Contacts of the helix formed by residues 224 - 234 (chain D) in PDB entry 2I6A
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 GLU 224 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D ASN* 1.3 89.5 - - - +
225D THR* 1.3 77.8 + - - +
227D ALA* 4.0 3.1 - - - +
228D ALA* 3.0 28.4 + - - +
241D ILE* 4.0 22.6 - - + +
265D THR 2.9 14.0 + - - +
266D GLN* 3.5 32.8 - - + +
267D GLY* 4.5 2.1 + - - -
295D THR* 5.9 3.1 - - - +
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Residues in contact with THR 225 (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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200D PRO* 4.5 14.3 - - - +
223D ASN* 3.4 14.3 + - - +
224D GLU* 1.3 91.1 + - - +
226D GLU* 1.3 61.1 + - - +
228D ALA* 3.6 6.1 - - - +
229D THR* 3.0 32.2 + - - -
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Residues in contact with GLU 226 (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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38D GLN* 3.8 9.0 + - - -
196D ASN* 4.2 1.4 - - - +
197D LEU* 3.8 18.7 - - + +
198D SER* 2.8 33.5 + - - +
199D ALA* 3.5 22.8 + - - +
200D PRO* 3.7 10.5 - - + +
203D SER* 4.3 3.0 + - - -
222D GLY* 3.6 7.3 - - - -
223D ASN* 2.7 51.5 + - - +
225D THR* 1.3 76.0 + - - +
227D ALA* 1.3 59.9 + - - +
229D THR* 3.3 6.1 + - - -
230D PHE* 2.9 28.9 + - - +
296D ASN* 5.5 0.2 + - - -
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Residues in contact with ALA 227 (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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197D LEU* 4.0 11.1 - - - +
223D ASN 2.9 16.2 + - - +
224D GLU* 4.0 6.1 - - - +
226D GLU* 1.3 72.7 - - - +
228D ALA* 1.3 62.3 + - - +
230D PHE* 3.0 3.6 + - - +
231D ALA* 2.8 32.8 + - - +
241D ILE* 5.0 5.4 - - + -
244D ILE* 4.0 10.1 - - + +
264D PHE* 3.6 39.5 - - + -
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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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224D GLU 3.0 18.8 + - - +
225D THR* 3.6 7.9 - - - +
227D ALA* 1.3 82.7 - - - +
229D THR* 1.4 61.6 + - - +
231D ALA* 3.4 8.6 + - - +
232D ARG* 3.3 18.9 + - - +
239D LYS* 5.7 4.7 - - - +
244D ILE* 4.4 9.2 - - + +
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Residues in contact with THR 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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200D PRO* 3.6 28.8 - - - +
203D SER* 3.6 20.9 - - - -
204D GLN* 3.8 22.5 + - + +
225D THR 3.0 21.6 + - - -
226D GLU 3.7 4.3 - - - -
227D ALA 3.3 0.2 - - - -
228D ALA* 1.4 74.9 - - - +
230D PHE* 1.3 63.7 + - - +
232D ARG* 3.3 8.0 + - + +
233D GLU* 3.0 27.2 + - + +
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Residues in contact with PHE 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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197D LEU* 4.0 16.6 - - + -
203D SER* 3.5 22.0 - - - +
210D LEU* 3.6 24.9 - - + -
211D MET* 3.9 17.7 - - + -
214D MET* 4.0 15.7 - - + -
220D LEU* 5.1 1.3 - - + -
226D GLU 2.9 18.9 + - - +
227D ALA* 3.0 6.7 + - - +
229D THR* 1.3 76.2 - - - +
231D ALA* 1.3 54.1 + - - +
233D GLU* 3.3 3.1 + - + +
234D GLN* 2.9 60.2 + - + +
236D PHE* 4.0 17.9 - + - -
244D ILE* 5.1 2.0 - - + -
248D THR* 3.8 32.3 - - + -
251D LEU* 4.1 6.3 - - + -
264D PHE* 5.7 0.7 - + - -
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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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227D ALA 2.8 14.5 + - - +
228D ALA* 3.4 7.0 - - - +
230D PHE* 1.3 75.1 - - - +
232D ARG* 1.3 53.8 + - - +
234D GLN 3.9 0.2 - - - -
235D GLY 3.2 2.8 + - - -
236D PHE* 2.7 47.9 + - + +
237D GLU 4.0 3.0 + - - -
238D THR 3.8 10.1 - - - +
244D ILE* 3.2 38.1 - - + -
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Residues in contact with ARG 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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228D ALA 3.3 9.1 + - - +
229D THR* 3.8 9.2 - - - +
230D PHE 3.3 0.6 - - - -
231D ALA* 1.3 75.8 - - - +
233D GLU* 1.3 76.4 + - - +
234D GLN 3.1 1.8 - - - -
235D GLY* 3.1 16.9 + - - +
237D GLU 5.7 0.7 - - - +
239D LYS* 5.8 6.3 - - - +
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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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203D SER* 3.8 18.8 - - - +
204D GLN* 3.9 24.0 + - - +
207D LYS* 2.2 57.0 + - + +
229D THR* 3.0 31.2 + - + +
230D PHE* 4.0 3.6 - - + +
232D ARG* 1.3 89.4 - - + +
234D GLN* 1.3 67.8 + - - +
235D GLY 3.3 0.7 - - - -
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Residues in contact with GLN 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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207D LYS* 4.4 13.0 - - - +
211D MET* 3.5 40.2 - - + +
230D PHE* 2.9 45.5 + - + +
233D GLU* 1.3 85.9 + - - +
235D GLY* 1.3 62.7 + - - +
236D PHE* 3.4 26.6 + - + -
251D LEU* 5.6 1.5 - - + +
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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