Contacts of the strand formed by residues 227 - 232 (chain A) in PDB entry 1ZKK
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 GLY 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A LEU* 3.6 11.6 - - - +
223A ILE 3.0 28.3 + - - +
226A LYS* 1.3 75.3 - - - +
228A ARG* 1.3 61.9 + - - -
2800A SAH 4.0 4.0 - - - -
276C GLN* 3.6 29.6 + - - -
281C THR* 5.2 0.6 + - - -
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Residues in contact with ARG 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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220A ILE* 4.0 22.1 - - + +
221A ASP 3.5 5.2 - - - -
222A LEU* 4.1 5.4 - - + -
227A GLY* 1.3 74.5 - - - -
229A GLY* 1.3 59.3 + - - +
271A TYR* 3.4 2.6 + - - -
289A GLU* 2.9 41.0 + - - -
296A LEU* 3.4 36.6 - - + +
298A ASN* 2.9 9.8 + - - +
2800A SAH 2.7 63.6 + - - +
339C ARG* 4.5 8.7 - - - +
19G ARG* 3.8 20.9 - - - +
23G ARG* 3.3 39.5 - - - +
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Residues in contact with GLY 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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220A ILE* 3.3 9.2 - - - +
221A ASP* 2.8 33.2 + - - -
223A ILE* 4.2 8.2 - - - +
227A GLY 3.9 0.4 + - - -
228A ARG* 1.3 75.4 - - - +
230A VAL* 1.3 65.3 + - - +
231A ILE* 5.0 0.4 - - - -
296A LEU* 3.6 6.3 - - - -
298A ASN* 3.4 16.4 - - - -
331A GLU* 3.9 6.3 - - - -
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Residues in contact with VAL 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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218A MET* 3.7 31.0 - - + -
219A LYS 3.3 12.3 - - - +
220A ILE* 5.0 1.3 - - + -
229A GLY* 1.3 78.8 - - - +
231A ILE* 1.3 63.0 + - - +
293A LEU* 3.6 37.5 - - + +
296A LEU* 3.7 17.6 + - + -
297A ILE* 3.8 19.2 - - + +
331A GLU* 3.6 7.0 + - - +
332A LEU* 2.8 40.6 + - + +
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Residues in contact with ILE 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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218A MET* 3.3 4.3 - - - -
219A LYS* 2.8 69.8 + - + +
221A ASP* 3.9 32.5 - - + +
223A ILE* 4.1 16.2 - - + -
230A VAL* 1.3 80.6 - - - +
232A ALA* 1.3 69.1 + - - +
329A GLY* 4.2 17.7 - - - +
330A GLU 3.4 10.8 - - - +
331A GLU* 4.0 14.4 - - + +
332A LEU* 4.7 2.0 - - - -
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Residues in contact with ALA 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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217A GLY 3.4 6.5 - - - -
218A MET* 4.6 0.2 - - - +
231A ILE* 1.3 76.6 - - - +
233A THR* 1.3 59.1 + - - +
234A LYS 3.4 18.6 - - - +
236A PHE* 4.0 10.5 - - + -
326A ILE* 4.0 15.9 - - + -
327A ALA 3.6 18.2 - - - +
329A GLY* 2.7 28.5 + - - -
330A GLU 2.9 11.6 + - - +
332A LEU* 4.5 6.9 - - + +
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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