Contacts of the helix formed by residues 223 - 240 (chain A) in PDB entry 1Z00
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 LEU 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A ALA 3.9 2.9 - - - +
221A ASP* 3.0 6.3 - - - -
222A LEU* 1.3 93.0 - - + +
224A MET* 1.3 78.0 + - + +
225A GLU* 3.7 28.7 - - + +
226A LYS* 3.6 32.2 - - + +
227A LEU* 3.0 25.9 + - - +
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Residues in contact with MET 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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221A ASP* 5.5 3.6 - - - +
223A LEU* 1.3 86.7 - - + +
225A GLU* 1.3 86.4 - - + +
226A LYS 3.1 2.0 - - - -
227A LEU* 3.1 23.3 + - + +
228A GLU* 3.2 18.9 + - - +
897B VAL* 4.9 4.8 - - + +
902B LYS* 4.2 23.8 + - + -
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Residues in contact with GLU 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 LEU* 3.9 24.9 - - + -
224A MET* 1.3 92.0 - - + +
226A LYS* 1.3 61.1 + - + +
228A GLU* 3.4 9.0 - - - +
229A GLN* 3.4 20.6 - - - +
902B LYS* 2.6 45.0 + - - +
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Residues in contact with LYS 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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223A LEU* 3.6 32.3 + - + +
225A GLU* 1.3 81.7 - - + +
227A LEU* 1.3 61.2 + - - +
228A GLU 3.3 0.7 - - - -
229A GLN* 3.2 16.7 + - + +
230A ASP* 2.9 32.7 + - + +
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Residues in contact with LEU 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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220A ALA* 3.3 38.6 - - + +
221A ASP* 4.4 18.2 - - - +
223A LEU 3.0 18.9 + - - +
224A MET* 3.4 17.0 - - + +
226A LYS* 1.3 78.8 - - - +
228A GLU* 1.3 57.8 + - - +
230A ASP* 3.8 5.9 - - + +
231A PHE* 2.8 39.9 + - + +
888B ASP* 5.7 3.8 - - - +
889B PHE* 6.1 5.8 - - + -
892B THR* 6.0 6.5 - - + -
897B VAL* 6.4 2.9 - - + -
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Residues in contact with GLU 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 MET 3.2 5.4 + - - +
225A GLU 3.4 16.8 - - - +
227A LEU* 1.3 78.7 - - - +
229A GLN* 1.3 78.6 + - - +
231A PHE* 3.6 8.2 - - - +
232A VAL* 2.9 36.9 + - + +
894B PHE* 5.2 1.6 - - - +
897B VAL* 3.8 27.4 - - + +
898B VAL* 4.2 24.3 - - + +
902B LYS* 2.6 35.8 + - - -
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Residues in contact with GLN 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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225A GLU 3.4 17.7 - - - +
226A LYS* 3.2 23.0 + - + +
228A GLU* 1.3 98.4 + - - +
230A ASP* 1.3 58.7 + - - +
232A VAL* 3.2 13.4 - - - +
233A SER* 2.7 34.5 + - - -
898B VAL* 5.7 1.6 - - - +
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Residues in contact with ASP 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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226A LYS 2.9 17.0 + - - +
227A LEU* 4.0 6.8 - - + +
229A GLN* 1.3 76.5 - - - +
231A PHE* 1.3 59.3 + - - +
233A SER* 3.1 7.6 - - - -
234A ARG* 2.8 56.9 + - - +
845B PRO* 5.8 3.5 - - - +
889B PHE* 5.5 1.9 - - - -
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Residues in contact with PHE 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 LEU* 2.8 26.8 + - + +
228A GLU* 3.6 6.5 - - - +
230A ASP* 1.3 77.0 + - - +
232A VAL* 1.3 57.7 + - - +
234A ARG* 3.1 1.9 + - - +
235A VAL* 2.8 51.2 + - + +
260A LEU* 4.3 4.9 - - + -
889B PHE* 3.0 57.0 - + + -
892B THR* 3.2 33.9 - - + -
893B SER 3.8 0.4 - - - -
894B PHE* 3.2 47.6 - + + -
897B VAL* 5.6 2.7 - - + -
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Residues in contact with VAL 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 GLU 2.9 22.5 + - - +
229A GLN* 3.2 28.3 - - - +
231A PHE* 1.3 71.7 - - - +
233A SER* 1.3 55.0 + - - +
235A VAL* 3.2 9.9 - - - +
236A THR* 2.6 39.1 + - - +
254A LEU* 4.3 12.7 - - + +
894B PHE* 3.6 28.7 - - + -
898B VAL* 4.6 14.1 - - + -
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Residues in contact with SER 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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229A GLN 2.7 18.7 + - - -
230A ASP* 3.1 15.4 - - - -
232A VAL* 1.3 79.7 - - - +
234A ARG* 1.3 66.3 + - - +
236A THR* 3.3 14.7 + - - -
237A GLU* 3.3 17.5 + - - +
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Residues in contact with ARG 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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230A ASP* 2.8 53.0 + - - +
231A PHE 3.6 4.3 - - - +
233A SER* 1.3 76.5 - - - +
235A VAL* 1.3 61.3 + - - +
237A GLU* 3.0 32.0 + - - +
238A CYS* 2.9 21.0 - - - -
842B LEU 4.8 1.8 + - - -
843B LYS* 2.7 40.2 + - - +
844B MET 3.4 13.2 + - - -
845B PRO* 4.9 7.6 + - + +
889B PHE* 3.7 24.2 - - + -
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Residues in contact with VAL 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 PHE* 2.8 47.5 + - + +
232A VAL* 3.2 20.2 - - - +
234A ARG* 1.3 73.9 - - - +
236A THR* 1.3 65.2 + - - +
238A CYS* 3.0 6.8 + - - +
239A LEU* 2.9 32.4 + - + +
254A LEU* 3.9 14.4 - - + -
260A LEU* 3.7 26.0 - - + -
263A LEU* 6.0 0.9 - - + -
889B PHE* 4.2 3.6 - - + -
894B PHE* 3.6 27.4 - - + -
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Residues in contact with THR 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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232A VAL* 2.6 24.6 + - - +
233A SER* 3.4 8.2 - - - -
235A VAL* 1.3 77.6 - - - +
237A GLU* 1.3 61.7 + - - +
239A LEU* 3.3 1.4 + - - +
240A THR* 2.9 33.1 + - + +
247A LYS* 4.8 11.7 - - + -
250A SER* 3.5 30.4 + - - +
254A LEU* 4.7 9.2 - - - +
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Residues in contact with GLU 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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233A SER* 3.3 11.3 + - - +
234A ARG* 3.0 39.2 + - - +
236A THR* 1.3 78.7 - - + +
238A CYS* 1.3 59.3 + - - +
240A THR* 3.0 12.5 + - - +
241A THR* 2.9 30.3 + - - +
843B LYS* 3.1 40.4 - - + +
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Residues in contact with CYS 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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234A ARG* 2.9 29.0 + - - -
235A VAL* 3.0 14.1 + - - +
237A GLU* 1.3 75.6 - - - +
239A LEU* 1.3 58.1 + - + +
241A THR* 2.6 29.6 + - - +
260A LEU* 4.5 5.6 - - + -
840B PHE* 3.0 41.5 - - + -
843B LYS* 3.4 32.5 - - - -
844B MET* 5.6 2.5 - - - -
889B PHE* 4.9 7.4 - - - -
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Residues in contact with LEU 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 VAL* 2.9 20.4 + - + +
236A THR 3.7 4.3 - - - +
238A CYS* 1.3 83.0 - - + +
240A THR* 1.3 58.6 + - - +
241A THR 3.1 4.7 + - - -
242A VAL* 3.8 2.1 - - - +
245A VAL* 3.2 29.5 - - + +
250A SER* 3.5 36.8 - - - +
253A LEU* 3.9 19.1 - - + -
254A LEU* 3.8 16.8 - - + -
260A LEU* 5.1 0.7 - - + -
263A LEU* 3.3 35.2 - - + -
285A LEU* 3.5 20.5 - - + +
289A LEU* 6.2 0.2 - - + -
840B PHE* 4.8 6.5 - - + -
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Residues in contact with THR 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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236A THR* 2.9 15.3 + - + +
237A GLU* 3.0 18.7 + - - +
239A LEU* 1.3 76.1 - - - +
241A THR* 1.4 54.7 + - - +
242A VAL 2.9 20.5 - - - +
245A VAL* 3.6 13.6 - - + +
246A ASN* 3.6 22.9 - - - +
247A LYS* 4.0 3.4 - - + +
250A SER* 3.0 26.9 - - - +
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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