* 3.3 22.0 + - - +
269O GLN 3.5 3.5 + - - -
311O ILE* 3.6 19.6 - - + +
312O ASP 3.8 24.0 - - - +
313O MET* 3.8 12.1 - - + -
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Residues in contact with LEU 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O TYR* 4.4 1.1 - - - +
27O ILE* 3.9 41.3 - - + -
31O ILE* 4.8 2.0 - - + -
221O GLY* 4.1 13.5 - - - -
258O VAL* 3.5 34.1 - - + -
262O HIS* 2.9 25.6 + - + +
263O VAL* 3.7 4.0 - - - +
265O PRO* 1.3 71.2 - - - +
267O LYS* 1.3 61.4 + - - +
268O THR 3.1 2.2 - - - -
269O GLN* 2.9 28.8 + - - +
270O LEU* 2.9 33.2 + - - +
313O MET* 3.8 22.0 - - + -
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Residues in contact with LYS 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O ILE* 4.6 17.9 - - + -
263O VAL* 3.1 34.6 + - + +
264O GLU* 3.0 43.2 + - - +
266O LEU* 1.3 76.9 - - - +
268O THR* 1.3 61.7 + - - +
270O LEU* 3.4 20.2 + - + +
271O GLU* 3.4 22.4 + - - +
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Residues in contact with THR 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264O GLU 3.5 8.9 + - - -
265O PRO* 3.3 12.7 + - - +
266O LEU 3.1 0.6 - - - -
267O LYS* 1.3 79.9 - - - +
269O GLN* 1.3 61.3 + - - +
271O GLU* 3.3 30.6 + - - +
272O ARG* 4.0 28.1 - - - +
311O ILE* 5.0 5.2 - - + -
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Residues in contact with GLN 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O TYR* 3.9 19.6 + - - -
24O LEU* 4.4 6.5 - - + +
27O ILE* 5.8 0.4 - - - -
66O LEU* 4.9 2.4 - - - +
68O THR* 2.7 42.1 + - - +
69O LYS* 3.7 26.7 - - - +
265O PRO 3.5 1.8 + - - +
266O LEU* 2.9 34.8 + - + +
268O THR* 1.3 75.5 - - - +
270O LEU* 1.3 54.9 + - + +
271O GLU 3.0 4.9 - - - -
272O ARG* 3.0 30.4 + - - +
311O ILE* 3.2 26.7 - - + +
313O MET* 4.3 2.6 - - - +
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Residues in contact with LEU 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O LEU* 3.4 49.8 - - + +
27O ILE* 4.2 13.5 - - + -
28O ARG* 3.6 45.8 + - + +
31O ILE* 4.4 20.6 - - + -
266O LEU* 2.9 19.9 + - + +
267O LYS* 3.6 20.4 - - + +
268O THR 3.3 0.2 - - - -
269O GLN* 1.3 76.6 - - + +
271O GLU* 1.3 60.1 + - + +
272O ARG 3.2 4.9 + - - +
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Residues in contact with GLU 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267O LYS* 3.4 19.9 - - - +
268O THR* 3.5 21.0 + - - +
269O GLN 3.0 1.2 - - - -
270O LEU* 1.3 77.5 - - + +
272O ARG* 1.3 61.6 + - + +
273O GLU* 3.9 1.2 + - - +
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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