Contacts of the helix formed by residues 262 - 271 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219F ASP* 3.6 29.0 + - - -
221F GLY* 4.0 4.2 - - - -
222F LEU* 3.7 22.0 - - + -
258F VAL* 4.1 2.7 - - + -
259F TYR* 2.8 27.0 + + + +
261F ASP* 1.3 94.9 + - - +
263F VAL* 1.3 64.9 + - - +
264F GLU 3.4 1.8 - - - -
265F PRO* 3.2 6.9 - - - +
266F LEU* 2.9 37.3 + - + +
313F MET* 3.7 32.0 - - + +
314F LYS 2.7 30.1 + - - -
315F MET* 5.3 0.2 - - - -
316F SER 5.9 0.4 - - - -
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Residues in contact with VAL 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ILE* 4.2 25.9 - - + +
46F VAL* 4.9 9.2 - - + -
258F VAL* 4.1 14.6 - - + +
259F TYR 3.8 8.1 - - - +
260F ARG* 3.5 23.0 + - - +
262F HIS* 1.3 78.5 - - - +
264F GLU* 1.3 71.1 + - + +
266F LEU* 3.3 2.3 + - - +
267F LYS* 3.1 50.1 + - - +
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Residues in contact with GLU 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260F ARG 5.0 0.6 + - - -
263F VAL* 1.3 81.4 - - + +
265F PRO* 1.3 73.1 - - + +
267F LYS* 2.9 55.0 + - - +
268F THR* 3.5 9.0 + - - -
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Residues in contact with PRO 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F ASP 3.7 17.0 - - - +
262F HIS* 3.2 14.8 - - - +
264F GLU* 1.3 96.7 - - + +
266F LEU* 1.3 59.3 + - - +
268F THR* 3.2 22.6 + - - +
269F GLN 3.4 3.6 + - - -
311F ILE* 3.7 18.6 - - + +
312F ASP 3.8 23.8 - - - +
313F MET* 3.8 13.0 - - + -
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Residues in contact with LEU 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F TYR* 4.4 1.1 - - - +
27F ILE* 3.9 42.8 - - + -
31F ILE* 4.8 1.8 - - + -
221F GLY* 4.1 14.1 - - - +
258F VAL* 3.5 34.1 - - + -
262F HIS* 2.9 22.4 + - + +
263F VAL* 3.7 4.7 - - - +
265F PRO* 1.3 74.7 - - - +
267F LYS* 1.3 60.0 + - - +
269F GLN* 2.9 29.3 + - + +
270F LEU* 2.8 34.2 + - - +
313F MET* 3.8 21.8 - - + -
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Residues in contact with LYS 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ILE* 4.6 18.2 - - + -
263F VAL* 3.1 32.2 + - + +
264F GLU* 2.9 43.1 + - - +
266F LEU* 1.3 76.0 - - - +
268F THR* 1.3 60.7 + - - +
270F LEU* 3.4 23.2 + - + +
271F GLU* 3.4 20.0 - - - +
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Residues in contact with THR 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264F GLU 3.5 8.9 + - - -
265F PRO* 3.2 12.5 + - - +
266F LEU 3.1 0.4 - - - -
267F LYS* 1.3 80.2 - - - +
269F GLN* 1.3 62.2 + - - +
271F GLU* 3.4 29.7 + - - +
272F ARG* 4.0 28.4 - - - +
311F ILE* 5.0 5.6 - - + -
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Residues in contact with GLN 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F TYR* 3.8 21.5 + - - -
24F LEU* 4.3 6.7 - - + +
27F ILE* 5.7 0.4 - - - -
66F LEU* 4.8 2.8 - - - +
68F THR* 2.8 42.6 + - - +
69F LYS* 3.7 26.2 - - - +
265F PRO 3.4 1.8 + - - -
266F LEU* 2.9 34.1 + - + +
268F THR* 1.3 80.9 - - - +
270F LEU* 1.3 57.3 + - + +
271F GLU 3.0 0.4 - - - -
272F ARG* 3.0 31.1 + - - +
311F ILE* 3.2 26.0 - - + +
313F MET* 4.3 2.6 - - - +
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Residues in contact with LEU 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F LEU* 3.4 51.1 - - + +
27F ILE* 4.2 23.6 - - + -
28F ARG* 3.6 43.1 + - + +
31F ILE* 4.3 11.7 - - + -
266F LEU* 2.8 19.3 + - + +
267F LYS* 3.6 20.2 - - + +
268F THR 3.3 0.2 - - - -
269F GLN* 1.3 76.0 - - + +
271F GLU* 1.3 60.3 + - + +
272F ARG 3.2 5.6 + - - +
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Residues in contact with GLU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F LYS* 3.4 19.4 - - - +
268F THR* 3.6 20.1 + - - +
269F GLN 3.0 0.6 + - - -
270F LEU* 1.3 77.5 - - + +
272F ARG* 1.3 61.3 + - + +
273F GLU 3.9 1.0 + - - -
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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