Contacts of the helix formed by residues 288 - 292 (chain G) in PDB entry 2I2X
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 GLY 288 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E GLU* 5.5 0.7 - - - +
287G GLU* 1.3 75.3 - - - +
289G LYS* 1.3 60.6 + - - -
290G THR 3.1 2.0 - - - -
291G SER* 2.9 29.4 + - - +
292G THR* 4.1 3.1 + - - +
295G HIS 5.3 0.7 - - - +
297G ASP* 3.4 19.3 - - - +
300G GLY* 3.4 16.8 - - - -
303G VAL* 3.6 5.2 - - - -
310G TRP* 3.3 9.7 - - - -
311G SER 4.6 0.6 + - - -
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Residues in contact with LYS 289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E LYS* 4.3 8.7 - - - +
332E THR* 2.6 35.1 + - + +
335E TYR* 3.6 36.6 - - + -
336E ASP* 2.9 33.7 + - - +
339E LEU* 4.6 10.9 - - - +
288G GLY* 1.3 72.2 - - - -
290G THR* 1.3 60.7 + - - +
291G SER 3.3 0.2 - - - -
292G THR* 3.3 12.8 - - - +
300G GLY* 2.9 21.0 + - - +
301G ASN* 3.0 28.6 - - - +
304G MET* 3.5 15.5 - - - +
310G TRP* 3.8 5.1 - - + -
336G ASP* 3.9 22.0 - - - -
339G LEU* 5.8 1.4 - - - +
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Residues in contact with THR 290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E THR* 4.3 4.3 - - + +
288G GLY 3.1 1.0 - - - -
289G LYS* 1.3 84.7 - - - +
291G SER* 1.3 57.9 + - - +
292G THR 3.5 1.8 - - - -
310G TRP* 3.6 6.5 + - - -
311G SER 4.2 2.0 - - - -
312G ASN* 3.2 21.1 - - - +
329G TRP* 3.7 23.7 - - + -
332G THR* 3.7 31.8 - - + +
333G LEU* 3.5 25.4 - - + +
336G ASP* 2.6 24.7 + - - +
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Residues in contact with SER 291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287G GLU* 3.6 11.0 - - - +
288G GLY* 2.9 30.0 + - - -
290G THR* 1.3 78.9 - - - +
292G THR* 1.3 56.9 + - - +
293G CYS* 3.2 3.4 - - - -
294G ALA* 3.1 17.4 + - - +
295G HIS* 3.1 19.9 + - - +
297G ASP* 4.2 4.5 + - - -
311G SER 3.7 8.3 - - - -
312G ASN 3.5 27.4 - - - -
313G GLU* 3.7 11.4 - - - -
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Residues in contact with THR 292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E ARG* 4.7 1.4 + - - -
322E GLY* 3.7 8.1 - - - +
328E CYS* 2.8 45.2 + - - +
331E GLU* 3.6 44.4 - - + +
332E THR* 2.9 10.6 + - - +
288G GLY 4.5 2.9 - - - +
289G LYS* 3.3 19.5 - - - +
290G THR 3.5 1.2 - - - -
291G SER* 1.3 73.8 - - - +
293G CYS* 1.3 66.6 + - - +
294G ALA 3.1 1.7 + - - -
295G HIS 3.1 15.2 - - - +
329G TRP* 3.5 7.4 - - - -
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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