Contacts of the helix formed by residues 227 - 238 (chain D) in PDB entry 2J2M
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 SER 227 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D ASP* 3.9 22.2 + - - -
186D ILE* 5.0 0.4 - - - -
226D LEU* 1.3 74.1 - - - +
228D ALA* 1.3 56.0 + - - +
229D ASP* 3.5 7.4 + - - +
230D GLU* 3.0 42.2 + - - +
231D ALA* 2.7 32.2 + - - +
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Residues in contact with ALA 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ARG* 4.5 15.6 - - - +
183D ASP* 4.8 0.8 + - - -
186D ILE* 4.8 2.2 - - - -
226D LEU 4.0 0.2 + - - -
227D SER* 1.3 72.6 - - - +
229D ASP* 1.3 58.8 + - - +
231D ALA* 3.4 6.7 + - - +
232D THR* 2.8 37.2 + - - +
442D ASN* 4.2 18.1 + - - +
445D ASN* 5.8 3.8 - - - +
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Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C LYS* 4.8 10.9 + - - -
227D SER* 3.2 6.3 + - - +
228D ALA* 1.3 78.9 - - - +
230D GLU* 1.3 61.1 + - + +
232D THR* 3.4 6.5 + - - +
233D GLU* 3.0 28.2 + - - +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D ASN 4.2 4.5 - - - +
226D LEU* 3.8 21.0 - - + -
227D SER* 3.0 40.4 + - - +
229D ASP* 1.3 73.3 - - + +
231D ALA* 1.3 59.2 + - - +
233D GLU* 3.3 7.7 + - - +
234D VAL* 2.9 35.8 + - + +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D THR* 3.3 31.6 - - - +
186D ILE* 3.6 24.0 - - + -
226D LEU* 4.0 12.4 - - + +
227D SER 2.7 19.3 + - - +
228D ALA* 3.6 4.3 - - - +
230D GLU* 1.3 73.2 - - - +
232D THR* 1.3 56.9 + - - +
235D GLN* 2.9 31.6 + - - +
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Residues in contact with THR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C GLY* 3.4 29.9 + - - +
237C LYS* 3.3 40.7 + - + +
228D ALA* 2.8 21.6 + - - +
229D ASP* 3.5 10.1 + - - +
230D GLU 3.2 0.4 - - - -
231D ALA* 1.3 75.0 - - - +
233D GLU* 1.3 63.5 + - - +
235D GLN* 3.5 1.9 + - - +
236D GLY* 3.4 16.6 + - - -
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Residues in contact with GLU 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ASP 3.0 16.0 + - - +
230D GLU* 3.3 6.2 + - - +
232D THR* 1.3 72.5 - - - +
234D VAL* 1.3 70.3 + - + +
236D GLY* 3.4 8.7 + - - -
237D LYS* 3.8 26.5 + - + +
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Residues in contact with VAL 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D THR* 3.5 22.7 - - + -
226D LEU* 4.3 18.8 - - + -
230D GLU* 2.9 22.4 + - + +
231D ALA* 4.4 0.7 - - - -
232D THR 3.4 0.2 - - - -
233D GLU* 1.3 77.8 - - + +
235D GLN* 1.3 62.8 + - - +
237D LYS* 2.9 16.7 + - - +
238D ASP* 3.0 14.6 + - + +
241D HIS* 3.5 33.7 - - + +
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Residues in contact with GLN 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235C GLN* 3.1 37.9 - - + +
236C GLY* 3.3 14.4 - - - +
237C LYS 4.7 1.0 - - - -
238C ASP 4.5 1.6 + - - -
239C PHE* 4.0 14.8 + - + -
104D PRO* 3.6 17.6 - - + +
106D THR* 2.5 35.4 + - - +
107D LEU* 3.3 24.1 - - - +
231D ALA 2.9 17.2 + - - +
232D THR* 3.7 6.5 - - - +
233D GLU 3.3 0.2 - - - -
234D VAL* 1.3 76.6 - - - +
236D GLY* 1.3 61.9 + - - +
237D LYS 3.2 0.9 + - - -
238D ASP 3.6 12.4 + - - -
239D PHE* 4.2 2.5 + - + +
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Residues in contact with GLY 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C THR* 3.5 47.3 + - - +
235C GLN* 3.4 13.5 - - - +
236C GLY* 3.6 12.5 - - - -
232D THR 3.4 8.2 + - - -
233D GLU 3.4 4.2 + - - -
234D VAL 3.2 1.0 - - - -
235D GLN* 1.3 78.3 - - - +
237D LYS* 1.3 58.2 + - - +
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Residues in contact with LYS 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232C THR* 4.0 23.9 + - + +
235C GLN* 4.8 2.5 - - - -
233D GLU* 3.8 24.5 + - + +
234D VAL* 2.9 8.3 + - - +
236D GLY* 1.3 80.5 - - - +
238D ASP* 1.3 63.5 + - + +
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Residues in contact with ASP 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 5.5 0.7 - - - +
106D THR* 4.6 0.5 - - - +
234D VAL* 3.0 18.8 + - + +
235D GLN* 3.6 6.1 + - - +
237D LYS* 1.3 84.7 - - + +
239D PHE* 1.3 61.5 + - - +
240D ASN* 2.8 32.5 + - - +
241D HIS* 3.5 33.0 + - + +
244D ASN* 3.2 26.1 + - - -
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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