Contacts of the helix formed by residues 224 - 234 (chain A) in PDB entry 1ZDT
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 PRO 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A ASN* 3.4 6.9 - - - +
223A VAL* 1.3 96.2 - - + +
225A GLU* 1.3 65.9 + - - +
226A LEU 3.3 1.8 - - - +
227A ILE* 3.1 20.8 + - + +
228A LEU* 3.1 10.0 + - - +
400A ALA* 3.4 44.9 - - + +
403A ASP* 4.0 18.2 - - + +
404A TYR* 4.1 15.7 - - + -
408A HIS* 5.6 0.7 - - + -
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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 VAL 3.5 2.8 + - - -
224A PRO* 1.3 73.8 - - - +
226A LEU* 1.3 67.5 + - + +
228A LEU* 3.1 15.2 + - + +
229A GLN* 2.9 49.3 + - - +
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Residues in contact with LEU 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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224A PRO* 3.3 1.0 - - + +
225A GLU* 1.3 81.4 - - + +
227A ILE* 1.3 58.2 + - - +
229A GLN* 3.4 11.4 + - - +
230A LEU* 3.0 36.0 + - + +
284A MET* 3.7 39.0 - - + -
285A VAL* 6.0 0.7 - - + -
370A CYS* 5.2 3.6 - - - -
373A PHE* 4.2 17.3 - - + -
396A LYS* 3.9 15.0 - - + +
397A ALA* 3.7 36.1 - - + +
400A ALA* 4.3 14.1 - - + -
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Residues in contact with ILE 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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223A VAL* 3.7 16.4 - - + -
224A PRO* 3.1 15.6 + - + +
226A LEU* 1.3 75.1 - - + +
228A LEU* 1.3 66.4 + - - +
230A LEU* 3.3 8.9 + - + +
231A LEU* 3.1 25.1 + - + +
366A GLN* 3.7 37.9 - - + +
367A GLU* 5.5 0.4 - - - -
369A VAL* 4.4 2.5 - - + -
370A CYS* 3.9 34.3 - - + -
400A ALA* 4.0 24.7 - - + +
401A LEU* 4.8 1.6 - - + -
404A TYR* 4.0 20.9 - - + -
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Residues in contact with LEU 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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223A VAL* 3.8 38.8 - - + +
224A PRO 3.1 13.1 + - - +
225A GLU* 3.1 16.0 + - + +
227A ILE* 1.3 77.6 - - - +
229A GLN* 1.3 62.9 + - + +
231A LEU* 3.3 24.8 + - + +
232A GLN* 3.3 18.4 + - + +
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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* 2.9 50.0 + - - +
226A LEU* 3.8 12.3 - - - +
228A LEU* 1.3 76.0 - - + +
230A LEU* 1.3 62.5 + - - +
232A GLN* 3.4 11.1 + - - +
233A LEU* 3.2 24.9 + - + +
284A MET* 3.3 25.3 - - + +
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Residues in contact with LEU 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 LEU* 3.0 31.5 + - + +
227A ILE* 3.7 3.1 - - - +
228A LEU 3.2 0.2 - - - -
229A GLN* 1.3 75.4 - - - +
231A LEU* 1.3 62.1 + - - +
233A LEU* 3.3 9.2 + - + +
234A GLU* 3.2 24.3 + - - +
279A TRP* 4.7 8.6 + - + +
283A CYS* 4.2 14.1 - - - -
284A MET* 3.5 25.8 - - + -
369A VAL* 3.5 43.8 - - + +
370A CYS* 4.2 7.0 - - + -
373A PHE* 3.7 29.4 - - + -
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Residues in contact with LEU 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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223A VAL* 5.4 0.2 - - + -
227A ILE* 3.1 23.0 + - + +
228A LEU* 3.3 23.3 + - + +
230A LEU* 1.3 77.2 - - - +
232A GLN* 1.3 66.8 + - + +
234A GLU* 3.2 21.9 + - + +
365A ARG* 3.7 49.5 + - + +
366A GLN* 4.1 28.9 - - + +
369A VAL* 4.2 10.5 - - + -
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Residues in contact with GLN 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 LEU 3.3 13.6 + - - +
229A GLN* 3.6 11.4 - - - +
230A LEU 3.2 0.4 - - - -
231A LEU* 1.3 81.3 - - + +
233A LEU* 1.3 62.7 + - + +
234A GLU 4.4 2.8 - - - +
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Residues in contact with LEU 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* 3.2 15.3 - - + +
230A LEU* 3.3 13.0 + - + +
231A LEU 3.2 0.4 - - - -
232A GLN* 1.3 80.3 - - + +
234A GLU* 1.3 66.7 + - - +
235A PRO* 3.0 4.2 - - - +
279A TRP* 4.7 8.0 - - - +
282A ARG* 3.0 61.4 + - + +
283A CYS* 3.7 18.4 - - - -
284A MET* 4.0 22.0 - - + +
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Residues in contact with GLU 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 LEU 3.2 9.2 + - - +
231A LEU* 3.2 21.8 + - - +
232A GLN 4.4 3.3 - - - +
233A LEU* 1.3 77.1 - - - +
235A PRO* 1.3 78.0 - - + +
236A ASP* 3.3 8.3 + - - +
279A TRP* 4.2 7.2 + - - -
365A ARG* 3.1 36.4 + - - +
368A PHE* 3.6 11.3 - - - -
369A VAL* 3.3 19.1 - - + +
372A LYS* 3.3 35.2 + - - -
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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