Contacts of the strand formed by residues 300 - 303 (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 PHE 300 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O LEU* 5.9 0.5 - - - +
77O ILE* 3.6 43.6 - - + +
80O LEU* 5.0 1.8 - - + -
81O LEU* 4.0 16.8 - - + -
233O LEU* 4.0 32.3 - - + -
237O MET* 3.8 29.8 - - + -
280O LEU* 4.2 9.2 - - + -
281O LYS 4.1 2.0 - - - -
282O TRP* 3.7 30.1 - + - -
295O PHE* 4.2 7.6 - + - -
296O LYS 3.3 20.4 - - - -
297O VAL 3.1 11.2 + - - +
298O GLU* 4.5 2.7 - - - +
299O ASP* 1.3 76.4 - - + +
301O VAL* 1.3 62.7 + - - +
302O VAL* 3.6 6.9 + - + +
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Residues in contact with VAL 301 (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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279O LYS 3.6 2.1 - - - +
280O LEU* 4.0 1.0 - - - +
281O LYS* 2.8 53.6 + - + +
282O TRP 4.4 0.7 - - - -
283O ALA* 3.9 30.7 - - + +
298O GLU 4.4 3.6 - - - +
300O PHE* 1.3 72.1 - - - +
302O VAL* 1.3 65.2 + - - +
303O GLU* 3.7 13.2 + - + +
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Residues in contact with VAL 302 (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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63O LEU* 3.9 22.2 - - + -
65O LEU* 4.7 2.0 - - + -
73O LEU* 3.5 36.6 - - + -
77O ILE* 5.2 0.2 - - + -
233O LEU* 5.6 0.7 - - + -
278O PRO* 3.7 31.0 - - + -
279O LYS 3.4 6.7 - - - +
280O LEU* 4.1 11.9 - - + -
300O PHE* 3.6 11.8 + - + +
301O VAL* 1.3 75.1 - - - +
303O GLU* 1.3 61.2 + - - +
305O TYR* 4.4 12.1 + - + +
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Residues in contact with GLU 303 (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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278O PRO* 3.4 1.7 - - - +
279O LYS* 2.9 47.8 + - + +
281O LYS* 3.0 42.2 - - + +
301O VAL* 4.6 10.9 - - + +
302O VAL* 1.3 74.8 - - - +
304O GLY* 1.3 63.4 + - - +
305O TYR 3.4 2.9 - - - -
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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
------------------------------------------------------------
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