Contacts of the helix formed by residues 222 - 226 (chain A) in PDB entry 4DAJ
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 ILE 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.7 25.1 - - + -
148A TYR* 3.6 29.6 - - + +
199A TRP* 5.0 2.5 - - + -
203A ILE* 3.5 33.7 - - + -
221A PHE* 1.3 84.0 - - - +
223A GLN* 1.3 69.3 + - - +
224A PHE* 3.2 36.3 - - + -
225A LEU* 3.2 42.7 + - + +
226A SER 3.9 0.9 + - - -
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Residues in contact with GLN 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A ILE* 5.6 4.9 + - - +
206A TRP* 3.1 32.8 + - + +
207A GLN* 3.2 32.9 + - - +
210A VAL* 4.4 8.9 - - - +
212A LYS 3.3 22.2 + - - -
213A ARG* 4.4 5.3 - - - +
214A THR* 3.9 33.2 + - - +
215A VAL* 4.5 12.7 - - + +
221A PHE* 3.4 6.9 + - - -
222A ILE* 1.3 74.6 - - - +
224A PHE* 1.3 57.6 + - - +
225A LEU 3.0 2.8 + - - -
226A SER* 2.9 26.0 + - - -
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Residues in contact with PHE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A TRP* 4.5 16.8 - + - -
202A ALA* 3.7 29.4 - - + -
203A ILE* 4.0 13.9 - - + -
206A TRP* 3.1 51.1 - + + +
222A ILE* 3.2 25.4 - - + -
223A GLN* 1.3 77.9 - - - +
225A LEU* 1.3 77.2 + - + +
226A SER* 3.3 3.3 + - - -
227A GLU* 4.5 0.9 + - - +
230A ILE* 3.4 41.3 - - + +
234A THR* 5.6 3.6 - - + -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A TYR* 4.6 6.7 - - + +
199A TRP* 4.8 4.9 - - + -
221A PHE* 5.8 0.7 - - - -
222A ILE* 3.2 44.8 + - + +
223A GLN 3.0 2.4 + - - -
224A PHE* 1.3 106.0 - - + +
226A SER* 1.3 66.5 + - - +
227A GLU 3.2 3.5 - - - +
230A ILE* 4.3 8.5 - - + +
231A THR* 2.9 45.1 + - + +
234A THR* 5.0 8.3 - - + +
2000A 0HK 4.3 20.2 - - + -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A THR* 4.2 14.1 - - - +
221A PHE* 4.0 19.0 - - - -
222A ILE 3.9 1.8 + - - -
223A GLN 2.9 17.5 + - - -
224A PHE 3.3 2.0 - - - -
225A LEU* 1.3 78.8 - - - +
227A GLU* 1.3 64.9 + - - +
228A PRO* 3.5 6.6 - - - +
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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