Contacts of the helix formed by residues 229 - 236 (chain N) in PDB entry 5X6E
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 CYS 229 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122N LYS* 3.1 38.0 - - - +
224N TRP* 4.3 15.0 - - - -
225N PHE* 2.9 17.4 - - + +
228N ALA* 1.3 74.6 - - - +
230N PRO* 1.3 69.3 - - - +
231N ALA* 3.3 3.4 - - - -
232N THR* 2.5 38.4 + - + +
233N TRP 3.4 1.2 + - - -
301N GSH 3.4 25.6 - - - +
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Residues in contact with PRO 230 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225N PHE 3.2 10.1 - - - +
226N TYR* 3.7 21.5 - - + +
227N LEU 4.7 4.7 - - - +
228N ALA* 3.4 4.9 - - - -
229N CYS* 1.3 87.8 - - - +
231N ALA* 1.3 64.9 + - + +
232N THR 3.3 0.2 - - - -
233N TRP* 3.1 8.1 + - + +
234N GLY* 3.0 24.3 + - - -
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Residues in contact with ALA 231 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229N CYS* 3.3 0.9 - - - -
230N PRO* 1.3 84.7 - - + +
232N THR* 1.3 59.7 + - + +
234N GLY* 3.0 16.7 + - - +
235N LYS* 3.5 28.0 + - - +
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Residues in contact with THR 232 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64N LYS* 5.7 4.3 - - - +
152N TYR* 4.8 13.2 - - - +
153N VAL* 5.2 13.4 - - + +
225N PHE* 4.0 12.7 - - - -
229N CYS* 2.5 39.5 + - + +
231N ALA* 1.3 77.7 - - + +
233N TRP* 1.3 59.4 + - - +
235N LYS* 3.9 16.4 + - - +
236N LEU* 3.6 24.3 - - - +
301N GSH 4.8 9.6 - - - +
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Residues in contact with TRP 233 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152N TYR* 3.2 33.6 + + - -
215N LYS* 5.7 5.8 - - + -
222N ASP* 3.0 38.0 + - - -
225N PHE* 3.1 35.9 - - + +
226N TYR* 3.9 35.0 - + + -
229N CYS 3.4 0.2 + - - -
230N PRO* 3.1 10.7 + - + +
232N THR* 1.3 82.6 + - - +
234N GLY* 1.3 67.1 + - - +
236N LEU* 3.8 2.2 + - - +
237N ASN* 2.8 53.3 + - - +
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Residues in contact with GLY 234 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230N PRO 3.0 12.3 + - - -
231N ALA* 3.0 7.2 + - - -
233N TRP* 1.3 85.0 - - - +
235N LYS* 1.3 63.2 + - - +
237N ASN* 3.1 17.7 + - - +
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Residues in contact with LYS 235 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157N GLU* 6.0 1.9 - - - +
231N ALA* 3.5 23.1 + - - +
232N THR* 3.9 15.0 + - - +
233N TRP 3.5 0.6 - - - -
234N GLY* 1.3 76.1 - - - +
236N LEU* 1.3 77.7 + - + +
237N ASN* 3.3 8.7 - - - +
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Residues in contact with LEU 236 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N THR* 4.0 14.8 - - + +
152N TYR* 3.7 45.8 - - + +
155N GLY* 4.8 3.8 - - - -
156N LYS 4.5 20.6 - - - +
157N GLU* 5.0 11.0 - - + -
162N ILE* 5.9 5.4 - - + -
211N LEU* 3.3 24.5 - - + +
232N THR 3.6 18.2 - - - +
233N TRP 3.8 1.6 + - - +
234N GLY 3.3 0.4 - - - -
235N LYS* 1.3 92.0 - - + +
237N ASN* 1.3 74.9 + - - +
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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