Contacts of the helix formed by residues 224 - 235 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ASN* 1.3 86.0 - - - +
225A THR* 1.3 73.6 + - - +
227A ALA* 3.3 2.6 + - - +
228A ALA* 2.8 29.5 + - - +
241A ILE* 4.3 15.3 - - + +
265A THR 3.0 4.2 + - - +
266A GLN* 3.4 51.8 - - + +
267A GLY* 4.1 3.3 + - - -
295A THR* 5.4 6.1 - - - +
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Residues in contact with THR 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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200A PRO* 4.5 13.1 - - - +
223A ASN* 3.0 23.9 + - - -
224A GLU* 1.3 89.0 + - - +
226A GLU* 1.3 57.3 + - - +
228A ALA* 3.3 6.3 + - - +
229A THR* 3.0 32.5 + - - -
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Residues in contact with GLU 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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38A GLN* 3.9 10.0 + - - -
196A ASN* 4.2 1.4 - - - +
197A LEU* 3.8 19.2 - - + +
198A SER* 3.0 30.2 + - - +
199A ALA* 3.5 28.1 + - - +
200A PRO* 3.7 10.3 - - + +
203A SER* 4.5 2.4 + - - -
222A GLY* 3.5 8.8 - - - -
223A ASN* 2.8 54.2 + - - +
225A THR* 1.3 69.1 + - - +
227A ALA* 1.3 58.7 + - - +
229A THR* 3.6 3.5 + - - -
230A PHE* 3.0 30.1 + - - +
296A ASN* 5.6 0.5 + - - -
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Residues in contact with ALA 227 (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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197A LEU* 4.2 8.5 - - - +
223A ASN 2.8 18.8 + - - +
224A GLU 3.6 0.7 - - - +
226A GLU* 1.3 77.5 - - - +
228A ALA* 1.3 56.3 + - - +
230A PHE* 3.8 2.3 - - - +
231A ALA* 3.0 29.1 + - - +
241A ILE* 3.5 29.8 - - + -
244A ILE* 3.7 9.6 - - + +
264A PHE* 3.5 25.1 - - + -
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Residues in contact with ALA 228 (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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224A GLU 2.8 17.3 + - - +
225A THR* 3.3 7.2 + - - +
227A ALA* 1.3 73.9 - - - +
229A THR* 1.3 61.1 + - - +
231A ALA* 3.4 2.9 + - - +
232A ARG* 3.0 28.8 + - - +
239A LYS* 5.9 6.3 - - + +
241A ILE* 5.6 0.2 - - - +
244A ILE* 4.4 11.7 - - + -
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Residues in contact with THR 229 (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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200A PRO* 3.6 42.3 - - + +
203A SER* 3.8 8.3 - - - -
204A GLN* 3.7 19.6 + - + +
225A THR 3.0 16.7 + - - -
226A GLU 3.9 4.0 - - - -
228A ALA* 1.3 77.7 - - - +
230A PHE* 1.3 57.7 + - - +
232A ARG* 3.4 5.5 + - - +
233A GLU* 2.9 41.7 + - + +
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Residues in contact with PHE 230 (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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197A LEU* 3.7 21.1 - - + -
203A SER* 3.4 24.7 - - - +
210A LEU* 3.7 12.6 - - + -
211A MET* 3.9 13.0 - - - -
214A MET* 3.4 32.8 - - + -
220A LEU* 5.1 0.2 - - + -
226A GLU 3.0 19.7 + - - +
227A ALA* 3.8 5.2 - - - +
228A ALA 3.3 0.2 - - - -
229A THR* 1.3 74.7 - - - +
231A ALA* 1.3 65.7 + - - +
233A GLU* 4.2 1.5 - - + +
234A GLN* 3.1 53.0 + - + +
236A PHE* 4.1 7.4 - + - -
244A ILE* 5.5 1.6 - - + -
248A THR* 3.8 28.3 - - + -
251A LEU* 4.0 14.4 - - + -
264A PHE* 5.9 0.9 - + - -
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Residues in contact with ALA 231 (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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227A ALA 3.0 17.4 + - - +
228A ALA 3.7 3.6 - - - +
230A PHE* 1.3 74.5 - - - +
232A ARG* 1.3 59.6 + - - +
234A GLN 3.2 1.4 + - - -
235A GLY 2.9 10.0 + - - -
236A PHE* 2.9 50.8 + - + -
237A GLU 5.0 1.1 - - - +
238A THR 3.7 7.0 - - - +
244A ILE* 3.6 31.4 - - + -
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Residues in contact with ARG 232 (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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228A ALA 3.0 17.7 + - - +
229A THR* 3.4 6.7 + - - +
231A ALA* 1.3 79.8 - - - +
233A GLU* 1.3 70.2 + - - +
235A GLY* 3.7 8.4 + - - -
236A PHE 5.1 0.2 - - - +
237A GLU 5.7 2.0 - - - +
239A LYS* 5.6 8.1 - - - +
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Residues in contact with GLU 233 (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 SER* 3.5 28.3 - - - +
204A GLN* 3.7 27.0 + - - +
207A LYS* 3.8 34.3 + - + +
229A THR* 2.9 31.1 + - + +
230A PHE* 4.4 2.0 - - - +
232A ARG* 1.3 88.7 - - + +
234A GLN* 1.3 70.3 + - - +
235A GLY 3.2 1.0 + - - -
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Residues in contact with GLN 234 (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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207A LYS* 4.6 11.6 - - - +
211A MET* 3.2 45.2 - - + +
230A PHE* 3.1 46.0 + - + +
231A ALA 3.9 0.2 - - - +
233A GLU* 1.3 84.1 - - - +
235A GLY* 1.3 60.0 + - - +
236A PHE* 3.8 24.5 - - + -
251A LEU* 5.4 3.9 - - + +
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Residues in contact with GLY 235 (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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231A ALA 2.9 3.9 + - - -
232A ARG* 3.7 8.2 + - - -
233A GLU 3.2 3.8 - - - -
234A GLN* 1.3 80.7 - - - +
236A PHE* 1.3 65.3 + - - +
237A GLU* 3.2 21.6 + - - +
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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