Contacts of the helix formed by residues 223 - 241 (chain A) in PDB entry 2IAG
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 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A SER 3.6 2.6 + - - -
222A LEU* 1.3 74.1 - - - +
224A VAL* 1.3 60.4 + - - +
225A GLY* 3.8 4.1 + - - -
226A ASP* 2.8 37.9 + - - -
227A LYS* 2.9 30.7 + - - +
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Residues in contact with VAL 224 (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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223A SER* 1.3 73.5 - - - +
225A GLY* 1.3 58.5 + - - +
227A LYS* 3.3 22.6 - - - +
228A ASP* 3.1 26.2 + - + +
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Residues in contact with GLY 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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223A SER* 3.3 4.6 + - - -
224A VAL* 1.3 79.4 - - - +
226A ASP* 1.3 53.7 + - - +
228A ASP* 3.2 6.8 + - - +
229A HIS* 2.8 34.7 + - - +
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Residues in contact with ASP 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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213A LEU* 4.4 12.5 - - + +
216A LYS* 3.9 24.4 + - - +
221A SER 4.9 0.5 - - - +
222A LEU* 3.8 21.5 - - + -
223A SER* 2.8 44.2 + - - +
225A GLY* 1.3 73.9 - - - +
227A LYS* 1.3 53.8 + - - +
229A HIS* 3.2 7.0 + - - +
230A MET* 2.7 40.7 + - - +
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Residues in contact with LYS 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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222A LEU* 3.2 41.7 + - + +
223A SER* 2.9 20.0 + - - +
224A VAL* 3.3 24.2 - - - +
226A ASP* 1.3 75.8 - - - +
228A ASP* 1.3 57.2 + - - +
230A MET* 3.4 2.1 + - - +
231A CYS* 2.9 41.2 + - - -
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Residues in contact with ASP 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 VAL* 3.1 12.1 + - + +
225A GLY* 3.7 9.4 - - - +
227A LYS* 1.3 75.9 - - - +
229A HIS* 1.3 66.4 + - - +
231A CYS* 3.5 6.2 + - - +
232A SER* 2.8 38.2 + - - -
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Residues in contact with HIS 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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209A GLN* 2.6 42.6 + - + -
213A LEU* 4.3 7.7 - - + +
225A GLY 2.8 20.9 + - - +
226A ASP* 3.6 6.7 + - - +
228A ASP* 1.3 74.5 + - - +
230A MET* 1.3 79.9 + - + +
232A SER* 3.3 7.5 + - - -
233A VAL* 3.0 38.2 + - + +
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Residues in contact with MET 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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209A GLN 3.4 21.5 - - - +
210A LEU* 3.8 17.7 - - - -
213A LEU* 3.3 32.3 - - + -
217A LEU* 3.9 23.8 - - + -
222A LEU* 4.1 15.7 - - + -
226A ASP 2.7 22.7 + - - +
227A LYS* 3.8 3.8 - - - +
229A HIS* 1.3 107.9 - - + +
231A CYS* 1.3 56.8 + - - +
233A VAL* 3.3 6.3 + - + +
234A LYS* 2.9 41.8 + - - +
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Residues in contact with CYS 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 LYS* 2.9 27.1 + - - +
228A ASP* 3.9 8.1 - - - +
230A MET* 1.3 77.5 - - - +
232A SER* 1.3 58.3 + - - +
234A LYS* 3.8 12.0 - - - +
235A SER* 2.9 29.1 + - - -
238A TRP* 5.5 1.6 - - - -
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Residues in contact with SER 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 ASP* 2.8 29.5 + - - -
229A HIS* 3.7 7.6 - - - -
231A CYS* 1.3 75.0 - - - +
233A VAL* 1.3 60.6 + - - +
235A SER* 3.5 7.4 + - - -
236A ARG* 3.0 27.4 + - - +
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Residues in contact with VAL 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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206A THR* 3.4 30.9 - - + +
209A GLN* 3.8 17.3 - - + +
210A LEU* 3.9 26.2 - - + +
229A HIS* 3.0 47.2 + - + +
230A MET* 3.3 8.7 + - + +
232A SER* 1.3 72.3 - - - +
234A LYS* 1.3 60.4 + - - +
236A ARG* 3.2 5.1 + - - +
237A LEU* 2.9 33.5 + - + +
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Residues in contact with LYS 234 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ARG 4.7 1.2 + - - -
107A ILE 2.9 27.1 + - - -
108A PHE* 4.8 2.5 - - - +
109A ASP* 2.9 32.5 + - - +
210A LEU* 4.0 28.9 - - + -
217A LEU* 3.9 18.2 - - - +
230A MET* 2.9 26.9 + - + +
231A CYS* 3.8 11.7 - - - +
233A VAL* 1.3 72.5 - - - +
235A SER* 1.3 56.7 + - - +
237A LEU* 3.0 7.1 + - - +
238A TRP* 2.7 65.6 + - + +
278A VAL* 6.0 1.3 - - + -
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Residues in contact with SER 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 CYS 2.9 20.1 + - - -
232A SER* 3.5 9.2 - - - -
233A VAL 3.4 0.2 - - - -
234A LYS* 1.3 74.4 - - - +
236A ARG* 1.3 62.4 + - - +
238A TRP* 3.6 14.7 + - - +
239A LYS* 3.3 21.8 + - - +
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Residues in contact with ARG 236 (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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202A ASP* 2.6 40.5 + - - -
206A THR* 3.9 18.5 + - + -
232A SER 3.0 14.0 + - - +
233A VAL* 3.7 7.2 - - - +
234A LYS 3.2 0.2 - - - -
235A SER* 1.3 74.1 - - - +
237A LEU* 1.3 60.9 + - - +
239A LYS* 3.1 9.4 + - - +
240A LEU* 2.9 51.2 + - + +
245A ARG* 5.4 4.0 - - - +
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Residues in contact with LEU 237 (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 VAL* 4.3 6.3 - - + +
206A THR* 3.6 19.5 - - + -
207A PHE* 3.9 31.9 - - + +
210A LEU* 3.8 29.4 - - + -
233A VAL* 2.9 29.0 + - + +
234A LYS* 3.6 4.7 - - - +
236A ARG* 1.3 75.5 - - - +
238A TRP* 1.3 58.2 - - - +
240A LEU* 3.3 12.3 + - + +
241A LEU* 3.0 32.5 + - + +
278A VAL* 3.5 30.1 - - + +
281A LEU* 4.8 10.5 - - + -
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Residues in contact with TRP 238 (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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108A PHE* 3.7 15.8 + - - -
109A ASP* 3.3 28.7 - - + -
231A CYS 5.5 1.3 - - - -
234A LYS* 2.7 49.5 + - + +
235A SER* 3.9 11.0 - - - +
237A LEU* 1.3 72.9 - - - +
239A LYS* 1.3 60.4 + - - +
242A SER* 3.4 10.0 + - - -
271A GLU 5.5 1.6 - - - +
274A ALA* 3.3 28.6 - - + +
275A ARG* 3.5 67.6 - - + +
278A VAL* 3.7 28.9 - - + +
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Residues in contact with LYS 239 (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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235A SER 3.3 11.4 + - - +
236A ARG* 3.1 13.1 + - + +
238A TRP* 1.3 78.1 - - - +
240A LEU* 1.3 66.1 + - + +
242A SER* 3.1 21.2 + - - +
245A ARG* 3.5 34.5 - - - +
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Residues in contact with LEU 240 (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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177A TYR* 4.8 4.5 + - - -
199A HIS* 4.1 25.9 - - + +
202A ASP* 3.6 24.9 - - - +
203A VAL* 4.3 14.4 - - + -
206A THR* 4.3 7.9 - - - +
236A ARG* 2.9 46.1 + - + +
237A LEU* 3.7 22.9 - - + +
239A LYS* 1.3 78.2 - - - +
241A LEU* 1.3 68.8 + - + +
242A SER 3.3 2.3 + - - -
245A ARG* 3.7 32.3 + - - +
246A LEU* 4.7 4.9 - - - +
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Residues in contact with LEU 241 (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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177A TYR* 4.0 24.7 - - + +
181A TYR* 3.6 32.1 - - + -
203A VAL* 4.3 14.6 - - + -
237A LEU* 3.0 19.5 + - + +
238A TRP 3.9 3.6 - - - -
240A LEU* 1.3 91.1 - - + +
242A SER* 1.3 62.7 + - - +
246A LEU* 4.3 8.5 - - + -
274A ALA* 3.6 7.3 - - - -
277A LEU* 3.5 42.6 - - + +
278A VAL* 4.0 14.4 - - + -
281A LEU* 4.1 15.3 - - + -
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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