Contacts of the helix formed by residues 262 - 271 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219L ASP* 3.7 28.7 + - - -
221L GLY* 4.1 3.6 - - - -
222L LEU* 3.8 21.1 - - + -
258L VAL* 4.2 2.9 - - + +
259L TYR* 2.8 27.9 + + + +
261L ASP* 1.3 94.9 + - - +
263L VAL* 1.3 66.4 + - - +
265L PRO* 3.2 9.5 - - - +
266L LEU* 2.9 38.1 + - + +
313L MET* 3.7 32.4 - - + +
314L LYS 2.7 29.0 + - - -
315L MET* 5.2 0.4 - - - -
316L SER 5.9 0.4 - - - -
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Residues in contact with VAL 263 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L ILE* 4.2 25.1 - - + +
46L VAL* 5.0 8.1 - - + -
258L VAL* 4.2 14.8 - - + +
259L TYR 3.5 9.2 + - - +
260L ARG* 3.5 22.2 + - - +
262L HIS* 1.3 78.2 - - - +
264L GLU* 1.3 71.1 + - + +
266L LEU* 3.4 2.6 + - - +
267L LYS* 3.1 50.2 + - - +
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Residues in contact with GLU 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260L ARG 5.0 0.6 + - - -
261L ASP 5.2 0.2 - - - -
263L VAL* 1.3 81.2 - - + +
265L PRO* 1.3 73.5 - - + +
267L LYS* 3.0 54.1 + - - +
268L THR* 3.5 8.5 + - - -
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Residues in contact with PRO 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261L ASP 3.7 17.7 - - - +
262L HIS* 3.2 15.9 - - - +
264L GLU* 1.3 93.5 - - + +
266L LEU* 1.3 60.4 + - - +
268L THR* 3.3 21.7 + - - +
269L GLN 3.5 3.5 + - - -
311L ILE* 3.7 23.8 - - + +
312L ASP 3.8 23.8 - - - +
313L MET* 3.9 7.9 - - + -
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Residues in contact with LEU 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 4.4 0.7 - - - +
27L ILE* 3.9 40.2 - - + -
31L ILE* 4.8 2.0 - - + -
221L GLY* 4.1 13.5 - - - +
258L VAL* 3.6 34.1 - - + -
262L HIS* 2.9 26.0 + - + +
263L VAL* 3.7 3.8 - - - +
265L PRO* 1.3 72.0 - - - +
267L LYS* 1.3 61.5 + - - +
268L THR 3.1 2.0 - - - -
269L GLN* 2.9 29.7 + - + +
270L LEU* 2.9 32.9 + - - +
313L MET* 3.8 23.1 - - + -
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Residues in contact with LYS 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L ILE* 4.6 18.2 - - + -
263L VAL* 3.1 34.7 + - + +
264L GLU* 3.0 42.9 + - - +
266L LEU* 1.3 76.0 - - - +
268L THR* 1.3 62.2 + - - +
270L LEU* 3.4 22.8 + - + +
271L GLU* 3.4 19.3 - - - +
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Residues in contact with THR 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264L GLU 3.5 8.2 + - - -
265L PRO* 3.3 12.7 + - - +
266L LEU 3.1 0.4 - - - -
267L LYS* 1.3 79.8 - - - +
269L GLN* 1.3 61.9 + - - +
271L GLU* 3.3 30.1 + - - +
272L ARG* 3.9 28.5 - - - +
311L ILE* 5.0 5.4 - - + -
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Residues in contact with GLN 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L TYR* 3.9 20.3 + - - -
24L LEU* 4.3 6.3 - - + +
27L ILE* 5.8 0.4 - - - -
66L LEU* 4.9 2.3 - - - +
68L THR* 2.7 42.4 + - - +
69L LYS* 3.7 25.0 - - - +
265L PRO 3.5 1.6 + - - -
266L LEU* 2.9 34.0 + - + +
268L THR* 1.3 76.5 - - - +
270L LEU* 1.3 58.2 + - + +
271L GLU 3.0 4.9 - - - -
272L ARG* 3.0 31.3 + - - +
311L ILE* 3.2 25.4 - - + +
313L MET* 4.3 3.4 - - - +
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Residues in contact with LEU 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L LEU* 3.4 50.5 - - + +
27L ILE* 4.2 23.8 - - + -
28L ARG* 3.6 45.2 + - + +
31L ILE* 4.4 9.2 - - + -
266L LEU 2.9 18.8 + - - +
267L LYS* 3.6 20.0 - - + +
268L THR 3.3 0.4 - - - -
269L GLN* 1.3 76.4 - - + +
271L GLU* 1.3 59.5 + - + +
272L ARG 3.2 5.4 + - - +
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Residues in contact with GLU 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267L LYS* 3.4 19.9 - - - +
268L THR* 3.5 22.6 + - - +
269L GLN 3.0 1.0 - - - -
270L LEU* 1.3 77.5 - - + +
272L ARG* 1.3 61.9 + - + +
273L 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