Contacts of the helix formed by residues 222 - 234 (chain H) in PDB entry 5ZRV
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 THR 222 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214H VAL 3.7 17.3 - - - -
215H SER* 4.1 1.6 - - - +
221H GLU* 1.3 76.8 - - - +
223H MET* 1.3 66.1 + - - +
224H GLY 3.2 3.7 + - - +
225H HIS* 3.8 10.0 + - - +
226H SER* 4.0 6.6 + - - -
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Residues in contact with MET 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214H VAL 4.2 6.1 + - - -
222H THR* 1.3 73.1 - - - +
224H GLY* 1.3 57.9 + - - +
226H SER* 3.5 2.8 + - - -
227H ALA* 3.0 23.6 + - - -
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Residues in contact with GLY 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H THR 3.2 1.4 - - - -
223H MET* 1.3 76.6 - - - +
225H HIS* 1.3 60.6 + - - +
227H ALA* 4.2 2.5 - - - -
228H ASP* 2.9 25.8 + - - -
296H PHE* 5.5 13.0 - - - -
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Residues in contact with HIS 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H THR* 3.8 8.0 + - - +
223H MET 3.4 0.4 - - - -
224H GLY* 1.3 75.9 - - - +
226H SER* 1.3 56.4 + - - +
228H ASP 3.5 0.3 + - - -
229H ARG* 3.0 25.8 + - - -
296H PHE 5.4 5.5 + - - -
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Residues in contact with SER 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H THR 4.0 7.0 + - - -
223H MET 3.5 5.2 + - - -
224H GLY 3.3 0.2 - - - -
225H HIS* 1.3 74.5 - - - +
227H ALA* 1.3 62.1 + - - +
229H ARG* 3.8 1.5 - - - +
230H LEU* 3.0 21.0 + - - -
351H LEU* 6.5 1.1 - - - +
352H LEU 5.7 5.0 + - - -
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Residues in contact with ALA 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223H MET 3.0 16.3 + - - -
224H GLY* 3.2 5.1 + - - -
225H HIS 3.2 0.6 - - - -
226H SER* 1.3 77.7 - - - +
228H ASP* 1.3 57.5 + - - +
230H LEU* 3.4 0.9 + - - -
231H ALA* 2.9 23.6 + - - -
385H GLN* 5.9 2.4 + - - -
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Residues in contact with ASP 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224H GLY 2.9 17.5 + - - -
225H HIS 4.2 0.4 - - - -
227H ALA* 1.3 69.7 - - - +
229H ARG* 1.3 61.0 + - - +
231H ALA* 3.6 3.8 - - - +
232H ALA* 2.8 25.3 + - - -
302H THR 5.9 4.3 - - - +
303H VAL* 5.8 7.9 - - - +
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Residues in contact with ARG 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G LEU* 6.0 4.7 - - - +
225H HIS 3.0 17.6 + - - -
226H SER* 3.8 2.0 - - - +
227H ALA 3.2 0.2 - - - -
228H ASP* 1.3 77.4 - - - +
230H LEU* 1.3 57.4 + - - +
232H ALA 3.8 0.5 - - - -
233H ALA* 2.9 27.2 + - - -
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Residues in contact with LEU 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226H SER 3.0 16.0 + - - -
227H ALA 3.8 0.9 - - - -
229H ARG* 1.3 75.6 - - - +
231H ALA* 1.3 62.5 + - - +
233H ALA* 3.6 6.9 + - - +
234H PHE* 3.7 8.3 + - - -
385H GLN* 6.3 1.3 - - - -
388H ALA* 5.5 6.1 - - - -
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Residues in contact with ALA 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H ALA 2.9 16.3 + - - -
228H ASP* 3.8 3.4 - - - +
229H ARG 3.1 0.2 - - - -
230H LEU* 1.3 80.1 - - - +
232H ALA* 1.3 60.7 + - - +
233H ALA 3.4 0.7 + - - -
234H PHE* 3.6 7.6 + - - -
236H VAL* 3.8 19.2 + - - -
384H GLY* 5.3 13.7 - - - -
385H GLN* 5.5 3.1 - - - +
388H ALA* 6.2 2.0 - - - +
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Residues in contact with ALA 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H ASP 2.8 20.0 + - - -
229H ARG* 3.8 0.9 - - - +
231H ALA* 1.3 72.4 - - - +
233H ALA* 1.3 61.3 + - - +
234H PHE 3.3 0.7 + - - -
235H ALA* 3.4 11.1 + - - +
236H VAL 5.0 6.7 - - - +
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Residues in contact with ALA 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227G PRO 4.6 13.2 - - - -
228G GLY* 4.1 16.3 - - - -
229G LEU 4.5 2.6 + - - -
229H ARG 2.9 16.7 + - - -
230H LEU* 3.6 3.8 + - - +
231H ALA 3.2 0.6 - - - -
232H ALA* 1.3 78.7 - - - +
234H PHE* 1.3 57.1 + - - +
235H ALA 3.5 1.3 + - - -
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Residues in contact with PHE 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228G GLY* 5.9 0.4 - - - -
229G LEU 5.6 3.6 - - - +
230H LEU 3.7 7.6 + - - -
231H ALA 3.6 6.9 + - - -
232H ALA 3.2 0.6 - - - -
233H ALA* 1.3 77.3 - - - +
235H ALA* 1.3 62.6 + - - +
236H VAL* 3.5 3.0 + - - -
388H ALA* 5.7 7.8 - - - +
391H LYS* 5.7 5.7 - - - -
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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